AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene049711


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene049711.t1 MTR_3g064750 92.537 201 14 1 1 201 75 274 6.68e-138 386
MS.gene049711.t1 MTR_3g064750 82.258 124 18 2 1 124 75 194 1.20e-66 203
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene049711.t1 AT2G01990 37.745 204 97 6 21 201 17 213 2.50e-33 119
MS.gene049711.t1 AT2G01990 37.745 204 97 6 21 201 48 244 8.03e-33 118
MS.gene049711.t1 AT1G14630 37.037 189 101 6 21 201 48 226 1.99e-28 106
MS.gene049711.t1 AT5G48720 43.373 83 38 3 120 201 192 266 1.22e-11 62.4
MS.gene049711.t1 AT5G48720 43.373 83 38 3 120 201 192 266 1.22e-11 62.4
MS.gene049711.t1 AT5G48720 43.373 83 38 3 120 201 226 300 1.33e-11 62.8
MS.gene049711.t1 AT5G48720 43.373 83 38 3 120 201 226 300 1.33e-11 62.8

Find 48 sgRNAs with CRISPR-Local

Find 91 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AACCGTGGTTATGGTATTTC+AGG 0.166700 3.3:+58414451 MS.gene049711:CDS
TATACATACCTTGAAGTAAT+TGG 0.169435 3.3:-58413723 None:intergenic
CAATCACTGGCTGGGATATT+TGG 0.233908 3.3:+58413491 MS.gene049711:CDS
TTTCCTTTCCTCCATGGAAT+TGG 0.298126 3.3:+58412913 None:intergenic
GAGGCTCCATTACCATTATT+AGG 0.327547 3.3:+58414515 MS.gene049711:CDS
TCAACCTTTAGTCCTAATAA+TGG 0.328259 3.3:-58414527 None:intergenic
TTGAAGTAATTGGGCTGCTT+TGG 0.351121 3.3:-58413713 None:intergenic
TGTATTTCAAACCGTGGTTA+TGG 0.353486 3.3:+58414442 MS.gene049711:CDS
GGATGTGGAATTGGCTTTGA+TGG 0.358593 3.3:-58414388 None:intergenic
ACAGCCACAGGATGTGGAAT+TGG 0.391650 3.3:-58414397 None:intergenic
ACTCATTCAGATTTAACTCT+TGG 0.392699 3.3:+58412947 MS.gene049711:CDS
CCAGGTTTCACCAGCTCAAA+TGG 0.394842 3.3:-58414310 None:intergenic
GAAGAAAATGTTGGAAATAG+AGG 0.396185 3.3:-58413691 None:intergenic
CTAGATGCACAACTTCTTTG+AGG 0.400638 3.3:-58414101 None:intergenic
TTGATGGACTCATCATCATT+TGG 0.401207 3.3:-58414372 None:intergenic
ATTACCATTATTAGGACTAA+AGG 0.415904 3.3:+58414523 MS.gene049711:CDS
ATACATACCTTGAAGTAATT+GGG 0.433333 3.3:-58413722 None:intergenic
AAGAAGTGGCAGCACTTACT+AGG 0.434363 3.3:+58414476 MS.gene049711:CDS
TTGAAGATGCAATCACTGGC+TGG 0.441092 3.3:+58413482 MS.gene049711:CDS
GTGAAACCTGGTGGAGTTGA+AGG 0.442086 3.3:+58414322 MS.gene049711:CDS
TTTAGTCCTAATAATGGTAA+TGG 0.443297 3.3:-58414521 None:intergenic
TATGATCTTGTGATGATGAT+AGG 0.443790 3.3:-58414049 None:intergenic
