AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0871290


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0871290 MtrunA17_Chr6g0458341 97.059 68 2 0 19 86 212 279 7.05e-42 137
Msa0871290 MtrunA17_Chr7g0230151 50.000 78 37 2 10 86 201 277 7.94e-19 77.8
Msa0871290 MtrunA17_Chr7g0230141 51.471 68 26 2 19 86 210 270 3.91e-14 65.1
Msa0871290 MtrunA17_Chr6g0458381 47.541 61 30 1 19 79 120 178 4.74e-12 58.5
Msa0871290 MtrunA17_Chr6g0458361 42.373 59 34 0 10 68 188 246 3.54e-11 57.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0871290 AT5G40670.1 62.069 58 20 2 19 76 210 265 2.16e-16 71.6

Find 32 sgRNAs with CRISPR-Local

Find 110 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AACCATTCTCCAAATCTTTA+AGG 0.070760 6_1:-6177888 Msa0871290:three_prime_UTR
GACTCTTGGGTGAATTTCTC+TGG 0.292974 6_1:-6178647 Msa0871290:CDS
GTTGTAAGGCCTTAAAGATT+TGG 0.308440 6_1:+6177879 None:intergenic
ATAATTCTCTTCTTGTTGTA+AGG 0.365692 6_1:+6177865 None:intergenic
ATGTTGTCATCGAGTTTAGA+AGG 0.377471 6_1:+6178242 None:intergenic
CATCCCCACTAACCTCATAA+TGG 0.393898 6_1:+6178056 None:intergenic
GGCCTTAAAGATTTGGAGAA+TGG 0.402110 6_1:+6177886 None:intergenic
TTTGAATTTGTAATTATGTT+TGG 0.432269 6_1:-6178169 Msa0871290:exon
ATCCCCACTAACCTCATAAT+GGG 0.432323 6_1:+6178057 None:intergenic
GTGAATTTCTCTGGGAACCT+TGG 0.434548 6_1:-6178638 Msa0871290:CDS
TGGAAAAGTATTGTTATCTC+TGG 0.434586 6_1:-6178618 Msa0871290:intron
GATTTGTGAAAGTGATTGTT+TGG 0.437640 6_1:-6177963 Msa0871290:three_prime_UTR
TCAGCCACCGGCACATTTGA+AGG 0.441029 6_1:+6178197 None:intergenic
GGTTAGTGGGGATGCTCTCT+TGG 0.442986 6_1:-6178047 Msa0871290:three_prime_UTR
GAACTGCGTGCTATACAGAT+AGG 0.448918 6_1:-6178022 Msa0871290:three_prime_UTR
TTGGAAGCTGTGAATATCAT+TGG 0.462634 6_1:-6177944 Msa0871290:three_prime_UTR
AATCCCCACCAACCTTATCA+TGG 0.468507 6_1:+6178082 None:intergenic
TTTCCCATTATGAGGTTAGT+GGG 0.483975 6_1:-6178060 Msa0871290:three_prime_UTR
ACAAGAAGAGAATTATACTT+TGG 0.492317 6_1:-6177858 Msa0871290:three_prime_UTR
CACACTAGCTAAAATCATAC+AGG 0.502798 6_1:+6178114 None:intergenic
TTCCCATGATAAGGTTGGTG+GGG 0.521220 6_1:-6178085 Msa0871290:three_prime_UTR
CAAGTCTCCTTCAAATGTGC+CGG 0.533047 6_1:-6178204 Msa0871290:CDS
ACTCTTGGGTGAATTTCTCT+GGG 0.540084 6_1:-6178646 Msa0871290:CDS
ATCCCCACCAACCTTATCAT+GGG 0.575454 6_1:+6178083 None:intergenic
GTCTCCTTCAAATGTGCCGG+TGG 0.578990 6_1:-6178201 Msa0871290:CDS
TTTCCCATGATAAGGTTGGT+GGG 0.581678 6_1:-6178086 Msa0871290:three_prime_UTR
AACTGCGTGCTATACAGATA+GGG 0.583379 6_1:-6178021 Msa0871290:three_prime_UTR
