AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene56189


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene56189.t1 MTR_3g007700 100.000 171 0 0 1 171 12 182 7.71e-126 351
MS.gene56189.t1 MTR_4g080740 98.830 171 2 0 1 171 11 181 6.76e-125 348
MS.gene56189.t1 MTR_8g046140 98.830 171 2 0 1 171 11 181 7.22e-125 348
MS.gene56189.t1 MTR_3g007690 81.287 171 31 1 1 170 71 241 3.77e-98 283
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene56189.t1 AT2G42740 95.906 171 7 0 1 171 11 181 2.23e-121 340
MS.gene56189.t1 AT5G45775 95.322 171 8 0 1 171 11 181 9.50e-121 338
MS.gene56189.t1 AT4G18730 95.322 171 8 0 1 171 11 181 9.50e-121 338
MS.gene56189.t1 AT3G58700 95.322 171 8 0 1 171 11 181 9.50e-121 338
MS.gene56189.t1 AT5G45775 95.322 171 8 0 1 171 1 171 1.51e-120 337

Find 49 sgRNAs with CRISPR-Local

Find 100 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GATCCTTCCACTGGTATTTA+TGG 0.136205 3.3:-3753538 MS.gene56189:CDS
CAATTGCCTGGGACTTGTTT+AGG 0.246867 3.3:+3753374 None:intergenic
CGACAAGGCAATGCAGCTTT+TGG 0.255810 3.3:-3753951 MS.gene56189:CDS
TTCAGTGATACCGGATGTTT+TGG 0.275627 3.3:-3753884 MS.gene56189:CDS
TATCCAGGAACATATTGATT+TGG 0.290604 3.3:-3753855 MS.gene56189:CDS
TGCACTTTGATTTCCCTCAT+TGG 0.303574 3.3:+3754894 None:intergenic
GCATGCTACGTCACTGTTAG+AGG 0.353505 3.3:-3753974 MS.gene56189:CDS
ATCCAGGAACATATTGATTT+GGG 0.366765 3.3:-3753854 MS.gene56189:CDS
TATGGATTTCTTTGTTGTCT+TGG 0.372237 3.3:-3753515 MS.gene56189:CDS
TTTAACTTGGAACCACTTCA+TGG 0.385179 3.3:+3753411 None:intergenic
TTCCCAAATCAATATGTTCC+TGG 0.396627 3.3:+3753852 None:intergenic
TCCGTTCCTTTGGTATTAGA+AGG 0.399311 3.3:-3754009 MS.gene56189:CDS
AGAAAATACCTTAGCGGCTC+TGG 0.400111 3.3:+3754824 None:intergenic
TTCCACTGGTATTTATGGTA+TGG 0.405174 3.3:-3753533 MS.gene56189:CDS
AAAATACCTTTGGAGAAAAC+AGG 0.431508 3.3:+3754698 None:intergenic
AGGTACACGGTCCGTTCCTT+TGG 0.433646 3.3:-3754019 MS.gene56189:CDS
GATCTCACTAAACAATTGCC+TGG 0.468826 3.3:+3753362 None:intergenic
TCACACCTTCATATTTAACT+TGG 0.469248 3.3:+3753398 None:intergenic
TTTGTTGTCTTGGAGCGCCC+TGG 0.474962 3.3:-3753505 MS.gene56189:CDS
AACATCTCCGTCGGTGAAAG+TGG 0.484770 3.3:-3754858 MS.gene56189:CDS
CGACGTCCCACACGATAACC+AGG 0.485872 3.3:+3753487 None:intergenic
CATCCTTTGTGACACGATGT+TGG 0.510267 3.3:+3753437 None:intergenic
AGGAGAAACTTCAGTGATAC+CGG 0.515104 3.3:-3753893 MS.gene56189:CDS
