AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene48868

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene48868.t1 MTR_4g007830 52.740 146 67 1 1 144 151 296 1.40e-45 152
MS.gene48868.t1 MTR_8g089760 48.673 113 56 1 34 144 1 113 3.38e-29 105
MS.gene48868.t1 MTR_4g040020 35.938 128 77 4 22 146 10 135 1.12e-19 81.3
MS.gene48868.t1 MTR_1g009820 89.474 38 4 0 109 146 1 38 6.92e-19 76.6
MS.gene48868.t1 MTR_5g022270 30.657 137 91 3 12 146 214 348 1.24e-16 75.9
MS.gene48868.t1 MTR_2g022080 30.469 128 85 3 21 146 223 348 4.38e-16 73.9
MS.gene48868.t1 MTR_6g035170 41.791 67 38 1 23 88 184 250 2.00e-13 66.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 32 sgRNAs with CRISPR-Local

Find 43 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCTTGACGTCCCAAACCTTT+TGG 0.174160 4.3:-71768062 None:intergenic
AACTGTTTCATTTGCCAAAA+TGG 0.193914 4.3:-71767602 None:intergenic
TGTCGTGGAATTCACCATTT+TGG 0.264921 4.3:+71767588 MS.gene48868:CDS
GTTGTTTCAGGCTATGTTTA+TGG 0.272519 4.3:+71767959 MS.gene48868:intron
TTTGTTTCAGGTAATAGATT+TGG 0.303954 4.3:+71767399 None:intergenic
AATAGTCACCCCAAAAGGTT+TGG 0.336042 4.3:+71768052 MS.gene48868:CDS
TCATCTACACTGGTTCCTTT+TGG 0.345121 4.3:+71767770 MS.gene48868:CDS
GTTTCTGCCAACAACTTTAA+CGG 0.369175 4.3:+71767477 MS.gene48868:CDS
GTTTATGGAGGAGTTCTTGA+TGG 0.373775 4.3:+71767974 MS.gene48868:CDS
CGTGAAGCACCGACGAACTT+TGG 0.382229 4.3:-71767836 None:intergenic
AAATTTACCGTTAAAGTTGT+TGG 0.410827 4.3:-71767484 None:intergenic
CAGTGTAGATGATCATATAT+TGG 0.446763 4.3:-71767759 None:intergenic
TTTAAAATAGTCACCCCAAA+AGG 0.463204 4.3:+71768047 MS.gene48868:CDS
CAAAGTTCGTCGGTGCTTCA+CGG 0.486634 4.3:+71767837 MS.gene48868:CDS
TTGATGGATCCATCTTTCCA+TGG 0.492954 4.3:+71767990 MS.gene48868:CDS
ATAGTCACCCCAAAAGGTTT+GGG 0.495339 4.3:+71768053 MS.gene48868:CDS
AAATGCGTCAACCTAAAACT+TGG 0.506791 4.3:+71767455 MS.gene48868:CDS
GCTAACTTACGATGCAAGAA+AGG 0.510769 4.3:+71767432 MS.gene48868:CDS
GGTTTGGGACGTCAAGGGGA+TGG 0.517176 4.3:+71768068 MS.gene48868:CDS
GAATCAGTGCCATGGAAAGA+TGG 0.518164 4.3:-71767999 None:intergenic
TCACAAAGTCAATAACCAAA+AGG 0.520836 4.3:-71767785 None:intergenic
GTTTCAGGCTATGTTTATGG+AGG 0.543768 4.3:+71767962 MS.gene48868:intron
CCAAAAGGTTTGGGACGTCA+AGG 0.551652 4.3:+71768062 MS.gene48868:CDS
CAAAAGGTTTGGGACGTCAA+GGG 0.561039 4.3:+71768063 MS.gene48868:CDS
GTTCGTCGGTGCTTCACGGA+AGG 0.563242 4.3:+71767841 MS.gene48868:CDS
AAAAGGTTTGGGACGTCAAG+GGG 0.574712 4.3:+71768064 MS.gene48868:CDS
TTTAGCGATATGTGCTGTCG+TGG 0.583539 4.3:+71767573 MS.gene48868:intron
CATAGTTTGAATCAGTGCCA+TGG 0.596462 4.3:-71768007 None:intergenic
ATTTATGGGAAATGCTGATG+TGG 0.609698 4.3:+71767637 MS.gene48868:CDS
AAATGCTGATGTGGTTTCAA+AGG 0.609916 4.3:+71767646 MS.gene48868:CDS
CAATATATGATCATCTACAC+TGG 0.632704 4.3:+71767760 MS.gene48868:CDS
TGACTCGTACCAAAGTTCGT+CGG 0.721179 4.3:+71767827 MS.gene48868:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! GATATCAAGTATCAAAAAAT+TGG + chr4.3:71767863-71767882 MS.gene48868:CDS 20.0%
!! TTCTACCAAAAAGAATTTAT+GGG + chr4.3:71767623-71767642 MS.gene48868:CDS 20.0%
