AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene051539


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene051539.t1 MTR_1g015040 85.253 217 30 2 1 216 24 239 1.34e-73 223
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 69 sgRNAs with CRISPR-Local

Find 89 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCTTCGCCTTCTTCGGGTTC+AGG 0.278379 1.3:+7124459 MS.gene051539:CDS
TGAGGCATAATAATAGTAAT+AGG 0.283637 1.3:-7124532 None:intergenic
TTTGAAATCTTCGCCTTCTT+CGG 0.306660 1.3:+7124452 MS.gene051539:CDS
GGTGGTCCACCAATTACTTT+AGG 0.326407 1.3:-7124492 None:intergenic
CAAGGACAACCTAAAGTAAT+TGG 0.337399 1.3:+7124483 MS.gene051539:CDS
TTGAAATCTTCGCCTTCTTC+GGG 0.338296 1.3:+7124453 MS.gene051539:CDS
GAATTTGATGAAGCAAGTTT+AGG 0.338870 1.3:-7124111 None:intergenic
AGTCCTTCGTCACATTCTTC+CGG 0.348481 1.3:+7124411 MS.gene051539:CDS
GTCCTTCGTCACATTCTTCC+GGG 0.349605 1.3:+7124412 MS.gene051539:CDS
ATTCATCGGATATTCTTTGC+TGG 0.356708 1.3:+7124609 MS.gene051539:CDS
TTTAGAAGTGGAGGAGGAGG+AGG 0.374484 1.3:-7124321 None:intergenic
TTTGATGATGTGAGTGGAAA+TGG 0.378894 1.3:-7124294 None:intergenic
TAATAATAGTAATAGGGATA+TGG 0.384788 1.3:-7124525 None:intergenic
TGTGTTAGGAGTGGAGTAGA+TGG 0.387212 1.3:-7124231 None:intergenic
GTTAATAGTGGAGGAGGTGG+AGG 0.430557 1.3:-7124258 None:intergenic
TGGGGTGTTATTAGTGGAAA+AGG 0.432885 1.3:-7124204 None:intergenic
TTGATGATGTGAGTGGAAAT+GGG 0.439050 1.3:-7124293 None:intergenic
CCTTCTTCGGGTTCAGGTCA+AGG 0.439335 1.3:+7124465 MS.gene051539:CDS
GGTGAATATGATGTTAATAG+TGG 0.445887 1.3:-7124270 None:intergenic
GAGGCATAATAATAGTAATA+GGG 0.446723 1.3:-7124531 None:intergenic
AGTGGAGTAGATGGAGGGTG+GGG 0.452281 1.3:-7124222 None:intergenic
GGAGGGTGGGGTGTTATTAG+TGG 0.452753 1.3:-7124210 None:intergenic
ATGCATAATAAACCACTTGA+AGG 0.460999 1.3:-7124045 None:intergenic
GGGGTGTTATTAGTGGAAAA+GGG 0.461571 1.3:-7124203 None:intergenic
TTCATCGGATATTCTTTGCT+GGG 0.468810 1.3:+7124610 MS.gene051539:CDS
GATGTTAATAGTGGAGGAGG+TGG 0.484497 1.3:-7124261 None:intergenic
AAAGAGAACATTGGAGATTG+AGG 0.496507 1.3:+7124005 MS.gene051539:CDS
GGGTGTTATTAGTGGAAAAG+GGG 0.496788 1.3:-7124202 None:intergenic
GAGTGGAGTAGATGGAGGGT+GGG 0.505478 1.3:-7124223 None:intergenic
GAAGAATGTGACGAAGGACT+TGG 0.508990 1.3:-7124408 None:intergenic
GGCGAAGATTTCAAAGGTGG+TGG 0.511485 1.3:-7124444 None:intergenic
GGAGTGGAGTAGATGGAGGG+TGG 0.519473 1.3:-7124224 None:intergenic
TTTGTTTGCAAAGAGAACAT+TGG 0.519949 1.3:+7123996 MS.gene051539:CDS
GGTGGTGGTGAACAAATTGT+AGG 0.526245 1.3:-7124087 None:intergenic