TTCATTCCTTCTAATACCAA+AGG 0.519643 3.3:+3754003 None:intergenic
CGTAGGTGCAAGGCAAGAGT+TGG 0.526727 3.3:-3753463 MS.gene56189:CDS
TCGTCTCACCAGAGCCGCTA+AGG 0.538952 3.3:-3754832 MS.gene56189:intron
GGAGAGCGGTTTGAAGGTCA+AGG 0.545050 3.3:-3753930 MS.gene56189:CDS
ATACTGAGAAAATACCTTAG+CGG 0.552318 3.3:+3754818 None:intergenic
GAGCGCCCTGGTTATCGTGT+GGG 0.552380 3.3:-3753493 MS.gene56189:CDS
TTCAGGTATGATCCTTCCAC+TGG 0.557425 3.3:-3753547 MS.gene56189:intron
GATACCGAAGCCAAAACATC+CGG 0.566708 3.3:+3753874 None:intergenic
TGGTTCCAAGTTAAATATGA+AGG 0.567557 3.3:-3753403 MS.gene56189:CDS
TCAAGGAATATGAGCTGTTG+AGG 0.569136 3.3:-3753913 MS.gene56189:CDS
GGAGCGCCCTGGTTATCGTG+TGG 0.572642 3.3:-3753494 MS.gene56189:CDS
ATCTCACTAAACAATTGCCT+GGG 0.574406 3.3:+3753363 None:intergenic
TAGGTTCTTGAACAGCTAAG+TGG 0.586306 3.3:-3754728 MS.gene56189:CDS
TGTGATCCTAAACAAGTCCC+AGG 0.593737 3.3:-3753380 MS.gene56189:CDS
GGGACGTCGTCGTAGGTGCA+AGG 0.607035 3.3:-3753473 MS.gene56189:CDS
ATCGTGTGGGACGTCGTCGT+AGG 0.611248 3.3:-3753480 MS.gene56189:CDS
TCCTTCTAATACCAAAGGAA+CGG 0.611594 3.3:+3754008 None:intergenic
CAAAGGATGATGCCATGAAG+TGG 0.613790 3.3:-3753423 MS.gene56189:CDS
ATCCATACCATAAATACCAG+TGG 0.620651 3.3:+3753531 None:intergenic
CTTATTGACAGCTAGGTACA+CGG 0.623398 3.3:-3754032 MS.gene56189:intron
CTTGTACTCAACATCTCCGT+CGG 0.623554 3.3:-3754867 MS.gene56189:CDS
CGTCACTGTTAGAGGCGACA+AGG 0.626392 3.3:-3753966 MS.gene56189:CDS
ATACCATAAATACCAGTGGA+AGG 0.634245 3.3:+3753535 None:intergenic
ACGATCTCCACTTTCACCGA+CGG 0.653039 3.3:+3754851 None:intergenic
AATCCAACATCGTGTCACAA+AGG 0.664970 3.3:-3753440 MS.gene56189:CDS
GACGTCCCACACGATAACCA+GGG 0.726452 3.3:+3753488 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TAAATTATAAAAAATACCTT+TGG + chr3.3:3753575-3753594 None:intergenic 10.0%
!! TTTATTTGAAGAAAAATATT+CGG - chr3.3:3754569-3754588 MS.gene56189:intron 10.0%
!!! AATATTTTTCTTCAAATAAA+AGG + chr3.3:3754569-3754588 None:intergenic 10.0%
!!! CAAATAACATTAATTTATTT+TGG - chr3.3:3753844-3753863 MS.gene56189:intron 10.0%
!! AAAAAAATATACAAAGCAAA+AGG + chr3.3:3754623-3754642 None:intergenic 15.0%
!!! AAAATATATGTACAAGTTTT+TGG + chr3.3:3753818-3753837 None:intergenic 15.0%
!!! CATAATTTTAAACATCAATA+TGG + chr3.3:3754692-3754711 None:intergenic 15.0%
!! AAGAAAAAATTACTTCATAC+AGG - chr3.3:3753883-3753902 MS.gene56189:CDS 20.0%
!! ACTTAGAAATACATATTTCA+AGG - chr3.3:3754082-3754101 MS.gene56189:intron 20.0%
