AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1303160


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1303160 MtrunA17_Chr4g0073201 95.028 181 5 2 1 181 1 177 3.20e-119 334
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1303160 AT4G30410.2 43.017 179 94 5 1 175 1 175 4.40e-30 108
Msa1303160 AT4G30410.1 43.017 179 94 5 1 175 1 175 4.40e-30 108
Msa1303160 AT5G57780.1 38.764 178 85 6 1 177 2 156 1.79e-28 104

Find 47 sgRNAs with CRISPR-Local

Find 122 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCTATTCTCTTTATAGAAAA+AGG 0.151336 8_3:-66004814 Msa1303160:CDS
TAAATCAGCAGAAAGCTTTA+TGG 0.212678 8_3:+66004979 None:intergenic
TCTTCACATAAGAAGGTAAT+AGG 0.223742 8_3:-66004854 Msa1303160:CDS
TTGTAGAAGTATTTGCAATT+AGG 0.236916 8_3:+66004909 None:intergenic
TGTAGAAGTATTTGCAATTA+GGG 0.288790 8_3:+66004910 None:intergenic
TGAGAGATTCTATATAATCT+AGG 0.292570 8_3:+66004633 None:intergenic
TTCATCGTGGATTTCATGAT+TGG 0.331477 8_3:-66004226 None:intergenic
ATTCCTAAGGAAATGGATAA+AGG 0.331543 8_3:-66005062 Msa1303160:CDS
TGCTTTCTATACATACATTA+AGG 0.340892 8_3:-66004377 Msa1303160:three_prime_UTR
TGTATAAATATATTAATTTA+CGG 0.360941 8_3:+66004551 None:intergenic
TGTAAAAGCTAATACTAGTA+TGG 0.361521 8_3:+66004497 None:intergenic
ATTCATGGATGATGCTTGTT+TGG 0.373687 8_3:-66004666 Msa1303160:CDS
GTTACCAGGTGGAAAATTCA+TGG 0.380790 8_3:-66004681 Msa1303160:CDS
AGCAAGAATTCCTAAGGAAA+TGG 0.389199 8_3:-66005069 Msa1303160:CDS
CTTCACATAAGAAGGTAATA+GGG 0.431570 8_3:-66004853 Msa1303160:CDS
TTCCTAAGGAAATGGATAAA+GGG 0.440057 8_3:-66005061 Msa1303160:CDS
CTAAAGACAAAACTACCCTT+TGG 0.442557 8_3:-66004940 Msa1303160:CDS
GACCCTTTATCCATTTCCTT+AGG 0.455134 8_3:+66005059 None:intergenic
GAAGAAGATAAAGTAGAAGA+TGG 0.455575 8_3:+66005320 None:intergenic
GAGAGATTCTATATAATCTA+GGG 0.474006 8_3:+66004634 None:intergenic
ATCTTTGCAAGCTAGAGGTA+TGG 0.477633 8_3:-66004410 Msa1303160:three_prime_UTR
AAAGATAAAGTGTAAATTGA+GGG 0.484799 8_3:+66004427 None:intergenic
GTCTTTAGACGTGGAAGCCA+TGG 0.491623 8_3:+66004955 None:intergenic
AACCTCATCTTCACATAAGA+AGG 0.491845 8_3:-66004861 Msa1303160:CDS
AGTGGAAAATGAGAAGATGA+TGG 0.523577 8_3:+66005416 None:intergenic
CAAAGATAAAGTGTAAATTG+AGG 0.535548 8_3:+66004426 None:intergenic
TGCTCAAGCAAGAATTCCTA+AGG 0.547032 8_3:-66005075 Msa1303160:CDS
ACTTTATCTTTGCAAGCTAG+AGG 0.555456 8_3:-66004415 Msa1303160:three_prime_UTR
TATACTTATAATCTATACAT+AGG 0.559609 8_3:+66004526 None:intergenic