CATTTGAAGGAGACTTGATG+AGG 0.590184 6_1:+6178210 None:intergenic
TTCCCATTATGAGGTTAGTG+GGG 0.606252 6_1:-6178059 Msa0871290:three_prime_UTR
ATCGACATTTGTCATAATCG+AGG 0.627549 6_1:-6177998 Msa0871290:three_prime_UTR
ATTTGAAGGAGACTTGATGA+GGG 0.629173 6_1:+6178211 None:intergenic
TTTGAAGGAGACTTGATGAG+GGG 0.680455 6_1:+6178212 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TATATAATGTAAACATTTTC+AGG - chr6_1:6178317-6178336 Msa0871290:CDS 15.0%
!! TTTGAATTTGTAATTATGTT+TGG - chr6_1:6178490-6178509 Msa0871290:intron 15.0%
!!! TATATAATGTAAACATTTTC+AGG - chr6_1:6178317-6178336 Msa0871290:CDS 15.0%
!! TTTGAATTTGTAATTATGTT+TGG - chr6_1:6178490-6178509 Msa0871290:intron 15.0%
!! ATGTTACTATAATGTGAATT+TGG + chr6_1:6177927-6177946 None:intergenic 20.0%
!!! TTTTTTTATTCTAGACTCTT+GGG - chr6_1:6177999-6178018 Msa0871290:three_prime_UTR 20.0%
!!! TATTCTAATGCAAATTTTGT+AGG + chr6_1:6178148-6178167 None:intergenic 20.0%
!! ATGTTACTATAATGTGAATT+TGG + chr6_1:6177927-6177946 None:intergenic 20.0%
!!! TTTTTTTATTCTAGACTCTT+GGG - chr6_1:6177999-6178018 Msa0871290:three_prime_UTR 20.0%
!!! TATTCTAATGCAAATTTTGT+AGG + chr6_1:6178148-6178167 None:intergenic 20.0%
!!! GTTTTTGAAAACATTGCTTA+AGG + chr6_1:6177878-6177897 None:intergenic 25.0%
!!! CTTTTTTTATTCTAGACTCT+TGG - chr6_1:6177998-6178017 Msa0871290:three_prime_UTR 25.0%
! CAAAATTGAAGTGAATGAAA+AGG + chr6_1:6178085-6178104 None:intergenic 25.0%
! AAGAAGCAGAAACATAAAAA+AGG + chr6_1:6178123-6178142 None:intergenic 25.0%
! TGAAAAATCGATTGCAAAAT+CGG - chr6_1:6178235-6178254 Msa0871290:CDS 25.0%
! ATACACGAGTAAGAAAATTA+AGG + chr6_1:6178298-6178317 None:intergenic 25.0%
!!! ATTGATGATGTTTTCTTTGA+TGG + chr6_1:6178393-6178412 None:intergenic 25.0%
!! ATAATTCTCTTCTTGTTGTA+AGG + chr6_1:6178797-6178816 None:intergenic 25.0%
! ACAAGAAGAGAATTATACTT+TGG - chr6_1:6178801-6178820 Msa0871290:CDS 25.0%
!!! GTTTTTGAAAACATTGCTTA+AGG + chr6_1:6177878-6177897 None:intergenic 25.0%
!!! CTTTTTTTATTCTAGACTCT+TGG - chr6_1:6177998-6178017 Msa0871290:three_prime_UTR 25.0%
! CAAAATTGAAGTGAATGAAA+AGG + chr6_1:6178085-6178104 None:intergenic 25.0%
! AAGAAGCAGAAACATAAAAA+AGG + chr6_1:6178123-6178142 None:intergenic 25.0%
! TGAAAAATCGATTGCAAAAT+CGG - chr6_1:6178235-6178254 Msa0871290:CDS 25.0%
! ATACACGAGTAAGAAAATTA+AGG + chr6_1:6178298-6178317 None:intergenic 25.0%
!!! ATTGATGATGTTTTCTTTGA+TGG + chr6_1:6178393-6178412 None:intergenic 25.0%
!! ATAATTCTCTTCTTGTTGTA+AGG + chr6_1:6178797-6178816 None:intergenic 25.0%
