AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene53910

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene53910.t1 MTR_3g030055 80.000 105 20 1 1 105 1 104 2.26e-54 166
MS.gene53910.t1 MTR_3g030055 77.570 107 20 1 1 107 8 110 4.83e-54 166
MS.gene53910.t1 MTR_3g034200 41.071 112 55 3 6 107 2 112 1.96e-17 73.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene53910.t1 AT5G13780 39.286 112 57 3 6 107 2 112 1.78e-16 71.6

Find 29 sgRNAs with CRISPR-Local

Find 41 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTTGGTTGGGTTGTTTCATT+AGG 0.229850 4.2:-60818328 MS.gene53910:CDS
TTCCACAATCTGCCAATATT+CGG 0.284634 4.2:+60818658 None:intergenic
CTCGTTACTCGCCCGAATAT+TGG 0.336302 4.2:-60818670 MS.gene53910:CDS
TCCACAATCTGCCAATATTC+GGG 0.340184 4.2:+60818659 None:intergenic
TGCATAAGAGTCGTAACATT+TGG 0.424993 4.2:-60818724 MS.gene53910:CDS
TTGGTTGGGTTGTTTCATTA+GGG 0.427007 4.2:-60818327 MS.gene53910:CDS
CATTTGGAGACGTATTAGAT+TGG 0.435564 4.2:-60818708 MS.gene53910:CDS
GGTTAGGTATGAAGCTTGGT+TGG 0.444494 4.2:-60818342 MS.gene53910:intron
TTGGGTTGTTTCATTAGGGA+TGG 0.451676 4.2:-60818323 MS.gene53910:CDS
GTTGCTTACCTCCTCTCTAA+AGG 0.454440 4.2:-60818595 MS.gene53910:CDS
AAAACACCATGGAAAAGGTT+AGG 0.456430 4.2:-60818474 MS.gene53910:intron
TGGGTTGTTTCATTAGGGAT+GGG 0.475902 4.2:-60818322 MS.gene53910:CDS
TGCCGAAAACACCATGGAAA+AGG 0.499281 4.2:-60818479 MS.gene53910:CDS
TTGTTTCATTAGGGATGGGA+AGG 0.502424 4.2:-60818318 MS.gene53910:CDS
TAATGGTTAGGTATGAAGCT+TGG 0.513302 4.2:-60818346 MS.gene53910:intron
TCTCTAAAGGTGAAGAGGAA+TGG 0.513826 4.2:-60818582 MS.gene53910:CDS
GCCCGAATATTGGCAGATTG+TGG 0.515192 4.2:-60818660 MS.gene53910:CDS
GTTAGGTATGAAGCTTGGTT+GGG 0.532684 4.2:-60818341 MS.gene53910:intron
CCTCTTCACCTTTAGAGAGG+AGG 0.539853 4.2:+60818587 None:intergenic
CCTCCTCTCTAAAGGTGAAG+AGG 0.541904 4.2:-60818587 MS.gene53910:CDS
AGGGAAAATGTCGTCAAAGA+AGG 0.547752 4.2:-60818749 None:intergenic
ATAGGTATGGTGAACAAAGA+GGG 0.575631 4.2:+60818537 None:intergenic
ATTCCTCTTCACCTTTAGAG+AGG 0.588352 4.2:+60818584 None:intergenic
TACCACATTTACGATAGGTA+TGG 0.589360 4.2:+60818524 None:intergenic
CACCATACCTATCGTAAATG+TGG 0.595431 4.2:-60818526 MS.gene53910:CDS
GATAGGTATGGTGAACAAAG+AGG 0.607709 4.2:+60818536 None:intergenic
CACTGCTGCCGAAAACACCA+TGG 0.615785 4.2:-60818485 MS.gene53910:CDS
CACATCGCGGATGATTGCAG+TGG 0.650393 4.2:-60818625 MS.gene53910:CDS
AGCGATACCACATTTACGAT+AGG 0.672035 4.2:+60818519 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATAATTTTGTTTTTTCGATT+AGG - chr4.2:60818620-60818639 MS.gene53910:CDS 15.0%
TCCATACATAACCAGTTAAA+AGG + chr4.2:60818679-60818698 None:intergenic 30.0%
! AATAAACCTAACCTTTTCCA+TGG + chr4.2:60818587-60818606 None:intergenic 30.0%
! TATGTATGGAGTTGGTTTAA+TGG - chr4.2:60818689-60818708 MS.gene53910:CDS 30.0%
!!! GTTTTTTCGATTAGCGTATA+AGG - chr4.2:60818642-60818661 MS.gene53910:CDS 30.0%
AAAACACCATGGAAAAGGTT+AGG - chr4.2:60818578-60818597 MS.gene53910:CDS 35.0%
ATAGGTATGGTGAACAAAGA+GGG + chr4.2:60818518-60818537 None:intergenic 35.0%
CATTTGGAGACGTATTAGAT+TGG - chr4.2:60818344-60818363 MS.gene53910:intron 35.0%
GAAAAAGCTTATTCACATCG+CGG - chr4.2:60818414-60818433 MS.gene53910:intron 35.0%
TAACTGGTTATGTATGGAGT+TGG - chr4.2:60818681-60818700 MS.gene53910:CDS 35.0%
TAATGGTTAGGTATGAAGCT+TGG - chr4.2:60818706-60818725 MS.gene53910:CDS 35.0%
TACCACATTTACGATAGGTA+TGG + chr4.2:60818531-60818550 None:intergenic 35.0%
TGCATAAGAGTCGTAACATT+TGG - chr4.2:60818328-60818347 MS.gene53910:CDS 35.0%
TTCCACAATCTGCCAATATT+CGG + chr4.2:60818397-60818416 None:intergenic 35.0%
! AACCTTTTCCATGGTGTTTT+CGG + chr4.2:60818578-60818597 None:intergenic 35.0%
! ATGGAGTTGGTTTAATGGTT+AGG - chr4.2:60818694-60818713 MS.gene53910:CDS 35.0%
! TTGGTTGGGTTGTTTCATTA+GGG - chr4.2:60818725-60818744 MS.gene53910:CDS 35.0%
!! GCCTTTTAACTGGTTATGTA+TGG - chr4.2:60818675-60818694 MS.gene53910:CDS 35.0%
AGCGATACCACATTTACGAT+AGG + chr4.2:60818536-60818555 None:intergenic 40.0%
CACCATACCTATCGTAAATG+TGG - chr4.2:60818526-60818545 MS.gene53910:CDS 40.0%
GATAGGTATGGTGAACAAAG+AGG + chr4.2:60818519-60818538 None:intergenic 40.0%
GTTAGGTATGAAGCTTGGTT+GGG - chr4.2:60818711-60818730 MS.gene53910:CDS 40.0%
TAGCGTATAAGGTGTGGTAT+AGG - chr4.2:60818653-60818672 MS.gene53910:CDS 40.0%
TCCACAATCTGCCAATATTC+GGG + chr4.2:60818396-60818415 None:intergenic 40.0%
TTCGATTAGCGTATAAGGTG+TGG - chr4.2:60818647-60818666 MS.gene53910:CDS 40.0%
TTGTTTCATTAGGGATGGGA+AGG - chr4.2:60818734-60818753 MS.gene53910:CDS 40.0%
! ATTCCTCTTCACCTTTAGAG+AGG + chr4.2:60818471-60818490 None:intergenic 40.0%
! CTTGGTTGGGTTGTTTCATT+AGG - chr4.2:60818724-60818743 MS.gene53910:CDS 40.0%
! TCTCTAAAGGTGAAGAGGAA+TGG - chr4.2:60818470-60818489 MS.gene53910:intron 40.0%
! TGGGTTGTTTCATTAGGGAT+GGG - chr4.2:60818730-60818749 MS.gene53910:CDS 40.0%
! TGTGGTATAGGCCTTTTAAC+TGG - chr4.2:60818665-60818684 MS.gene53910:CDS 40.0%
! TTGGGTTGTTTCATTAGGGA+TGG - chr4.2:60818729-60818748 MS.gene53910:CDS 40.0%
GGTTAGGTATGAAGCTTGGT+TGG - chr4.2:60818710-60818729 MS.gene53910:CDS 45.0%
GTTGCTTACCTCCTCTCTAA+AGG - chr4.2:60818457-60818476 MS.gene53910:intron 45.0%
TGCCGAAAACACCATGGAAA+AGG - chr4.2:60818573-60818592 MS.gene53910:CDS 45.0%
CTCGTTACTCGCCCGAATAT+TGG - chr4.2:60818382-60818401 MS.gene53910:intron 50.0%
GCCCGAATATTGGCAGATTG+TGG - chr4.2:60818392-60818411 MS.gene53910:intron 50.0%
! CCTCCTCTCTAAAGGTGAAG+AGG - chr4.2:60818465-60818484 MS.gene53910:intron 50.0%
! CCTCTTCACCTTTAGAGAGG+AGG + chr4.2:60818468-60818487 None:intergenic 50.0%
CACATCGCGGATGATTGCAG+TGG - chr4.2:60818427-60818446 MS.gene53910:intron 55.0%
CACTGCTGCCGAAAACACCA+TGG - chr4.2:60818567-60818586 MS.gene53910:CDS 55.0%


