AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene27294


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene27294.t1 MTR_1g022395 88.811 143 14 1 1 141 1 143 1.21e-90 259
MS.gene27294.t1 MTR_3g111970 62.238 143 45 5 1 140 1 137 6.61e-54 166
MS.gene27294.t1 MTR_3g111970 63.636 121 35 5 1 118 1 115 1.95e-44 141
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene27294.t1 AT1G19530 41.860 129 56 3 1 128 1 111 3.43e-18 75.1
MS.gene27294.t1 AT1G19530 41.860 129 56 3 1 128 1 111 3.43e-18 75.1

Find 34 sgRNAs with CRISPR-Local

Find 101 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAGATGAAATTGATGCTTAT+TGG 0.156482 1.2:-2154322 MS.gene27294:CDS
AATCATATGGTACCTGATTT+AGG 0.175839 1.2:+2154503 None:intergenic
GAACGTACTTGACACAAATT+TGG 0.215908 1.2:-2153179 MS.gene27294:CDS
GTCAAGTACGTTCATATTAA+AGG 0.224800 1.2:+2153189 None:intergenic
CTGAATAGTCTCTGACAAAT+TGG 0.254276 1.2:+2154256 None:intergenic
CTGTCTCAGCCATACTTAAA+AGG 0.269763 1.2:-2154361 MS.gene27294:intron
CAATTTGTCAGAGACTATTC+AGG 0.322635 1.2:-2154255 MS.gene27294:intron
GCAGGTGGACTAAGAGTAAC+TGG 0.334701 1.2:-2152989 MS.gene27294:intron
TCAAGTACGTTCATATTAAA+GGG 0.359264 1.2:+2153190 None:intergenic
TCTTCAATTGATCCTAAATC+AGG 0.362673 1.2:-2154515 MS.gene27294:intron
TTGGATGCAGCTTCCATCAT+TGG 0.363993 1.2:+2152948 None:intergenic
ACAGTTTCACGTTGCCAGTT+TGG 0.389711 1.2:-2152913 MS.gene27294:CDS
GGGTTCTCTTATGGCAGGAT+GGG 0.445491 1.2:-2154543 MS.gene27294:CDS
TCTGAATGAGCCACCAATGA+TGG 0.467236 1.2:-2152961 MS.gene27294:CDS
CCATGCCCGTGGCCCACGTA+AGG 0.471373 1.2:-2153216 MS.gene27294:CDS
GGGTCCCTTACGTGGGCCAC+GGG 0.472849 1.2:+2153211 None:intergenic
GGGGTCCCTTACGTGGGCCA+CGG 0.474803 1.2:+2153210 None:intergenic
CCTTACGTGGGCCACGGGCA+TGG 0.492032 1.2:+2153216 None:intergenic
GGTTCTCTTATGGCAGGATG+GGG 0.492223 1.2:-2154542 MS.gene27294:CDS
CAATCACTAACTTCATCTAC+GGG 0.495529 1.2:+2152873 None:intergenic
GAAATCAAAGAAGAAGATAG+AGG 0.499005 1.2:-2154300 MS.gene27294:CDS
GATGCAGCTTCCATCATTGG+TGG 0.505474 1.2:+2152951 None:intergenic
TGGGTTCTCTTATGGCAGGA+TGG 0.507870 1.2:-2154544 MS.gene27294:CDS
TCAATCACTAACTTCATCTA+CGG 0.513170 1.2:+2152872 None:intergenic
AAACTGTGCTGCATACTTGT+TGG 0.515262 1.2:+2152929 None:intergenic
TATTAAAGGGGTCCCTTACG+TGG 0.530982 1.2:+2153203 None:intergenic
AAAATGGGTTCTCTTATGGC+AGG 0.548408 1.2:-2154548 MS.gene27294:CDS
CATGCCCGTGGCCCACGTAA+GGG 0.568293 1.2:-2153215 MS.gene27294:CDS
ACAAATTGGAAATTGCTGTA+AGG 0.584160 1.2:+2154270 None:intergenic
GAAGTCAATGACCATGCCCG+TGG 0.649977 1.2:-2153227 MS.gene27294:CDS
CAAGTACGTTCATATTAAAG+GGG 0.651488 1.2:+2153191 None:intergenic
ATTAAAGGGGTCCCTTACGT+GGG 0.678500 1.2:+2153204 None:intergenic