! ACAAGAAGAGAATTATACTT+TGG - chr6_1:6178801-6178820 Msa0871290:CDS 25.0%
! GAGATAACAATACTTTTCCA+AGG + chr6_1:6178041-6178060 None:intergenic 30.0%
!! TGGAAAAGTATTGTTATCTC+TGG - chr6_1:6178041-6178060 Msa0871290:three_prime_UTR 30.0%
GAAGTGAATGAAAAGGTAAA+GGG + chr6_1:6178078-6178097 None:intergenic 30.0%
TGAAGTGAATGAAAAGGTAA+AGG + chr6_1:6178079-6178098 None:intergenic 30.0%
GATTTGTGAAAGTGATTGTT+TGG - chr6_1:6178696-6178715 Msa0871290:intron 30.0%
AACCATTCTCCAAATCTTTA+AGG - chr6_1:6178771-6178790 Msa0871290:intron 30.0%
! GAGATAACAATACTTTTCCA+AGG + chr6_1:6178041-6178060 None:intergenic 30.0%
!! TGGAAAAGTATTGTTATCTC+TGG - chr6_1:6178041-6178060 Msa0871290:three_prime_UTR 30.0%
GAAGTGAATGAAAAGGTAAA+GGG + chr6_1:6178078-6178097 None:intergenic 30.0%
TGAAGTGAATGAAAAGGTAA+AGG + chr6_1:6178079-6178098 None:intergenic 30.0%
GATTTGTGAAAGTGATTGTT+TGG - chr6_1:6178696-6178715 Msa0871290:intron 30.0%
AACCATTCTCCAAATCTTTA+AGG - chr6_1:6178771-6178790 Msa0871290:intron 30.0%
TGATGCATCAAGTGATCATT+TGG + chr6_1:6177951-6177970 None:intergenic 35.0%
!! TTGCAATCGATTTTTCAACC+TGG + chr6_1:6178232-6178251 None:intergenic 35.0%
ATGTTGTCATCGAGTTTAGA+AGG + chr6_1:6178420-6178439 None:intergenic 35.0%
ATTTGAAGGAGACTTGATGA+GGG + chr6_1:6178451-6178470 None:intergenic 35.0%
! ATTCAAACATTTTCAGCCAC+CGG + chr6_1:6178477-6178496 None:intergenic 35.0%
CACACTAGCTAAAATCATAC+AGG + chr6_1:6178548-6178567 None:intergenic 35.0%
! GTGTAGATTTTCCCATGATA+AGG - chr6_1:6178565-6178584 Msa0871290:intron 35.0%
! AGATTTTCCCATGATAAGGT+TGG - chr6_1:6178569-6178588 Msa0871290:intron 35.0%
! TTTTCCCATTATGAGGTTAG+TGG - chr6_1:6178598-6178617 Msa0871290:intron 35.0%
TTTCCCATTATGAGGTTAGT+GGG - chr6_1:6178599-6178618 Msa0871290:intron 35.0%
ATCGACATTTGTCATAATCG+AGG - chr6_1:6178661-6178680 Msa0871290:intron 35.0%
TTGGAAGCTGTGAATATCAT+TGG - chr6_1:6178715-6178734 Msa0871290:intron 35.0%
GTTGTAAGGCCTTAAAGATT+TGG + chr6_1:6178783-6178802 None:intergenic 35.0%
TGATGCATCAAGTGATCATT+TGG + chr6_1:6177951-6177970 None:intergenic 35.0%
!! TTGCAATCGATTTTTCAACC+TGG + chr6_1:6178232-6178251 None:intergenic 35.0%
ATGTTGTCATCGAGTTTAGA+AGG + chr6_1:6178420-6178439 None:intergenic 35.0%
ATTTGAAGGAGACTTGATGA+GGG + chr6_1:6178451-6178470 None:intergenic 35.0%
! ATTCAAACATTTTCAGCCAC+CGG + chr6_1:6178477-6178496 None:intergenic 35.0%
CACACTAGCTAAAATCATAC+AGG + chr6_1:6178548-6178567 None:intergenic 35.0%
! GTGTAGATTTTCCCATGATA+AGG - chr6_1:6178565-6178584 Msa0871290:intron 35.0%
! AGATTTTCCCATGATAAGGT+TGG - chr6_1:6178569-6178588 Msa0871290:intron 35.0%
