AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene52188

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene52188.t1 MTR_7g076530 96.296 81 3 0 1 81 1 81 1.99e-56 168
MS.gene52188.t1 MTR_2g436800 95.062 81 4 0 1 81 1 81 3.00e-55 165
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene52188.t1 AT5G27700 85.185 81 12 0 1 81 1 81 8.26e-51 154
MS.gene52188.t1 AT3G53890 80.247 81 16 0 1 81 1 81 1.61e-48 148
MS.gene52188.t1 AT3G53890 80.247 81 16 0 1 81 1 81 1.61e-48 148

Find 13 sgRNAs with CRISPR-Local

Find 82 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGCTCTACATTCCCAGAAAA+TGG 0.339849 7.4:+29122206 MS.gene52188:CDS
TCAGCTTAACATCGGTCATT+TGG 0.359324 7.4:+29122358 MS.gene52188:CDS
CTGTGGCTTCACTCGCGCAC+AGG 0.458896 7.4:+29122424 MS.gene52188:CDS
TACTGCCAAGGATCACGCTT+CGG 0.492236 7.4:+29122334 MS.gene52188:CDS
GAAGCCACAGAGGGCAAAAG+TGG 0.538865 7.4:-29122411 None:intergenic
CTGAACCGAAGCGTGATCCT+TGG 0.542452 7.4:-29122339 None:intergenic
AAATCGATTGATTACTGCCA+AGG 0.573907 7.4:+29122322 MS.gene52188:CDS
TGCGCGAGTGAAGCCACAGA+GGG 0.586789 7.4:-29122420 None:intergenic
TTCCAGGGAGATGCTGACAG+TGG 0.628839 7.4:+29123686 MS.gene52188:intron
GATGAAAGCAGTGTCTACAA+TGG 0.659648 7.4:+29122380 MS.gene52188:CDS
GCTTCGGTTCAGCTTAACAT+CGG 0.677252 7.4:+29122350 MS.gene52188:CDS
ACAGTGGAATTGATCGCTTG+TGG 0.696079 7.4:+29123702 MS.gene52188:CDS
GTGCGCGAGTGAAGCCACAG+AGG 0.703435 7.4:-29122421 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ACATAATTTTAATTAGCTTT+AGG + chr7.4:29122583-29122602 MS.gene52188:intron 15.0%
!! AAATAGTTCCTTAATTAAGA+TGG + chr7.4:29122949-29122968 MS.gene52188:intron 20.0%
!! ATCAGGAAATAAAGTTAAAA+TGG + chr7.4:29122632-29122651 MS.gene52188:intron 20.0%
!! ATCTTAATTAAGGAACTATT+TGG - chr7.4:29122950-29122969 None:intergenic 20.0%
!! ATTCAATACTAATCATGTTT+AGG + chr7.4:29122476-29122495 MS.gene52188:intron 20.0%
!! GATATAAACAGAATACAATA+TGG - chr7.4:29123565-29123584 None:intergenic 20.0%
!! TTCAATACTAATCATGTTTA+GGG + chr7.4:29122477-29122496 MS.gene52188:intron 20.0%
!!! CAAAAAAGAGCTTTTTATAA+GGG - chr7.4:29123004-29123023 None:intergenic 20.0%
!!! CTTATAAAAAGCTCTTTTTT+GGG + chr7.4:29123003-29123022 MS.gene52188:intron 20.0%
!!! TTATAAAAAGCTCTTTTTTG+GGG + chr7.4:29123004-29123023 MS.gene52188:intron 20.0%
!!! TTATGTCATTTTTATTTCCA+GGG + chr7.4:29123671-29123690 MS.gene52188:intron 20.0%
!!! TTTATATTTTGTGTAGTATC+TGG + chr7.4:29123037-29123056 MS.gene52188:intron 20.0%
!!! TTTTATGAATTGCATTTCTA+AGG + chr7.4:29123635-29123654 MS.gene52188:intron 20.0%
! AGAATCAACCATCTTAATTA+AGG - chr7.4:29122960-29122979 None:intergenic 25.0%