AACCTACTCTCAAGATCAAA+AGG 0.460972 3.3:+58413534 MS.gene049711:CDS
AAAGCAGCCCAATTACTTCA+AGG 0.465374 3.3:+58413715 MS.gene049711:CDS
TCTTCTACAGCCACAGGATG+TGG 0.472779 3.3:-58414403 None:intergenic
GTCTCCCCTTCAACTCCACC+AGG 0.476119 3.3:-58414328 None:intergenic
CACTTACTAGGATTCAAACT+AGG 0.484716 3.3:+58414488 MS.gene049711:CDS
CCTGTGGCTGTAGAAGATTA+TGG 0.497843 3.3:+58414409 MS.gene049711:CDS
CCATTTGAGCTGGTGAAACC+TGG 0.512570 3.3:+58414310 MS.gene049711:CDS
GATTCCAATGTCCAATTCCA+TGG 0.514674 3.3:-58412924 None:intergenic
ACTTACTAGGATTCAAACTA+GGG 0.519902 3.3:+58414489 MS.gene049711:CDS
TCCTCCATGGAATTGGACAT+TGG 0.529804 3.3:+58412920 None:intergenic
AGGATTCAAACTAGGGGTAG+AGG 0.539013 3.3:+58414496 MS.gene049711:CDS
GCTGCTTTGGAAGAAAATGT+TGG 0.550147 3.3:-58413700 None:intergenic
TGAAGATGCAATCACTGGCT+GGG 0.560320 3.3:+58413483 MS.gene049711:CDS
AATAGCTTATCCATTTGAGC+TGG 0.561873 3.3:+58414300 MS.gene049711:CDS
TGAAACCTGGTGGAGTTGAA+GGG 0.567199 3.3:+58414323 MS.gene049711:CDS
CCATAATCTTCTACAGCCAC+AGG 0.574350 3.3:-58414409 None:intergenic
TATCTTGAAGATGCAATCAC+TGG 0.588676 3.3:+58413478 MS.gene049711:CDS
CAAAGAAGTTGTGCATCTAG+AGG 0.590256 3.3:+58414104 MS.gene049711:CDS
TGGTATTTCAGGAAAAGAAG+TGG 0.597344 3.3:+58414462 MS.gene049711:CDS
TTTGCAGCTGATACATCAAG+TGG 0.606270 3.3:+58413454 MS.gene049711:CDS
GAAACCTGGTGGAGTTGAAG+GGG 0.620257 3.3:+58414324 MS.gene049711:CDS
CATCAATGTATTTCAAACCG+TGG 0.631525 3.3:+58414436 MS.gene049711:CDS
TTCCTGAAATACCATAACCA+CGG 0.632367 3.3:-58414453 None:intergenic
AAAGCCAATTCCACATCCTG+TGG 0.636787 3.3:+58414393 MS.gene049711:CDS
TTTGAGCTGGTGAAACCTGG+TGG 0.670776 3.3:+58414313 MS.gene049711:CDS
CTTACTAGGATTCAAACTAG+GGG 0.738551 3.3:+58414490 MS.gene049711:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TAATAAAAAAACAAAATGTT+TGG + chr3.3:58413657-58413676 MS.gene049711:intron 10.0%
!! CAATCATTTGAAAATAATTT+CGG + chr3.3:58413810-58413829 MS.gene049711:intron 15.0%
!!! TAGGTTATTATTTCTAATTT+TGG + chr3.3:58413942-58413961 MS.gene049711:intron 15.0%
!! TAACCTAAAGTTAAAATGTT+AGG - chr3.3:58413929-58413948 None:intergenic 20.0%
!!! ATTATGTTTTGATGTAACTA+GGG + chr3.3:58414263-58414282 MS.gene049711:intron 20.0%
! ACCATAAAAAATTCAACACT+AGG + chr3.3:58414024-58414043 MS.gene049711:CDS 25.0%
! ATACATACCTTGAAGTAATT+GGG - chr3.3:58413725-58413744 None:intergenic 25.0%
