AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1420140


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1420140 MtrunA17_Chr1g0179671 94.404 411 23 0 1 411 1 411 0.0 764
Msa1420140 MtrunA17_Chr8g0340991 23.611 360 232 8 12 336 22 373 8.04e-19 88.6
Msa1420140 MtrunA17_Chr2g0330791 21.622 407 241 7 10 366 9 387 8.18e-16 79.3
Msa1420140 MtrunA17_Chr5g0422391 26.087 276 184 3 98 366 125 387 9.69e-14 73.2
Msa1420140 MtrunA17_Chr1g0198861 25.097 259 168 3 96 335 124 375 4.26e-12 68.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1420140 AT2G36650.1 30.154 325 181 3 11 335 13 291 2.99e-34 131
Msa1420140 AT3G25690.5 25.100 251 188 0 98 348 130 380 2.79e-15 78.6
Msa1420140 AT3G25690.1 25.100 251 188 0 98 348 128 378 3.08e-15 78.6
Msa1420140 AT3G25690.2 25.100 251 188 0 98 348 128 378 3.08e-15 78.6
Msa1420140 AT3G25690.6 25.100 251 188 0 98 348 128 378 3.08e-15 78.6
Msa1420140 AT3G25690.4 25.100 251 188 0 98 348 128 378 3.08e-15 78.6
Msa1420140 AT1G52080.2 26.812 276 180 4 98 366 138 398 3.95e-12 68.6
Msa1420140 AT1G52080.1 26.812 276 180 4 98 366 138 398 3.95e-12 68.6

Find 38 sgRNAs with CRISPR-Local

Find 108 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGAAGATTAATGTTTGTTTA+AGG 0.192588 tig0024758:-45490 Msa1420140:CDS
TAGAGAGCTGAAAAGGGTTT+TGG 0.249773 tig0024758:-45726 Msa1420140:CDS
TGACCCTTCTAGTTCCAAAA+AGG 0.258156 tig0024758:-45384 Msa1420140:CDS
GGCTCAATCTCATTTGATTA+AGG 0.274337 tig0024758:-45849 Msa1420140:CDS
ACACCAGCTTTGAGGATAAT+AGG 0.296488 tig0024758:+46418 None:intergenic
TTTCAATAATCTTAAGGTAT+TGG 0.311191 tig0024758:+45942 None:intergenic
TTATTGAAAAGCTTGAATAT+TGG 0.323357 tig0024758:-45928 Msa1420140:CDS
CAACAAGATTCTGAATGAAT+TGG 0.330904 tig0024758:-45564 Msa1420140:CDS
ATGAAATTAGAGAGCTGAAA+AGG 0.337337 tig0024758:-45733 Msa1420140:CDS
ACATCATGAGAATTGACTTC+AGG 0.356940 tig0024758:+46295 None:intergenic
CTTGAGACATCAGAAGAATA+TGG 0.358484 tig0024758:-45665 Msa1420140:CDS
TCTTTCTGAGAGATTTGGTT+TGG 0.365727 tig0024758:-46185 Msa1420140:CDS
AGTGTTCTTTCTGAGAGATT+TGG 0.368051 tig0024758:-46190 Msa1420140:CDS
AGTAATGAAATTAAGTGCTT+TGG 0.382181 tig0024758:-45287 Msa1420140:CDS
TTTGTCAAATTGTAAAGTTA+AGG 0.415691 tig0024758:+46105 None:intergenic
GAGCAAAACCTTGGAGTAGT+TGG 0.436041 tig0024758:+45251 None:intergenic