! AAATTTACCGTTAAAGTTGT+TGG - chr4.3:71767487-71767506 None:intergenic 25.0%
! GTTCTACCAAAAAGAATTTA+TGG + chr4.3:71767622-71767641 MS.gene48868:CDS 25.0%
!! CATTTCCCATAAATTCTTTT+TGG - chr4.3:71767631-71767650 None:intergenic 25.0%
AACTGTTTCATTTGCCAAAA+TGG - chr4.3:71767605-71767624 None:intergenic 30.0%
CAATATATGATCATCTACAC+TGG + chr4.3:71767760-71767779 MS.gene48868:CDS 30.0%
CAGTGTAGATGATCATATAT+TGG - chr4.3:71767762-71767781 None:intergenic 30.0%
TCACAAAGTCAATAACCAAA+AGG - chr4.3:71767788-71767807 None:intergenic 30.0%
! TTTAAAATAGTCACCCCAAA+AGG + chr4.3:71768047-71768066 MS.gene48868:CDS 30.0%
!! CAAATTTCAAGTGTTGTTTC+AGG + chr4.3:71767947-71767966 MS.gene48868:intron 30.0%
AAATGCGTCAACCTAAAACT+TGG + chr4.3:71767455-71767474 MS.gene48868:CDS 35.0%
AAATGCTGATGTGGTTTCAA+AGG + chr4.3:71767646-71767665 MS.gene48868:CDS 35.0%
AGCACATATCGCTAAATAGA+TGG - chr4.3:71767569-71767588 None:intergenic 35.0%
ATTTATGGGAAATGCTGATG+TGG + chr4.3:71767637-71767656 MS.gene48868:CDS 35.0%
GTTTCTGCCAACAACTTTAA+CGG + chr4.3:71767477-71767496 MS.gene48868:CDS 35.0%
TAAACATGTATGAGCGCATA+GGG - chr4.3:71767542-71767561 None:intergenic 35.0%
TTAAACATGTATGAGCGCAT+AGG - chr4.3:71767543-71767562 None:intergenic 35.0%
! GTTGTTTCAGGCTATGTTTA+TGG + chr4.3:71767959-71767978 MS.gene48868:intron 35.0%
AAACATGTATGAGCGCATAG+GGG - chr4.3:71767541-71767560 None:intergenic 40.0%
AATAGTCACCCCAAAAGGTT+TGG + chr4.3:71768052-71768071 MS.gene48868:CDS 40.0%
ATAGTCACCCCAAAAGGTTT+GGG + chr4.3:71768053-71768072 MS.gene48868:CDS 40.0%
CATAGTTTGAATCAGTGCCA+TGG - chr4.3:71768010-71768029 None:intergenic 40.0%
GCTAACTTACGATGCAAGAA+AGG + chr4.3:71767432-71767451 MS.gene48868:CDS 40.0%
GTTTATGGAGGAGTTCTTGA+TGG + chr4.3:71767974-71767993 MS.gene48868:CDS 40.0%
GTTTCAGGCTATGTTTATGG+AGG + chr4.3:71767962-71767981 MS.gene48868:intron 40.0%
! GTTGGCAGAAACCAAGTTTT+AGG - chr4.3:71767469-71767488 None:intergenic 40.0%
! TGTCGTGGAATTCACCATTT+TGG + chr4.3:71767588-71767607 MS.gene48868:CDS 40.0%
! TTGATGGATCCATCTTTCCA+TGG + chr4.3:71767990-71768009 MS.gene48868:CDS 40.0%
!!! TCATCTACACTGGTTCCTTT+TGG + chr4.3:71767770-71767789 MS.gene48868:CDS 40.0%
GAATCAGTGCCATGGAAAGA+TGG - chr4.3:71768002-71768021 None:intergenic 45.0%
TGACTCGTACCAAAGTTCGT+CGG + chr4.3:71767827-71767846 MS.gene48868:CDS 45.0%
TTTAGCGATATGTGCTGTCG+TGG + chr4.3:71767573-71767592 MS.gene48868:intron 45.0%
! AAAAGGTTTGGGACGTCAAG+GGG + chr4.3:71768064-71768083 MS.gene48868:CDS 45.0%
! CAAAAGGTTTGGGACGTCAA+GGG + chr4.3:71768063-71768082 MS.gene48868:CDS 45.0%
! CTTGACGTCCCAAACCTTTT+GGG - chr4.3:71768064-71768083 None:intergenic 45.0%
! TTGACGTCCCAAACCTTTTG+GGG - chr4.3:71768063-71768082 None:intergenic 45.0%
! CAAAGTTCGTCGGTGCTTCA+CGG + chr4.3:71767837-71767856 MS.gene48868:CDS 50.0%
! CCAAAAGGTTTGGGACGTCA+AGG + chr4.3:71768062-71768081 MS.gene48868:CDS 50.0%
! CCTTGACGTCCCAAACCTTT+TGG - chr4.3:71768065-71768084 None:intergenic 50.0%
!! CGTGAAGCACCGACGAACTT+TGG - chr4.3:71767839-71767858 None:intergenic 55.0%
! GGTTTGGGACGTCAAGGGGA+TGG + chr4.3:71768068-71768087 MS.gene48868:CDS 60.0%
! GTTCGTCGGTGCTTCACGGA+AGG + chr4.3:71767841-71767860 MS.gene48868:CDS 60.0%


