AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene035825


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene035825.t1 MTR_3g053540 100.000 101 0 0 1 101 1 101 1.20e-72 211
MS.gene035825.t1 MTR_3g053520 98.020 101 2 0 1 101 1 101 2.23e-71 207
MS.gene035825.t1 MTR_8g010480 59.459 74 30 0 21 94 165 238 2.35e-27 102
MS.gene035825.t1 MTR_8g010480 61.972 71 27 0 23 93 244 314 1.33e-22 89.4
MS.gene035825.t1 MTR_8g010480 55.128 78 31 1 20 93 83 160 9.56e-22 87.0
MS.gene035825.t1 MTR_8g010480 43.678 87 46 2 15 100 2 86 5.60e-16 71.6
MS.gene035825.t1 MTR_8g010490 46.237 93 49 1 3 95 10 101 1.60e-26 97.1
MS.gene035825.t1 MTR_8g010490 52.632 76 36 0 23 98 108 183 7.15e-22 85.1
MS.gene035825.t1 MTR_8g085340 38.710 93 56 1 10 101 14 106 2.91e-18 74.3
MS.gene035825.t1 MTR_8g085320 33.333 99 65 1 1 98 1 99 8.80e-18 72.4
MS.gene035825.t1 MTR_3g053640 50.000 70 35 0 20 89 82 151 1.19e-15 70.9
MS.gene035825.t1 MTR_3g053640 51.562 64 31 0 29 92 15 78 1.71e-15 70.5
MS.gene035825.t1 MTR_0007s0030 64.103 39 14 0 48 86 1 39 1.53e-14 62.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene035825.t1 AT4G26840 90.000 90 9 0 7 96 2 91 3.86e-57 171
MS.gene035825.t1 AT5G55160 90.426 94 6 2 5 98 2 92 4.53e-57 171
MS.gene035825.t1 AT5G55160 79.439 107 6 3 5 98 2 105 1.64e-53 163
MS.gene035825.t1 AT5G55856 49.438 89 45 0 10 98 2 90 1.38e-26 94.4
MS.gene035825.t1 AT5G55170 51.685 89 41 1 12 98 5 93 1.03e-25 92.8
MS.gene035825.t1 AT5G55855 47.674 86 45 0 13 98 5 90 2.13e-24 89.0
MS.gene035825.t1 AT5G48710 46.591 88 46 1 12 98 17 104 9.67e-23 85.1
MS.gene035825.t1 AT5G48710 46.591 88 46 1 12 98 17 104 9.67e-23 85.1
MS.gene035825.t1 AT5G48710 46.591 88 46 1 12 98 17 104 9.67e-23 85.1
MS.gene035825.t1 AT5G55170 48.315 89 40 2 12 98 5 89 2.83e-21 81.3
MS.gene035825.t1 AT2G32765 37.778 90 55 1 10 98 14 103 1.98e-20 79.0
MS.gene035825.t1 AT5G55170 49.296 71 34 1 12 80 5 75 7.39e-18 72.4
MS.gene035825.t1 AT5G48700 42.222 90 50 2 11 98 19 108 9.23e-18 72.4
MS.gene035825.t1 AT5G48710 39.437 71 42 1 12 81 17 87 5.73e-14 62.4

Find 28 sgRNAs with CRISPR-Local

Find 99 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GATGTGAGCACCACCTGCTT+CGG 0.338312 3.3:+43722780 None:intergenic
TTCTTGTCTTCCTCGGTGTT+GGG 0.340524 3.3:+43722805 None:intergenic
ATGTGAGCACCACCTGCTTC+GGG 0.344186 3.3:+43722781 None:intergenic
CTTCTTGTCTTCCTCGGTGT+TGG 0.351501 3.3:+43722804 None:intergenic