GTCAACAAAGGAGGAGGTGA+AGG 0.526752 1.3:-7124168 None:intergenic
TTTGATGAAGCAAGTTTAGG+AGG 0.539473 1.3:-7124108 None:intergenic
GATGAAGCAAGTTTAGGAGG+TGG 0.545014 1.3:-7124105 None:intergenic
GAAGATTTCAAAGGTGGTGG+AGG 0.554576 1.3:-7124441 None:intergenic
GAATGTGACGAAGGACTTGG+TGG 0.555897 1.3:-7124405 None:intergenic
CCTTGACCTGAACCCGAAGA+AGG 0.567300 1.3:-7124465 None:intergenic
TATGATGTTAATAGTGGAGG+AGG 0.568744 1.3:-7124264 None:intergenic
GGACAACCTAAAGTAATTGG+TGG 0.583322 1.3:+7124486 MS.gene051539:CDS
GAAGCAAGTTTAGGAGGTGG+TGG 0.584772 1.3:-7124102 None:intergenic
TGATGATGTGAGTGGAAATG+GGG 0.585770 1.3:-7124292 None:intergenic
AAAGTTGAAGAGCCTTCAAG+TGG 0.589794 1.3:+7124033 MS.gene051539:CDS
AGGTGGTGGAGGAGTTTCCC+CGG 0.592101 1.3:-7124430 None:intergenic
GTGGTGGAAGACTTAGTGAT+GGG 0.594811 1.3:-7124356 None:intergenic
GTTAGGAGTGGAGTAGATGG+AGG 0.597422 1.3:-7124228 None:intergenic
TTAGGAGTGGAGTAGATGGA+GGG 0.598597 1.3:-7124227 None:intergenic
TTTGGTGTCAACAAAGGAGG+AGG 0.602071 1.3:-7124174 None:intergenic
GGTGCATTTGGTGTCAACAA+AGG 0.602133 1.3:-7124180 None:intergenic
GAAGGACTTGGTGGAGATGG+TGG 0.605778 1.3:-7124396 None:intergenic
GGTGGAAGACTTAGTGATGG+GGG 0.608316 1.3:-7124354 None:intergenic
GACGAAGGACTTGGTGGAGA+TGG 0.610720 1.3:-7124399 None:intergenic
GAATATGATGTTAATAGTGG+AGG 0.611804 1.3:-7124267 None:intergenic
GGTAGAGTCAACAATGGTGG+TGG 0.613265 1.3:-7124372 None:intergenic
GGACTTGGTGGAGATGGTGG+CGG 0.623426 1.3:-7124393 None:intergenic
GGAGAATTTGATGATGTGAG+TGG 0.631413 1.3:-7124300 None:intergenic
GCATTTGGTGTCAACAAAGG+AGG 0.639121 1.3:-7124177 None:intergenic
TCCTTCGTCACATTCTTCCG+GGG 0.641768 1.3:+7124413 MS.gene051539:CDS
TGGTGGAAGACTTAGTGATG+GGG 0.649103 1.3:-7124355 None:intergenic
GAAGAAGGCGAAGATTTCAA+AGG 0.649156 1.3:-7124450 None:intergenic
GAAGGCGAAGATTTCAAAGG+TGG 0.657373 1.3:-7124447 None:intergenic
GGCGGTAGAGTCAACAATGG+TGG 0.660549 1.3:-7124375 None:intergenic
GGTGGTGGAAGACTTAGTGA+TGG 0.666350 1.3:-7124357 None:intergenic
GGTGTTATTAGTGGAAAAGG+GGG 0.675151 1.3:-7124201 None:intergenic
TCCCCGGAAGAATGTGACGA+AGG 0.679405 1.3:-7124414 None:intergenic
GATGATGTGAGTGGAAATGG+GGG 0.687997 1.3:-7124291 None:intergenic
GGTGGCGGTAGAGTCAACAA+TGG 0.730976 1.3:-7124378 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TAATAATAGTAATAGGGATA+TGG - chr1.3:7124528-7124547 None:intergenic 20.0%
! GAGGCATAATAATAGTAATA+GGG - chr1.3:7124534-7124553 None:intergenic 25.0%
! TGAGGCATAATAATAGTAAT+AGG - chr1.3:7124535-7124554 None:intergenic 25.0%
!! TTGTACTTTTGTTCATTCAT+CGG + chr1.3:7124595-7124614 MS.gene051539:CDS 25.0%