! AGTAAACAACATAAATGATC+AGG + chr7.4:29122615-29122634 MS.gene52188:intron 25.0%
! AGTGAAAAACTAAAAGTGAA+TGG + chr7.4:29123284-29123303 MS.gene52188:intron 25.0%
! CAACTAATACTTATAATCTG+CGG + chr7.4:29123241-29123260 MS.gene52188:intron 25.0%
! TAATTCCAACGTGTTTATAA+AGG - chr7.4:29123533-29123552 None:intergenic 25.0%
! TGAAAATTGATATGTTGCAA+TGG + chr7.4:29123346-29123365 MS.gene52188:intron 25.0%
! TGTTGAAAGTTAATGAAGTT+GGG + chr7.4:29123482-29123501 MS.gene52188:intron 25.0%
! TTAACAAATTATTATCGACG+TGG + chr7.4:29122829-29122848 MS.gene52188:intron 25.0%
! TTTAACCTTTATAAACACGT+TGG + chr7.4:29123525-29123544 MS.gene52188:intron 25.0%
!! CAAAGTATATACCATTTTCT+GGG - chr7.4:29122220-29122239 None:intergenic 25.0%
!! CATGTTTAGGGTATTTAAAT+TGG + chr7.4:29122489-29122508 MS.gene52188:intron 25.0%
!! CCAAAAAAGAGCTTTTTATA+AGG - chr7.4:29123005-29123024 None:intergenic 25.0%
!! TCAAAGTATATACCATTTTC+TGG - chr7.4:29122221-29122240 None:intergenic 25.0%
!!! CCTTATAAAAAGCTCTTTTT+TGG + chr7.4:29123002-29123021 MS.gene52188:intron 25.0%
!!! CGTTATTTGTTGATTTGATT+TGG + chr7.4:29122250-29122269 MS.gene52188:intron 25.0%
!!! GTTATGTCATTTTTATTTCC+AGG + chr7.4:29123670-29123689 MS.gene52188:intron 25.0%
!!! TTGTTGATTTGATTTGGTTA+TGG + chr7.4:29122256-29122275 MS.gene52188:intron 25.0%
GAACAACATAGTATGTTCAA+TGG - chr7.4:29123590-29123609 None:intergenic 30.0%
GTGTTGAAAGTTAATGAAGT+TGG + chr7.4:29123481-29123500 MS.gene52188:intron 30.0%
TCATAAAACCTGAATCATCA+AGG - chr7.4:29123623-29123642 None:intergenic 30.0%
! ATTGGATTTTGCATTTCTCT+TGG + chr7.4:29122507-29122526 MS.gene52188:intron 30.0%
! GTTGATTCTGTTTCTCATAA+TGG + chr7.4:29122971-29122990 MS.gene52188:intron 30.0%
! TTGGATTTTGCATTTCTCTT+GGG + chr7.4:29122508-29122527 MS.gene52188:intron 30.0%
AAATCGATTGATTACTGCCA+AGG + chr7.4:29122322-29122341 MS.gene52188:CDS 35.0%
AAGTGAACAAAGAAGGACAA+TGG + chr7.4:29123157-29123176 MS.gene52188:intron 35.0%
ACAACCATTTGCAAAGTTGT+GGG - chr7.4:29122903-29122922 None:intergenic 35.0%
ACTTTGTCATACTCTTCTTG+CGG - chr7.4:29123267-29123286 None:intergenic 35.0%
ATTGTCCTTCTTTGTTCACT+TGG - chr7.4:29123158-29123177 None:intergenic 35.0%
GTTAATGAAGTTGGGAACTA+TGG + chr7.4:29123490-29123509 MS.gene52188:intron 35.0%
TCATAGGTTGTGAGACTATT+TGG - chr7.4:29122716-29122735 None:intergenic 35.0%
TGATTCCAAGTGAACAAAGA+AGG + chr7.4:29123150-29123169 MS.gene52188:intron 35.0%
TTGTCCTGTATTTCATTCTG+TGG + chr7.4:29123071-29123090 MS.gene52188:intron 35.0%
! TTGATACACCTTGATGATTC+AGG + chr7.4:29123612-29123631 MS.gene52188:intron 35.0%
!!! GCTCTTTTTTGGGGAAAATT+TGG + chr7.4:29123013-29123032 MS.gene52188:intron 35.0%
AGCTCCACAGAATGAAATAC+AGG - chr7.4:29123078-29123097 None:intergenic 40.0%
