AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene54892

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene54892.t1 MTR_4g039380 83.761 117 18 1 1 116 1 117 1.08e-60 181
MS.gene54892.t1 MTR_4g039340 74.809 131 18 2 1 116 1 131 4.47e-56 170
MS.gene54892.t1 MTR_4g039640 77.778 117 25 1 1 116 1 117 5.21e-47 147
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 16 sgRNAs with CRISPR-Local

Find 26 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCTGGTTCAGGCTGGTTATT+TGG 0.175696 4.4:+65770337 None:intergenic
TCTCATTCATCTGGTGTATA+AGG 0.203991 4.4:+65770136 None:intergenic
CTAGATTCTAATATATAATC+TGG 0.344499 4.4:+65770376 None:intergenic
CTCATTCATCTGGTGTATAA+GGG 0.375685 4.4:+65770137 None:intergenic
TCAGGCTGGTTATTTGGTGG+TGG 0.452210 4.4:+65770343 None:intergenic
TTGAGGTCGAAAGCTTGAAC+AGG 0.493044 4.4:+65770163 None:intergenic
GGAGGCTGGTTCAAGTCAAA+TGG 0.506887 4.4:+65770184 None:intergenic
GGTTCAGGCTGGTTATTTGG+TGG 0.509510 4.4:+65770340 None:intergenic
CGAAAGCTTGAACAGGAGGC+TGG 0.520977 4.4:+65770170 None:intergenic
AAGTCAAATGGTTGCACATG+TGG 0.522527 4.4:+65770196 None:intergenic
AATGGTTGCACATGTGGAGG+TGG 0.555990 4.4:+65770202 None:intergenic
ACTGCTAAAGCTTCTCGAGA+TGG 0.596385 4.4:+65770421 None:intergenic
CTGGTGTATAAGGGAGATTG+AGG 0.611261 4.4:+65770146 None:intergenic
AGGTCGAAAGCTTGAACAGG+AGG 0.614849 4.4:+65770166 None:intergenic
ATATTAGAATCTAGTAAACA+AGG 0.648272 4.4:-65770367 MS.gene54892:CDS
TCAAATGGTTGCACATGTGG+AGG 0.671560 4.4:+65770199 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATATTAGAATCTAGTAAACA+AGG - chr4.4:65770237-65770256 MS.gene54892:CDS 20.0%
!! CTAGATTCTAATATATAATC+TGG + chr4.4:65770231-65770250 None:intergenic 20.0%
! TGATGTTCAACATTTTGTGG+TGG + chr4.4:65770306-65770325 None:intergenic 35.0%
! TGTTCAACATTTTGTGGTTG+AGG + chr4.4:65770303-65770322 None:intergenic 35.0%
!! GGTTGATGTTCAACATTTTG+TGG + chr4.4:65770309-65770328 None:intergenic 35.0%
AAGTCAAATGGTTGCACATG+TGG + chr4.4:65770411-65770430 None:intergenic 40.0%
ACTGCTAAAGCTTCTCGAGA+TGG + chr4.4:65770186-65770205 None:intergenic 45.0%
CTGGTGTATAAGGGAGATTG+AGG + chr4.4:65770461-65770480 None:intergenic 45.0%
TCAAATGGTTGCACATGTGG+AGG + chr4.4:65770408-65770427 None:intergenic 45.0%
TTGAGGTCGAAAGCTTGAAC+AGG + chr4.4:65770444-65770463 None:intergenic 45.0%
! TCTGGTTCAGGCTGGTTATT+TGG + chr4.4:65770270-65770289 None:intergenic 45.0%
!! TCAACATTTTGTGGTGGAGC+TGG + chr4.4:65770342-65770361 None:intergenic 45.0%
AATGGTTGCACATGTGGAGG+TGG + chr4.4:65770405-65770424 None:intergenic 50.0%
AGGTCGAAAGCTTGAACAGG+AGG + chr4.4:65770441-65770460 None:intergenic 50.0%
! GGAGGCTGGTTCAAGTCAAA+TGG + chr4.4:65770423-65770442 None:intergenic 50.0%
! GGTTCAGGCTGGTTATTTGG+TGG + chr4.4:65770267-65770286 None:intergenic 50.0%
! GGTTGAGGCTGAGCATTTTC+TGG + chr4.4:65770288-65770307 None:intergenic 50.0%
! TCAGGCTGGTTATTTGGTGG+TGG + chr4.4:65770264-65770283 None:intergenic 50.0%
! TGTGGAGGTGGTGCATTTTG+TGG + chr4.4:65770393-65770412 None:intergenic 50.0%
!!! GAGCATTTTCTGGTTCAGGC+TGG + chr4.4:65770278-65770297 None:intergenic 50.0%
!!! GGCTGAGCATTTTCTGGTTC+AGG + chr4.4:65770282-65770301 None:intergenic 50.0%
CGAAAGCTTGAACAGGAGGC+TGG + chr4.4:65770437-65770456 None:intergenic 55.0%
! GGAGGTGGTGCATTTTGTGG+TGG + chr4.4:65770390-65770409 None:intergenic 55.0%
! GGTGGAGCTGGTGCATTTTG+TGG + chr4.4:65770330-65770349 None:intergenic 55.0%
!! GGTGCATTTTGTGGTGGAGC+TGG + chr4.4:65770384-65770403 None:intergenic 55.0%
!! GGTGGAGCTGGAGCATTTTG+TGG + chr4.4:65770372-65770391 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr4.4 gene 65770138 65770488 65770138 ID=MS.gene54892
chr4.4 mRNA 65770138 65770488 65770138 ID=MS.gene54892.t1;Parent=MS.gene54892
chr4.4 exon 65770138 65770488 65770138 ID=MS.gene54892.t1.exon1;Parent=MS.gene54892.t1
chr4.4 CDS 65770138 65770488 65770138 ID=cds.MS.gene54892.t1;Parent=MS.gene54892.t1
Gene Sequence

>MS.gene54892

ATGTCAAAGCTAGAATTCTTATGCAGTGAATGTGACACAATGTTTCCATCTCGAGAAGCTTTAGCAGTGCATGTTATCGAAGAACATCATCCAGATTATATATTAGAATCTAGTAAACAAGGTCCACCACCAAATAACCAGCCTGAACCAGAAAATGCTCAGCCTCAACCACAAAATGTTGAACATCAACCACAAAATGCACCAGCTCCACCACAAAATGTTGAACATCAACCACAAAATGCTCCAGCTCCACCACAAAATGCACCACCTCCACATGTGCAACCATTTGACTTGAACCAGCCTCCTGTTCAAGCTTTCGACCTCAATCTCCCTTATACACCAGATGAATGA
Protein sequence

>MS.gene54892.t1

MSKLEFLCSECDTMFPSREALAVHVIEEHHPDYILESSKQGPPPNNQPEPENAQPQPQNVEHQPQNAPAPPQNVEHQPQNAPAPPQNAPPPHVQPFDLNQPPVQAFDLNLPYTPDE