Chromosome Type Strat End Strand Name
chr4.3 gene 71767409 71768093 71767409 ID=MS.gene48868
chr4.3 mRNA 71767409 71768093 71767409 ID=MS.gene48868.t1;Parent=MS.gene48868
chr4.3 exon 71767409 71767498 71767409 ID=MS.gene48868.t1.exon1;Parent=MS.gene48868.t1
chr4.3 CDS 71767409 71767498 71767409 ID=cds.MS.gene48868.t1;Parent=MS.gene48868.t1
chr4.3 exon 71767578 71767667 71767578 ID=MS.gene48868.t1.exon2;Parent=MS.gene48868.t1
chr4.3 CDS 71767578 71767667 71767578 ID=cds.MS.gene48868.t1;Parent=MS.gene48868.t1
chr4.3 exon 71767750 71767884 71767750 ID=MS.gene48868.t1.exon3;Parent=MS.gene48868.t1
chr4.3 CDS 71767750 71767884 71767750 ID=cds.MS.gene48868.t1;Parent=MS.gene48868.t1
chr4.3 exon 71767969 71768093 71767969 ID=MS.gene48868.t1.exon4;Parent=MS.gene48868.t1
chr4.3 CDS 71767969 71768093 71767969 ID=cds.MS.gene48868.t1;Parent=MS.gene48868.t1
Gene Sequence

>MS.gene48868

GTAATAGATTTGGCTGCGTGCATGCTAACTTACGATGCAAGAAAGGAAATGCGTCAACCTAAAACTTGGTTTCTGCCAACAACTTTAACGGTAAATTTTTAATGCTAACTATTTTTAATATTTGTTTGTCCCCTATGCGCTCATACATGTTTAAAATCCATCTATTTAGCGATATGTGCTGTCGTGGAATTCACCATTTTGGCAAATGAAACAGTTCTACCAAAAAGAATTTATGGGAAATGCTGATGTGGTTTCAAAGGTAATTAGTCTGTATTAATTAAAGCAATATTTCTTTACTCATTGCTTATATGTTTGTGAAACTAATGTTTAAATATAATCAGATCTTTTTACCAATATATGATCATCTACACTGGTTCCTTTTGGTTATTGACTTTGTGAGAAAAGAATTAGTATATCTTGACTCGTACCAAAGTTCGTCGGTGCTTCACGGAAGGATATCAAGTATCAAAAAATTGGTAAAAAAATTAATTAAACTATATTTTTATCTTACATATTCATCAACGTAGAAAATCATTAACAAATTTCAAGTGTTGTTTCAGGCTATGTTTATGGAGGAGTTCTTGATGGATCCATCTTTCCATGGCACTGATTCAAACTATGACTATAAAATAACAAAGTTTAAAATAGTCACCCCAAAAGGTTTGGGACGTCAAGGGGATGGATC
Protein sequence

>MS.gene48868.t1

VIDLAACMLTYDARKEMRQPKTWFLPTTLTRYVLSWNSPFWQMKQFYQKEFMGNADVVSKIFLPIYDHLHWFLLVIDFVRKELVYLDSYQSSSVLHGRISSIKKLAMFMEEFLMDPSFHGTDSNYDYKITKFKIVTPKGLGRQGDG