CAGGTGGACTAAGAGTAACT+GGG 0.688506 1.2:-2152988 MS.gene27294:CDS
AATCACTAACTTCATCTACG+GGG 0.796732 1.2:+2152874 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TGAAATAAAAACATTAAAAT+TGG + chr1.2:2154092-2154111 None:intergenic 10.0%
!!! TACAAAATCATATATATTTT+TGG + chr1.2:2153923-2153942 None:intergenic 10.0%
!!! TTTATTTTTTTGGAAAAATT+TGG + chr1.2:2153265-2153284 None:intergenic 10.0%
!! AATAAATAAAATACATACGA+AGG - chr1.2:2153279-2153298 MS.gene27294:intron 15.0%
!! ATAATACTATAATATGACTA+AGG - chr1.2:2153619-2153638 MS.gene27294:intron 15.0%
!! TAATACTATAATATGACTAA+GGG - chr1.2:2153620-2153639 MS.gene27294:intron 15.0%
!! TATAGTATTATATATAGTGT+TGG + chr1.2:2153610-2153629 None:intergenic 15.0%
!!! AAATACATCTTTAATTTCAT+TGG - chr1.2:2153434-2153453 MS.gene27294:intron 15.0%
!!! TTAATGTTTTTATTTCATGA+TGG - chr1.2:2154095-2154114 MS.gene27294:intron 15.0%
!! ATAACTATAATTAGAAGAGT+AGG + chr1.2:2154298-2154317 None:intergenic 20.0%
!! CATAAACATTATTTCAAACT+TGG + chr1.2:2154135-2154154 None:intergenic 20.0%
!! CATATGCATAATTCATATAT+AGG + chr1.2:2154383-2154402 None:intergenic 20.0%
!! CTATATATGAATTATGCATA+TGG - chr1.2:2154381-2154400 MS.gene27294:intron 20.0%
!! TTTACACACAATGTTAAAAT+TGG + chr1.2:2154061-2154080 None:intergenic 20.0%
!!! AAGTATCGTTATTAATCATA+TGG + chr1.2:2152930-2152949 None:intergenic 20.0%
!!! AGGTTGATATAGAAATTAAT+AGG + chr1.2:2153833-2153852 None:intergenic 20.0%
!!! CTACTATTTTCTTTTTCTTT+TGG + chr1.2:2153578-2153597 None:intergenic 20.0%
!!! GGTTGATATAGAAATTAATA+GGG + chr1.2:2153832-2153851 None:intergenic 20.0%
!!! GTGCTTATTATTTTATGTTA+TGG - chr1.2:2152972-2152991 MS.gene27294:CDS 20.0%
!!! TATATTTTTGGATTTCACTT+AGG + chr1.2:2153911-2153930 None:intergenic 20.0%
!!! TATTAATTTAATTTGAGTGC+AGG - chr1.2:2154410-2154429 MS.gene27294:intron 20.0%
!!! TTTTACCATTTTTCTAGTAA+TGG - chr1.2:2153485-2153504 MS.gene27294:intron 20.0%
! AAGATGAAATTGATGCTTAT+TGG - chr1.2:2153095-2153114 MS.gene27294:intron 25.0%
! ACACGACAAACATTAATTAT+TGG - chr1.2:2153763-2153782 MS.gene27294:intron 25.0%
! ACACTTGAAAAAATCAACAA+GGG - chr1.2:2153546-2153565 MS.gene27294:intron 25.0%
! ATAAGGTAGTTATATTGATG+AGG - chr1.2:2153021-2153040 MS.gene27294:intron 25.0%
! ATTACTCTAGTAGAAGAATA+TGG + chr1.2:2153733-2153752 None:intergenic 25.0%
! GAACCCTAATAATTGTTAAT+TGG + chr1.2:2153352-2153371 None:intergenic 25.0%
! GCTCCAATTAACAATTATTA+GGG - chr1.2:2153346-2153365 MS.gene27294:intron 25.0%
! TAAGGTAGTTATATTGATGA+GGG - chr1.2:2153022-2153041 MS.gene27294:intron 25.0%
! TACACTTGAAAAAATCAACA+AGG - chr1.2:2153545-2153564 MS.gene27294:intron 25.0%
! TCAAGTACGTTCATATTAAA+GGG + chr1.2:2154230-2154249 None:intergenic 25.0%