!!! ATGAAGTAATTTTTTCTTTC+CGG + chr3.3:3753881-3753900 None:intergenic 20.0%
!!! TCAATATTTGCTAGTTTTTT+AGG - chr3.3:3753786-3753805 MS.gene56189:intron 20.0%
!!! TTTGATTTTTTATGTCAATG+TGG - chr3.3:3754529-3754548 MS.gene56189:intron 20.0%
! AGGTTAGTAATGAAATTGAA+AGG + chr3.3:3753497-3753516 None:intergenic 25.0%
! ATACTAATGTTGTCAAAAAG+TGG - chr3.3:3753953-3753972 MS.gene56189:CDS 25.0%
! TAGTAATGAAATTGAAAGGA+AGG + chr3.3:3753493-3753512 None:intergenic 25.0%
!! ATATGTATTTCTAAGTGCAA+CGG + chr3.3:3754078-3754097 None:intergenic 25.0%
!! GATGTTTAAAATTATGCTTC+AGG - chr3.3:3754696-3754715 MS.gene56189:intron 25.0%
!!! GTTGTTTTCTTATGTTTCAA+AGG - chr3.3:3754652-3754671 MS.gene56189:intron 25.0%
!!! TGAAGTAATTTTTTCTTTCC+GGG + chr3.3:3753880-3753899 None:intergenic 25.0%
ATACTGAGAAAATACCTTAG+CGG + chr3.3:3753445-3753464 None:intergenic 30.0%
GAGTCAAATTCTCATCATTT+AGG - chr3.3:3754109-3754128 MS.gene56189:intron 30.0%
TAGAAAATGAAGAACCAATC+AGG + chr3.3:3754203-3754222 None:intergenic 30.0%
TCACACCTTCATATTTAACT+TGG + chr3.3:3754865-3754884 None:intergenic 30.0%
TGGTTCCAAGTTAAATATGA+AGG - chr3.3:3754857-3754876 MS.gene56189:CDS 30.0%
TTCATTCCTTCTAATACCAA+AGG + chr3.3:3754260-3754279 None:intergenic 30.0%
! AAAATACCTTTGGAGAAAAC+AGG + chr3.3:3753565-3753584 None:intergenic 30.0%
! GTGTCTTAAAATAGGGTTTT+TGG - chr3.3:3754024-3754043 MS.gene56189:CDS 30.0%
! TATCCAGGAACATATTGATT+TGG - chr3.3:3754405-3754424 MS.gene56189:intron 30.0%
! TATGGATTTCTTTGTTGTCT+TGG - chr3.3:3754745-3754764 MS.gene56189:intron 30.0%
!! ATCCAGGAACATATTGATTT+GGG - chr3.3:3754406-3754425 MS.gene56189:intron 30.0%
!!! TATTTTGGTTGACAAATTCC+CGG - chr3.3:3753859-3753878 MS.gene56189:CDS 30.0%
ACAGTTCTTTACATGCGTAT+TGG - chr3.3:3754155-3754174 MS.gene56189:intron 35.0%
ACATGCGTATTGGATATCTT+GGG - chr3.3:3754165-3754184 MS.gene56189:intron 35.0%
ACCTATGAGAAAGAGAAAAC+AGG + chr3.3:3753517-3753536 None:intergenic 35.0%
ATACCATAAATACCAGTGGA+AGG + chr3.3:3754728-3754747 None:intergenic 35.0%
ATCCATACCATAAATACCAG+TGG + chr3.3:3754732-3754751 None:intergenic 35.0%
ATGTACAGAACATGTCTACT+AGG + chr3.3:3753683-3753702 None:intergenic 35.0%
TACATGCGTATTGGATATCT+TGG - chr3.3:3754164-3754183 MS.gene56189:intron 35.0%
TATTGTGCTTATTGACAGCT+AGG - chr3.3:3754221-3754240 MS.gene56189:intron 35.0%
TCCTTCTAATACCAAAGGAA+CGG + chr3.3:3754255-3754274 None:intergenic 35.0%