TACCTTCTTATGTGAAGATG+AGG 0.560965 8_3:+66004859 None:intergenic
CTTCTTCAAGAGTTTGAGCA+AGG 0.564795 8_3:-66005304 Msa1303160:intron
GCTTTCTGCTGATTTAGCCA+TGG 0.566451 8_3:-66004972 Msa1303160:CDS
AGATGATGGATTAATGTGAG+AGG 0.573671 8_3:+66005430 None:intergenic
GATGAGAGATGGAAGCAAAG+TGG 0.576621 8_3:+66005398 None:intergenic
GCTAGAGGTATGGAGGAAAG+AGG 0.602380 8_3:-66004400 Msa1303160:three_prime_UTR
CTCAAGAGTTTGTTACCAGG+TGG 0.612619 8_3:-66004692 Msa1303160:CDS
AGGCTCAAGAGTTTGTTACC+AGG 0.621754 8_3:-66004695 Msa1303160:CDS
TTTGCAAGCTAGAGGTATGG+AGG 0.634967 8_3:-66004407 Msa1303160:three_prime_UTR
TGGTTAAGAAAAGAACAAGA+AGG 0.644687 8_3:-66004715 Msa1303160:CDS
GTTGAGAAGAAATCGTGCAA+AGG 0.662740 8_3:-66004771 Msa1303160:CDS
TACATTAAGGCAATGTACAG+AGG 0.665796 8_3:-66004364 Msa1303160:three_prime_UTR
TCGTGCAAAGGAAAGAGTTG+AGG 0.666359 8_3:-66004759 Msa1303160:CDS
GCTTGAAAGATGAGAGTGGT+GGG 0.668443 8_3:+66005465 None:intergenic
ATAAATATATTAATTTACGG+TGG 0.671525 8_3:+66004554 None:intergenic
AAGTGCTTGAAAGATGAGAG+TGG 0.681389 8_3:+66005461 None:intergenic
TGGACTAATGAAGAGTTCAG+AGG 0.697145 8_3:+66004574 None:intergenic
TGCTTGAAAGATGAGAGTGG+TGG 0.719348 8_3:+66005464 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATGACGTTTTTTTTTTTTTT+TGG + chr8_3:66004343-66004362 None:intergenic 15.0%
!! ATATATGATATAATATGCTA+GGG + chr8_3:66004535-66004554 None:intergenic 15.0%
!! ATAAATATATTAATTTACGG+TGG + chr8_3:66005141-66005160 None:intergenic 15.0%
!! TATACTTATAATCTATACAT+AGG + chr8_3:66005169-66005188 None:intergenic 15.0%
!!! ATGACGTTTTTTTTTTTTTT+TGG + chr8_3:66004343-66004362 None:intergenic 15.0%
!! ATATATGATATAATATGCTA+GGG + chr8_3:66004535-66004554 None:intergenic 15.0%
!! ATAAATATATTAATTTACGG+TGG + chr8_3:66005141-66005160 None:intergenic 15.0%
!! TATACTTATAATCTATACAT+AGG + chr8_3:66005169-66005188 None:intergenic 15.0%
!! CATATATGATATAATATGCT+AGG + chr8_3:66004536-66004555 None:intergenic 20.0%
!! CAAATTAAAAAAAAATACGC+AGG + chr8_3:66004577-66004596 None:intergenic 20.0%
!! CTTTATAGAAAAAGGATAAT+TGG - chr8_3:66004886-66004905 Msa1303160:CDS 20.0%
!! AAAGATAAAGTGTAAATTGA+GGG + chr8_3:66005268-66005287 None:intergenic 20.0%
!! ATCATGAAAAGTAAAAACTT+AGG + chr8_3:66005378-66005397 None:intergenic 20.0%
!! CATATATGATATAATATGCT+AGG + chr8_3:66004536-66004555 None:intergenic 20.0%
!! CAAATTAAAAAAAAATACGC+AGG + chr8_3:66004577-66004596 None:intergenic 20.0%
!! CTTTATAGAAAAAGGATAAT+TGG - chr8_3:66004886-66004905 Msa1303160:CDS 20.0%