! TGCTCCAATTAACAATTATT+AGG - chr1.2:2153345-2153364 MS.gene27294:intron 25.0%
! TTACTCTAGTAGAAGAATAT+GGG + chr1.2:2153732-2153751 None:intergenic 25.0%
! TTGAATCTAGTAAAAGAAGT+TGG + chr1.2:2153808-2153827 None:intergenic 25.0%
!! AGTATTATATATAGTGTTGG+TGG + chr1.2:2153607-2153626 None:intergenic 25.0%
!! TAGTTTTCTAATATGCAAGA+AGG + chr1.2:2153862-2153881 None:intergenic 25.0%
!!! GTATTATATATAGTGTTGGT+GGG + chr1.2:2153606-2153625 None:intergenic 25.0%
!!! TATTATATATAGTGTTGGTG+GGG + chr1.2:2153605-2153624 None:intergenic 25.0%
!!! TTTTTTGGAAAAATTTGGTG+TGG + chr1.2:2153260-2153279 None:intergenic 25.0%
AACTTATCAACAAAAATGGC+TGG - chr1.2:2154264-2154283 MS.gene27294:CDS 30.0%
AATATGCAAGAAGGACTAAA+AGG + chr1.2:2153853-2153872 None:intergenic 30.0%
AATCATATGGTACCTGATTT+AGG + chr1.2:2152917-2152936 None:intergenic 30.0%
ACAAATTGGAAATTGCTGTA+AGG + chr1.2:2153150-2153169 None:intergenic 30.0%
AGTGACCATTACTAGAAAAA+TGG + chr1.2:2153493-2153512 None:intergenic 30.0%
CAAGTACGTTCATATTAAAG+GGG + chr1.2:2154229-2154248 None:intergenic 30.0%
GAAATCAAAGAAGAAGATAG+AGG - chr1.2:2153117-2153136 MS.gene27294:intron 30.0%
GAGCAACTTATCAACAAAAA+TGG - chr1.2:2154260-2154279 MS.gene27294:CDS 30.0%
GTCAAGTACGTTCATATTAA+AGG + chr1.2:2154231-2154250 None:intergenic 30.0%
TCAATCACTAACTTCATCTA+CGG + chr1.2:2154548-2154567 None:intergenic 30.0%
TCGTACTAGAACTTACTATA+AGG - chr1.2:2153004-2153023 MS.gene27294:intron 30.0%
TCTTCAATTGATCCTAAATC+AGG - chr1.2:2152902-2152921 MS.gene27294:CDS 30.0%
! TTTCATCTTTTGTAAGTGAC+TGG + chr1.2:2153084-2153103 None:intergenic 30.0%
!! TAATTTAATTTGAGTGCAGG+TGG - chr1.2:2154413-2154432 MS.gene27294:intron 30.0%
AATCACTAACTTCATCTACG+GGG + chr1.2:2154546-2154565 None:intergenic 35.0%
ATGTTTGTCGTGTCTCTAAT+AGG + chr1.2:2153756-2153775 None:intergenic 35.0%
CAATCACTAACTTCATCTAC+GGG + chr1.2:2154547-2154566 None:intergenic 35.0%
CAATTTGTCAGAGACTATTC+AGG - chr1.2:2153162-2153181 MS.gene27294:CDS 35.0%
CTGAATAGTCTCTGACAAAT+TGG + chr1.2:2153164-2153183 None:intergenic 35.0%
GAACGTACTTGACACAAATT+TGG - chr1.2:2154238-2154257 MS.gene27294:intron 35.0%
!! TGAAACTTCTTTTCAGGATC+AGG + chr1.2:2154170-2154189 None:intergenic 35.0%
!! TGACTGGTTCCTTTTAAGTA+TGG + chr1.2:2153068-2153087 None:intergenic 35.0%
!!! CAATTTTGTCGATTCCAAAC+TGG + chr1.2:2154521-2154540 None:intergenic 35.0%
!!! GACTTCTGAAACTTCTTTTC+AGG + chr1.2:2154176-2154195 None:intergenic 35.0%
AAACTGTGCTGCATACTTGT+TGG + chr1.2:2154491-2154510 None:intergenic 40.0%
AAAGAAGAAGCAGACAGAGT+TGG + chr1.2:2153468-2153487 None:intergenic 40.0%
CTGTCTCAGCCATACTTAAA+AGG - chr1.2:2153056-2153075 MS.gene27294:intron 40.0%
