AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1343760


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1343760 MtrunA17_Chr8g0343841 96.970 33 1 0 1 33 1 33 3.33e-17 67.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1343760 AT3G13970.3 83.871 31 5 0 3 33 2 32 8.41e-13 55.8
Msa1343760 AT3G13970.2 83.871 31 5 0 3 33 2 32 8.41e-13 55.8
Msa1343760 AT3G13970.1 83.871 31 5 0 3 33 2 32 1.53e-12 55.8
Msa1343760 AT3G13970.4 83.871 31 5 0 3 33 2 32 1.84e-12 55.5
Msa1343760 AT1G54210.2 86.207 29 4 0 4 32 5 33 3.29e-12 53.9
Msa1343760 AT1G54210.3 83.333 30 5 0 4 33 5 34 6.38e-12 54.3
Msa1343760 AT1G54210.1 83.333 30 5 0 4 33 5 34 6.38e-12 54.3

Find 19 sgRNAs with CRISPR-Local

Find 98 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGTTCTTCTTCACAGAAAAT+AGG 0.214719 tig0006506:+89562 Msa1343760:intron
AAAAGACCCATTAATTAAAA+AGG 0.285555 tig0006506:-89802 Msa1343760:intergenic
TCAGTGTTCGTTCTTCTTCA+TGG 0.287098 tig0006506:+89588 Msa1343760:exon
GTTCTTCTTCACAGAAAATA+GGG 0.316856 tig0006506:+89563 Msa1343760:intron
AACTTGGATTGTTTGAGAAT+AGG 0.443789 tig0006506:-89767 Msa1343760:intergenic
AAGGAAAAGTACCTTGAACT+TGG 0.453341 tig0006506:-89783 Msa1343760:intergenic
TCTCAAACAATCCAAGTTCA+AGG 0.453483 tig0006506:+89772 Msa1343760:CDS
TAACCTTTACGAACAGAAGT+TGG 0.498862 tig0006506:-89625 Msa1343760:intergenic
ATCTGAAGTTTGAGAAAGGA+AGG 0.503034 tig0006506:+88928 Msa1343760:five_prime_UTR
TCTCCAACTTCTGTTCGTAA+AGG 0.513941 tig0006506:+89622 Msa1343760:CDS
AACGTGAAGGTTGAGAAAAC+AGG 0.515362 tig0006506:+88959 Msa1343760:five_prime_UTR
TCAGATCTGAAGTTTGAGAA+AGG 0.555866 tig0006506:+88924 Msa1343760:five_prime_UTR
GTTGTTCATCTTAGAGCCAC+CGG 0.557111 tig0006506:+89737 Msa1343760:CDS
TTTGAGAATAGGAGCATCAC+CGG 0.562343 tig0006506:-89756 Msa1343760:intergenic
CGTGACACGTAGGATTGACT+AGG 0.584555 tig0006506:+89418 Msa1343760:five_prime_UTR
CTGTGTGATGATGATGAAGA+AGG 0.625613 tig0006506:-88889 Msa1343760:intergenic
GAAGGAGAGAACGAACGTGA+AGG 0.658917 tig0006506:+88946 Msa1343760:five_prime_UTR
AGTTATGTGGCGTGACACGT+AGG 0.687465 tig0006506:+89408 Msa1343760:five_prime_UTR
GAGAATAGGAGCATCACCGG+TGG 0.697312 tig0006506:-89753 Msa1343750:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATATAATTCTTGATATAAT+TGG + tig0006506:89227-89246 Msa1343760:intron 10.0%
!! ATATAATTCTTGATATAATT+GGG + tig0006506:89228-89247 Msa1343760:intron 10.0%
!! AATATAATTCTTGATATAAT+TGG + tig0006506:89227-89246 Msa1343760:intron 10.0%
!! ATATAATTCTTGATATAATT+GGG + tig0006506:89228-89247 Msa1343760:intron 10.0%
!! AAAAAATAAGTAAATCAAGA+GGG - tig0006506:89127-89146 Msa1343760:intergenic 15.0%
!! GGAAGAATTAAATTATATTA+AGG + tig0006506:89168-89187 Msa1343760:intron 15.0%
!! GAATTAAATTATATTAAGGA+TGG + tig0006506:89172-89191 Msa1343760:intron 15.0%