TCGTAAACACAAACCTCATC+TGG 0.362733 3.3:+43721305 None:intergenic
ATGGGAATGAAGTGTTCTTC+AGG 0.382849 3.3:-43721445 MS.gene035825:CDS
GAACCTGGCCTTTGACTTTG+AGG 0.404598 3.3:+43722755 None:intergenic
TTCGGGCTTCTTGTCTTCCT+CGG 0.415650 3.3:+43722798 None:intergenic
GAAGACAAGAAGCCCGAAGC+AGG 0.445397 3.3:-43722793 MS.gene035825:CDS
CGGAAACTGAAGATGTCGTC+AGG 0.500483 3.3:-43722838 None:intergenic
TTGCAGCTGGAAATGGAAGA+TGG 0.502872 3.3:-43721201 MS.gene035825:intron
CGTAAACACAAACCTCATCT+GGG 0.526755 3.3:+43721306 None:intergenic
CATCTGGGGTCTGCTCTGCA+CGG 0.560850 3.3:+43721321 None:intergenic
TGCAGCTGGAAATGGAAGAT+GGG 0.572615 3.3:-43721200 MS.gene035825:intron
GATGCCATGCTTCATCAGAC+AGG 0.575586 3.3:-43721168 MS.gene035825:CDS
CACATCAACCTCAAAGTCAA+AGG 0.580464 3.3:-43722763 MS.gene035825:CDS
ACCTCCTGTCTGATGAAGCA+TGG 0.580486 3.3:+43721164 None:intergenic
CCCATCAAATAGAAAAGCAA+TGG 0.583133 3.3:+43721352 None:intergenic
CAACCTCAAAGTCAAAGGCC+AGG 0.584554 3.3:-43722758 MS.gene035825:intron
AAGTGTTCTTCAGGATCAAG+AGG 0.592447 3.3:-43721436 MS.gene035825:CDS
GCCATGCTTCATCAGACAGG+AGG 0.614785 3.3:-43721165 MS.gene035825:CDS
GACAAGAAGCCCGAAGCAGG+TGG 0.627526 3.3:-43722790 MS.gene035825:CDS
TGCAGAGCAGACCCCAGATG+AGG 0.644394 3.3:-43721318 MS.gene035825:intron
TTACTGTGATCGTCAGTCTG+TGG 0.670146 3.3:-43721384 MS.gene035825:CDS
CTGGGGTCTGCTCTGCACGG+AGG 0.678982 3.3:+43721324 None:intergenic
GCAGCTGGAAATGGAAGATG+GGG 0.689173 3.3:-43721199 MS.gene035825:intron
GTAAACACAAACCTCATCTG+GGG 0.707969 3.3:+43721307 None:intergenic
TGCAGCTGCTCCCAACACCG+AGG 0.715016 3.3:-43722815 MS.gene035825:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAAATACAATAAAAATGTT+TGG + chr3.3:43722108-43722127 None:intergenic 10.0%
!!! ATTTTATATGTTTAGATTAA+CGG - chr3.3:43721453-43721472 MS.gene035825:intron 10.0%
!! ATTTGATAAAAAATACACTT+TGG + chr3.3:43722047-43722066 None:intergenic 15.0%
!! TGAATTATATACAATTTGTA+AGG - chr3.3:43721619-43721638 MS.gene035825:intron 15.0%
!!! TTTTATATGTTTAGATTAAC+GGG - chr3.3:43721454-43721473 MS.gene035825:intron 15.0%
!! AATAAAAATGTTTGGATTGA+CGG + chr3.3:43722100-43722119 None:intergenic 20.0%
!! ACAAGATAACAATATCATAT+AGG + chr3.3:43722299-43722318 None:intergenic 20.0%
!! TTTATATGTTTAGATTAACG+GGG - chr3.3:43721455-43721474 MS.gene035825:intron 20.0%
!!! ATTCGATCGTTAATTTTTTA+GGG - chr3.3:43721307-43721326 MS.gene035825:intron 20.0%