TGAAATTAGAGAGCTGAAAA+GGG 0.459539 tig0024758:-45732 Msa1420140:CDS
CTATAGGAACACCAGCTTTG+AGG 0.462456 tig0024758:+46410 None:intergenic
TGCTTAAGAAGCAAGATTGA+AGG 0.471674 tig0024758:-46148 Msa1420140:CDS
TTGCTGGTTTGATCTATGCA+TGG 0.476381 tig0024758:-46378 Msa1420140:CDS
TGAATCAAGAGATGTTATGA+AGG 0.483238 tig0024758:-45594 Msa1420140:CDS
CCAGCAAAAGAAACAGCTAT+AGG 0.492610 tig0024758:+46394 None:intergenic
AAGAACACTACTATCTATAG+AGG 0.498832 tig0024758:+46204 None:intergenic
ATCTGCAAATAATATTTCAA+AGG 0.499256 tig0024758:+45617 None:intergenic
TTGGGTGGATGGTAGTGAAA+AGG 0.500899 tig0024758:-45336 Msa1420140:CDS
CATCAAAATGTGTCTTGCAT+TGG 0.501895 tig0024758:-45425 Msa1420140:CDS
ATGAGAGTCAGTTTCTGAAA+AGG 0.515828 tig0024758:+46321 None:intergenic
TGAATTGGAGCAAGTTAAGA+AGG 0.519910 tig0024758:-45549 Msa1420140:CDS
CAAACTTTGATGATCAAAGA+AGG 0.530552 tig0024758:-45824 Msa1420140:CDS
TTGAAGAACTTATTTACTTG+AGG 0.545043 tig0024758:-45511 Msa1420140:CDS
CATCATGAGAATTGACTTCA+GGG 0.556455 tig0024758:+46296 None:intergenic
AAGCCTATTATCCTCAAAGC+TGG 0.568812 tig0024758:-46421 Msa1420140:CDS
TCATAGAAACAGAAACTATG+AGG 0.580497 tig0024758:-45982 Msa1420140:CDS
GAAGCTACTTAAGAAATCAA+AGG 0.584610 tig0024758:-45870 Msa1420140:CDS
TAAGCACTAGAGCAAAACCT+TGG 0.616488 tig0024758:+45242 None:intergenic
AAGGTTAAAGTGAAACCAGA+AGG 0.618245 tig0024758:-45317 Msa1420140:CDS
ATTCTGCTCCAACTACTCCA+AGG 0.627578 tig0024758:-45259 Msa1420140:CDS
ATCATGAGAATTGACTTCAG+GGG 0.687779 tig0024758:+46297 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTGATAACTTTTCTTCTA+TGG - tig0024758:45441-45460 Msa1420140:CDS 20.0%
!! TTTGTCAAATTGTAAAGTTA+AGG + tig0024758:45593-45612 None:intergenic 20.0%
!! AATCAAAAACATGTTATCAT+TGG - tig0024758:45651-45670 Msa1420140:CDS 20.0%
!! TTTCAATAATCTTAAGGTAT+TGG + tig0024758:45756-45775 None:intergenic 20.0%
!! TTATTGAAAAGCTTGAATAT+TGG - tig0024758:45767-45786 Msa1420140:CDS 20.0%
!! ATCTGCAAATAATATTTCAA+AGG + tig0024758:46081-46100 None:intergenic 20.0%
!! TGATTAAAAAGCTGAAAAAT+TGG - tig0024758:46340-46359 Msa1420140:CDS 20.0%
!! GATTAAAAAGCTGAAAAATT+GGG - tig0024758:46341-46360 Msa1420140:CDS 20.0%
!!! TTTTGATAACTTTTCTTCTA+TGG - tig0024758:45441-45460 Msa1420140:CDS 20.0%
!! TTTGTCAAATTGTAAAGTTA+AGG + tig0024758:45593-45612 None:intergenic 20.0%
!! AATCAAAAACATGTTATCAT+TGG - tig0024758:45651-45670 Msa1420140:CDS 20.0%
