AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene54897

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene54897.t1 MTR_4g039380 82.906 117 19 1 1 116 1 117 4.91e-60 180
MS.gene54897.t1 MTR_4g039340 74.046 131 19 2 1 116 1 131 1.94e-55 169
MS.gene54897.t1 MTR_4g039640 78.632 117 24 1 1 116 1 117 2.42e-48 150
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
TCTGGTTCAGGCTGGTTATT+TGG 0.175696 4.4:+65829496 None:intergenic
TCTCATTCATCTGGTGTATA+AGG 0.203991 4.4:+65829295 None:intergenic
ACTCGATTCTAATATAAAAT+CGG 0.323743 4.4:+65829534 None:intergenic
CTCATTCATCTGGTGTATAA+GGG 0.375685 4.4:+65829296 None:intergenic
CTCGATTCTAATATAAAATC+GGG 0.421980 4.4:+65829535 None:intergenic
TCAGGCTGGTTATTTGGTGG+TGG 0.452210 4.4:+65829502 None:intergenic
GGAGGTTGGTTCAAGTCAAA+TGG 0.461699 4.4:+65829343 None:intergenic
TTGAGGTCGAAAGCTCGAAC+AGG 0.496472 4.4:+65829322 None:intergenic
GGTTCAGGCTGGTTATTTGG+TGG 0.509510 4.4:+65829499 None:intergenic
AAGTCAAATGGTTGCACATG+TGG 0.522527 4.4:+65829355 None:intergenic
AATGGTTGCACATGTGGAGG+TGG 0.555990 4.4:+65829361 None:intergenic
CGAAAGCTCGAACAGGAGGT+TGG 0.564077 4.4:+65829329 None:intergenic
ACTGCTAAAGCTTCTCGAGA+TGG 0.596385 4.4:+65829580 None:intergenic
CTGGTGTATAAGGGAGATTG+AGG 0.611261 4.4:+65829305 None:intergenic
ATATTAGAATCGAGTAAACA+AGG 0.624706 4.4:-65829526 MS.gene54897:CDS
AGGTCGAAAGCTCGAACAGG+AGG 0.636300 4.4:+65829325 None:intergenic
TCAAATGGTTGCACATGTGG+AGG 0.671560 4.4:+65829358 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ACTCGATTCTAATATAAAAT+CGG + chr4.4:65829391-65829410 None:intergenic 20.0%
! ATATTAGAATCGAGTAAACA+AGG - chr4.4:65829396-65829415 MS.gene54897:CDS 25.0%
! CTCGATTCTAATATAAAATC+GGG + chr4.4:65829390-65829409 None:intergenic 25.0%
! TGTTCAACATTTTGTGGTTG+AGG + chr4.4:65829462-65829481 None:intergenic 35.0%
! TGTTGTTCAACATTTTGTGG+TGG + chr4.4:65829507-65829526 None:intergenic 35.0%
!! GGTTGATGTTCAACATTTTG+TGG + chr4.4:65829468-65829487 None:intergenic 35.0%
!! GGTTGTTGTTCAACATTTTG+TGG + chr4.4:65829510-65829529 None:intergenic 35.0%
AAGTCAAATGGTTGCACATG+TGG + chr4.4:65829570-65829589 None:intergenic 40.0%
ACTGCTAAAGCTTCTCGAGA+TGG + chr4.4:65829345-65829364 None:intergenic 45.0%
CTGGTGTATAAGGGAGATTG+AGG + chr4.4:65829620-65829639 None:intergenic 45.0%
TCAAATGGTTGCACATGTGG+AGG + chr4.4:65829567-65829586 None:intergenic 45.0%
! GGAGGTTGGTTCAAGTCAAA+TGG + chr4.4:65829582-65829601 None:intergenic 45.0%
! TCTGGTTCAGGCTGGTTATT+TGG + chr4.4:65829429-65829448 None:intergenic 45.0%
!! TCAACATTTTGTGGTGGAGC+TGG + chr4.4:65829501-65829520 None:intergenic 45.0%
AATGGTTGCACATGTGGAGG+TGG + chr4.4:65829564-65829583 None:intergenic 50.0%
TTGAGGTCGAAAGCTCGAAC+AGG + chr4.4:65829603-65829622 None:intergenic 50.0%
! GGTTCAGGCTGGTTATTTGG+TGG + chr4.4:65829426-65829445 None:intergenic 50.0%
! GGTTGAGGCTGAGCATTTTC+TGG + chr4.4:65829447-65829466 None:intergenic 50.0%
! TCAGGCTGGTTATTTGGTGG+TGG + chr4.4:65829423-65829442 None:intergenic 50.0%
! TGTGGAGGTGGTGCATTTTG+TGG + chr4.4:65829552-65829571 None:intergenic 50.0%
!!! GAGCATTTTCTGGTTCAGGC+TGG + chr4.4:65829437-65829456 None:intergenic 50.0%
!!! GGCTGAGCATTTTCTGGTTC+AGG + chr4.4:65829441-65829460 None:intergenic 50.0%
AGGTCGAAAGCTCGAACAGG+AGG + chr4.4:65829600-65829619 None:intergenic 55.0%
CGAAAGCTCGAACAGGAGGT+TGG + chr4.4:65829596-65829615 None:intergenic 55.0%
! GGAGGTGGTGCATTTTGTGG+TGG + chr4.4:65829549-65829568 None:intergenic 55.0%
! GGTGGAGCTGGTGCATTTTG+TGG + chr4.4:65829489-65829508 None:intergenic 55.0%
!! GGTGCATTTTGTGGTGGAGC+TGG + chr4.4:65829543-65829562 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr4.4 gene 65829297 65829647 65829297 ID=MS.gene54897
chr4.4 mRNA 65829297 65829647 65829297 ID=MS.gene54897.t1;Parent=MS.gene54897
chr4.4 exon 65829297 65829647 65829297 ID=MS.gene54897.t1.exon1;Parent=MS.gene54897.t1
chr4.4 CDS 65829297 65829647 65829297 ID=cds.MS.gene54897.t1;Parent=MS.gene54897.t1
Gene Sequence

>MS.gene54897

ATGTCAAAGCTAGAATTCTTATGCAGTGAATGTGACACAATGTTTCCATCTCGAGAAGCTTTAGCAGTGCATGTTATCGAAGAACATCATCCCGATTTTATATTAGAATCGAGTAAACAAGGTCCACCACCAAATAACCAGCCTGAACCAGAAAATGCTCAGCCTCAACCACAAAATGTTGAACATCAACCACAAAATGCACCAGCTCCACCACAAAATGTTGAACAACAACCACAAAATGCACCAGCTCCACCACAAAATGCACCACCTCCACATGTGCAACCATTTGACTTGAACCAACCTCCTGTTCGAGCTTTCGACCTCAATCTCCCTTATACACCAGATGAATGA
Protein sequence

>MS.gene54897.t1

MSKLEFLCSECDTMFPSREALAVHVIEEHHPDFILESSKQGPPPNNQPEPENAQPQPQNVEHQPQNAPAPPQNVEQQPQNAPAPPQNAPPPHVQPFDLNQPPVRAFDLNLPYTPDE