AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene025596

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene025596.t1 MTR_4g039380 83.761 117 18 1 1 116 1 117 1.64e-61 184
MS.gene025596.t1 MTR_4g039340 74.809 131 18 2 1 116 1 131 8.09e-57 172
MS.gene025596.t1 MTR_4g039640 77.778 117 25 1 1 116 1 117 4.28e-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 28 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCTGGTTCGGGCTGGTTATT+TGG 0.202950 4.3:+61503018 None:intergenic
TCTCATTCATCTGGTGTATA+AGG 0.203991 4.3:+61502817 None:intergenic
ACTCGATTCTAATATAAAAT+CGG 0.323743 4.3:+61503056 None:intergenic
CTCATTCATCTGGTGTATAA+GGG 0.375685 4.3:+61502818 None:intergenic
CTCGATTCTAATATAAAATC+GGG 0.421980 4.3:+61503057 None:intergenic
GGAGGTTGGTTCAAGTCAAA+TGG 0.461699 4.3:+61502865 None:intergenic
TTGAGGTCGAAAGCTCGAAC+AGG 0.496472 4.3:+61502844 None:intergenic
TCGGGCTGGTTATTTGGTGG+TGG 0.505201 4.3:+61503024 None:intergenic
AAGTCAAATGGTTGCACATG+TGG 0.522527 4.3:+61502877 None:intergenic
AATGGTTGCACATGTGGAGG+TGG 0.555990 4.3:+61502883 None:intergenic
GGTTCGGGCTGGTTATTTGG+TGG 0.558588 4.3:+61503021 None:intergenic
CGAAAGCTCGAACAGGAGGT+TGG 0.564077 4.3:+61502851 None:intergenic
CTGGTGTATAAGGGAGATTG+AGG 0.611261 4.3:+61502827 None:intergenic
ACTGCTAAAGCTTCACGAGA+TGG 0.614779 4.3:+61503102 None:intergenic
ATATTAGAATCGAGTAAACA+AGG 0.624706 4.3:-61503048 MS.gene025596:CDS
AGGTCGAAAGCTCGAACAGG+AGG 0.636300 4.3:+61502847 None:intergenic
TCAAATGGTTGCACATGTGG+AGG 0.671560 4.3:+61502880 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ACTCGATTCTAATATAAAAT+CGG + chr4.3:61502913-61502932 None:intergenic 20.0%
! ATATTAGAATCGAGTAAACA+AGG - chr4.3:61502918-61502937 MS.gene025596:CDS 25.0%
! CTCGATTCTAATATAAAATC+GGG + chr4.3:61502912-61502931 None:intergenic 25.0%
! TGTTCAACATTTTGTGGTTG+AGG + chr4.3:61502984-61503003 None:intergenic 35.0%
! TGTTGTTCAACATTTTGTGG+TGG + chr4.3:61503029-61503048 None:intergenic 35.0%
!! GGTTGATGTTCAACATTTTG+TGG + chr4.3:61502990-61503009 None:intergenic 35.0%
!! GGTTGTTGTTCAACATTTTG+TGG + chr4.3:61503032-61503051 None:intergenic 35.0%
AAGTCAAATGGTTGCACATG+TGG + chr4.3:61503092-61503111 None:intergenic 40.0%
ACTGCTAAAGCTTCACGAGA+TGG + chr4.3:61502867-61502886 None:intergenic 45.0%
CTGGTGTATAAGGGAGATTG+AGG + chr4.3:61503142-61503161 None:intergenic 45.0%
TCAAATGGTTGCACATGTGG+AGG + chr4.3:61503089-61503108 None:intergenic 45.0%
! GGAGGTTGGTTCAAGTCAAA+TGG + chr4.3:61503104-61503123 None:intergenic 45.0%
!!! AGGCTGAGCATTTTCTGGTT+CGG + chr4.3:61502964-61502983 None:intergenic 45.0%
AATGGTTGCACATGTGGAGG+TGG + chr4.3:61503086-61503105 None:intergenic 50.0%
TTGAGGTCGAAAGCTCGAAC+AGG + chr4.3:61503125-61503144 None:intergenic 50.0%
! GGTGGAGCTAGTGCATTTTG+TGG + chr4.3:61503011-61503030 None:intergenic 50.0%
! GGTTGAGGCTGAGCATTTTC+TGG + chr4.3:61502969-61502988 None:intergenic 50.0%
! TGTGGAGGTGGTGCATTTTG+TGG + chr4.3:61503074-61503093 None:intergenic 50.0%
!! TCTGGTTCGGGCTGGTTATT+TGG + chr4.3:61502951-61502970 None:intergenic 50.0%
!!! GGCTGAGCATTTTCTGGTTC+GGG + chr4.3:61502963-61502982 None:intergenic 50.0%
AGGTCGAAAGCTCGAACAGG+AGG + chr4.3:61503122-61503141 None:intergenic 55.0%
CGAAAGCTCGAACAGGAGGT+TGG + chr4.3:61503118-61503137 None:intergenic 55.0%
! GGAGGTGGTGCATTTTGTGG+TGG + chr4.3:61503071-61503090 None:intergenic 55.0%
! GGTGGAGCTGGTGCATTTTG+TGG + chr4.3:61503053-61503072 None:intergenic 55.0%
!! GGTGCATTTTGTGGTGGAGC+TGG + chr4.3:61503065-61503084 None:intergenic 55.0%
!! GGTTCGGGCTGGTTATTTGG+TGG + chr4.3:61502948-61502967 None:intergenic 55.0%
!! TCGGGCTGGTTATTTGGTGG+TGG + chr4.3:61502945-61502964 None:intergenic 55.0%
!!! GAGCATTTTCTGGTTCGGGC+TGG + chr4.3:61502959-61502978 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr4.3 gene 61502819 61503169 61502819 ID=MS.gene025596
chr4.3 mRNA 61502819 61503169 61502819 ID=MS.gene025596.t1;Parent=MS.gene025596
chr4.3 exon 61502819 61503169 61502819 ID=MS.gene025596.t1.exon1;Parent=MS.gene025596.t1
chr4.3 CDS 61502819 61503169 61502819 ID=cds.MS.gene025596.t1;Parent=MS.gene025596.t1
Gene Sequence

>MS.gene025596

ATGTCAAAGCTAGAATTCTTATGCAGTGAATGTGACACAATGTTTCCATCTCGTGAAGCTTTAGCAGTGCATGTTATCGAAGAACATCATCCCGATTTTATATTAGAATCGAGTAAACAAGGTCCACCACCAAATAACCAGCCCGAACCAGAAAATGCTCAGCCTCAACCACAAAATGTTGAACATCAACCACAAAATGCACTAGCTCCACCACAAAATGTTGAACAACAACCACAAAATGCACCAGCTCCACCACAAAATGCACCACCTCCACATGTGCAACCATTTGACTTGAACCAACCTCCTGTTCGAGCTTTCGACCTCAATCTCCCTTATACACCAGATGAATGA
Protein sequence

>MS.gene025596.t1

MSKLEFLCSECDTMFPSREALAVHVIEEHHPDFILESSKQGPPPNNQPEPENAQPQPQNVEHQPQNALAPPQNVEQQPQNAPAPPQNAPPPHVQPFDLNQPPVRAFDLNLPYTPDE