AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene034902

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene034902.t1 MTR_1g060700 94.872 312 13 3 1 311 178 487 0.0 602
MS.gene034902.t1 MTR_2g067000 81.424 323 23 11 1 311 1 298 1.21e-161 452
MS.gene034902.t1 MTR_8g093500 58.491 53 22 0 181 233 125 177 3.45e-13 68.9
MS.gene034902.t1 MTR_3g101810 58.491 53 22 0 181 233 182 234 2.44e-12 66.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene034902.t1 AT1G30670 44.118 170 93 1 135 304 95 262 2.22e-33 124
MS.gene034902.t1 AT2G34820 41.315 213 116 3 97 304 81 289 8.23e-29 112
MS.gene034902.t1 AT3G21330 60.377 53 21 0 181 233 280 332 2.34e-13 70.5
MS.gene034902.t1 AT5G01305 50.000 58 29 0 181 238 48 105 1.26e-12 65.5
MS.gene034902.t1 AT4G00120 54.717 53 24 0 181 233 123 175 2.21e-12 65.5

Find 50 sgRNAs with CRISPR-Local

Find 92 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGTTGGAATTCTTCAACTTA+TGG 0.193552 1.2:+46514311 MS.gene034902:CDS
ATCTCTGCTGTGTTCATCTT+TGG 0.238213 1.2:-46514246 None:intergenic
TTGGTGAAATCTTCCTCATT+TGG 0.290806 1.2:-46513928 None:intergenic
ATCAAAACCTACCATTCTTA+AGG 0.300143 1.2:+46515322 MS.gene034902:CDS
AAATAAAACTATTCTTGCTT+TGG 0.325467 1.2:-46515383 None:intergenic
TGGTGAAATCTTCCTCATTT+GGG 0.332786 1.2:-46513927 None:intergenic
AGTTTCATTCAAATAGTTAG+AGG 0.343349 1.2:-46513761 None:intergenic
TCTCCTCGTAGCATAGCTTT+TGG 0.368098 1.2:-46513972 None:intergenic
AGTTGATCTTGACAAGGGTT+AGG 0.369040 1.2:-46513844 None:intergenic
TCAAAGGAAGCAAAAGGGTT+AGG 0.369513 1.2:-46514063 None:intergenic
GTAGTTTGAATAGGTTGATA+AGG 0.378786 1.2:-46513667 None:intergenic
TACAGTTTCTCTTGAACAAA+TGG 0.383908 1.2:-46515233 None:intergenic
AAGGGTCTGAAACAGCTTGC+TGG 0.388228 1.2:+46515341 MS.gene034902:CDS
AGTAGTGACTTCTGAGTTGT+TGG 0.390115 1.2:-46513689 None:intergenic
AATGTGGTGACAAACTCTTT+TGG 0.390869 1.2:-46515278 None:intergenic
GAGCTTGGGAAGTTGGTTCC+TGG 0.392352 1.2:+46514219 MS.gene034902:CDS
GACACAAGAGCTTGGGAAGT+TGG 0.397999 1.2:+46514212 MS.gene034902:CDS
TTGATTATTTCAGGAAGAAA+AGG 0.406675 1.2:+46515169 MS.gene034902:intron
GAGTTGTTGGTAGTTTGAAT+AGG 0.425759 1.2:-46513676 None:intergenic
TAGTTTGAATAGGTTGATAA+GGG 0.429054 1.2:-46513666 None:intergenic
GTTGATCTTGACAAGGGTTA+GGG 0.453473 1.2:-46513843 None:intergenic
AGAGCATCGCGGCGAGAGAA+AGG 0.454679 1.2:+46514169 MS.gene034902:CDS