!! AAAGATAAAGTGTAAATTGA+GGG + chr8_3:66005268-66005287 None:intergenic 20.0%
!! ATCATGAAAAGTAAAAACTT+AGG + chr8_3:66005378-66005397 None:intergenic 20.0%
!!! TGTAGAAGTATTTGCAATTA+GGG + chr8_3:66004785-66004804 None:intergenic 25.0%
!!! TTGTAGAAGTATTTGCAATT+AGG + chr8_3:66004786-66004805 None:intergenic 25.0%
!! CCTTTTTCTATAAAGAGAAT+AGG + chr8_3:66004881-66004900 None:intergenic 25.0%
! CCTATTCTCTTTATAGAAAA+AGG - chr8_3:66004878-66004897 Msa1303160:CDS 25.0%
! ATAGAAAAAGGATAATTGGA+AGG - chr8_3:66004890-66004909 Msa1303160:CDS 25.0%
! GAGAGATTCTATATAATCTA+GGG + chr8_3:66005061-66005080 None:intergenic 25.0%
! TGAGAGATTCTATATAATCT+AGG + chr8_3:66005062-66005081 None:intergenic 25.0%
! TGTAAAAGCTAATACTAGTA+TGG + chr8_3:66005198-66005217 None:intergenic 25.0%
! CAAAGATAAAGTGTAAATTG+AGG + chr8_3:66005269-66005288 None:intergenic 25.0%
! TGCTTTCTATACATACATTA+AGG - chr8_3:66005315-66005334 Msa1303160:five_prime_UTR 25.0%
!!! AACTTTTTTTTCTTTCATCG+TGG - chr8_3:66005453-66005472 Msa1303160:five_prime_UTR 25.0%
!!! TGTAGAAGTATTTGCAATTA+GGG + chr8_3:66004785-66004804 None:intergenic 25.0%
!!! TTGTAGAAGTATTTGCAATT+AGG + chr8_3:66004786-66004805 None:intergenic 25.0%
!! CCTTTTTCTATAAAGAGAAT+AGG + chr8_3:66004881-66004900 None:intergenic 25.0%
! CCTATTCTCTTTATAGAAAA+AGG - chr8_3:66004878-66004897 Msa1303160:CDS 25.0%
! ATAGAAAAAGGATAATTGGA+AGG - chr8_3:66004890-66004909 Msa1303160:CDS 25.0%
! GAGAGATTCTATATAATCTA+GGG + chr8_3:66005061-66005080 None:intergenic 25.0%
! TGAGAGATTCTATATAATCT+AGG + chr8_3:66005062-66005081 None:intergenic 25.0%
! TGTAAAAGCTAATACTAGTA+TGG + chr8_3:66005198-66005217 None:intergenic 25.0%
! CAAAGATAAAGTGTAAATTG+AGG + chr8_3:66005269-66005288 None:intergenic 25.0%
! TGCTTTCTATACATACATTA+AGG - chr8_3:66005315-66005334 Msa1303160:five_prime_UTR 25.0%
!!! AACTTTTTTTTCTTTCATCG+TGG - chr8_3:66005453-66005472 Msa1303160:five_prime_UTR 25.0%
GAAGAAGATAAAGTAGAAGA+TGG + chr8_3:66004375-66004394 None:intergenic 30.0%
GGGCTTAATATAGTTATTCT+TGG + chr8_3:66004515-66004534 None:intergenic 30.0%
ATTCCTAAGGAAATGGATAA+AGG - chr8_3:66004630-66004649 Msa1303160:CDS 30.0%
TTCCTAAGGAAATGGATAAA+GGG - chr8_3:66004631-66004650 Msa1303160:CDS 30.0%
TAAATCAGCAGAAAGCTTTA+TGG + chr8_3:66004716-66004735 None:intergenic 30.0%
TCTTCACATAAGAAGGTAAT+AGG - chr8_3:66004838-66004857 Msa1303160:CDS 30.0%
CTTCACATAAGAAGGTAATA+GGG - chr8_3:66004839-66004858 Msa1303160:CDS 30.0%