! ATGAAACAGAGAAGATAAAT+TGG - chr3.3:58413849-58413868 None:intergenic 25.0%
! ATTACCATTATTAGGACTAA+AGG + chr3.3:58414523-58414542 MS.gene049711:CDS 25.0%
! CAATCATGTATTACTAGATT+TGG + chr3.3:58413782-58413801 MS.gene049711:intron 25.0%
! CTAAAGTTAAAATGTTAGGT+TGG - chr3.3:58413925-58413944 None:intergenic 25.0%
! CTAGTTACATCAAAACATAA+TGG - chr3.3:58414264-58414283 None:intergenic 25.0%
! TAATAAATCAGCAAGTGAAA+AGG - chr3.3:58412985-58413004 None:intergenic 25.0%
! TATACATACCTTGAAGTAAT+TGG - chr3.3:58413726-58413745 None:intergenic 25.0%
! TCAAAACATAATGGTACAAA+AGG - chr3.3:58414255-58414274 None:intergenic 25.0%
! TTCAATGTAATCACAAATGT+CGG - chr3.3:58413293-58413312 None:intergenic 25.0%
! TTTAGTCCTAATAATGGTAA+TGG - chr3.3:58414524-58414543 None:intergenic 25.0%
!!! CAACCTAACATTTTAACTTT+AGG + chr3.3:58413923-58413942 MS.gene049711:intron 25.0%
!!! CATTATGTTTTGATGTAACT+AGG + chr3.3:58414262-58414281 MS.gene049711:intron 25.0%
!!! TCCTAGTGTTGAATTTTTTA+TGG - chr3.3:58414028-58414047 None:intergenic 25.0%
!!! TTATGTTTTGATGTAACTAG+GGG + chr3.3:58414264-58414283 MS.gene049711:intron 25.0%
ACTCATTCAGATTTAACTCT+TGG + chr3.3:58412947-58412966 MS.gene049711:CDS 30.0%
ACTTACTAGGATTCAAACTA+GGG + chr3.3:58414489-58414508 MS.gene049711:CDS 30.0%
ATATACTACTAGATGACACT+TGG + chr3.3:58413057-58413076 MS.gene049711:intron 30.0%
ATTCTACTTGTTTGTGATCT+TGG + chr3.3:58413095-58413114 MS.gene049711:intron 30.0%
CAAGTAGAATAAGATCATAG+TGG - chr3.3:58413085-58413104 None:intergenic 30.0%
GAAGAAAATGTTGGAAATAG+AGG - chr3.3:58413694-58413713 None:intergenic 30.0%
GATTCAGCAGCTATATAATA+AGG + chr3.3:58413876-58413895 MS.gene049711:intron 30.0%
GTCATCTAGTAGTATATTCT+TGG - chr3.3:58413054-58413073 None:intergenic 30.0%
TCAACCTTTAGTCCTAATAA+TGG - chr3.3:58414530-58414549 None:intergenic 30.0%
TTCTGATTGAAGATGTGTTT+CGG + chr3.3:58413244-58413263 MS.gene049711:intron 30.0%
! TATGATCTTGTGATGATGAT+AGG - chr3.3:58414052-58414071 None:intergenic 30.0%
!!! TATGTTTTGATGTAACTAGG+GGG + chr3.3:58414265-58414284 MS.gene049711:intron 30.0%
AACAAAATGTTTGGTTGAGC+AGG + chr3.3:58413666-58413685 MS.gene049711:intron 35.0%
AACCTACTCTCAAGATCAAA+AGG + chr3.3:58413534-58413553 MS.gene049711:CDS 35.0%
AATAGCTTATCCATTTGAGC+TGG + chr3.3:58414300-58414319 MS.gene049711:CDS 35.0%
AATCAGAAATGTCTGCAACA+AGG - chr3.3:58413232-58413251 None:intergenic 35.0%
CACTTACTAGGATTCAAACT+AGG + chr3.3:58414488-58414507 MS.gene049711:CDS 35.0%