!!! ATTTCTGTTATTAGTTTCAT+TGG - chr3.3:43722180-43722199 MS.gene035825:intron 20.0%
!!! ATTTTAATATGTTCTAGGAT+GGG - chr3.3:43722515-43722534 MS.gene035825:intron 20.0%
!!! GTATTTTTTATCAAATCACT+TGG - chr3.3:43722051-43722070 MS.gene035825:intron 20.0%
!!! TATTCGATCGTTAATTTTTT+AGG - chr3.3:43721306-43721325 MS.gene035825:intron 20.0%
!!! TTTGTAAGGAATTTTTGTTT+TGG - chr3.3:43721633-43721652 MS.gene035825:intron 20.0%
!!! TTTTTATTGAATTTGTGTGT+TGG - chr3.3:43722124-43722143 MS.gene035825:intron 20.0%
! TGCATTCATGTAAAACATAT+TGG - chr3.3:43722340-43722359 MS.gene035825:intron 25.0%
! TTTCTGTTATCAGTTTCATT+AGG - chr3.3:43721807-43721826 MS.gene035825:intron 25.0%
!! GAGTTATGTATGCTAATTTT+TGG - chr3.3:43722491-43722510 MS.gene035825:intron 25.0%
!! TATATTTGAAACTCTTGACA+TGG - chr3.3:43722399-43722418 MS.gene035825:intron 25.0%
!! TTTGTTTAAAACGTTGGTTA+GGG - chr3.3:43721771-43721790 MS.gene035825:intron 25.0%
!!! CATTTTAATATGTTCTAGGA+TGG - chr3.3:43722514-43722533 MS.gene035825:intron 25.0%
!!! GTATATGATTTGGTGAAAAT+AGG - chr3.3:43721936-43721955 MS.gene035825:intron 25.0%
!!! TTGGCATTTTAATATGTTCT+AGG - chr3.3:43722510-43722529 MS.gene035825:intron 25.0%
!!! TTTTTTTGAACAAGCCATAT+AGG + chr3.3:43722268-43722287 None:intergenic 25.0%
AACAATCACAAACACAACAA+AGG + chr3.3:43721343-43721362 None:intergenic 30.0%
AATCCAAACATAATTGAGAC+TGG - chr3.3:43721575-43721594 MS.gene035825:intron 30.0%
AATTATGTTTGGATTGACGA+TGG + chr3.3:43721570-43721589 None:intergenic 30.0%
ATCCAAAAAGTCCTAACATA+TGG + chr3.3:43722162-43722181 None:intergenic 30.0%
ATTCCAGTCTCAATTATGTT+TGG + chr3.3:43721581-43721600 None:intergenic 30.0%
CAAATATTGATGTTGCGTTA+TGG + chr3.3:43721727-43721746 None:intergenic 30.0%
GATAACAGAAACCCAAAAAA+AGG + chr3.3:43721798-43721817 None:intergenic 30.0%
TACGATATTGTTGAAGAACT+GGG - chr3.3:43721895-43721914 MS.gene035825:intron 30.0%
TAGTTCTTATCAGAATCACT+TGG - chr3.3:43721524-43721543 MS.gene035825:intron 30.0%
TGATTCTGATAAGAACTACA+CGG + chr3.3:43721522-43721541 None:intergenic 30.0%
! CTTTGTTTAAAACGTTGGTT+AGG - chr3.3:43721770-43721789 MS.gene035825:intron 30.0%
! GATTGTTTGTTGAAGAACTA+GGG - chr3.3:43721356-43721375 MS.gene035825:CDS 30.0%
! TACCATATGTTAGGACTTTT+TGG - chr3.3:43722157-43722176 MS.gene035825:intron 30.0%
! TGATTGTTTGTTGAAGAACT+AGG - chr3.3:43721355-43721374 MS.gene035825:CDS 30.0%
!! AAAATATGTTTTGTTGCAGC+TGG - chr3.3:43722764-43722783 MS.gene035825:CDS 30.0%
!! ACCAACGTTTTAAACAAAGT+TGG + chr3.3:43721769-43721788 None:intergenic 30.0%