!! ATCCAACTTATGGTTTGGTG+CGG - chr1.2:2153228-2153247 MS.gene27294:CDS 40.0%
!! TGACTAAGGGCACTACAATT+TGG - chr1.2:2153633-2153652 MS.gene27294:intron 40.0%
ACAGTTTCACGTTGCCAGTT+TGG - chr1.2:2154504-2154523 MS.gene27294:intron 45.0%
ATTAAAGGGGTCCCTTACGT+GGG + chr1.2:2154216-2154235 None:intergenic 45.0%
GGCAGATCCAACTTATGGTT+TGG - chr1.2:2153223-2153242 MS.gene27294:CDS 45.0%
TATTAAAGGGGTCCCTTACG+TGG + chr1.2:2154217-2154236 None:intergenic 45.0%
TCTGAATGAGCCACCAATGA+TGG - chr1.2:2154456-2154475 MS.gene27294:intron 45.0%
TTGGATGCAGCTTCCATCAT+TGG + chr1.2:2154472-2154491 None:intergenic 45.0%
! AAGAAGCAGACAGAGTTGGT+GGG + chr1.2:2153464-2153483 None:intergenic 45.0%
!! CAGGTGGACTAAGAGTAACT+GGG - chr1.2:2154429-2154448 MS.gene27294:intron 45.0%
!! AATTATAGTTATATAATAAT+TGG - chr1.2:2154306-2154325 MS.gene27294:CDS 5.0%
!!! ATGTATTTTATTTATTTTTT+TGG + chr1.2:2153275-2153294 None:intergenic 5.0%
AACCTCTACTTGCCACCTTC+CGG - chr1.2:2153196-2153215 MS.gene27294:CDS 50.0%
AGCCGCACCAAACCATAAGT+TGG + chr1.2:2153233-2153252 None:intergenic 50.0%
GAAGAAGCAGACAGAGTTGG+TGG + chr1.2:2153465-2153484 None:intergenic 50.0%
GATGCAGCTTCCATCATTGG+TGG + chr1.2:2154469-2154488 None:intergenic 50.0%
GCATGGGCAGATCCAACTTA+TGG - chr1.2:2153218-2153237 MS.gene27294:CDS 50.0%
GGGTTCTCTTATGGCAGGAT+GGG - chr1.2:2152874-2152893 MS.gene27294:CDS 50.0%
GGTTCTCTTATGGCAGGATG+GGG - chr1.2:2152875-2152894 MS.gene27294:CDS 50.0%
TGGGTTCTCTTATGGCAGGA+TGG - chr1.2:2152873-2152892 MS.gene27294:CDS 50.0%
! TAAGTTGGATCTGCCCATGC+CGG + chr1.2:2153218-2153237 None:intergenic 50.0%
!! AGAAGCAGACAGAGTTGGTG+GGG + chr1.2:2153463-2153482 None:intergenic 50.0%
!! GCAGGTGGACTAAGAGTAAC+TGG - chr1.2:2154428-2154447 MS.gene27294:intron 50.0%
GAAGTCAATGACCATGCCCG+TGG - chr1.2:2154190-2154209 MS.gene27294:intron 55.0%
TACTTGCCACCTTCCGGCAT+GGG - chr1.2:2153202-2153221 MS.gene27294:CDS 55.0%
CTACTTGCCACCTTCCGGCA+TGG - chr1.2:2153201-2153220 MS.gene27294:CDS 60.0%
TGCCGGAAGGTGGCAAGTAG+AGG + chr1.2:2153201-2153220 None:intergenic 60.0%
TTGGATCTGCCCATGCCGGA+AGG + chr1.2:2153214-2153233 None:intergenic 60.0%
CATGCCCGTGGCCCACGTAA+GGG - chr1.2:2154202-2154221 MS.gene27294:intron 65.0%
GATCTGCCCATGCCGGAAGG+TGG + chr1.2:2153211-2153230 None:intergenic 65.0%
CCATGCCCGTGGCCCACGTA+AGG - chr1.2:2154201-2154220 MS.gene27294:intron 70.0%
CCTTACGTGGGCCACGGGCA+TGG + chr1.2:2154204-2154223 None:intergenic 70.0%
GGGGTCCCTTACGTGGGCCA+CGG + chr1.2:2154210-2154229 None:intergenic 70.0%
GGGTCCCTTACGTGGGCCAC+GGG + chr1.2:2154209-2154228 None:intergenic 70.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 2152872 2154567 2152872 ID=MS.gene27294