CATCAATGTATTTCAAACCG+TGG + chr3.3:58414436-58414455 MS.gene049711:CDS 35.0%
CTTACTAGGATTCAAACTAG+GGG + chr3.3:58414490-58414509 MS.gene049711:CDS 35.0%
GGTTAACTAACAACTATGCA+TGG + chr3.3:58413555-58413574 MS.gene049711:intron 35.0%
TATCTTGAAGATGCAATCAC+TGG + chr3.3:58413478-58413497 MS.gene049711:CDS 35.0%
TGGTATTTCAGGAAAAGAAG+TGG + chr3.3:58414462-58414481 MS.gene049711:CDS 35.0%
TGTATATATATACCCCCTTG+TGG + chr3.3:58413740-58413759 MS.gene049711:intron 35.0%
TGTATTTCAAACCGTGGTTA+TGG + chr3.3:58414442-58414461 MS.gene049711:CDS 35.0%
TTCCTGAAATACCATAACCA+CGG - chr3.3:58414456-58414475 None:intergenic 35.0%
! AAAGTAATTTGCAGTGTCAG+TGG - chr3.3:58413997-58414016 None:intergenic 35.0%
! AACCTTTTGATCTTGAGAGT+AGG - chr3.3:58413539-58413558 None:intergenic 35.0%
! GTGACTTTTCTCAATCATGA+TGG - chr3.3:58413163-58413182 None:intergenic 35.0%
! TTTTGATCTTGAGAGTAGGT+TGG - chr3.3:58413535-58413554 None:intergenic 35.0%
!! TTGATGGACTCATCATCATT+TGG - chr3.3:58414375-58414394 None:intergenic 35.0%
!!! GTCTGCTTATTTTGTCTCTA+TGG + chr3.3:58413409-58413428 MS.gene049711:intron 35.0%
AAAGCAGCCCAATTACTTCA+AGG + chr3.3:58413715-58413734 MS.gene049711:CDS 40.0%
AACCGTGGTTATGGTATTTC+AGG + chr3.3:58414451-58414470 MS.gene049711:CDS 40.0%
CAAAGAAGTTGTGCATCTAG+AGG + chr3.3:58414104-58414123 MS.gene049711:CDS 40.0%
CTAGATGCACAACTTCTTTG+AGG - chr3.3:58414104-58414123 None:intergenic 40.0%
GAGGCTCCATTACCATTATT+AGG + chr3.3:58414515-58414534 MS.gene049711:CDS 40.0%
TCACACTTTGAACCTTCTCA+CGG + chr3.3:58413179-58413198 MS.gene049711:intron 40.0%
TTGAAGTAATTGGGCTGCTT+TGG - chr3.3:58413716-58413735 None:intergenic 40.0%
TTTGCAGCTGATACATCAAG+TGG + chr3.3:58413454-58413473 MS.gene049711:CDS 40.0%
!! GCTGCTTTGGAAGAAAATGT+TGG - chr3.3:58413703-58413722 None:intergenic 40.0%
AAAGCCAATTCCACATCCTG+TGG + chr3.3:58414393-58414412 MS.gene049711:CDS 45.0%
AAGAAGTGGCAGCACTTACT+AGG + chr3.3:58414476-58414495 MS.gene049711:CDS 45.0%
AGGATTCAAACTAGGGGTAG+AGG + chr3.3:58414496-58414515 MS.gene049711:CDS 45.0%
ATATACCCCCTTGTGGAATG+TGG + chr3.3:58413747-58413766 MS.gene049711:intron 45.0%
ATGCAACCACATTCCACAAG+GGG - chr3.3:58413756-58413775 None:intergenic 45.0%
CAGCAAACACAACACTGACA+CGG - chr3.3:58413356-58413375 None:intergenic 45.0%
CCATAATCTTCTACAGCCAC+AGG - chr3.3:58414412-58414431 None:intergenic 45.0%