!! TTTCAATAATCTTAAGGTAT+TGG + tig0024758:45756-45775 None:intergenic 20.0%
!! TTATTGAAAAGCTTGAATAT+TGG - tig0024758:45767-45786 Msa1420140:CDS 20.0%
!! ATCTGCAAATAATATTTCAA+AGG + tig0024758:46081-46100 None:intergenic 20.0%
!! TGATTAAAAAGCTGAAAAAT+TGG - tig0024758:46340-46359 Msa1420140:CDS 20.0%
!! GATTAAAAAGCTGAAAAATT+GGG - tig0024758:46341-46360 Msa1420140:CDS 20.0%
!! CAAGCTTTTCAATAATCTTA+AGG + tig0024758:45762-45781 None:intergenic 25.0%
! ACTATGATGAATTGCAAAAA+AGG - tig0024758:45914-45933 Msa1420140:CDS 25.0%
! CTATGATGAATTGCAAAAAA+GGG - tig0024758:45915-45934 Msa1420140:CDS 25.0%
! TTGAAGAACTTATTTACTTG+AGG - tig0024758:46184-46203 Msa1420140:CDS 25.0%
! GGAAGATTAATGTTTGTTTA+AGG - tig0024758:46205-46224 Msa1420140:CDS 25.0%
!!! TGAATTGCATTGTTCTTTTT+TGG - tig0024758:46245-46264 Msa1420140:CDS 25.0%
!! TTTAATCAACTTTCCCTTTT+TGG + tig0024758:46328-46347 None:intergenic 25.0%
! AGTAATGAAATTAAGTGCTT+TGG - tig0024758:46408-46427 Msa1420140:CDS 25.0%
!! CAAGCTTTTCAATAATCTTA+AGG + tig0024758:45762-45781 None:intergenic 25.0%
! ACTATGATGAATTGCAAAAA+AGG - tig0024758:45914-45933 Msa1420140:CDS 25.0%
! CTATGATGAATTGCAAAAAA+GGG - tig0024758:45915-45934 Msa1420140:CDS 25.0%
! TTGAAGAACTTATTTACTTG+AGG - tig0024758:46184-46203 Msa1420140:CDS 25.0%
! GGAAGATTAATGTTTGTTTA+AGG - tig0024758:46205-46224 Msa1420140:CDS 25.0%
!!! TGAATTGCATTGTTCTTTTT+TGG - tig0024758:46245-46264 Msa1420140:CDS 25.0%
!! TTTAATCAACTTTCCCTTTT+TGG + tig0024758:46328-46347 None:intergenic 25.0%
! AGTAATGAAATTAAGTGCTT+TGG - tig0024758:46408-46427 Msa1420140:CDS 25.0%
AAGAACACTACTATCTATAG+AGG + tig0024758:45494-45513 None:intergenic 30.0%
TCATAGAAACAGAAACTATG+AGG - tig0024758:45713-45732 Msa1420140:CDS 30.0%
GAAGCTACTTAAGAAATCAA+AGG - tig0024758:45825-45844 Msa1420140:CDS 30.0%
! CAAACTTTGATGATCAAAGA+AGG - tig0024758:45871-45890 Msa1420140:CDS 30.0%
ATGAAATTAGAGAGCTGAAA+AGG - tig0024758:45962-45981 Msa1420140:CDS 30.0%
TGAAATTAGAGAGCTGAAAA+GGG - tig0024758:45963-45982 Msa1420140:CDS 30.0%
TGAATCAAGAGATGTTATGA+AGG - tig0024758:46101-46120 Msa1420140:CDS 30.0%
CAACAAGATTCTGAATGAAT+TGG - tig0024758:46131-46150 Msa1420140:CDS 30.0%
TAAAAAGCTGAAAAATTGGG+TGG - tig0024758:46344-46363 Msa1420140:CDS 30.0%
AAGAACACTACTATCTATAG+AGG + tig0024758:45494-45513 None:intergenic 30.0%