TCAAAACCTACCATTCTTAA+GGG 0.456430 1.2:+46515323 MS.gene034902:CDS
CAAAGGAAGCAAAAGGGTTA+GGG 0.461232 1.2:-46514062 None:intergenic
TCTGCCTCAAAGGAAGCAAA+AGG 0.471457 1.2:-46514069 None:intergenic
TTGTGTAGATCTTCACTTGG+AGG 0.473071 1.2:-46515197 None:intergenic
TGTAGATCTTCACTTGGAGG+AGG 0.494574 1.2:-46515194 None:intergenic
GTGTTCATCTTTGGTCCACC+AGG 0.499817 1.2:-46514237 None:intergenic
ACTGAGAAGACACAAGAGCT+TGG 0.499993 1.2:+46514204 MS.gene034902:CDS
CTGAGAAGACACAAGAGCTT+GGG 0.500383 1.2:+46514205 MS.gene034902:CDS
TATAGTTGAAGTATGTGCTA+AGG 0.501324 1.2:-46513636 None:intergenic
CTGTTTCAGACCCTTAAGAA+TGG 0.516519 1.2:-46515333 None:intergenic
AGCAAAGGGTTCTGCCTCAA+AGG 0.518713 1.2:-46514079 None:intergenic
AGGGTCTGAAACAGCTTGCT+GGG 0.522554 1.2:+46515342 MS.gene034902:CDS
ATAGTTGAAGTATGTGCTAA+GGG 0.550447 1.2:-46513635 None:intergenic
CTTGGGAAGTTGGTTCCTGG+TGG 0.551828 1.2:+46514222 MS.gene034902:CDS
ACTTATGGAAACATTTAGCA+AGG 0.569731 1.2:+46514326 MS.gene034902:CDS
TCGCGGCGAGAGAAAGGAGA+AGG 0.580062 1.2:+46514175 MS.gene034902:CDS
AGTTTGTGTAGATCTTCACT+TGG 0.582386 1.2:-46515200 None:intergenic
TTCAGACCCTTAAGAATGGT+AGG 0.583734 1.2:-46515329 None:intergenic
GAGTTCAAAAGCTCTTGTTG+TGG 0.586358 1.2:-46514006 None:intergenic
AAGTTTCTTCAAGCTCAAGT+TGG 0.590061 1.2:+46514294 MS.gene034902:CDS
GTGAGAAGAAAGTTGCTGAA+AGG 0.592639 1.2:+46514133 MS.gene034902:CDS
CTGCCTCAAAGGAAGCAAAA+GGG 0.606158 1.2:-46514068 None:intergenic
ACAAGTAGTTGATCTTGACA+AGG 0.633389 1.2:-46513850 None:intergenic
CAAGTAGTTGATCTTGACAA+GGG 0.656926 1.2:-46513849 None:intergenic
ATCATTATGATTGCTCAATG+TGG 0.666694 1.2:-46515294 None:intergenic
ATGCTACGAGGAGAAAAGAG+AGG 0.681365 1.2:+46513981 MS.gene034902:CDS
ACGCCAAAAGCTATGCTACG+AGG 0.715032 1.2:+46513969 MS.gene034902:CDS
TATCTCGTCGCAGAGCATCG+CGG 0.776153 1.2:+46514158 MS.gene034902:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TATTGTTGTAAATATCTAAA+TGG + chr1.2:46514673-46514692 MS.gene034902:intron 15.0%
!! CATAATAACACTACAATAAA+TGG - chr1.2:46514648-46514667 None:intergenic 20.0%
!! CGTTTGATAAAAAAATATAG+AGG + chr1.2:46514617-46514636 MS.gene034902:intron 20.0%
!! TTTACTCCATGAAAATATTT+AGG + chr1.2:46514808-46514827 MS.gene034902:intron 20.0%
!!! TTTTGCTAATTGATTATTTC+AGG + chr1.2:46515160-46515179 MS.gene034902:intron 20.0%
! AAACTCATCCACAAAAAAAT+TGG - chr1.2:46514034-46514053 None:intergenic 25.0%