CCTGTGGCTGTAGAAGATTA+TGG + chr3.3:58414409-58414428 MS.gene049711:CDS 45.0%
GATGCAACCACATTCCACAA+GGG - chr3.3:58413757-58413776 None:intergenic 45.0%
GTCTCTATGAAGCACAGACA+CGG - chr3.3:58413380-58413399 None:intergenic 45.0%
TCTGCAACAAGGACTCAGTT+TGG - chr3.3:58413221-58413240 None:intergenic 45.0%
TGAAACCTGGTGGAGTTGAA+GGG + chr3.3:58414323-58414342 MS.gene049711:CDS 45.0%
TGATGCAACCACATTCCACA+AGG - chr3.3:58413758-58413777 None:intergenic 45.0%
TTGAAGATGCAATCACTGGC+TGG + chr3.3:58413482-58413501 MS.gene049711:CDS 45.0%
! CAATCACTGGCTGGGATATT+TGG + chr3.3:58413491-58413510 MS.gene049711:CDS 45.0%
! GTAATTTGCAGTGTCAGTGG+TGG - chr3.3:58413994-58414013 None:intergenic 45.0%
! GTGCTTTTACAGCTGAGTCT+TGG + chr3.3:58413431-58413450 MS.gene049711:intron 45.0%
! TGAAGATGCAATCACTGGCT+GGG + chr3.3:58413483-58413502 MS.gene049711:CDS 45.0%
!! GGATGTGGAATTGGCTTTGA+TGG - chr3.3:58414391-58414410 None:intergenic 45.0%
ACAGCCACAGGATGTGGAAT+TGG - chr3.3:58414400-58414419 None:intergenic 50.0%
ATCACGACAACACCGTGAGA+AGG - chr3.3:58413194-58413213 None:intergenic 50.0%
CCAGGTTTCACCAGCTCAAA+TGG - chr3.3:58414313-58414332 None:intergenic 50.0%
CCATTTGAGCTGGTGAAACC+TGG + chr3.3:58414310-58414329 MS.gene049711:CDS 50.0%
GAAACCTGGTGGAGTTGAAG+GGG + chr3.3:58414324-58414343 MS.gene049711:CDS 50.0%
GTGAAACCTGGTGGAGTTGA+AGG + chr3.3:58414322-58414341 MS.gene049711:CDS 50.0%
TCTTCTACAGCCACAGGATG+TGG - chr3.3:58414406-58414425 None:intergenic 50.0%
TGATGTAACTAGGGGGACAG+TGG + chr3.3:58414272-58414291 MS.gene049711:intron 50.0%
TGCAACCACATTCCACAAGG+GGG - chr3.3:58413755-58413774 None:intergenic 50.0%
TTTGAGCTGGTGAAACCTGG+TGG + chr3.3:58414313-58414332 MS.gene049711:CDS 50.0%
GTCTCCCCTTCAACTCCACC+AGG - chr3.3:58414331-58414350 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr3.3 gene 58412926 58414549 58412926 ID=MS.gene049711
chr3.3 mRNA 58412926 58414549 58412926 ID=MS.gene049711.t1;Parent=MS.gene049711
chr3.3 exon 58412926 58412968 58412926 ID=MS.gene049711.t1.exon1;Parent=MS.gene049711.t1
chr3.3 CDS 58412926 58412968 58412926 ID=cds.MS.gene049711.t1;Parent=MS.gene049711.t1
chr3.3 exon 58413443 58413555 58413443 ID=MS.gene049711.t1.exon2;Parent=MS.gene049711.t1
chr3.3 CDS 58413443 58413555 58413443 ID=cds.MS.gene049711.t1;Parent=MS.gene049711.t1
chr3.3 exon 58413685 58413736 58413685 ID=MS.gene049711.t1.exon3;Parent=MS.gene049711.t1