TGCCATGGTGTCTTAAAATA+GGG - chr3.3:3754017-3754036 MS.gene56189:CDS 35.0%
TTCCACTGGTATTTATGGTA+TGG - chr3.3:3754727-3754746 MS.gene56189:CDS 35.0%
TTCCCAAATCAATATGTTCC+TGG + chr3.3:3754411-3754430 None:intergenic 35.0%
! ACCTGTTTTCTCTTTCTCAT+AGG - chr3.3:3753513-3753532 MS.gene56189:CDS 35.0%
!! TTTAACTTGGAACCACTTCA+TGG + chr3.3:3754852-3754871 None:intergenic 35.0%
!!! AACCCTATTTTAAGACACCA+TGG + chr3.3:3754022-3754041 None:intergenic 35.0%
AAAGTGGCCATAGAAGATTG+CGG - chr3.3:3753969-3753988 MS.gene56189:CDS 40.0%
AATCCAACATCGTGTCACAA+AGG - chr3.3:3754820-3754839 MS.gene56189:intron 40.0%
AGGAGAAACTTCAGTGATAC+CGG - chr3.3:3754367-3754386 MS.gene56189:intron 40.0%
CTGCCATGGTGTCTTAAAAT+AGG - chr3.3:3754016-3754035 MS.gene56189:CDS 40.0%
CTTATTGACAGCTAGGTACA+CGG - chr3.3:3754228-3754247 MS.gene56189:intron 40.0%
GATCCTTCCACTGGTATTTA+TGG - chr3.3:3754722-3754741 MS.gene56189:CDS 40.0%
GGTTGTGTTTGTATCCTGAT+TGG - chr3.3:3754186-3754205 MS.gene56189:intron 40.0%
TAGGTTCTTGAACAGCTAAG+TGG - chr3.3:3753532-3753551 MS.gene56189:CDS 40.0%
TCAAGGAATATGAGCTGTTG+AGG - chr3.3:3754347-3754366 MS.gene56189:intron 40.0%
TCCGTTCCTTTGGTATTAGA+AGG - chr3.3:3754251-3754270 MS.gene56189:intron 40.0%
! CAAACACCTGTTTTCTCCAA+AGG - chr3.3:3753556-3753575 MS.gene56189:intron 40.0%
! TTCAGTGATACCGGATGTTT+TGG - chr3.3:3754376-3754395 MS.gene56189:intron 40.0%
!!! GTGGAGTTTTTTATTGCCAC+CGG - chr3.3:3753991-3754010 MS.gene56189:CDS 40.0%
AACTCCACCGCAATCTTCTA+TGG + chr3.3:3753979-3753998 None:intergenic 45.0%
AGAAAATACCTTAGCGGCTC+TGG + chr3.3:3753439-3753458 None:intergenic 45.0%
CAAAGGATGATGCCATGAAG+TGG - chr3.3:3754837-3754856 MS.gene56189:CDS 45.0%
CATCCTTTGTGACACGATGT+TGG + chr3.3:3754826-3754845 None:intergenic 45.0%
CTTGTACTCAACATCTCCGT+CGG - chr3.3:3753393-3753412 MS.gene56189:CDS 45.0%
GATACCGAAGCCAAAACATC+CGG + chr3.3:3754389-3754408 None:intergenic 45.0%
TGTGATCCTAAACAAGTCCC+AGG - chr3.3:3754880-3754899 MS.gene56189:CDS 45.0%
TTAAGACACCATGGCAGAAC+CGG + chr3.3:3754013-3754032 None:intergenic 45.0%
TTCAGGTATGATCCTTCCAC+TGG - chr3.3:3754713-3754732 MS.gene56189:CDS 45.0%
! CAATTGCCTGGGACTTGTTT+AGG + chr3.3:3754889-3754908 None:intergenic 45.0%
!!! ATGTTTTGGCTTCGGTATCC+AGG - chr3.3:3754390-3754409 MS.gene56189:intron 45.0%
!!! GATACCGGATGTTTTGGCTT+CGG - chr3.3:3754382-3754401 MS.gene56189:intron 45.0%
!! ATAAAAATTAAATAATAGAA+AGG + chr3.3:3753617-3753636 None:intergenic 5.0%