!! TATAATTCTTGATATAATTG+GGG + tig0006506:89229-89248 Msa1343760:intron 15.0%
!! AAAAAATAAGTAAATCAAGA+GGG - tig0006506:89127-89146 Msa1343760:intergenic 15.0%
!! GGAAGAATTAAATTATATTA+AGG + tig0006506:89168-89187 Msa1343760:intron 15.0%
!! GAATTAAATTATATTAAGGA+TGG + tig0006506:89172-89191 Msa1343760:intron 15.0%
!! TATAATTCTTGATATAATTG+GGG + tig0006506:89229-89248 Msa1343760:intron 15.0%
!! CAAAAAATAAGTAAATCAAG+AGG - tig0006506:89128-89147 Msa1343760:intergenic 20.0%
!!! AAATTGAGATTTTGCAAAAT+GGG + tig0006506:89444-89463 Msa1343760:five_prime_UTR 20.0%
!! CAAAAAATAAGTAAATCAAG+AGG - tig0006506:89128-89147 Msa1343760:intergenic 20.0%
!!! AAATTGAGATTTTGCAAAAT+GGG + tig0006506:89444-89463 Msa1343760:five_prime_UTR 20.0%
! ATTCTTCCAATTGACATATA+TGG - tig0006506:89156-89175 Msa1343760:intergenic 25.0%
!! TTTGATTGTTACGAATTTTC+TGG + tig0006506:89300-89319 Msa1343760:intron 25.0%
!! TTGATTGTTACGAATTTTCT+GGG + tig0006506:89301-89320 Msa1343760:intron 25.0%
!! TAATTCTAGAAATACACTTG+TGG + tig0006506:89336-89355 Msa1343760:intron 25.0%
! AAATTCAAAAAATACACAGC+TGG + tig0006506:89375-89394 Msa1343760:intron 25.0%
!! CAAATTGAGATTTTGCAAAA+TGG + tig0006506:89443-89462 Msa1343760:five_prime_UTR 25.0%
!! AATTGAGATTTTGCAAAATG+GGG + tig0006506:89445-89464 Msa1343760:five_prime_UTR 25.0%
!! TTTTTATCTTTTTGTGACAG+TGG + tig0006506:89715-89734 Msa1343760:intron 25.0%
! ATTCTTCCAATTGACATATA+TGG - tig0006506:89156-89175 Msa1343760:intergenic 25.0%
!! TTTGATTGTTACGAATTTTC+TGG + tig0006506:89300-89319 Msa1343760:intron 25.0%
!! TTGATTGTTACGAATTTTCT+GGG + tig0006506:89301-89320 Msa1343760:intron 25.0%
!! TAATTCTAGAAATACACTTG+TGG + tig0006506:89336-89355 Msa1343760:intron 25.0%
! AAATTCAAAAAATACACAGC+TGG + tig0006506:89375-89394 Msa1343760:intron 25.0%
!! CAAATTGAGATTTTGCAAAA+TGG + tig0006506:89443-89462 Msa1343760:five_prime_UTR 25.0%
!! AATTGAGATTTTGCAAAATG+GGG + tig0006506:89445-89464 Msa1343760:five_prime_UTR 25.0%
!! TTTTTATCTTTTTGTGACAG+TGG + tig0006506:89715-89734 Msa1343760:intron 25.0%
TCTTCAAAAATCTGGAAAAG+AGG + tig0006506:88837-88856 Msa1343760:five_prime_UTR 30.0%
AAAAATCTGGAAAAGAGGAA+GGG + tig0006506:88842-88861 Msa1343760:five_prime_UTR 30.0%
! TTTTGTAATTGATGCGAATC+TGG + tig0006506:89076-89095 Msa1343760:intron 30.0%
GATCAACCATATATGTCAAT+TGG + tig0006506:89147-89166 Msa1343760:intron 30.0%
!!! GAGAAGATGATTTTCTAGTT+TGG + tig0006506:89263-89282 Msa1343760:intron 30.0%
!!! TGGCAAGTTTTTAAGTTATG+TGG + tig0006506:89395-89414 Msa1343760:five_prime_UTR 30.0%
AGTTCTTCTTCACAGAAAAT+AGG + tig0006506:89562-89581 Msa1343760:intron 30.0%
GTTCTTCTTCACAGAAAATA+GGG + tig0006506:89563-89582 Msa1343760:intron 30.0%
AACTTGGATTGTTTGAGAAT+AGG - tig0006506:89770-89789 Msa1343760:intergenic 30.0%