TCATAGAAACAGAAACTATG+AGG - tig0024758:45713-45732 Msa1420140:CDS 30.0%
GAAGCTACTTAAGAAATCAA+AGG - tig0024758:45825-45844 Msa1420140:CDS 30.0%
! CAAACTTTGATGATCAAAGA+AGG - tig0024758:45871-45890 Msa1420140:CDS 30.0%
ATGAAATTAGAGAGCTGAAA+AGG - tig0024758:45962-45981 Msa1420140:CDS 30.0%
TGAAATTAGAGAGCTGAAAA+GGG - tig0024758:45963-45982 Msa1420140:CDS 30.0%
TGAATCAAGAGATGTTATGA+AGG - tig0024758:46101-46120 Msa1420140:CDS 30.0%
CAACAAGATTCTGAATGAAT+TGG - tig0024758:46131-46150 Msa1420140:CDS 30.0%
TAAAAAGCTGAAAAATTGGG+TGG - tig0024758:46344-46363 Msa1420140:CDS 30.0%
! ATGAGAGTCAGTTTCTGAAA+AGG + tig0024758:45377-45396 None:intergenic 35.0%
! ATCATGAGAATTGACTTCAG+GGG + tig0024758:45401-45420 None:intergenic 35.0%
! CATCATGAGAATTGACTTCA+GGG + tig0024758:45402-45421 None:intergenic 35.0%
! ACATCATGAGAATTGACTTC+AGG + tig0024758:45403-45422 None:intergenic 35.0%
! AGTGTTCTTTCTGAGAGATT+TGG - tig0024758:45505-45524 Msa1420140:CDS 35.0%
! TCTTTCTGAGAGATTTGGTT+TGG - tig0024758:45510-45529 Msa1420140:CDS 35.0%
TGCTTAAGAAGCAAGATTGA+AGG - tig0024758:45547-45566 Msa1420140:CDS 35.0%
GGCTCAATCTCATTTGATTA+AGG - tig0024758:45846-45865 Msa1420140:CDS 35.0%
CTTGAGACATCAGAAGAATA+TGG - tig0024758:46030-46049 Msa1420140:CDS 35.0%
TGAATTGGAGCAAGTTAAGA+AGG - tig0024758:46146-46165 Msa1420140:CDS 35.0%
CATCAAAATGTGTCTTGCAT+TGG - tig0024758:46270-46289 Msa1420140:CDS 35.0%
!!! TTCCCTTTTTGGAACTAGAA+GGG + tig0024758:46317-46336 None:intergenic 35.0%
!!! TTTCCCTTTTTGGAACTAGA+AGG + tig0024758:46318-46337 None:intergenic 35.0%
AAGGTTAAAGTGAAACCAGA+AGG - tig0024758:46378-46397 Msa1420140:CDS 35.0%
!! TCATTACTGCTTTTACCTTC+TGG + tig0024758:46396-46415 None:intergenic 35.0%
! ATGAGAGTCAGTTTCTGAAA+AGG + tig0024758:45377-45396 None:intergenic 35.0%
! ATCATGAGAATTGACTTCAG+GGG + tig0024758:45401-45420 None:intergenic 35.0%
! CATCATGAGAATTGACTTCA+GGG + tig0024758:45402-45421 None:intergenic 35.0%
! ACATCATGAGAATTGACTTC+AGG + tig0024758:45403-45422 None:intergenic 35.0%
! AGTGTTCTTTCTGAGAGATT+TGG - tig0024758:45505-45524 Msa1420140:CDS 35.0%
! TCTTTCTGAGAGATTTGGTT+TGG - tig0024758:45510-45529 Msa1420140:CDS 35.0%
TGCTTAAGAAGCAAGATTGA+AGG - tig0024758:45547-45566 Msa1420140:CDS 35.0%
GGCTCAATCTCATTTGATTA+AGG - tig0024758:45846-45865 Msa1420140:CDS 35.0%
CTTGAGACATCAGAAGAATA+TGG - tig0024758:46030-46049 Msa1420140:CDS 35.0%