! AAAGACAAAATTGAGACAAT+AGG - chr1.2:46514761-46514780 None:intergenic 25.0%
! AGAAAAACATCAAATTCACT+TGG - chr1.2:46514454-46514473 None:intergenic 25.0%
! AGTTTCATTCAAATAGTTAG+AGG - chr1.2:46513764-46513783 None:intergenic 25.0%
! GGAACTGTTATAAAAATTGA+CGG + chr1.2:46514829-46514848 MS.gene034902:intron 25.0%
! GTTTCATTTGAGTAAAAACA+AGG - chr1.2:46513820-46513839 None:intergenic 25.0%
! TAACTGTTTAACAAGGAATT+TGG + chr1.2:46515025-46515044 MS.gene034902:intron 25.0%
! TCAAATAGTTAGAGGAAAAA+TGG - chr1.2:46513756-46513775 None:intergenic 25.0%
! TGTTAGGTTTAAGAAAATGT+TGG + chr1.2:46514859-46514878 MS.gene034902:intron 25.0%
! TTGATTATTTCAGGAAGAAA+AGG + chr1.2:46515169-46515188 MS.gene034902:intron 25.0%
! TTGTTTGTTCATTGCATATT+TGG + chr1.2:46514549-46514568 MS.gene034902:intron 25.0%
!! ACAGTTCCTAAATATTTTCA+TGG - chr1.2:46514817-46514836 None:intergenic 25.0%
!! TATTTTCATGGAGTAAAAGT+TGG - chr1.2:46514805-46514824 None:intergenic 25.0%
!!! AATTTTTTTTGAAGCAGCAA+AGG - chr1.2:46514097-46514116 None:intergenic 25.0%
!!! ATTACTTGTTTTGTGTTCTT+AGG + chr1.2:46514413-46514432 MS.gene034902:intron 25.0%
!!! ATTTTTTTTGAAGCAGCAAA+GGG - chr1.2:46514096-46514115 None:intergenic 25.0%
!!! TAGTTTGAATAGGTTGATAA+GGG - chr1.2:46513669-46513688 None:intergenic 25.0%
!!! TTACTTGTTTTGTGTTCTTA+GGG + chr1.2:46514414-46514433 MS.gene034902:intron 25.0%
AATAGTTAGAGGAAAAATGG+TGG - chr1.2:46513753-46513772 None:intergenic 30.0%
ACTCAAATGATTACAAGCAA+GGG - chr1.2:46514591-46514610 None:intergenic 30.0%
ACTTATGGAAACATTTAGCA+AGG + chr1.2:46514326-46514345 MS.gene034902:CDS 30.0%
AGTTGGAATTCTTCAACTTA+TGG + chr1.2:46514311-46514330 MS.gene034902:CDS 30.0%
ATAGTTGAAGTATGTGCTAA+GGG - chr1.2:46513638-46513657 None:intergenic 30.0%
ATCAAAACCTACCATTCTTA+AGG + chr1.2:46515322-46515341 MS.gene034902:CDS 30.0%
ATCATTATGATTGCTCAATG+TGG - chr1.2:46515297-46515316 None:intergenic 30.0%
CTGTTATAAAAATTGACGGA+TGG + chr1.2:46514833-46514852 MS.gene034902:intron 30.0%
TAATGCTGTTGTTGTAGATT+TGG + chr1.2:46514700-46514719 MS.gene034902:intron 30.0%
TACAGTTTCTCTTGAACAAA+TGG - chr1.2:46515236-46515255 None:intergenic 30.0%
TACTCAAATGATTACAAGCA+AGG - chr1.2:46514592-46514611 None:intergenic 30.0%
TATAGTTGAAGTATGTGCTA+AGG - chr1.2:46513639-46513658 None:intergenic 30.0%
TCAAAACCTACCATTCTTAA+GGG + chr1.2:46515323-46515342 MS.gene034902:CDS 30.0%