!!! TTTATTATATTTTTTTTTTC+TGG - chr3.3:3753708-3753727 MS.gene56189:intron 5.0%
AACATCTCCGTCGGTGAAAG+TGG - chr3.3:3753402-3753421 MS.gene56189:CDS 50.0%
ACGATCTCCACTTTCACCGA+CGG + chr3.3:3753412-3753431 None:intergenic 50.0%
GCATGCTACGTCACTGTTAG+AGG - chr3.3:3754286-3754305 MS.gene56189:intron 50.0%
! CGACAAGGCAATGCAGCTTT+TGG - chr3.3:3754309-3754328 MS.gene56189:intron 50.0%
!! GCAATGCAGCTTTTGGAGAG+CGG - chr3.3:3754316-3754335 MS.gene56189:intron 50.0%
!! GCTTTTGGAGAGCGGTTTGA+AGG - chr3.3:3754324-3754343 MS.gene56189:intron 50.0%
!! GTGCAACGGATTGCAGAAGA+CGG + chr3.3:3754064-3754083 None:intergenic 50.0%
!! TGCAACGGATTGCAGAAGAC+GGG + chr3.3:3754063-3754082 None:intergenic 50.0%
AGGTACACGGTCCGTTCCTT+TGG - chr3.3:3754241-3754260 MS.gene56189:intron 55.0%
CGTAGGTGCAAGGCAAGAGT+TGG - chr3.3:3754797-3754816 MS.gene56189:intron 55.0%
CGTCACTGTTAGAGGCGACA+AGG - chr3.3:3754294-3754313 MS.gene56189:intron 55.0%
GACGTCCCACACGATAACCA+GGG + chr3.3:3754775-3754794 None:intergenic 55.0%
GATTGCAGAAGACGGGCCAT+GGG + chr3.3:3754056-3754075 None:intergenic 55.0%
GGAGAGCGGTTTGAAGGTCA+AGG - chr3.3:3754330-3754349 MS.gene56189:intron 55.0%
GTGGCCATAGAAGATTGCGG+TGG - chr3.3:3753972-3753991 MS.gene56189:CDS 55.0%
! TTTGTTGTCTTGGAGCGCCC+TGG - chr3.3:3754755-3754774 MS.gene56189:intron 55.0%
!! TATTGCCACCGGTTCTGCCA+TGG - chr3.3:3754002-3754021 MS.gene56189:CDS 55.0%
!!! GGGTTTTTGGCCTTTGCCCA+TGG - chr3.3:3754037-3754056 MS.gene56189:intron 55.0%
AGAAGACGGGCCATGGGCAA+AGG + chr3.3:3754050-3754069 None:intergenic 60.0%
AGACACCATGGCAGAACCGG+TGG + chr3.3:3754010-3754029 None:intergenic 60.0%
ATCGTGTGGGACGTCGTCGT+AGG - chr3.3:3754780-3754799 MS.gene56189:intron 60.0%
CGACGTCCCACACGATAACC+AGG + chr3.3:3754776-3754795 None:intergenic 60.0%
GAGCGCCCTGGTTATCGTGT+GGG - chr3.3:3754767-3754786 MS.gene56189:intron 60.0%
GGATTGCAGAAGACGGGCCA+TGG + chr3.3:3754057-3754076 None:intergenic 60.0%
TCGTCTCACCAGAGCCGCTA+AGG - chr3.3:3753428-3753447 MS.gene56189:CDS 60.0%
GGGACGTCGTCGTAGGTGCA+AGG - chr3.3:3754787-3754806 MS.gene56189:intron 65.0%
! GGAGCGCCCTGGTTATCGTG+TGG - chr3.3:3754766-3754785 MS.gene56189:intron 65.0%


Chromosome Type Strat End Strand Name
chr3.3 gene 3753369 3754913 3753369 ID=MS.gene56189
chr3.3 mRNA 3753369 3754913 3753369 ID=MS.gene56189.t1;Parent=MS.gene56189
chr3.3 exon 3754833 3754913 3754833 ID=MS.gene56189.t1.exon1;Parent=MS.gene56189.t1