TGAATTGGAGCAAGTTAAGA+AGG - tig0024758:46146-46165 Msa1420140:CDS 35.0%
CATCAAAATGTGTCTTGCAT+TGG - tig0024758:46270-46289 Msa1420140:CDS 35.0%
!!! TTCCCTTTTTGGAACTAGAA+GGG + tig0024758:46317-46336 None:intergenic 35.0%
!!! TTTCCCTTTTTGGAACTAGA+AGG + tig0024758:46318-46337 None:intergenic 35.0%
AAGGTTAAAGTGAAACCAGA+AGG - tig0024758:46378-46397 Msa1420140:CDS 35.0%
!! TCATTACTGCTTTTACCTTC+TGG + tig0024758:46396-46415 None:intergenic 35.0%
AAGCCTATTATCCTCAAAGC+TGG - tig0024758:45274-45293 Msa1420140:CDS 40.0%
!! ACACCAGCTTTGAGGATAAT+AGG + tig0024758:45280-45299 None:intergenic 40.0%
CCAGCAAAAGAAACAGCTAT+AGG + tig0024758:45304-45323 None:intergenic 40.0%
!!! CCTATAGCTGTTTCTTTTGC+TGG - tig0024758:45301-45320 Msa1420140:CDS 40.0%
!! TTGCTGGTTTGATCTATGCA+TGG - tig0024758:45317-45336 Msa1420140:CDS 40.0%
! TAGAGAGCTGAAAAGGGTTT+TGG - tig0024758:45969-45988 Msa1420140:CDS 40.0%
!! TGACCCTTCTAGTTCCAAAA+AGG - tig0024758:46311-46330 Msa1420140:CDS 40.0%
!! GACCCTTCTAGTTCCAAAAA+GGG - tig0024758:46312-46331 Msa1420140:CDS 40.0%
AAGCTGAAAAATTGGGTGGA+TGG - tig0024758:46348-46367 Msa1420140:CDS 40.0%
TAAGCACTAGAGCAAAACCT+TGG + tig0024758:46456-46475 None:intergenic 40.0%
AAGCCTATTATCCTCAAAGC+TGG - tig0024758:45274-45293 Msa1420140:CDS 40.0%
!! ACACCAGCTTTGAGGATAAT+AGG + tig0024758:45280-45299 None:intergenic 40.0%
CCAGCAAAAGAAACAGCTAT+AGG + tig0024758:45304-45323 None:intergenic 40.0%
!!! CCTATAGCTGTTTCTTTTGC+TGG - tig0024758:45301-45320 Msa1420140:CDS 40.0%
!! TTGCTGGTTTGATCTATGCA+TGG - tig0024758:45317-45336 Msa1420140:CDS 40.0%
! TAGAGAGCTGAAAAGGGTTT+TGG - tig0024758:45969-45988 Msa1420140:CDS 40.0%
!! TGACCCTTCTAGTTCCAAAA+AGG - tig0024758:46311-46330 Msa1420140:CDS 40.0%
!! GACCCTTCTAGTTCCAAAAA+GGG - tig0024758:46312-46331 Msa1420140:CDS 40.0%
AAGCTGAAAAATTGGGTGGA+TGG - tig0024758:46348-46367 Msa1420140:CDS 40.0%
TAAGCACTAGAGCAAAACCT+TGG + tig0024758:46456-46475 None:intergenic 40.0%
CTATAGGAACACCAGCTTTG+AGG + tig0024758:45288-45307 None:intergenic 45.0%
! TTGGGTGGATGGTAGTGAAA+AGG - tig0024758:46359-46378 Msa1420140:CDS 45.0%
ATTCTGCTCCAACTACTCCA+AGG - tig0024758:46436-46455 Msa1420140:CDS 45.0%
GAGCAAAACCTTGGAGTAGT+TGG + tig0024758:46447-46466 None:intergenic 45.0%
CTATAGGAACACCAGCTTTG+AGG + tig0024758:45288-45307 None:intergenic 45.0%
! TTGGGTGGATGGTAGTGAAA+AGG - tig0024758:46359-46378 Msa1420140:CDS 45.0%
