AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1420220

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1420220 MtrunA17_Chr5g0404111 88.462 78 8 1 1 78 1 77 8.57e-46 142
Msa1420220 MtrunA17_Chr3g0081641 36.559 93 55 2 14 105 1 90 7.05e-14 62.0
Msa1420220 MtrunA17_Chr1g0173721 35.106 94 48 3 14 106 1 82 2.19e-13 60.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1420220 AT2G21640.1 35.052 97 56 2 14 103 1 97 6.30e-12 57.4
Msa1420220 AT4G39235.2 34.783 69 37 1 14 82 1 61 3.19e-11 55.1
Msa1420220 AT4G39235.1 34.783 69 37 1 14 82 1 61 3.19e-11 55.1

Find 23 sgRNAs with CRISPR-Local

Find 30 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTTAATGCATCAAAGGATTT+TGG 0.124757 tig0024770:+27546 Msa1420220:CDS
CTTGAATGTTACACATTAAT+TGG 0.152502 tig0024770:-27766 None:intergenic
CATACAATACAATTGTTTAC+AGG 0.285310 tig0024770:+27738 Msa1420220:three_prime_UTR
TCAGCTTTAACTTTCTCCTT+TGG 0.324540 tig0024770:+27854 Msa1420220:three_prime_UTR
TTAACTATGTTGATGTCAAC+TGG 0.344256 tig0024770:+27219 None:intergenic
ACAGTTTCATATGATTATCA+TGG 0.433286 tig0024770:+27798 Msa1420220:three_prime_UTR
AGTCAATCATGTGTTCTCTA+AGG 0.438611 tig0024770:-27700 None:intergenic
CAGAATGTGACTCTTTGTGC+TGG 0.447400 tig0024770:-27312 None:intergenic
TTCTGTCAAAGAAACAAGTC+CGG 0.465521 tig0024770:+27330 Msa1420220:CDS
TCATGTGTTCTCTAAGGTCT+TGG 0.473675 tig0024770:-27694 None:intergenic
CTTGAGAAACACAATTCAAA+AGG 0.489220 tig0024770:+27431 Msa1420220:CDS
ATTAATGTGTAACATTCAAG+TGG 0.494096 tig0024770:+27769 Msa1420220:three_prime_UTR
ACAGATATTTAATGCATCAA+AGG 0.510172 tig0024770:+27539 Msa1420220:intron
TCTGTCAAAGAAACAAGTCC+GGG 0.516482 tig0024770:+27331 Msa1420220:CDS
CAAAGAAACAAGTCCGGGGA+TGG 0.518949 tig0024770:+27336 Msa1420220:CDS
TGTGTTCATCAACGGATGCA+TGG 0.564961 tig0024770:-27401 None:intergenic
AGTCACAAAACTCCCATCCC+CGG 0.586279 tig0024770:-27349 None:intergenic
AAAGAAACAAGTCCGGGGAT+GGG 0.589500 tig0024770:+27337 Msa1420220:CDS
GCATCTCCTGTGTTCATCAA+CGG 0.594973 tig0024770:-27409 None:intergenic
TTAATGTGTAACATTCAAGT+GGG 0.633879 tig0024770:+27770 Msa1420220:three_prime_UTR
ATGCATCCGTTGATGAACAC+AGG 0.635825 tig0024770:+27403 Msa1420220:CDS
TATAAACGAAGATGAAAACT+CGG 0.670859 tig0024770:+27584 Msa1420220:CDS
CTGTCAAAGAAACAAGTCCG+GGG 0.697051 tig0024770:+27332 Msa1420220:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! TATTGATGTATATACATCCA+CGG - tig0024770:27468-27487 None:intergenic 25.0%
! TTGTTAGCATAATAATCGAA+GGG - tig0024770:27493-27512 None:intergenic 25.0%
! ACAGATATTTAATGCATCAA+AGG + tig0024770:27539-27558 Msa1420220:intron 25.0%
!! TTTAATGCATCAAAGGATTT+TGG + tig0024770:27546-27565 Msa1420220:CDS 25.0%
! TATAAACGAAGATGAAAACT+CGG + tig0024770:27584-27603 Msa1420220:CDS 25.0%
!! TTTTCTGAATCATTAGTAGA+TGG + tig0024770:27641-27660 Msa1420220:three_prime_UTR 25.0%
! CATACAATACAATTGTTTAC+AGG + tig0024770:27738-27757 Msa1420220:three_prime_UTR 25.0%