AGCTCTACATTCCCAGAAAA+TGG + chr7.4:29122206-29122225 MS.gene52188:CDS 40.0%
ATAGCCCACAACTTTGCAAA+TGG + chr7.4:29122896-29122915 MS.gene52188:intron 40.0%
CAACTTTGCAAATGGTTGTG+TGG + chr7.4:29122904-29122923 MS.gene52188:intron 40.0%
CACAACCATTTGCAAAGTTG+TGG - chr7.4:29122904-29122923 None:intergenic 40.0%
GATGAAAGCAGTGTCTACAA+TGG + chr7.4:29122380-29122399 MS.gene52188:CDS 40.0%
TATTATCGACGTGGACTTGT+CGG + chr7.4:29122838-29122857 MS.gene52188:intron 40.0%
TCAGCTTAACATCGGTCATT+TGG + chr7.4:29122358-29122377 MS.gene52188:CDS 40.0%
!! TTTTCTGGGAATGTAGAGCT+CGG - chr7.4:29122206-29122225 None:intergenic 40.0%
ACAGTGGAATTGATCGCTTG+TGG + chr7.4:29123702-29123721 MS.gene52188:CDS 45.0%
ATGAAGCACGGAAACAAACC+CGG - chr7.4:29122878-29122897 None:intergenic 45.0%
GCTTCGGTTCAGCTTAACAT+CGG + chr7.4:29122350-29122369 MS.gene52188:CDS 45.0%
GTCTCACAACCTATGAAGCA+CGG + chr7.4:29122720-29122739 MS.gene52188:intron 45.0%
! AAGTTGTGGGCTATGAAGCA+CGG - chr7.4:29122890-29122909 None:intergenic 45.0%
!! TTTTCCACTTTTGCCCTCTG+TGG + chr7.4:29122407-29122426 MS.gene52188:CDS 45.0%
!!! TATGTTTATTTTATTTTTTT+TGG + chr7.4:29123428-29123447 MS.gene52188:intron 5.0%
TACTGCCAAGGATCACGCTT+CGG + chr7.4:29122334-29122353 MS.gene52188:CDS 50.0%
TATGAAGCACGGACACTCCT+CGG + chr7.4:29122731-29122750 MS.gene52188:intron 50.0%
! GTCGGTGTCTATGTCATGTC+CGG + chr7.4:29122856-29122875 MS.gene52188:intron 50.0%
! TCGGTGTCTATGTCATGTCC+GGG + chr7.4:29122857-29122876 MS.gene52188:intron 50.0%
CTGAACCGAAGCGTGATCCT+TGG - chr7.4:29122342-29122361 None:intergenic 55.0%
GAAGCCACAGAGGGCAAAAG+TGG - chr7.4:29122414-29122433 None:intergenic 55.0%
GATTAGGTCTGTCCCGGTGT+CGG + chr7.4:29122753-29122772 MS.gene52188:intron 55.0%
TTCCACTGTCAGCATCTCCC+TGG - chr7.4:29123691-29123710 None:intergenic 55.0%
TTCCAGGGAGATGCTGACAG+TGG + chr7.4:29123686-29123705 MS.gene52188:intron 55.0%
! TCCTCGGATTAGGTCTGTCC+CGG + chr7.4:29122747-29122766 MS.gene52188:intron 55.0%
!! GAGGAGTGTCCGTGCTTCAT+AGG - chr7.4:29122732-29122751 None:intergenic 55.0%
ACCGGGACAGACCTAATCCG+AGG - chr7.4:29122751-29122770 None:intergenic 60.0%
GCACGGACACTCCTCGGATT+AGG + chr7.4:29122737-29122756 MS.gene52188:intron 60.0%
TGCGCGAGTGAAGCCACAGA+GGG - chr7.4:29122423-29122442 None:intergenic 60.0%
ACCAACGCGTGTCCGACACC+GGG - chr7.4:29122768-29122787 None:intergenic 65.0%
CACCAACGCGTGTCCGACAC+CGG - chr7.4:29122769-29122788 None:intergenic 65.0%
CTGTGGCTTCACTCGCGCAC+AGG + chr7.4:29122424-29122443 MS.gene52188:CDS 65.0%
GTGCGCGAGTGAAGCCACAG+AGG - chr7.4:29122424-29122443 None:intergenic 65.0%
! TCCCGGTGTCGGACACGCGT+TGG + chr7.4:29122764-29122783 MS.gene52188:intron 70.0%