! GAATGAAATTTTCCCAAATG+AGG + chr1.2:46513915-46513934 MS.gene034902:CDS 30.0%
! TTTTGGACATGTAAGGTAAT+TGG - chr1.2:46513950-46513969 None:intergenic 30.0%
!! ACTTTTTCTTCTCAAAACGA+TGG + chr1.2:46513880-46513899 MS.gene034902:CDS 30.0%
!! CAATAAACGAGAGAGTATTT+AGG + chr1.2:46514969-46514988 MS.gene034902:intron 30.0%
!! GTAGTTTGAATAGGTTGATA+AGG - chr1.2:46513670-46513689 None:intergenic 30.0%
!!! ATCGTTTTGAGAAGAAAAAG+TGG - chr1.2:46513881-46513900 None:intergenic 30.0%
!!! GAACTCAACCAATTTTTTTG+TGG + chr1.2:46514023-46514042 MS.gene034902:CDS 30.0%
AAGTTTCTTCAAGCTCAAGT+TGG + chr1.2:46514294-46514313 MS.gene034902:CDS 35.0%
ACAAGTAGTTGATCTTGACA+AGG - chr1.2:46513853-46513872 None:intergenic 35.0%
AGGAAACGGTTAATAAGAAG+AGG + chr1.2:46514939-46514958 MS.gene034902:intron 35.0%
AGTTTGTGTAGATCTTCACT+TGG - chr1.2:46515203-46515222 None:intergenic 35.0%
ATTGAGACAATAGGTAGTCA+TGG - chr1.2:46514752-46514771 None:intergenic 35.0%
CAAGTAGTTGATCTTGACAA+GGG - chr1.2:46513852-46513871 None:intergenic 35.0%
CAAGTGTATATCAAATGAGC+TGG + chr1.2:46514997-46515016 MS.gene034902:intron 35.0%
CGGTTAATAAGAAGAGGAAA+TGG + chr1.2:46514945-46514964 MS.gene034902:intron 35.0%
GCAATGAACAAACAAACTCT+AGG - chr1.2:46514544-46514563 None:intergenic 35.0%
GGCTATGTAACTGTTTAACA+AGG + chr1.2:46515018-46515037 MS.gene034902:intron 35.0%
TGGTGAAATCTTCCTCATTT+GGG - chr1.2:46513930-46513949 None:intergenic 35.0%
TTGGTGAAATCTTCCTCATT+TGG - chr1.2:46513931-46513950 None:intergenic 35.0%
! AATGTGGTGACAAACTCTTT+TGG - chr1.2:46515281-46515300 None:intergenic 35.0%
! AATTGACGGATGGAATTGTT+AGG + chr1.2:46514843-46514862 MS.gene034902:intron 35.0%
!! GAGTTGTTGGTAGTTTGAAT+AGG - chr1.2:46513679-46513698 None:intergenic 35.0%
AGTAGTGACTTCTGAGTTGT+TGG - chr1.2:46513692-46513711 None:intergenic 40.0%
AGTTGATCTTGACAAGGGTT+AGG - chr1.2:46513847-46513866 None:intergenic 40.0%
ATCTCTGCTGTGTTCATCTT+TGG - chr1.2:46514249-46514268 None:intergenic 40.0%
CAAAGGAAGCAAAAGGGTTA+GGG - chr1.2:46514065-46514084 None:intergenic 40.0%
CTGTTTCAGACCCTTAAGAA+TGG - chr1.2:46515336-46515355 None:intergenic 40.0%
GAGTTCAAAAGCTCTTGTTG+TGG - chr1.2:46514009-46514028 None:intergenic 40.0%
GTGAGAAGAAAGTTGCTGAA+AGG + chr1.2:46514133-46514152 MS.gene034902:CDS 40.0%
GTTGATCTTGACAAGGGTTA+GGG - chr1.2:46513846-46513865 None:intergenic 40.0%