!! CAACGTTTTAAACAAAGTTG+GGG + chr3.3:43721767-43721786 None:intergenic 30.0%
!! CCAACGTTTTAAACAAAGTT+GGG + chr3.3:43721768-43721787 None:intergenic 30.0%
!! CCATTGCTTTTCTATTTGAT+GGG - chr3.3:43722626-43722645 MS.gene035825:intron 30.0%
!! TGGAAATGATGCATTGATTT+CGG - chr3.3:43721653-43721672 MS.gene035825:intron 30.0%
AAAAATGTTTGGATTGACGG+TGG + chr3.3:43722097-43722116 None:intergenic 35.0%
AACAAAAACCCTAGAATCGA+AGG + chr3.3:43721260-43721279 None:intergenic 35.0%
ACGATATTGTTGAAGAACTG+GGG - chr3.3:43721896-43721915 MS.gene035825:intron 35.0%
ATATAGGAGACAAGTTAGAG+TGG + chr3.3:43722252-43722271 None:intergenic 35.0%
CCCATCAAATAGAAAAGCAA+TGG + chr3.3:43722629-43722648 None:intergenic 35.0%
CTGTTTGCATACCATATGTT+AGG - chr3.3:43722148-43722167 MS.gene035825:intron 35.0%
GTACGATATTGTTGAAGAAC+TGG - chr3.3:43721894-43721913 MS.gene035825:intron 35.0%
GTTCTTCAACAATATCGTAC+AGG + chr3.3:43721894-43721913 None:intergenic 35.0%
! ACTCTAACTTGTCTCCTATA+TGG - chr3.3:43722251-43722270 MS.gene035825:intron 35.0%
! CACACTAGGAGTATATGATT+TGG - chr3.3:43721926-43721945 MS.gene035825:intron 35.0%
! CCCAACTTTGTTTAAAACGT+TGG - chr3.3:43721765-43721784 MS.gene035825:intron 35.0%
!! GCCATTGCTTTTCTATTTGA+TGG - chr3.3:43722625-43722644 MS.gene035825:intron 35.0%
!!! TTGGTTAGGGTCCTTTTTTT+GGG - chr3.3:43721784-43721803 MS.gene035825:intron 35.0%
AAGTGTTCTTCAGGATCAAG+AGG - chr3.3:43722542-43722561 MS.gene035825:intron 40.0%
CACATCAACCTCAAAGTCAA+AGG - chr3.3:43721215-43721234 MS.gene035825:intron 40.0%
CGTAAACACAAACCTCATCT+GGG + chr3.3:43722675-43722694 None:intergenic 40.0%
GTAAACACAAACCTCATCTG+GGG + chr3.3:43722674-43722693 None:intergenic 40.0%
GTTTGGATTGACGATGGAAT+TGG + chr3.3:43721564-43721583 None:intergenic 40.0%
TCGTAAACACAAACCTCATC+TGG + chr3.3:43722676-43722695 None:intergenic 40.0%
TGTCTCTTCCTTCGATTCTA+GGG - chr3.3:43721249-43721268 MS.gene035825:intron 40.0%
TTGAAGAACTAGGGTTTCTC+TGG - chr3.3:43721365-43721384 MS.gene035825:CDS 40.0%
TTGTCTCTTCCTTCGATTCT+AGG - chr3.3:43721248-43721267 MS.gene035825:intron 40.0%
! AAAGTTCCGCAGTGATTTTG+TGG + chr3.3:43721485-43721504 None:intergenic 40.0%
! ATGGGAATGAAGTGTTCTTC+AGG - chr3.3:43722533-43722552 MS.gene035825:intron 40.0%
! TGATGTTGCGTTATGGATTG+CGG + chr3.3:43721720-43721739 None:intergenic 40.0%
!! TGTTTTGTTGCAGCTGGAAA+TGG - chr3.3:43722770-43722789 MS.gene035825:CDS 40.0%