! TTTTCCCATTATGAGGTTAG+TGG - chr6_1:6178598-6178617 Msa0871290:intron 35.0%
TTTCCCATTATGAGGTTAGT+GGG - chr6_1:6178599-6178618 Msa0871290:intron 35.0%
ATCGACATTTGTCATAATCG+AGG - chr6_1:6178661-6178680 Msa0871290:intron 35.0%
TTGGAAGCTGTGAATATCAT+TGG - chr6_1:6178715-6178734 Msa0871290:intron 35.0%
GTTGTAAGGCCTTAAAGATT+TGG + chr6_1:6178783-6178802 None:intergenic 35.0%
ACTCTTGGGTGAATTTCTCT+GGG - chr6_1:6178013-6178032 Msa0871290:three_prime_UTR 40.0%
TAGACATCGATGTAGTTACC+AGG - chr6_1:6178211-6178230 Msa0871290:CDS 40.0%
TTTGAAGGAGACTTGATGAG+GGG + chr6_1:6178450-6178469 None:intergenic 40.0%
CATTTGAAGGAGACTTGATG+AGG + chr6_1:6178452-6178471 None:intergenic 40.0%
! TTTTCCCATGATAAGGTTGG+TGG - chr6_1:6178572-6178591 Msa0871290:intron 40.0%
! TTTCCCATGATAAGGTTGGT+GGG - chr6_1:6178573-6178592 Msa0871290:intron 40.0%
TTCCCATTATGAGGTTAGTG+GGG - chr6_1:6178600-6178619 Msa0871290:intron 40.0%
ATCCCCACTAACCTCATAAT+GGG + chr6_1:6178605-6178624 None:intergenic 40.0%
AACTGCGTGCTATACAGATA+GGG - chr6_1:6178638-6178657 Msa0871290:CDS 40.0%
GGCCTTAAAGATTTGGAGAA+TGG + chr6_1:6178776-6178795 None:intergenic 40.0%
ACTCTTGGGTGAATTTCTCT+GGG - chr6_1:6178013-6178032 Msa0871290:three_prime_UTR 40.0%
TAGACATCGATGTAGTTACC+AGG - chr6_1:6178211-6178230 Msa0871290:CDS 40.0%
TTTGAAGGAGACTTGATGAG+GGG + chr6_1:6178450-6178469 None:intergenic 40.0%
CATTTGAAGGAGACTTGATG+AGG + chr6_1:6178452-6178471 None:intergenic 40.0%
! TTTTCCCATGATAAGGTTGG+TGG - chr6_1:6178572-6178591 Msa0871290:intron 40.0%
! TTTCCCATGATAAGGTTGGT+GGG - chr6_1:6178573-6178592 Msa0871290:intron 40.0%
TTCCCATTATGAGGTTAGTG+GGG - chr6_1:6178600-6178619 Msa0871290:intron 40.0%
ATCCCCACTAACCTCATAAT+GGG + chr6_1:6178605-6178624 None:intergenic 40.0%
AACTGCGTGCTATACAGATA+GGG - chr6_1:6178638-6178657 Msa0871290:CDS 40.0%
GGCCTTAAAGATTTGGAGAA+TGG + chr6_1:6178776-6178795 None:intergenic 40.0%
GACTCTTGGGTGAATTTCTC+TGG - chr6_1:6178012-6178031 Msa0871290:three_prime_UTR 45.0%
! GTGAATTTCTCTGGGAACCT+TGG - chr6_1:6178021-6178040 Msa0871290:three_prime_UTR 45.0%
CAAGTCTCCTTCAAATGTGC+CGG - chr6_1:6178455-6178474 Msa0871290:intron 45.0%
!! TTCCCATGATAAGGTTGGTG+GGG - chr6_1:6178574-6178593 Msa0871290:intron 45.0%
ATCCCCACCAACCTTATCAT+GGG + chr6_1:6178579-6178598 None:intergenic 45.0%
AATCCCCACCAACCTTATCA+TGG + chr6_1:6178580-6178599 None:intergenic 45.0%
! GTGGGGATTTTCCCATTATG+AGG - chr6_1:6178591-6178610 Msa0871290:intron 45.0%
CATCCCCACTAACCTCATAA+TGG + chr6_1:6178606-6178625 None:intergenic 45.0%