ATTCTGCTCCAACTACTCCA+AGG - tig0024758:46436-46455 Msa1420140:CDS 45.0%
GAGCAAAACCTTGGAGTAGT+TGG + tig0024758:46447-46466 None:intergenic 45.0%
Chromosome Type Strat End Strand Name
tig0024758 gene 45241 46476 45241 ID=Msa1420140;Name=Msa1420140
tig0024758 mRNA 45241 46476 45241 ID=Msa1420140-mRNA-1;Parent=Msa1420140;Name=Msa1420140-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|411
tig0024758 exon 45241 46476 45241 ID=Msa1420140-mRNA-1:exon:1277;Parent=Msa1420140-mRNA-1
tig0024758 CDS 45241 46476 45241 ID=Msa1420140-mRNA-1:cds;Parent=Msa1420140-mRNA-1
Gene Sequence

>Msa1420140

ATGGAAAACTCAACGCTTAAAGCTGAGAATCTAAAGCCTATTATCCTCAAAGCTGGTGTTCCTATAGCTGTTTCTTTTGCTGGTTTGATCTATGCATGGATCATAACAAAGAAAAGCTTATCAAATGTCTCTTCCTTTTCAGAAACTGACTCTCATACCCCTGAAGTCAATTCTCATGATGTAACTCAACATGAAGAAAGTTTTGATAACTTTTCTTCTATGGAAGATGAAGAAAAAGAAGAATACACTACCTCTATAGATAGTAGTGTTCTTTCTGAGAGATTTGGTTTGGAACAAGAGATTGCTTGCTTAAGAAGCAAGATTGAAGGTATGCAAATGAGAGAATTAGCCTTAACTTTACAATTTGACAAATATTGTGAAATGAAAGAAAAAGAATCTATGCTTAGAGAAATCAAAAACATGTTATCATTGGAGACATCTCGTGTCGAATTCTTCGATAGAGAGATTTCATTCATAGAAACAGAAACTATGAGGTTAGAGAATTTTGTAATCCAATACCTTAAGATTATTGAAAAGCTTGAATATTGGAAATCAGAGAATAGATTGCTTCAGAAGAAAGTTCAGAAGCTACTTAAGAAATCAAAGGCTCAATCTCATTTGATTAAGGAGCAAACTTTGATGATCAAAGAAGGAGAAGAAGAAATCTTGAGAAACTATGATGAATTGCAAAAAAGGGCTAATATGATTCATAAGTTAGAAGATGAAATTAGAGAGCTGAAAAGGGTTTTGGATGATTTTCAAGATGAGAAGAATGAACTTGTGAAGAAGCTTGAGACATCAGAAGAATATGGATGTAAAGAAGAGCTACATAAAAAGCCTTTGAAATATTATTTGCAGATTGAATCAAGAGATGTTATGAAGGAAGATTACAACAAGATTCTGAATGAATTGGAGCAAGTTAAGAAGGAACATGAAAATGAAATTGAAGAACTTATTTACTTGAGGAAGATTAATGTTTGTTTAAGGCAAGAGTTAATGAAGCATGAATTGCATTGTTCTTTTTTGGATCATCAAAATGTGTCTTGCATTGGTTCTTCTAGTTTTCATTGTGACCCTTCTAGTTCCAAAAAGGGAAAGTTGATTAAAAAGCTGAAAAATTGGGTGGATGGTAGTGAAAAGGTTAAAGTGAAACCAGAAGGTAAAAGCAGTAATGAAATTAAGTGCTTTGGTATGAATTCTGCTCCAACTACTCCAAGGTTTTGCTCTAGTGCTTAG

Protein sequence

>Msa1420140

MENSTLKAENLKPIILKAGVPIAVSFAGLIYAWIITKKSLSNVSSFSETDSHTPEVNSHDVTQHEESFDNFSSMEDEEKEEYTTSIDSSVLSERFGLEQEIACLRSKIEGMQMRELALTLQFDKYCEMKEKESMLREIKNMLSLETSRVEFFDREISFIETETMRLENFVIQYLKIIEKLEYWKSENRLLQKKVQKLLKKSKAQSHLIKEQTLMIKEGEEEILRNYDELQKRANMIHKLEDEIRELKRVLDDFQDEKNELVKKLETSEEYGCKEELHKKPLKYYLQIESRDVMKEDYNKILNELEQVKKEHENEIEELIYLRKINVCLRQELMKHELHCSFLDHQNVSCIGSSSFHCDPSSSKKGKLIKKLKNWVDGSEKVKVKPEGKSSNEIKCFGMNSAPTTPRFCSSA*