TGGTTAAGAAAAGAACAAGA+AGG - chr8_3:66004977-66004996 Msa1303160:CDS 30.0%
GAAGAAGATAAAGTAGAAGA+TGG + chr8_3:66004375-66004394 None:intergenic 30.0%
GGGCTTAATATAGTTATTCT+TGG + chr8_3:66004515-66004534 None:intergenic 30.0%
ATTCCTAAGGAAATGGATAA+AGG - chr8_3:66004630-66004649 Msa1303160:CDS 30.0%
TTCCTAAGGAAATGGATAAA+GGG - chr8_3:66004631-66004650 Msa1303160:CDS 30.0%
TAAATCAGCAGAAAGCTTTA+TGG + chr8_3:66004716-66004735 None:intergenic 30.0%
TCTTCACATAAGAAGGTAAT+AGG - chr8_3:66004838-66004857 Msa1303160:CDS 30.0%
CTTCACATAAGAAGGTAATA+GGG - chr8_3:66004839-66004858 Msa1303160:CDS 30.0%
TGGTTAAGAAAAGAACAAGA+AGG - chr8_3:66004977-66004996 Msa1303160:CDS 30.0%
!! AGATGATGGATTAATGTGAG+AGG + chr8_3:66004265-66004284 None:intergenic 35.0%
AGTGGAAAATGAGAAGATGA+TGG + chr8_3:66004279-66004298 None:intergenic 35.0%
!! GACGAAATTTTGATGAGAGA+TGG + chr8_3:66004308-66004327 None:intergenic 35.0%
AGCAAGAATTCCTAAGGAAA+TGG - chr8_3:66004623-66004642 Msa1303160:CDS 35.0%
CTAAAGACAAAACTACCCTT+TGG - chr8_3:66004752-66004771 Msa1303160:CDS 35.0%
! AATTAGGGCTTTTCTCCAAA+GGG + chr8_3:66004770-66004789 None:intergenic 35.0%
AACCTCATCTTCACATAAGA+AGG - chr8_3:66004831-66004850 Msa1303160:CDS 35.0%
TACCTTCTTATGTGAAGATG+AGG + chr8_3:66004836-66004855 None:intergenic 35.0%
ATTCATGGATGATGCTTGTT+TGG - chr8_3:66005026-66005045 Msa1303160:CDS 35.0%
ACTTTATCTTTGCAAGCTAG+AGG - chr8_3:66005277-66005296 Msa1303160:intron 35.0%
TACATTAAGGCAATGTACAG+AGG - chr8_3:66005328-66005347 Msa1303160:five_prime_UTR 35.0%
!! AGATGATGGATTAATGTGAG+AGG + chr8_3:66004265-66004284 None:intergenic 35.0%
AGTGGAAAATGAGAAGATGA+TGG + chr8_3:66004279-66004298 None:intergenic 35.0%
!! GACGAAATTTTGATGAGAGA+TGG + chr8_3:66004308-66004327 None:intergenic 35.0%
AGCAAGAATTCCTAAGGAAA+TGG - chr8_3:66004623-66004642 Msa1303160:CDS 35.0%
CTAAAGACAAAACTACCCTT+TGG - chr8_3:66004752-66004771 Msa1303160:CDS 35.0%
! AATTAGGGCTTTTCTCCAAA+GGG + chr8_3:66004770-66004789 None:intergenic 35.0%
AACCTCATCTTCACATAAGA+AGG - chr8_3:66004831-66004850 Msa1303160:CDS 35.0%
TACCTTCTTATGTGAAGATG+AGG + chr8_3:66004836-66004855 None:intergenic 35.0%
ATTCATGGATGATGCTTGTT+TGG - chr8_3:66005026-66005045 Msa1303160:CDS 35.0%
ACTTTATCTTTGCAAGCTAG+AGG - chr8_3:66005277-66005296 Msa1303160:intron 35.0%
TACATTAAGGCAATGTACAG+AGG - chr8_3:66005328-66005347 Msa1303160:five_prime_UTR 35.0%
AAGTGCTTGAAAGATGAGAG+TGG + chr8_3:66004234-66004253 None:intergenic 40.0%