!!! GTTGGTTAGGGTCCTTTTTT+TGG - chr3.3:43721783-43721802 MS.gene035825:intron 40.0%
AAGGAAGAGACAAACGAACC+TGG + chr3.3:43721241-43721260 None:intergenic 45.0%
ACTGGGGTTAATCTCACACT+AGG - chr3.3:43721912-43721931 MS.gene035825:intron 45.0%
CTGTGAGTTCGACAAACTCA+CGG - chr3.3:43721998-43722017 MS.gene035825:intron 45.0%
GGAGTTCCACAAAATCACTG+CGG - chr3.3:43721476-43721495 MS.gene035825:intron 45.0%
GTTTGGATTGACGGTGGAAT+TGG + chr3.3:43722091-43722110 None:intergenic 45.0%
TGCAGCTGGAAATGGAAGAT+GGG - chr3.3:43722778-43722797 MS.gene035825:CDS 45.0%
TTACTGTGATCGTCAGTCTG+TGG - chr3.3:43722594-43722613 MS.gene035825:intron 45.0%
TTGCAGCTGGAAATGGAAGA+TGG - chr3.3:43722777-43722796 MS.gene035825:CDS 45.0%
!! TTCTTGTCTTCCTCGGTGTT+GGG + chr3.3:43721176-43721195 None:intergenic 45.0%
ACAAAGTTGGGGCTGCGTTA+AGG + chr3.3:43721756-43721775 None:intergenic 50.0%
ACCTCCTGTCTGATGAAGCA+TGG + chr3.3:43722817-43722836 None:intergenic 50.0%
CAACCTCAAAGTCAAAGGCC+AGG - chr3.3:43721220-43721239 MS.gene035825:intron 50.0%
GATGCCATGCTTCATCAGAC+AGG - chr3.3:43722810-43722829 MS.gene035825:CDS 50.0%
GCAGCTGGAAATGGAAGATG+GGG - chr3.3:43722779-43722798 MS.gene035825:CDS 50.0%
TGAGTTCGACAAACTCACGG+TGG - chr3.3:43722001-43722020 MS.gene035825:intron 50.0%
TTCGGGCTTCTTGTCTTCCT+CGG + chr3.3:43721183-43721202 None:intergenic 50.0%
! CTTCTTGTCTTCCTCGGTGT+TGG + chr3.3:43721177-43721196 None:intergenic 50.0%
! GAACCTGGCCTTTGACTTTG+AGG + chr3.3:43721226-43721245 None:intergenic 50.0%
! GTTGCGTTATGGATTGCGGT+CGG + chr3.3:43721716-43721735 None:intergenic 50.0%
ATGTGAGCACCACCTGCTTC+GGG + chr3.3:43721200-43721219 None:intergenic 55.0%
GAAGACAAGAAGCCCGAAGC+AGG - chr3.3:43721185-43721204 MS.gene035825:CDS 55.0%
GATGTGAGCACCACCTGCTT+CGG + chr3.3:43721201-43721220 None:intergenic 55.0%
GCCATGCTTCATCAGACAGG+AGG - chr3.3:43722813-43722832 MS.gene035825:CDS 55.0%
GACAAGAAGCCCGAAGCAGG+TGG - chr3.3:43721188-43721207 MS.gene035825:CDS 60.0%
TGCAGAGCAGACCCCAGATG+AGG - chr3.3:43722660-43722679 MS.gene035825:intron 60.0%
! CATCTGGGGTCTGCTCTGCA+CGG + chr3.3:43722660-43722679 None:intergenic 60.0%
TGCAGCTGCTCCCAACACCG+AGG - chr3.3:43721163-43721182 MS.gene035825:CDS 65.0%
CTGGGGTCTGCTCTGCACGG+AGG + chr3.3:43722657-43722676 None:intergenic 70.0%


Chromosome Type Strat End Strand Name
chr3.3 gene 43721152 43722848 43721152 ID=MS.gene035825
chr3.3 mRNA 43721152 43722848 43721152 ID=MS.gene035825.t1;Parent=MS.gene035825