ATGCATAATAAACCACTTGA+AGG - chr1.3:7124048-7124067 None:intergenic 30.0%
GAATATGATGTTAATAGTGG+AGG - chr1.3:7124270-7124289 None:intergenic 30.0%
GAATTTGATGAAGCAAGTTT+AGG - chr1.3:7124114-7124133 None:intergenic 30.0%
GGTGAATATGATGTTAATAG+TGG - chr1.3:7124273-7124292 None:intergenic 30.0%
TTTGTTTGCAAAGAGAACAT+TGG + chr1.3:7123996-7124015 MS.gene051539:CDS 30.0%
AAAGAGAACATTGGAGATTG+AGG + chr1.3:7124005-7124024 MS.gene051539:CDS 35.0%
AGAAAAATGAGATGCACTTG+AGG - chr1.3:7124553-7124572 None:intergenic 35.0%
ATTCATCGGATATTCTTTGC+TGG + chr1.3:7124609-7124628 MS.gene051539:CDS 35.0%
CAAGGACAACCTAAAGTAAT+TGG + chr1.3:7124483-7124502 MS.gene051539:CDS 35.0%
TTCATCGGATATTCTTTGCT+GGG + chr1.3:7124610-7124629 MS.gene051539:CDS 35.0%
TTTGATGAAGCAAGTTTAGG+AGG - chr1.3:7124111-7124130 None:intergenic 35.0%
! TATGATGTTAATAGTGGAGG+AGG - chr1.3:7124267-7124286 None:intergenic 35.0%
! TTTGAAATCTTCGCCTTCTT+CGG + chr1.3:7124452-7124471 MS.gene051539:CDS 35.0%
!! GGAGGATATGATTTTAGAAG+TGG - chr1.3:7124336-7124355 None:intergenic 35.0%
!! GGATATGATTTTAGAAGTGG+AGG - chr1.3:7124333-7124352 None:intergenic 35.0%
!! TAGGGATATGGATAGTTTTG+TGG - chr1.3:7124516-7124535 None:intergenic 35.0%
!! TATGATTTTAGAAGTGGAGG+AGG - chr1.3:7124330-7124349 None:intergenic 35.0%
!! TTGATGATGTGAGTGGAAAT+GGG - chr1.3:7124296-7124315 None:intergenic 35.0%
!! TTTGATGATGTGAGTGGAAA+TGG - chr1.3:7124297-7124316 None:intergenic 35.0%
AAAGTTGAAGAGCCTTCAAG+TGG + chr1.3:7124033-7124052 MS.gene051539:CDS 40.0%
GAAGAAGGCGAAGATTTCAA+AGG - chr1.3:7124453-7124472 None:intergenic 40.0%
GGACAACCTAAAGTAATTGG+TGG + chr1.3:7124486-7124505 MS.gene051539:CDS 40.0%
TTGAAATCTTCGCCTTCTTC+GGG + chr1.3:7124453-7124472 MS.gene051539:CDS 40.0%
! AGGTGAAGGATTTTGTGTTG+GGG - chr1.3:7124157-7124176 None:intergenic 40.0%
! GAGGTGAAGGATTTTGTGTT+GGG - chr1.3:7124158-7124177 None:intergenic 40.0%
! TGATGATGTGAGTGGAAATG+GGG - chr1.3:7124295-7124314 None:intergenic 40.0%
!! GGAGAATTTGATGATGTGAG+TGG - chr1.3:7124303-7124322 None:intergenic 40.0%
!! GGGGTGTTATTAGTGGAAAA+GGG - chr1.3:7124206-7124225 None:intergenic 40.0%
!! GGGTGTTATTAGTGGAAAAG+GGG - chr1.3:7124205-7124224 None:intergenic 40.0%
!! GGTGTTATTAGTGGAAAAGG+GGG - chr1.3:7124204-7124223 None:intergenic 40.0%
!! TGGGGTGTTATTAGTGGAAA+AGG - chr1.3:7124207-7124226 None:intergenic 40.0%
!!! GGATATGGATAGTTTTGTGG+TGG - chr1.3:7124513-7124532 None:intergenic 40.0%
AGTCCTTCGTCACATTCTTC+CGG + chr1.3:7124411-7124430 MS.gene051539:CDS 45.0%
GAAGAATGTGACGAAGGACT+TGG - chr1.3:7124411-7124430 None:intergenic 45.0%