TCTTCAAAAATCTGGAAAAG+AGG + tig0006506:88837-88856 Msa1343760:five_prime_UTR 30.0%
AAAAATCTGGAAAAGAGGAA+GGG + tig0006506:88842-88861 Msa1343760:five_prime_UTR 30.0%
! TTTTGTAATTGATGCGAATC+TGG + tig0006506:89076-89095 Msa1343760:intron 30.0%
GATCAACCATATATGTCAAT+TGG + tig0006506:89147-89166 Msa1343760:intron 30.0%
!!! GAGAAGATGATTTTCTAGTT+TGG + tig0006506:89263-89282 Msa1343760:intron 30.0%
!!! TGGCAAGTTTTTAAGTTATG+TGG + tig0006506:89395-89414 Msa1343760:five_prime_UTR 30.0%
AGTTCTTCTTCACAGAAAAT+AGG + tig0006506:89562-89581 Msa1343760:intron 30.0%
GTTCTTCTTCACAGAAAATA+GGG + tig0006506:89563-89582 Msa1343760:intron 30.0%
AACTTGGATTGTTTGAGAAT+AGG - tig0006506:89770-89789 Msa1343760:intergenic 30.0%
CAAAAATCTGGAAAAGAGGA+AGG + tig0006506:88841-88860 Msa1343760:five_prime_UTR 35.0%
! TCAGATCTGAAGTTTGAGAA+AGG + tig0006506:88924-88943 Msa1343760:five_prime_UTR 35.0%
! ATCTGAAGTTTGAGAAAGGA+AGG + tig0006506:88928-88947 Msa1343760:five_prime_UTR 35.0%
TAATTGATGCGAATCTGGTT+GGG + tig0006506:89081-89100 Msa1343760:intron 35.0%
TAACCTTTACGAACAGAAGT+TGG - tig0006506:89628-89647 Msa1343760:intergenic 35.0%
TCTCAAACAATCCAAGTTCA+AGG + tig0006506:89772-89791 Msa1343760:CDS 35.0%
!! AAGGAAAAGTACCTTGAACT+TGG - tig0006506:89786-89805 Msa1343760:intergenic 35.0%
CAAAAATCTGGAAAAGAGGA+AGG + tig0006506:88841-88860 Msa1343760:five_prime_UTR 35.0%
! TCAGATCTGAAGTTTGAGAA+AGG + tig0006506:88924-88943 Msa1343760:five_prime_UTR 35.0%
! ATCTGAAGTTTGAGAAAGGA+AGG + tig0006506:88928-88947 Msa1343760:five_prime_UTR 35.0%
TAATTGATGCGAATCTGGTT+GGG + tig0006506:89081-89100 Msa1343760:intron 35.0%
TAACCTTTACGAACAGAAGT+TGG - tig0006506:89628-89647 Msa1343760:intergenic 35.0%
TCTCAAACAATCCAAGTTCA+AGG + tig0006506:89772-89791 Msa1343760:CDS 35.0%
!! AAGGAAAAGTACCTTGAACT+TGG - tig0006506:89786-89805 Msa1343760:intergenic 35.0%
! CTGTGTGATGATGATGAAGA+AGG - tig0006506:88892-88911 Msa1343760:intergenic 40.0%
AACGTGAAGGTTGAGAAAAC+AGG + tig0006506:88959-88978 Msa1343760:five_prime_UTR 40.0%
GTAATTGATGCGAATCTGGT+TGG + tig0006506:89080-89099 Msa1343760:intron 40.0%
CAAGAGGGATACAAGTTACA+CGG - tig0006506:89112-89131 Msa1343760:intergenic 40.0%
!! TCTAGTTTGGTGCTTGAAGA+TGG + tig0006506:89276-89295 Msa1343760:intron 40.0%
!! CTAGTTTGGTGCTTGAAGAT+GGG + tig0006506:89277-89296 Msa1343760:intron 40.0%
TGCTACTGTTGCAAACTTAG+AGG + tig0006506:89480-89499 Msa1343760:intron 40.0%
GCTACTGTTGCAAACTTAGA+GGG + tig0006506:89481-89500 Msa1343760:intron 40.0%
TCAGTGTTCGTTCTTCTTCA+TGG + tig0006506:89588-89607 Msa1343760:exon 40.0%
TCTCCAACTTCTGTTCGTAA+AGG + tig0006506:89622-89641 Msa1343760:CDS 40.0%
!! TTTGAGAATAGGAGCATCAC+CGG - tig0006506:89759-89778 Msa1343760:intergenic 40.0%
! CTGTGTGATGATGATGAAGA+AGG - tig0006506:88892-88911 Msa1343760:intergenic 40.0%