TCAAAGGAAGCAAAAGGGTT+AGG - chr1.2:46514066-46514085 None:intergenic 40.0%
TTCAGACCCTTAAGAATGGT+AGG - chr1.2:46515332-46515351 None:intergenic 40.0%
TTGTGTAGATCTTCACTTGG+AGG - chr1.2:46515200-46515219 None:intergenic 40.0%
! GAGAGAGTGTGTTAAGGAAA+CGG + chr1.2:46514925-46514944 MS.gene034902:intron 40.0%
! TAACCCTTTTGCTTCCTTTG+AGG + chr1.2:46514065-46514084 MS.gene034902:CDS 40.0%
! TAGCATAGCTTTTGGCGTTT+TGG - chr1.2:46513967-46513986 None:intergenic 40.0%
!! TTTGGCGTTTTGGACATGTA+AGG - chr1.2:46513957-46513976 None:intergenic 40.0%
ACTGAGAAGACACAAGAGCT+TGG + chr1.2:46514204-46514223 MS.gene034902:CDS 45.0%
ATGCTACGAGGAGAAAAGAG+AGG + chr1.2:46513981-46514000 MS.gene034902:CDS 45.0%
CTGAGAAGACACAAGAGCTT+GGG + chr1.2:46514205-46514224 MS.gene034902:CDS 45.0%
CTGCCTCAAAGGAAGCAAAA+GGG - chr1.2:46514071-46514090 None:intergenic 45.0%
TCTGCCTCAAAGGAAGCAAA+AGG - chr1.2:46514072-46514091 None:intergenic 45.0%
TGTAGATCTTCACTTGGAGG+AGG - chr1.2:46515197-46515216 None:intergenic 45.0%
! GAGAGAGAGAGAGTGTGTTA+AGG + chr1.2:46514919-46514938 MS.gene034902:intron 45.0%
! TCTCCTCGTAGCATAGCTTT+TGG - chr1.2:46513975-46513994 None:intergenic 45.0%
ACGCCAAAAGCTATGCTACG+AGG + chr1.2:46513969-46513988 MS.gene034902:CDS 50.0%
AGCAAAGGGTTCTGCCTCAA+AGG - chr1.2:46514082-46514101 None:intergenic 50.0%
GACACAAGAGCTTGGGAAGT+TGG + chr1.2:46514212-46514231 MS.gene034902:CDS 50.0%
GTGTTCATCTTTGGTCCACC+AGG - chr1.2:46514240-46514259 None:intergenic 50.0%
! AAGGGTCTGAAACAGCTTGC+TGG + chr1.2:46515341-46515360 MS.gene034902:CDS 50.0%
! AGGGTCTGAAACAGCTTGCT+GGG + chr1.2:46515342-46515361 MS.gene034902:CDS 50.0%
! CTTGGGAAGTTGGTTCCTGG+TGG + chr1.2:46514222-46514241 MS.gene034902:CDS 55.0%
! GAGCTTGGGAAGTTGGTTCC+TGG + chr1.2:46514219-46514238 MS.gene034902:CDS 55.0%
!! TATCTCGTCGCAGAGCATCG+CGG + chr1.2:46514158-46514177 MS.gene034902:CDS 55.0%
TCGCGGCGAGAGAAAGGAGA+AGG + chr1.2:46514175-46514194 MS.gene034902:CDS 60.0%
!! AGAGCATCGCGGCGAGAGAA+AGG + chr1.2:46514169-46514188 MS.gene034902:CDS 60.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 46513628 46515397 46513628 ID=MS.gene034902
chr1.2 mRNA 46513628 46515397 46513628 ID=MS.gene034902.t1;Parent=MS.gene034902
chr1.2 exon 46513628 46514347 46513628 ID=MS.gene034902.t1.exon1;Parent=MS.gene034902.t1
chr1.2 CDS 46513628 46514347 46513628 ID=cds.MS.gene034902.t1;Parent=MS.gene034902.t1