chr3.3 CDS 58413685 58413736 58413685 ID=cds.MS.gene049711.t1;Parent=MS.gene049711.t1
chr3.3 exon 58414024 58414155 58414024 ID=MS.gene049711.t1.exon4;Parent=MS.gene049711.t1
chr3.3 CDS 58414024 58414155 58414024 ID=cds.MS.gene049711.t1;Parent=MS.gene049711.t1
chr3.3 exon 58414284 58414549 58414284 ID=MS.gene049711.t1.exon5;Parent=MS.gene049711.t1
chr3.3 CDS 58414284 58414549 58414284 ID=cds.MS.gene049711.t1;Parent=MS.gene049711.t1
Gene Sequence

>MS.gene049711

ATGGAATTGGACATTGGAATCACTCATTCAGATTTAACTCTTGGTATTTTTGCTATCCTTTTCACTTGCTGATTTATTATTTATCTTTATTTTTTTCATTTTCATTTTCTTTGATTCACTTGTTACCAAGAATATACTACTAGATGACACTTGGCACCACTATGATCTTATTCTACTTGTTTGTGATCTTGGTCTATATTTAGATTGACAGTGAATCTAGTAGAATCACATTTGCCATCATGATTGAGAAAAGTCACACTTTGAACCTTCTCACGGTGTTGTCGTGATTTTGCCAAACTGAGTCCTTGTTGCAGACATTTCTGATTGAAGATGTGTTTCGGTATCAGACACTTATCGTACTACACCGACATTTGTGATTACATTGAATTATGTTATTTAAAATAAAAAAAAAACTGTGTCAACGTGTCCGTGTCAGTGTTGTGTTTGCTGTCCGTGTCTGTGCTTCATAGAGACTCACTGTATGTCTGCTTATTTTGTCTCTATGGTGCTTTTACAGCTGAGTCTTGGTTTGCAGCTGATACATCAAGTGGATATCTTGAAGATGCAATCACTGGCTGGGATATTTGGTGCAAGCAAAATAACTTACCAACCTACTCTCAAGATCAAAAGGTTAACTAACAACTATGCATGGTTTCATGTTCTTTACATTTGCTTAATTGTTATTTCATAGTTTTTATTTGTCAAATATGTTGAAACTTTATAAGATATATTAATAAAAAAACAAAATGTTTGGTTGAGCAGGAACCTCTATTTCCAACATTTTCTTCCAAAGCAGCCCAATTACTTCAAGGTATGTATATATATACCCCCTTGTGGAATGTGGTTGCATCACTTTCAATCATGTATTACTAGATTTGGAAAATCAATCATTTGAAAATAATTTCGGTTATTTATCTAGTCCAATTTATCTTCTCTGTTTCATGTTTACTGATTCAGCAGCTATATAATAAGGAGTTAAGAATTTGCAATAAATGACCAACCTAACATTTTAACTTTAGGTTATTATTTCTAATTTTGGTAGTATTGAAAGTAATTGAACTATATCCACCACTGACACTGCAAATTACTTTTTTACAGACCATAAAAAATTCAACACTAGGAACCTATCATCATCACAAGATCATACACATTCAGCTGCAGTAAATCATGATTCACCTCAAAGAAGTTGTGCATCTAGAGGATCAAATGAAAATGTTGCTTCTGTTTCAAGTACAAAATTCTTTTACTGTTTTAACACAAGAACAATTTCTTGATCAATCATTTCATGTCTCTTTTCTAAAGTAATTTTTTATGACTAAAATGTGTCCTTTTGTACCATTATGTTTTGATGTAACTAGGGGGACAGTGGAAGAAAATAGCTTATCCATTTGAGCTGGTGAAACCTGGTGGAGTTGAAGGGGAGACAACAATTAAAGATATAAATCACCAAATGATGATGAGTCCATCAAAGCCAATTCCACATCCTGTGGCTGTAGAAGATTATGGTACTCATCAATGTATTTCAAACCGTGGTTATGGTATTTCAGGAAAAGAAGTGGCAGCACTTACTAGGATTCAAACTAGGGGTAGAGGCTCCATTACCATTATTAGGACTAAAGGTTGA

Protein sequence

>MS.gene049711.t1

MELDIGITHSDLTLAESWFAADTSSGYLEDAITGWDIWCKQNNLPTYSQDQKQEPLFPTFSSKAAQLLQDHKKFNTRNLSSSQDHTHSAAVNHDSPQRSCASRGSNENVASVSRGQWKKIAYPFELVKPGGVEGETTIKDINHQMMMSPSKPIPHPVAVEDYGTHQCISNRGYGISGKEVAALTRIQTRGRGSITIIRTKG