Chromosome Type Strat End Strand Name
chr7.4 gene 29122178 29123754 29122178 ID=MS.gene52188
chr7.4 mRNA 29122178 29123754 29122178 ID=MS.gene52188.t1;Parent=MS.gene52188
chr7.4 exon 29122178 29122227 29122178 ID=MS.gene52188.t1.exon1;Parent=MS.gene52188.t1
chr7.4 CDS 29122178 29122227 29122178 ID=cds.MS.gene52188.t1;Parent=MS.gene52188.t1
chr7.4 exon 29122313 29122445 29122313 ID=MS.gene52188.t1.exon2;Parent=MS.gene52188.t1
chr7.4 CDS 29122313 29122445 29122313 ID=cds.MS.gene52188.t1;Parent=MS.gene52188.t1
chr7.4 exon 29123692 29123754 29123692 ID=MS.gene52188.t1.exon3;Parent=MS.gene52188.t1
chr7.4 CDS 29123692 29123754 29123692 ID=cds.MS.gene52188.t1;Parent=MS.gene52188.t1
Gene Sequence

>MS.gene52188

ATGCAGAACGAAGAAGGGCAAATCACCGAGCTCTACATTCCCAGAAAATGGTATATACTTTGATCATAATCTCGTTATTTGTTGATTTGATTTGGTTATGGAATTTGAAAATCTGTGTTTGTCGATTTTGTTCAGTTCTGCTACAAATCGATTGATTACTGCCAAGGATCACGCTTCGGTTCAGCTTAACATCGGTCATTTGGATGAAAGCAGTGTCTACAATGGTCAATTTTCCACTTTTGCCCTCTGTGGCTTCACTCGCGCACAGGTCTCTAATTGTTAATTTACTGTGTTTTATATTCAATACTAATCATGTTTAGGGTATTTAAATTGGATTTTGCATTTCTCTTGGGTGATTTTGAATTGTTGTTGAGTTATGTTTGTGTAGTATTGTGTTATGTATGAACATAATTTTAATTAGCTTTAGGCTCTGTTTGAGTAAACAACATAAATGATCAGGAAATAAAGTTAAAATGGTTTTCGTATAGCTATATTAGCTATATGTTGTTGTTATATGCTCTTTTCATTAGCTTTTCCAAATAGTCTCACAACCTATGAAGCACGGACACTCCTCGGATTAGGTCTGTCCCGGTGTCGGACACGCGTTGGTGTTTGACACAGACACATATGATTACACTAAATTATGTCATTTTAACAAATTATTATCGACGTGGACTTGTCGGTGTCTATGTCATGTCCGGGTTTGTTTCCGTGCTTCATAGCCCACAACTTTGCAAATGGTTGTGTGGATAAGTTCGAATAACTCAATCCAAATAGTTCCTTAATTAAGATGGTTGATTCTGTTTCTCATAATGGTATTTTACCCTTATAAAAAGCTCTTTTTTGGGGAAAATTTGGTTTTATATTTTGTGTAGTATCTGGTGTTGTTTTAATTGTCCTGTATTTCATTCTGTGGAGCTTCTATTAGTTTAGATTGTATTTTTTTAGTCGATAGATTACAACATATTAATGTGATTCCAAGTGAACAAAGAAGGACAATGGCAGATAGAATTGTCAAGAATTTCATTGCATGAATTCTGAGTAAATTTGAACTGATAGTATACAACTAATACTTATAATCTGCGGCCGCAAGAAGAGTATGACAAAGTGAAAAACTAAAAGTGAATGGAACTAACATTGTCAACTTTTGTAAGAAAAAAAACGTAACTGAAAATTGATATGTTGCAATGGTTTTTATTCTTTAGAAACATATTGAAATATTGCTTTTAGTTTGTGTGACTGAATCATGATATGTTTATTTTATTTTTTTTGGTACAAGAATCATGATATTTTTATTAATGCTGTGTTGAAAGTTAATGAAGTTGGGAACTATGGTTGAAAAAAATATTTAACCTTTATAAACACGTTGGAATTACTCTCTGTACCATATTGTATTCTGTTTATATCAGCCATTGAACATACTATGTTGTTCTCTTGATACACCTTGATGATTCAGGTTTTATGAATTGCATTTCTAAGGTGCTGATTTCATGTTATGTCATTTTTATTTCCAGGGAGATGCTGACAGTGGAATTGATCGCTTGTGGCAGAAAAAGAAAGCTGAAATTAAGCAATAG
Protein sequence

>MS.gene52188.t1

MQNEEGQITELYIPRKCSATNRLITAKDHASVQLNIGHLDESSVYNGQFSTFALCGFTRAQGDADSGIDRLWQKKKAEIKQ