chr1.2 exon 46515182 46515397 46515182 ID=MS.gene034902.t1.exon2;Parent=MS.gene034902.t1
chr1.2 CDS 46515182 46515397 46515182 ID=cds.MS.gene034902.t1;Parent=MS.gene034902.t1
Gene Sequence

>MS.gene034902

ATGGGAGCCCTTAGCACATACTTCAACTATATTTGTTACCCTTATCAACCTATTCAAACTACCAACAACTCAGAAGTCACTACTTTTCAACATCATGAACAAGAACAACTTATGCAACAAAACCACCATTTTTCCTCTAACTATTTGAATGAAACTTCTCTTTTAGATGAAAGCTTCATTTTTCAAACTCCTTGTTTTTACTCAAATGAAACTTACCCTAACCCTTGTCAAGATCAACTACTTGTTGACTCCACTTTTTCTTCTCAAAACGATGGCTTCGTTTCAATGAATGAAATTTTCCCAAATGAGGAAGATTTCACCAATTACCTTACATGTCCAAAACGCCAAAAGCTATGCTACGAGGAGAAAAGAGAGGAACCACAACAAGAGCTTTTGAACTCAACCAATTTTTTTGTGGATGAGTTTATGACTAACCCTAACCCTTTTGCTTCCTTTGAGGCAGAACCCTTTGCTGCTTCAAAAAAAATTGTTGATGTTGTTCAATGTGAGAAGAAAGTTGCTGAAAGGACTATCTCGTCGCAGAGCATCGCGGCGAGAGAAAGGAGAAGGAAGATAACTGAGAAGACACAAGAGCTTGGGAAGTTGGTTCCTGGTGGACCAAAGATGAACACAGCAGAGATGCTTAATGCTGCTGCTAATTATGTTAAGTTTCTTCAAGCTCAAGTTGGAATTCTTCAACTTATGGAAACATTTAGCAAGGTAACTGTTTTTGTTTTTTTATTGTTGCAATGTTCTTATATTATTAGAGCTCATAGTTGAATTTAATTACTTGTTTTGTGTTCTTAGGGTCTTATGTAACACTCCAAGTGAATTTGATGTTTTTCTTTTGAATGATGTTTTTTGCTTTTTACGTTATGCTATGCTACTTCATTTAGTTTTTGAGTTTATAATACCTAGAGTTTGTTTGTTCATTGCATATTTGGTTACTTTGTGTGAAGACCCTTGCTTGTAATCATTTGAGTACATGTCGTTTGATAAAAAAATATAGAGGATATGCCATTTATTGTAGTGTTATTATGTCATGTATTGTTGTAAATATCTAAATGGATATTAATGCTGTTGTTGTAGATTTGGTTAGTTTTATCATTTATGTATGTAATCCATGACTACCTATTGTCTCAATTTTGTCTTTTTTATATTGATTTTTTTCATACCAACTTTTACTCCATGAAAATATTTAGGAACTGTTATAAAAATTGACGGATGGAATTGTTAGGTTTAAGAAAATGTTGGTTACAATGTATGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGTGTGTTAAGGAAACGGTTAATAAGAAGAGGAAATGGTCAATAAACGAGAGAGTATTTAGGAACAGCAAGTGTATATCAAATGAGCTGGCTATGTAACTGTTTAACAAGGAATTTGGCAATTTTGCAATATTTAAATTTAAATATTCACTATTTAGTGCAACATTTTTGTAAAAGCTAAATTTCTAGTGTAACTTATATAATAAAAAGAATTCACGTATATATCTTAGATTTTGCTAATTGATTATTTCAGGAAGAAAAGGAACCTCCTCCAAGTGAAGATCTACACAAACTTCTTCTTTCTCCATTTGTTCAAGAGAAACTGTATTCAGAAGAAAAGTGCTTTGTTCCAAAAGAGTTTGTCACCACATTGAGCAATCATAATGATGTTCAATCAAAACCTACCATTCTTAAGGGTCTGAAACAGCTTGCTGGGACTGAGATTGAGAAGAAACCAAAGCAAGAATAG
Protein sequence

>MS.gene034902.t1

MGALSTYFNYICYPYQPIQTTNNSEVTTFQHHEQEQLMQQNHHFSSNYLNETSLLDESFIFQTPCFYSNETYPNPCQDQLLVDSTFSSQNDGFVSMNEIFPNEEDFTNYLTCPKRQKLCYEEKREEPQQELLNSTNFFVDEFMTNPNPFASFEAEPFAASKKIVDVVQCEKKVAERTISSQSIAARERRRKITEKTQELGKLVPGGPKMNTAEMLNAAANYVKFLQAQVGILQLMETFSKEEKEPPPSEDLHKLLLSPFVQEKLYSEEKCFVPKEFVTTLSNHNDVQSKPTILKGLKQLAGTEIEKKPKQE