GAAGGCGAAGATTTCAAAGG+TGG - chr1.3:7124450-7124469 None:intergenic 45.0%
GATGAAGCAAGTTTAGGAGG+TGG - chr1.3:7124108-7124127 None:intergenic 45.0%
GATGATGTGAGTGGAAATGG+GGG - chr1.3:7124294-7124313 None:intergenic 45.0%
GGTGGTCCACCAATTACTTT+AGG - chr1.3:7124495-7124514 None:intergenic 45.0%
TGGTGGAAGACTTAGTGATG+GGG - chr1.3:7124358-7124377 None:intergenic 45.0%
TGTGTTAGGAGTGGAGTAGA+TGG - chr1.3:7124234-7124253 None:intergenic 45.0%
TTAGGAGTGGAGTAGATGGA+GGG - chr1.3:7124230-7124249 None:intergenic 45.0%
! GAAGATTTCAAAGGTGGTGG+AGG - chr1.3:7124444-7124463 None:intergenic 45.0%
! GAGGTGGAGGATTTTGTGTT+AGG - chr1.3:7124248-7124267 None:intergenic 45.0%
! GATGTTAATAGTGGAGGAGG+TGG - chr1.3:7124264-7124283 None:intergenic 45.0%
! GGAGGATTTTGTGTTAGGAG+TGG - chr1.3:7124243-7124262 None:intergenic 45.0%
! GGAGGTGAAGGATTTTGTGT+TGG - chr1.3:7124159-7124178 None:intergenic 45.0%
! GGTGAAGGATTTTGTGTTGG+GGG - chr1.3:7124156-7124175 None:intergenic 45.0%
! GGTGGTGGTGAACAAATTGT+AGG - chr1.3:7124090-7124109 None:intergenic 45.0%
! GTGGTGGAAGACTTAGTGAT+GGG - chr1.3:7124359-7124378 None:intergenic 45.0%
!! GATTTTAGAAGTGGAGGAGG+AGG - chr1.3:7124327-7124346 None:intergenic 45.0%
!! GCATTTGGTGTCAACAAAGG+AGG - chr1.3:7124180-7124199 None:intergenic 45.0%
!! GGTGCATTTGGTGTCAACAA+AGG - chr1.3:7124183-7124202 None:intergenic 45.0%
!! TTTGGTGTCAACAAAGGAGG+AGG - chr1.3:7124177-7124196 None:intergenic 45.0%
GAAGCAAGTTTAGGAGGTGG+TGG - chr1.3:7124105-7124124 None:intergenic 50.0%
GAATGTGACGAAGGACTTGG+TGG - chr1.3:7124408-7124427 None:intergenic 50.0%
GGCGAAGATTTCAAAGGTGG+TGG - chr1.3:7124447-7124466 None:intergenic 50.0%
GGTAGAGTCAACAATGGTGG+TGG - chr1.3:7124375-7124394 None:intergenic 50.0%
GGTGGAAGACTTAGTGATGG+GGG - chr1.3:7124357-7124376 None:intergenic 50.0%
GTCAACAAAGGAGGAGGTGA+AGG - chr1.3:7124171-7124190 None:intergenic 50.0%
GTCCTTCGTCACATTCTTCC+GGG + chr1.3:7124412-7124431 MS.gene051539:CDS 50.0%
GTTAGGAGTGGAGTAGATGG+AGG - chr1.3:7124231-7124250 None:intergenic 50.0%
TCCTTCGTCACATTCTTCCG+GGG + chr1.3:7124413-7124432 MS.gene051539:CDS 50.0%
TTTAGAAGTGGAGGAGGAGG+AGG - chr1.3:7124324-7124343 None:intergenic 50.0%
! AGTGGAAAAGGGGGTGCATT+TGG - chr1.3:7124195-7124214 None:intergenic 50.0%
! GGATTTTGTGTTGGGGGTGA+AGG - chr1.3:7124150-7124169 None:intergenic 50.0%
! GTTAATAGTGGAGGAGGTGG+AGG - chr1.3:7124261-7124280 None:intergenic 50.0%
! TTTTGTGTTGGGGGTGAAGG+AGG - chr1.3:7124147-7124166 None:intergenic 50.0%
!! GGTGGTGGAAGACTTAGTGA+TGG - chr1.3:7124360-7124379 None:intergenic 50.0%