chr3.3 exon 43722759 43722848 43722759 ID=MS.gene035825.t1.exon1;Parent=MS.gene035825.t1
chr3.3 CDS 43722759 43722848 43722759 ID=cds.MS.gene035825.t1;Parent=MS.gene035825.t1
chr3.3 exon 43721319 43721468 43721319 ID=MS.gene035825.t1.exon2;Parent=MS.gene035825.t1
chr3.3 CDS 43721319 43721468 43721319 ID=cds.MS.gene035825.t1;Parent=MS.gene035825.t1
chr3.3 exon 43721152 43721217 43721152 ID=MS.gene035825.t1.exon3;Parent=MS.gene035825.t1
chr3.3 CDS 43721152 43721217 43721152 ID=cds.MS.gene035825.t1;Parent=MS.gene035825.t1
Gene Sequence

>MS.gene035825

ATGTCGTCAGGTGCAGCTGCTCCCAACACCGAGGAAGACAAGAAGCCCGAAGCAGGTGGTGCTCACATCAACCTCAAAGTCAAAGGCCAGGTTCGTTTGTCTCTTCCTTCGATTCTAGGGTTTTTGTTTTTTTATGAATCGTCTTATTCAAACGTATTCGATCGTTAATTTTTTAGGGTTTTTTTTTGCCTTTGTTGTGTTTGTGATTGTTTGTTGAAGAACTAGGGTTTCTCTGGTTTAATTTGATTGCTATTTGTGTTATATAGCATAAGTATGAAAAATTTTAAAAATAAAAAGAGAAATTTTATATGTTTAGATTAACGGGGAGTTCCACAAAATCACTGCGGAACTTTGATTTTGTGTAATTCCGTGTAGTTCTTATCAGAATCACTTGGTCACTGTGATTTTGCCAATTCCATCGTCAATCCAAACATAATTGAGACTGGAATTTATAGTGTTAATTTTATTGAATTATATACAATTTGTAAGGAATTTTTGTTTTGGAAATGATGCATTGATTTCGGTAAGATTTGTGCAATGTTATAATTAAATCACATCGCGCCGACCGCAATCCATAACGCAACATCAATATTTGCGAAATCCTTAACGCAGCCCCAACTTTGTTTAAAACGTTGGTTAGGGTCCTTTTTTTGGGTTTCTGTTATCAGTTTCATTAGGAAACTTTAGATGCTATGTATTAGTGTTCATTCTTCAGTTTATCGATCACTCTAACTTGTTTCCTGTACGATATTGTTGAAGAACTGGGGTTAATCTCACACTAGGAGTATATGATTTGGTGAAAATAGGATAATCACTAATGCTATTTTTTAAACATGTTTAAATTAACTGTGAGTTCGACAAACTCACGGTGGCACTTTGATTTAATGAAGTTCCAAAGTGTATTTTTTATCAAATCACTTGGTCACTGTGATTTTGCCAATTCCACCGTCAATCCAAACATTTTTATTGTATTTTTTATTGAATTTGTGTGTTGGACTGTTTGCATACCATATGTTAGGACTTTTTGGATTTCTGTTATTAGTTTCATTGGTAAACTTTAGATGCTATGTATTAGTGTTCATTCTTCAGTTTATCTACCACTCTAACTTGTCTCCTATATGGCTTGTTCAAAAAAAACATGTCTCCTATATGATATTGTTATCTTGTTCTTCGTTCGTTTCTTTATGTTGCATTCATGTAAAACATATTGGTCTAATCTTAAGTTATAACTTTTCAGAAATCGAAGTTATATTTGAAACTCTTGACATGGTTATAGTTTTCTATATTATTAGTCTTAGTTACTGTCAAAAGTTTTTAGTCATCATTGAAATTAGCATCAGAGTTATGTATGCTAATTTTTGGCATTTTAATATGTTCTAGGATGGGAATGAAGTGTTCTTCAGGATCAAGAGGAACACTCAACTGAAAAAGCTTATGAATGCTTACTGTGATCGTCAGTCTGTGGATTTCAATGCCATTGCTTTTCTATTTGATGGGCGTCGCCTCCGTGCAGAGCAGACCCCAGATGAGGTTTGTGTTTACGACATTTTTTCATCACTTTTTCTCTATCATAATGTTCAAATAAGTCTAACATTTGTGTTTTTATGACTTGAAAATATGTTTTGTTGCAGCTGGAAATGGAAGATGGGGACGAAATCGATGCCATGCTTCATCAGACAGGAGGTTCTGTTGTCTGA

Protein sequence

>MS.gene035825.t1

MSSGAAAPNTEEDKKPEAGGAHINLKVKGQDGNEVFFRIKRNTQLKKLMNAYCDRQSVDFNAIAFLFDGRRLRAEQTPDELEMEDGDEIDAMLHQTGGSVV