! CTTGAATGTTACACATTAAT+TGG - tig0024770:27769-27788 None:intergenic 25.0%
! ATTAATGTGTAACATTCAAG+TGG + tig0024770:27769-27788 Msa1420220:three_prime_UTR 25.0%
! TTAATGTGTAACATTCAAGT+GGG + tig0024770:27770-27789 Msa1420220:three_prime_UTR 25.0%
! ACAGTTTCATATGATTATCA+TGG + tig0024770:27798-27817 Msa1420220:three_prime_UTR 25.0%
! AACTGGATTAACTTTTCTTC+AGG + tig0024770:27236-27255 Msa1420220:CDS 30.0%
! AACTTTTCTTCAGGTGTTAA+TGG + tig0024770:27245-27264 Msa1420220:CDS 30.0%
!!! GTTTTAGTTTTTCATCAGTC+TGG - tig0024770:27284-27303 None:intergenic 30.0%
CTTGAGAAACACAATTCAAA+AGG + tig0024770:27431-27450 Msa1420220:CDS 30.0%
!! AAAAGGTATATTTTCTACCG+TGG + tig0024770:27448-27467 Msa1420220:intron 30.0%
CTTGTTAGCATAATAATCGA+AGG - tig0024770:27494-27513 None:intergenic 30.0%
TTCTGTCAAAGAAACAAGTC+CGG + tig0024770:27330-27349 Msa1420220:CDS 35.0%
AGTCAATCATGTGTTCTCTA+AGG - tig0024770:27703-27722 None:intergenic 35.0%
! TCAGCTTTAACTTTCTCCTT+TGG + tig0024770:27854-27873 Msa1420220:three_prime_UTR 35.0%
TCTGTCAAAGAAACAAGTCC+GGG + tig0024770:27331-27350 Msa1420220:CDS 40.0%
!! TCATGTGTTCTCTAAGGTCT+TGG - tig0024770:27697-27716 None:intergenic 40.0%
CAGAATGTGACTCTTTGTGC+TGG - tig0024770:27315-27334 None:intergenic 45.0%
CTGTCAAAGAAACAAGTCCG+GGG + tig0024770:27332-27351 Msa1420220:CDS 45.0%
AAAGAAACAAGTCCGGGGAT+GGG + tig0024770:27337-27356 Msa1420220:CDS 45.0%
TGTGTTCATCAACGGATGCA+TGG - tig0024770:27404-27423 None:intergenic 45.0%
! ATGCATCCGTTGATGAACAC+AGG + tig0024770:27403-27422 Msa1420220:CDS 45.0%
GCATCTCCTGTGTTCATCAA+CGG - tig0024770:27412-27431 None:intergenic 45.0%
CAAAGAAACAAGTCCGGGGA+TGG + tig0024770:27336-27355 Msa1420220:CDS 50.0%
AGTCACAAAACTCCCATCCC+CGG - tig0024770:27352-27371 None:intergenic 50.0%
Chromosome Type Strat End Strand Name
tig0024770 gene 27225 27888 27225 ID=Msa1420220;Name=Msa1420220
tig0024770 mRNA 27225 27888 27225 ID=Msa1420220-mRNA-1;Parent=Msa1420220;Name=Msa1420220-mRNA-1;_AED=0.08;_eAED=0.08;_QI=0|1|0.5|1|1|1|2|253|106
tig0024770 exon 27225 27452 27225 ID=Msa1420220-mRNA-1:exon:1359;Parent=Msa1420220-mRNA-1
tig0024770 exon 27543 27888 27543 ID=Msa1420220-mRNA-1:exon:1360;Parent=Msa1420220-mRNA-1
tig0024770 CDS 27225 27452 27225 ID=Msa1420220-mRNA-1:cds;Parent=Msa1420220-mRNA-1
tig0024770 CDS 27543 27635 27543 ID=Msa1420220-mRNA-1:cds;Parent=Msa1420220-mRNA-1
tig0024770 three_prime_UTR 27636 27888 27636 ID=Msa1420220-mRNA-1:three_prime_utr;Parent=Msa1420220-mRNA-1
Gene Sequence

>Msa1420220

ATGTTGATGTCAACTGGATTAACTTTTCTTCAGGTGTTAATGGATTCAAACAGCAACCAGACTGATGAAAAACTAAAACAAGTCAAGCCAGCACAAAGAGTCACATTCTGTCAAAGAAACAAGTCCGGGGATGGGAGTTTTGTGACTAAATTAAGAAATCATTTTCATGAATTTATCCATGCATCCGTTGATGAACACAGGAGATGCTTGAGAAACACAATTCAAAAGATATTTAATGCATCAAAGGATTTTGGAAATAACAGTGAAAGTATAAACGAAGATGAAAACTCGGTACAACTTCATTCATCTACAAAGAACTAG
Protein sequence

>Msa1420220

MLMSTGLTFLQVLMDSNSNQTDEKLKQVKPAQRVTFCQRNKSGDGSFVTKLRNHFHEFIHASVDEHRRCLRNTIQKIFNASKDFGNNSESINEDENSVQLHSSTKN*