chr1.2 mRNA 2152872 2154567 2152872 ID=MS.gene27294.t1;Parent=MS.gene27294
chr1.2 exon 2154516 2154567 2154516 ID=MS.gene27294.t1.exon1;Parent=MS.gene27294.t1
chr1.2 CDS 2154516 2154567 2154516 ID=cds.MS.gene27294.t1;Parent=MS.gene27294.t1
chr1.2 exon 2154256 2154374 2154256 ID=MS.gene27294.t1.exon2;Parent=MS.gene27294.t1
chr1.2 CDS 2154256 2154374 2154256 ID=cds.MS.gene27294.t1;Parent=MS.gene27294.t1
chr1.2 exon 2153154 2153272 2153154 ID=MS.gene27294.t1.exon3;Parent=MS.gene27294.t1
chr1.2 CDS 2153154 2153272 2153154 ID=cds.MS.gene27294.t1;Parent=MS.gene27294.t1
chr1.2 exon 2152872 2153007 2152872 ID=MS.gene27294.t1.exon4;Parent=MS.gene27294.t1
chr1.2 CDS 2152872 2153007 2152872 ID=cds.MS.gene27294.t1;Parent=MS.gene27294.t1
Gene Sequence

>MS.gene27294

ATGGGTTCTCTTATGGCAGGATGGGGCTCTTCTTCAATTGATCCTAAATCAGGTACCATATGATTAATAACGATACTTATATTATACACATATATGCTTTGTGCTTATTATTTTATGTTATGGAACAATTAATCGTACTAGAACTTACTATAAGGTAGTTATATTGATGAGGGAACTTTTTTCACTGTCTCAGCCATACTTAAAAGGAACCAGTCACTTACAAAAGATGAAATTGATGCTTATTGGAAATCAAAGAAGAAGATAGAGGAAGAACACCTTACAGCAATTTCCAATTTGTCAGAGACTATTCAGGTTTGATATTCAAACCTCTACTTGCCACCTTCCGGCATGGGCAGATCCAACTTATGGTTTGGTGCGGCTACTGCCACACCAAATTTTTCCAAAAAAATAAATAAAATACATACGAAGGATTTCTATAAAAATGAAATGTTAGAGAAATTGACAAATCATTTTGCTCCAATTAACAATTATTAGGGTTCAAATGCATTTGAGCTAATAAAACTAAAAAAAAAACTATAAAAATTGTTATTTTAAGTGAAATAAATACATCTTTAATTTCATTGGACACCCCACCAACTCTGTCTGCTTCTTCTTTTACCATTTTTCTAGTAATGGTCACTACTAAATTATAGAAATGAATTAAAGATTTTTTTACACTTGAAAAAATCAACAAGGGATAAGACCAAAAGAAAAAGAAAATAGTAGCACACCCCACCAACACTATATATAATACTATAATATGACTAAGGGCACTACAATTTGGATCGTGATTGTGAATTTTTAATCTCTATATTTTTTTATTATTAATCTTTGTATCAATTTTTTTCTTCATTTTTCCCATATTCTTCTACTAGAGTAATCCTATTAGAGACACGACAAACATTAATTATTGGTTCGATTGATTGTGAAATTCCAACTTCTTTTACTAGATTCAATCCCTATTAATTTCTATATCAACCTTTTAGTCCTTCTTGCATATTAGAAAACTAAGTGACTAGAAAATATAGTTATGTCACCTAAGTGAAATCCAAAAATATATATGATTTTGTAATTTTTAGTAATTAAAAGACGAATACAAGACTAAAAAACAACTTGTCAAAAAAAAGACTAAAAAACAAATTCAATATATCTATAAAGATAAAAAATATATTTAACTCATTAATTTCCAATTTTAACATTGTGTGTAAAAAAAAAAACCAATTTTAATGTTTTTATTTCATGATGGAGTAACAGACAATTCCAAGTTTGAAATAATGTTTATGATGATGATGCAGCCTGATCCTGAAAAGAAGTTTCAGAAGTCAATGACCATGCCCGTGGCCCACGTAAGGGACCCCTTTAATATGAACGTACTTGACACAAATTTGGAGCAACTTATCAACAAAAATGGCTGGTAAATTAACCTACTCTTCTAATTATAGTTATATAATAATTGGTTAGTTTAATATTTTTATACTTTTATTGCTATTTTTGCTAGAGAAAGTACTCCTATATATGAATTATGCATATGGATCATATATTAATTTAATTTGAGTGCAGGTGGACTAAGAGTAACTGGGCATTTCTGAATGAGCCACCAATGATGGAAGCTGCATCCAACAAGTATGCAGCACAGTTTCACGTTGCCAGTTTGGAATCGACAAAATTGAACCCCGTAGATGAAGTTAGTGATTGA

Protein sequence

>MS.gene27294.t1

MGSLMAGWGSSSIDPKSAILKRNQSLTKDEIDAYWKSKKKIEEEHLTAISNLSETIQPDPEKKFQKSMTMPVAHVRDPFNMNVLDTNLEQLINKNGWWTKSNWAFLNEPPMMEAASNKYAAQFHVASLESTKLNPVDEVSD