CTTCTTCAAGAGTTTGAGCA+AGG - chr8_3:66004388-66004407 Msa1303160:three_prime_UTR 40.0%
TGCTCAAGCAAGAATTCCTA+AGG - chr8_3:66004617-66004636 Msa1303160:CDS 40.0%
GACCCTTTATCCATTTCCTT+AGG + chr8_3:66004636-66004655 None:intergenic 40.0%
!!! GGTAGTTTTGTCTTTAGACG+TGG + chr8_3:66004749-66004768 None:intergenic 40.0%
! CAATTAGGGCTTTTCTCCAA+AGG + chr8_3:66004771-66004790 None:intergenic 40.0%
GTTGAGAAGAAATCGTGCAA+AGG - chr8_3:66004921-66004940 Msa1303160:CDS 40.0%
GTTACCAGGTGGAAAATTCA+TGG - chr8_3:66005011-66005030 Msa1303160:CDS 40.0%
! TCATCCATGAATTTTCCACC+TGG + chr8_3:66005018-66005037 None:intergenic 40.0%
TGGACTAATGAAGAGTTCAG+AGG + chr8_3:66005121-66005140 None:intergenic 40.0%
ATCTTTGCAAGCTAGAGGTA+TGG - chr8_3:66005282-66005301 Msa1303160:intron 40.0%
AAGTGCTTGAAAGATGAGAG+TGG + chr8_3:66004234-66004253 None:intergenic 40.0%
CTTCTTCAAGAGTTTGAGCA+AGG - chr8_3:66004388-66004407 Msa1303160:three_prime_UTR 40.0%
TGCTCAAGCAAGAATTCCTA+AGG - chr8_3:66004617-66004636 Msa1303160:CDS 40.0%
GACCCTTTATCCATTTCCTT+AGG + chr8_3:66004636-66004655 None:intergenic 40.0%
!!! GGTAGTTTTGTCTTTAGACG+TGG + chr8_3:66004749-66004768 None:intergenic 40.0%
! CAATTAGGGCTTTTCTCCAA+AGG + chr8_3:66004771-66004790 None:intergenic 40.0%
GTTGAGAAGAAATCGTGCAA+AGG - chr8_3:66004921-66004940 Msa1303160:CDS 40.0%
GTTACCAGGTGGAAAATTCA+TGG - chr8_3:66005011-66005030 Msa1303160:CDS 40.0%
! TCATCCATGAATTTTCCACC+TGG + chr8_3:66005018-66005037 None:intergenic 40.0%
TGGACTAATGAAGAGTTCAG+AGG + chr8_3:66005121-66005140 None:intergenic 40.0%
ATCTTTGCAAGCTAGAGGTA+TGG - chr8_3:66005282-66005301 Msa1303160:intron 40.0%
GATGAGAGATGGAAGCAAAG+TGG + chr8_3:66004297-66004316 None:intergenic 45.0%
!! GCTTTCTGCTGATTTAGCCA+TGG - chr8_3:66004720-66004739 Msa1303160:CDS 45.0%
TCGTGCAAAGGAAAGAGTTG+AGG - chr8_3:66004933-66004952 Msa1303160:CDS 45.0%
!! AGGCGAGTTTTATAGCGACA+CGG - chr8_3:66004953-66004972 Msa1303160:CDS 45.0%
!! GAGTTTTATAGCGACACGGT+TGG - chr8_3:66004957-66004976 Msa1303160:CDS 45.0%
!! AGGCTCAAGAGTTTGTTACC+AGG - chr8_3:66004997-66005016 Msa1303160:CDS 45.0%
!! CTCAAGAGTTTGTTACCAGG+TGG - chr8_3:66005000-66005019 Msa1303160:CDS 45.0%
! TTTGCAAGCTAGAGGTATGG+AGG - chr8_3:66005285-66005304 Msa1303160:intron 45.0%
GATGAGAGATGGAAGCAAAG+TGG + chr8_3:66004297-66004316 None:intergenic 45.0%
!! GCTTTCTGCTGATTTAGCCA+TGG - chr8_3:66004720-66004739 Msa1303160:CDS 45.0%
TCGTGCAAAGGAAAGAGTTG+AGG - chr8_3:66004933-66004952 Msa1303160:CDS 45.0%