GAACTGCGTGCTATACAGAT+AGG - chr6_1:6178637-6178656 Msa0871290:CDS 45.0%
GACTCTTGGGTGAATTTCTC+TGG - chr6_1:6178012-6178031 Msa0871290:three_prime_UTR 45.0%
! GTGAATTTCTCTGGGAACCT+TGG - chr6_1:6178021-6178040 Msa0871290:three_prime_UTR 45.0%
CAAGTCTCCTTCAAATGTGC+CGG - chr6_1:6178455-6178474 Msa0871290:intron 45.0%
!! TTCCCATGATAAGGTTGGTG+GGG - chr6_1:6178574-6178593 Msa0871290:intron 45.0%
ATCCCCACCAACCTTATCAT+GGG + chr6_1:6178579-6178598 None:intergenic 45.0%
AATCCCCACCAACCTTATCA+TGG + chr6_1:6178580-6178599 None:intergenic 45.0%
! GTGGGGATTTTCCCATTATG+AGG - chr6_1:6178591-6178610 Msa0871290:intron 45.0%
CATCCCCACTAACCTCATAA+TGG + chr6_1:6178606-6178625 None:intergenic 45.0%
GAACTGCGTGCTATACAGAT+AGG - chr6_1:6178637-6178656 Msa0871290:CDS 45.0%
GTCTCCTTCAAATGTGCCGG+TGG - chr6_1:6178458-6178477 Msa0871290:intron 55.0%
TCAGCCACCGGCACATTTGA+AGG + chr6_1:6178465-6178484 None:intergenic 55.0%
GGTTAGTGGGGATGCTCTCT+TGG - chr6_1:6178612-6178631 Msa0871290:intron 55.0%
GTCTCCTTCAAATGTGCCGG+TGG - chr6_1:6178458-6178477 Msa0871290:intron 55.0%
TCAGCCACCGGCACATTTGA+AGG + chr6_1:6178465-6178484 None:intergenic 55.0%
GGTTAGTGGGGATGCTCTCT+TGG - chr6_1:6178612-6178631 Msa0871290:intron 55.0%
Chromosome Type Strat End Strand Name
chr6_1 gene 6177855 6178826 6177855 ID=Msa0871290;Name=Msa0871290
chr6_1 mRNA 6177855 6178826 6177855 ID=Msa0871290-mRNA-1;Parent=Msa0871290;Name=Msa0871290-mRNA-1;_AED=0.29;_eAED=0.29;_QI=0|0.5|0.33|0.66|0|0.66|3|332|86
chr6_1 exon 6177855 6178342 6177855 ID=Msa0871290-mRNA-1:exon:1912;Parent=Msa0871290-mRNA-1
chr6_1 exon 6178619 6178668 6178619 ID=Msa0871290-mRNA-1:exon:1911;Parent=Msa0871290-mRNA-1
chr6_1 exon 6178772 6178826 6178772 ID=Msa0871290-mRNA-1:exon:1910;Parent=Msa0871290-mRNA-1
chr6_1 CDS 6178772 6178826 6178772 ID=Msa0871290-mRNA-1:cds;Parent=Msa0871290-mRNA-1
chr6_1 CDS 6178619 6178668 6178619 ID=Msa0871290-mRNA-1:cds;Parent=Msa0871290-mRNA-1
chr6_1 CDS 6178187 6178342 6178187 ID=Msa0871290-mRNA-1:cds;Parent=Msa0871290-mRNA-1
chr6_1 three_prime_UTR 6177855 6178186 6177855 ID=Msa0871290-mRNA-1:three_prime_utr;Parent=Msa0871290-mRNA-1
Gene Sequence

>Msa0871290

ATGTCATTTTTCATGTACTGCCTTAAGCAATGTTTTCAAAAACGAACACATTATAACTCTTGGGTGAATTTCTCTGGGAACCTTGGAAAAGTATTGTTATCTCTGGTTTGTATGTTCTTTGATCTTCTTTTCATGTGTCAACATTATGTGTTGTATCCATCAAAGAAAACATCATCAATTTCTCCTTCTAAACTCGATGACAACATCAAAGAGCCCCTCATCAAGTCTCCTTCAAATGTGCCGGTGGCTGAAAATGTTTGA

Protein sequence

>Msa0871290

MSFFMYCLKQCFQKRTHYNSWVNFSGNLGKVLLSLVCMFFDLLFMCQHYVLYPSKKTSSISPSKLDDNIKEPLIKSPSNVPVAENV*