AGTGGAGTAGATGGAGGGTG+GGG - chr1.3:7124225-7124244 None:intergenic 55.0%
CCTTGACCTGAACCCGAAGA+AGG - chr1.3:7124468-7124487 None:intergenic 55.0%
GAGTGGAGTAGATGGAGGGT+GGG - chr1.3:7124226-7124245 None:intergenic 55.0%
GGCGGTAGAGTCAACAATGG+TGG - chr1.3:7124378-7124397 None:intergenic 55.0%
TCCCCGGAAGAATGTGACGA+AGG - chr1.3:7124417-7124436 None:intergenic 55.0%
! CCTTCTTCGGGTTCAGGTCA+AGG + chr1.3:7124465-7124484 MS.gene051539:CDS 55.0%
! GGAAGACTTAGTGATGGGGG+AGG - chr1.3:7124354-7124373 None:intergenic 55.0%
! GGTGGCGGTAGAGTCAACAA+TGG - chr1.3:7124381-7124400 None:intergenic 55.0%
! TCTTCGCCTTCTTCGGGTTC+AGG + chr1.3:7124459-7124478 MS.gene051539:CDS 55.0%
!! GAAGGACTTGGTGGAGATGG+TGG - chr1.3:7124399-7124418 None:intergenic 55.0%
!! GACGAAGGACTTGGTGGAGA+TGG - chr1.3:7124402-7124421 None:intergenic 55.0%
!! GGAGGGTGGGGTGTTATTAG+TGG - chr1.3:7124213-7124232 None:intergenic 55.0%
GGAGTGGAGTAGATGGAGGG+TGG - chr1.3:7124227-7124246 None:intergenic 60.0%
GTGTTGGGGGTGAAGGAGGA+GGG - chr1.3:7124143-7124162 None:intergenic 60.0%
TGTGTTGGGGGTGAAGGAGG+AGG - chr1.3:7124144-7124163 None:intergenic 60.0%
!! AGGTGGTGGAGGAGTTTCCC+CGG - chr1.3:7124433-7124452 None:intergenic 60.0%
!! GGACTTGGTGGAGATGGTGG+CGG - chr1.3:7124396-7124415 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr1.3 gene 7123985 7124635 7123985 ID=MS.gene051539
chr1.3 mRNA 7123985 7124635 7123985 ID=MS.gene051539.t1;Parent=MS.gene051539
chr1.3 exon 7123985 7124635 7123985 ID=MS.gene051539.t1.exon1;Parent=MS.gene051539.t1
chr1.3 CDS 7123985 7124635 7123985 ID=cds.MS.gene051539.t1;Parent=MS.gene051539.t1
Gene Sequence

>MS.gene051539

ATGTTGTTGGTTTTGTTTGCAAAGAGAACATTGGAGATTGAGGACAACAAAGTTGAAGAGCCTTCAAGTGGTTTATTATGCATTAGTGAATGTGTCACATGTCCTACAATTTGTTCACCACCACCTCCTAAACTTGCTTCATCAAATTCAAATCACCCTCCTCCTTCACCCCCAACACAAAATCCTTCACCTCCTCCTTTGTTGACACCAAATGCACCCCCTTTTCCACTAATAACACCCCACCCTCCATCTACTCCACTCCTAACACAAAATCCTCCACCTCCTCCACTATTAACATCATATTCACCCCCATTTCCACTCACATCATCAAATTCTCCTCCTCCTCCTCCACTTCTAAAATCATATCCTCCCCCATCACTAAGTCTTCCACCACCATTGTTGACTCTACCGCCACCATCTCCACCAAGTCCTTCGTCACATTCTTCCGGGGAAACTCCTCCACCACCTTTGAAATCTTCGCCTTCTTCGGGTTCAGGTCAAGGACAACCTAAAGTAATTGGTGGACCACCACAAAACTATCCATATCCCTATTACTATTATTATGCCTCAAGTGCATCTCATTTTTCTAATCATGTTGTACTCTTCTTTATTGTACTTTTGTTCATTCATCGGATATTCTTTGCTGGGTAA

Protein sequence

>MS.gene051539.t1

MLLVLFAKRTLEIEDNKVEEPSSGLLCISECVTCPTICSPPPPKLASSNSNHPPPSPPTQNPSPPPLLTPNAPPFPLITPHPPSTPLLTQNPPPPPLLTSYSPPFPLTSSNSPPPPPLLKSYPPPSLSLPPPLLTLPPPSPPSPSSHSSGETPPPPLKSSPSSGSGQGQPKVIGGPPQNYPYPYYYYYASSASHFSNHVVLFFIVLLFIHRIFFAG