chr3.3 CDS 3754833 3754913 3754833 ID=cds.MS.gene56189.t1;Parent=MS.gene56189.t1
chr3.3 exon 3754705 3754747 3754705 ID=MS.gene56189.t1.exon2;Parent=MS.gene56189.t1
chr3.3 CDS 3754705 3754747 3754705 ID=cds.MS.gene56189.t1;Parent=MS.gene56189.t1
chr3.3 exon 3753848 3754043 3753848 ID=MS.gene56189.t1.exon3;Parent=MS.gene56189.t1
chr3.3 CDS 3753848 3754043 3753848 ID=cds.MS.gene56189.t1;Parent=MS.gene56189.t1
chr3.3 exon 3753369 3753564 3753369 ID=MS.gene56189.t1.exon4;Parent=MS.gene56189.t1
chr3.3 CDS 3753369 3753564 3753369 ID=cds.MS.gene56189.t1;Parent=MS.gene56189.t1
Gene Sequence

>MS.gene56189

ATGAGGGAAATCAAAGTGCAAAAACTTGTACTCAACATCTCCGTCGGTGAAAGTGGAGATCGTCTCACCAGAGCCGCTAAGGTATTTTCTCAGTATCATTTTCACATAGACTCTCTCAATTCCTTCCTTTCAATTTCATTACTAACCTGTTTTCTCTTTCTCATAGGTTCTTGAACAGCTAAGTGGACAAACACCTGTTTTCTCCAAAGGTATTTTTTATAATTTAATTTTGATTTTACATTTTTCCTTTCTATTATTTAATTTTTATATTCTATTGTGTTTAACATGTTATTTCATATCAATTTGAAAAACCTAGTAGACATGTTCTGTACATATATTTTTATTATATTTTTTTTTTCTGGTATAATTATTCTGATATATTCTTACTGCAGAGTGTAAAAACATAATTATTATGTATCAATATTTGCTAGTTTTTTAGGTTTTAACCAAAAACTTGTACATATATTTTCATAAGCAAATAACATTAATTTATTTTGGTTGACAAATTCCCGGAAAGAAAAAATTACTTCATACAGGTCTTAGTATCAAAGATAAACTGTGTTGTAACTATTTCGATAGACGATATACTAATGTTGTCAAAAAGTGGCCATAGAAGATTGCGGTGGAGTTTTTTATTGCCACCGGTTCTGCCATGGTGTCTTAAAATAGGGTTTTTGGCCTTTGCCCATGGCCCGTCTTCTGCAATCCGTTGCACTTAGAAATACATATTTCAAGGCTTTGAGTCAAATTCTCATCATTTAGGACTCGTAGACTAGCATAAATATGACAGTTCTTTACATGCGTATTGGATATCTTGGGTTGTGTTTGTATCCTGATTGGTTCTTCATTTTCTATTGTGCTTATTGACAGCTAGGTACACGGTCCGTTCCTTTGGTATTAGAAGGAATGAAAAGATTGCATGCTACGTCACTGTTAGAGGCGACAAGGCAATGCAGCTTTTGGAGAGCGGTTTGAAGGTCAAGGAATATGAGCTGTTGAGGAGAAACTTCAGTGATACCGGATGTTTTGGCTTCGGTATCCAGGAACATATTGATTTGGGAATCAAGTAAGTTGAAAAAACAGTTCTATTTATACTGAAGTTATTTGTTAGAATACTCATGATTATTGCAAAGTCATTTCTTTCATTCTTTTGTATAATTTTTGATTTTTTATGTCAATGTGGTTTATCTTATGAAACCTTTTATTTGAAGAAAAATATTCGGAATTCAATCTGCTGTCTGTGTATCAATTCCTTTTGCTTTGTATATTTTTTTTTGTTTGTCGTTGTTTTCTTATGTTTCAAAGGATGATTGTGTTTTACCATATTGATGTTTAAAATTATGCTTCAGGTATGATCCTTCCACTGGTATTTATGGTATGGATTTCTTTGTTGTCTTGGAGCGCCCTGGTTATCGTGTGGGACGTCGTCGTAGGTGCAAGGCAAGAGTTGGAATCCAACATCGTGTCACAAAGGATGATGCCATGAAGTGGTTCCAAGTTAAATATGAAGGTGTGATCCTAAACAAGTCCCAGGCAATTGTTTAG

Protein sequence

>MS.gene56189.t1

MREIKVQKLVLNISVGESGDRLTRAAKVLEQLSGQTPVFSKARYTVRSFGIRRNEKIACYVTVRGDKAMQLLESGLKVKEYELLRRNFSDTGCFGFGIQEHIDLGIKYDPSTGIYGMDFFVVLERPGYRVGRRRRCKARVGIQHRVTKDDAMKWFQVKYEGVILNKSQAIV