AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene025589

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene025589.t1 MTR_4g039380 76.923 117 19 2 1 109 1 117 1.51e-52 160
MS.gene025589.t1 MTR_4g039340 68.702 131 19 3 1 109 1 131 1.38e-47 149
MS.gene025589.t1 MTR_4g039640 67.742 124 18 3 1 109 1 117 8.75e-45 141
MS.gene025589.t1 MTR_4g039400 41.818 110 35 2 1 109 1 82 3.38e-12 57.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 17 sgRNAs with CRISPR-Local

Find 27 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCTCATTCATCTGGTGTATA+AGG 0.183369 4.3:+61220206 None:intergenic
TCGGGTTCAGGCTGGTTATT+TGG 0.220105 4.3:+61220386 None:intergenic
CTCGATTCTAATATAAAATC+TGG 0.312947 4.3:+61220425 None:intergenic
CTCATTCATCTGGTGTATAA+GGG 0.358870 4.3:+61220207 None:intergenic
TCAGGCTGGTTATTTGGTGG+TGG 0.474246 4.3:+61220392 None:intergenic
TTGAGGTCGAAAGCTCGAAC+AGG 0.496472 4.3:+61220233 None:intergenic
GGAGGCTGGTTCAAGTCAAA+TGG 0.506887 4.3:+61220254 None:intergenic
AAGTCAAATGGTTGCACATG+TGG 0.522527 4.3:+61220266 None:intergenic
GGTTCAGGCTGGTTATTTGG+TGG 0.524862 4.3:+61220389 None:intergenic
CGAAAGCTCGAACAGGAGGC+TGG 0.528604 4.3:+61220240 None:intergenic
AATGGTTGCACATGTGGAGG+TGG 0.555990 4.3:+61220272 None:intergenic
TTGTGTCACATTCACTGCAT+AGG 0.586276 4.3:+61220498 None:intergenic
ACTGCTAAAGCTTCTCGAGA+TGG 0.596385 4.3:+61220470 None:intergenic
CTGGTGTATAAGGGAGATTG+AGG 0.611261 4.3:+61220216 None:intergenic
ATATTAGAATCGAGTAAACA+AGG 0.624706 4.3:-61220416 MS.gene025589:CDS
AGGTCGAAAGCTCGAACAGG+AGG 0.629084 4.3:+61220236 None:intergenic
TCAAATGGTTGCACATGTGG+AGG 0.671560 4.3:+61220269 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! ATATTAGAATCGAGTAAACA+AGG - chr4.3:61220307-61220326 MS.gene025589:CDS 25.0%
! CTCGATTCTAATATAAAATC+TGG + chr4.3:61220301-61220320 None:intergenic 25.0%
! TGTTGATGTTCAACATTTTG+TGG + chr4.3:61220400-61220419 None:intergenic 30.0%
! TGATGTTCAACATTTTGTGG+TGG + chr4.3:61220397-61220416 None:intergenic 35.0%
AAGTCAAATGGTTGCACATG+TGG + chr4.3:61220460-61220479 None:intergenic 40.0%
TTGTGTCACATTCACTGCAT+AGG + chr4.3:61220228-61220247 None:intergenic 40.0%
!! TCAACATTTTGTGGTGGAGT+TGG + chr4.3:61220391-61220410 None:intergenic 40.0%
ACTGCTAAAGCTTCTCGAGA+TGG + chr4.3:61220256-61220275 None:intergenic 45.0%
CTGGTGTATAAGGGAGATTG+AGG + chr4.3:61220510-61220529 None:intergenic 45.0%
TCAAATGGTTGCACATGTGG+AGG + chr4.3:61220457-61220476 None:intergenic 45.0%
! GTTGGTGCATTTTGTGGTTG+AGG + chr4.3:61220373-61220392 None:intergenic 45.0%
! TGGTTGAGGCTGAGCATTTT+CGG + chr4.3:61220359-61220378 None:intergenic 45.0%
AATGGTTGCACATGTGGAGG+TGG + chr4.3:61220454-61220473 None:intergenic 50.0%
TTGAGGTCGAAAGCTCGAAC+AGG + chr4.3:61220493-61220512 None:intergenic 50.0%
! GGAGGCTGGTTCAAGTCAAA+TGG + chr4.3:61220472-61220491 None:intergenic 50.0%
! GGTTCAGGCTGGTTATTTGG+TGG + chr4.3:61220337-61220356 None:intergenic 50.0%
! GGTTGAGGCTGAGCATTTTC+GGG + chr4.3:61220358-61220377 None:intergenic 50.0%
! TCAGGCTGGTTATTTGGTGG+TGG + chr4.3:61220334-61220353 None:intergenic 50.0%
! TCGGGTTCAGGCTGGTTATT+TGG + chr4.3:61220340-61220359 None:intergenic 50.0%
! TGTGGAGGTGGTGCATTTTG+TGG + chr4.3:61220442-61220461 None:intergenic 50.0%
!!! GGTGGAGTTGGTGCATTTTG+TGG + chr4.3:61220379-61220398 None:intergenic 50.0%
AGGTCGAAAGCTCGAACAGG+AGG + chr4.3:61220490-61220509 None:intergenic 55.0%
! GGAGGTGGTGCATTTTGTGG+TGG + chr4.3:61220439-61220458 None:intergenic 55.0%
!! GGTGCATTTTGTGGTGGAGC+TGG + chr4.3:61220433-61220452 None:intergenic 55.0%
!!! GAGCATTTTCGGGTTCAGGC+TGG + chr4.3:61220348-61220367 None:intergenic 55.0%
!!! GGCTGAGCATTTTCGGGTTC+AGG + chr4.3:61220352-61220371 None:intergenic 55.0%
CGAAAGCTCGAACAGGAGGC+TGG + chr4.3:61220486-61220505 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr4.3 gene 61220208 61220537 61220208 ID=MS.gene025589
chr4.3 mRNA 61220208 61220537 61220208 ID=MS.gene025589.t1;Parent=MS.gene025589
chr4.3 exon 61220208 61220537 61220208 ID=MS.gene025589.t1.exon1;Parent=MS.gene025589.t1
chr4.3 CDS 61220208 61220537 61220208 ID=cds.MS.gene025589.t1;Parent=MS.gene025589.t1
Gene Sequence

>MS.gene025589

ATGTCAAAGCTAGAATTCCTATGCAGTGAATGTGACACAATGTTTCCATCTCGAGAAGCTTTAGCAGTGCATGTTATCGAAGAACATCATCCAGATTTTATATTAGAATCGAGTAAACAAGGTCCACCACCAAATAACCAGCCTGAACCCGAAAATGCTCAGCCTCAACCACAAAATGCACCAACTCCACCACAAAATGTTGAACATCAACAACAAAATGCACCAGCTCCACCACAAAATGCACCACCTCCACATGTGCAACCATTTGACTTGAACCAGCCTCCTGTTCGAGCTTTCGACCTCAATCTCCCTTATACACCAGATGAATGA
Protein sequence

>MS.gene025589.t1

MSKLEFLCSECDTMFPSREALAVHVIEEHHPDFILESSKQGPPPNNQPEPENAQPQPQNAPTPPQNVEHQQQNAPAPPQNAPPPHVQPFDLNQPPVRAFDLNLPYTPDE