!! AGGCGAGTTTTATAGCGACA+CGG - chr8_3:66004953-66004972 Msa1303160:CDS 45.0%
!! GAGTTTTATAGCGACACGGT+TGG - chr8_3:66004957-66004976 Msa1303160:CDS 45.0%
!! AGGCTCAAGAGTTTGTTACC+AGG - chr8_3:66004997-66005016 Msa1303160:CDS 45.0%
!! CTCAAGAGTTTGTTACCAGG+TGG - chr8_3:66005000-66005019 Msa1303160:CDS 45.0%
! TTTGCAAGCTAGAGGTATGG+AGG - chr8_3:66005285-66005304 Msa1303160:intron 45.0%
!! TGTATAAATATATTAATTTA+CGG + chr8_3:66005144-66005163 None:intergenic 5.0%
!! TGTATAAATATATTAATTTA+CGG + chr8_3:66005144-66005163 None:intergenic 5.0%
GTCTTTAGACGTGGAAGCCA+TGG + chr8_3:66004740-66004759 None:intergenic 50.0%
! GCTAGAGGTATGGAGGAAAG+AGG - chr8_3:66005292-66005311 Msa1303160:intron 50.0%
GTCTTTAGACGTGGAAGCCA+TGG + chr8_3:66004740-66004759 None:intergenic 50.0%
! GCTAGAGGTATGGAGGAAAG+AGG - chr8_3:66005292-66005311 Msa1303160:intron 50.0%
Chromosome Type Strat End Strand Name
chr8_3 gene 66004229 66005485 66004229 ID=Msa1303160;Name=Msa1303160
chr8_3 mRNA 66004229 66005485 66004229 ID=Msa1303160-mRNA-1;Parent=Msa1303160;Name=Msa1303160-mRNA-1;_AED=0.00;_eAED=0.00;_QI=181|0|0.5|1|0|0.5|2|339|181
chr8_3 exon 66004229 66005113 66004229 ID=Msa1303160-mRNA-1:exon:20095;Parent=Msa1303160-mRNA-1
chr8_3 exon 66005305 66005485 66005305 ID=Msa1303160-mRNA-1:exon:20094;Parent=Msa1303160-mRNA-1
chr8_3 five_prime_UTR 66005305 66005485 66005305 ID=Msa1303160-mRNA-1:five_prime_utr;Parent=Msa1303160-mRNA-1
chr8_3 CDS 66004568 66005113 66004568 ID=Msa1303160-mRNA-1:cds;Parent=Msa1303160-mRNA-1
chr8_3 three_prime_UTR 66004229 66004567 66004229 ID=Msa1303160-mRNA-1:three_prime_utr;Parent=Msa1303160-mRNA-1
Gene Sequence

>Msa1303160

ATGCGAAATTTGAGCTTGCTCAAGCAAGAATTCCTAAGGAAATGGATAAAGGGTCTAAAAAAATATTATAACTCTCAAAAGAAGAATATGAACTTGTTCGAGAGAAAGAAAGCCATAAAGCTTTCTGCTGATTTAGCCATGGCTTCCACGTCTAAAGACAAAACTACCCTTTGGAGAAAAGCCCTAATTGCAAATACTTCTACAAGCATAGATGAACAAGACATATCAACAACCTCATCTTCACATAAGAAGGTAATAGGGAAAAACTCGACGAATTCCTATTCTCTTTATAGAAAAAGGATAATTGGAAGGAGAAAGACGTTGAGAAGAAATCGTGCAAAGGAAAGAGTTGAGGCGAGTTTTATAGCGACACGGTTGGTTAAGAAAAGAACAAGAAGGCTCAAGAGTTTGTTACCAGGTGGAAAATTCATGGATGATGCTTGTTTGGTTGATGAAACCCTAGATTATATAGAATCTCTCAAAGCTCAAGTTGAAGTGATGAGATGTCTTGTTACTGCCTCTGAACTCTTCATTAGTCCACCGTAA

Protein sequence

>Msa1303160

MRNLSLLKQEFLRKWIKGLKKYYNSQKKNMNLFERKKAIKLSADLAMASTSKDKTTLWRKALIANTSTSIDEQDISTTSSSHKKVIGKNSTNSYSLYRKRIIGRRKTLRRNRAKERVEASFIATRLVKKRTRRLKSLLPGGKFMDDACLVDETLDYIESLKAQVEVMRCLVTASELFISPP*