Chromosome Type Strat End Strand Name
chr4.2 gene 60818310 60818764 60818310 ID=MS.gene53910
chr4.2 mRNA 60818310 60818764 60818310 ID=MS.gene53910.t1;Parent=MS.gene53910
chr4.2 exon 60818475 60818764 60818475 ID=MS.gene53910.t1.exon1;Parent=MS.gene53910.t1
chr4.2 CDS 60818475 60818764 60818475 ID=cds.MS.gene53910.t1;Parent=MS.gene53910.t1
chr4.2 exon 60818310 60818358 60818310 ID=MS.gene53910.t1.exon2;Parent=MS.gene53910.t1
chr4.2 CDS 60818310 60818358 60818310 ID=cds.MS.gene53910.t1;Parent=MS.gene53910.t1
Gene Sequence

>MS.gene53910

ATGTCGTCAAAGAAGGTGTGCATAAGAGTCGTAACATTTGGAGACGTATTAGATTGGAACAGTAACAACAATCTCGTTACTCGCCCGAATATTGGCAGATTGTGGAAAAAGCTTATTCACATCGCGGATGATTGCAGTGGTTGTATTGTTGCTTACCTCCTCTCTAAAGGTGAAGAGGAATGGAATGATCACTTTAGCATCACTTCCCTCTTTGTTCACCATACCTATCGTAAATGTGGTATCGCTACTGATCTTATCACTGCTGCCGAAAACACCATGGAAAAGGTTAGGTTTATTTCTTTATTCTGTTATAATTTTGTTTTTTCGATTAGGTTTTTTCGATTAGCGTATAAGGTGTGGTATAGGCCTTTTAACTGGTTATGTATGGAGTTGGTTTAATGGTTAGGTATGAAGCTTGGTTGGGTTGTTTCATTAGGGATGGGAAGGCTGAGTAA
Protein sequence

>MS.gene53910.t1

MSSKKVCIRVVTFGDVLDWNSNNNLVTRPNIGRLWKKLIHIADDCSGCIVAYLLSKGEEEWNDHFSITSLFVHHTYRKCGIATDLITAAENTMEKVRYEAWLGCFIRDGKAE