AACGTGAAGGTTGAGAAAAC+AGG + tig0006506:88959-88978 Msa1343760:five_prime_UTR 40.0%
GTAATTGATGCGAATCTGGT+TGG + tig0006506:89080-89099 Msa1343760:intron 40.0%
CAAGAGGGATACAAGTTACA+CGG - tig0006506:89112-89131 Msa1343760:intergenic 40.0%
!! TCTAGTTTGGTGCTTGAAGA+TGG + tig0006506:89276-89295 Msa1343760:intron 40.0%
!! CTAGTTTGGTGCTTGAAGAT+GGG + tig0006506:89277-89296 Msa1343760:intron 40.0%
TGCTACTGTTGCAAACTTAG+AGG + tig0006506:89480-89499 Msa1343760:intron 40.0%
GCTACTGTTGCAAACTTAGA+GGG + tig0006506:89481-89500 Msa1343760:intron 40.0%
TCAGTGTTCGTTCTTCTTCA+TGG + tig0006506:89588-89607 Msa1343760:exon 40.0%
TCTCCAACTTCTGTTCGTAA+AGG + tig0006506:89622-89641 Msa1343760:CDS 40.0%
!! TTTGAGAATAGGAGCATCAC+CGG - tig0006506:89759-89778 Msa1343760:intergenic 40.0%
GGTTGAGAAAACAGGTCTGA+AGG + tig0006506:88967-88986 Msa1343760:intron 45.0%
GTTGTTCATCTTAGAGCCAC+CGG + tig0006506:89737-89756 Msa1343760:CDS 45.0%
GGTTGAGAAAACAGGTCTGA+AGG + tig0006506:88967-88986 Msa1343760:intron 45.0%
GTTGTTCATCTTAGAGCCAC+CGG + tig0006506:89737-89756 Msa1343760:CDS 45.0%
GAAGGAGAGAACGAACGTGA+AGG + tig0006506:88946-88965 Msa1343760:five_prime_UTR 50.0%
AGTTATGTGGCGTGACACGT+AGG + tig0006506:89408-89427 Msa1343760:five_prime_UTR 50.0%
CGTGACACGTAGGATTGACT+AGG + tig0006506:89418-89437 Msa1343760:five_prime_UTR 50.0%
GAAGGAGAGAACGAACGTGA+AGG + tig0006506:88946-88965 Msa1343760:five_prime_UTR 50.0%
AGTTATGTGGCGTGACACGT+AGG + tig0006506:89408-89427 Msa1343760:five_prime_UTR 50.0%
CGTGACACGTAGGATTGACT+AGG + tig0006506:89418-89437 Msa1343760:five_prime_UTR 50.0%
!! GAGAATAGGAGCATCACCGG+TGG - tig0006506:89756-89775 Msa1343760:intergenic 55.0%
!! GAGAATAGGAGCATCACCGG+TGG - tig0006506:89756-89775 Msa1343760:intergenic 55.0%
Chromosome Type Strat End Strand Name
tig0006506 gene 88835 89811 88835 ID=Msa1343760;Name=Msa1343760
tig0006506 mRNA 88835 89811 88835 ID=Msa1343760-mRNA-1;Parent=Msa1343760;Name=Msa1343760-mRNA-1;_AED=0.25;_eAED=0.25;_QI=249|1|0.75|1|0.33|0.25|4|0|38
tig0006506 exon 88835 88980 88835 ID=Msa1343760-mRNA-1:exon:4262;Parent=Msa1343760-mRNA-1
tig0006506 exon 89394 89466 89394 ID=Msa1343760-mRNA-1:exon:4263;Parent=Msa1343760-mRNA-1
tig0006506 exon 89577 89643 89577 ID=Msa1343760-mRNA-1:exon:4264;Parent=Msa1343760-mRNA-1
tig0006506 exon 89735 89811 89735 ID=Msa1343760-mRNA-1:exon:4265;Parent=Msa1343760-mRNA-1
tig0006506 five_prime_UTR 88835 88980 88835 ID=Msa1343760-mRNA-1:five_prime_utr;Parent=Msa1343760-mRNA-1
tig0006506 five_prime_UTR 89394 89466 89394 ID=Msa1343760-mRNA-1:five_prime_utr;Parent=Msa1343760-mRNA-1
tig0006506 five_prime_UTR 89577 89606 89577 ID=Msa1343760-mRNA-1:five_prime_utr;Parent=Msa1343760-mRNA-1
tig0006506 CDS 89607 89643 89607 ID=Msa1343760-mRNA-1:cds;Parent=Msa1343760-mRNA-1
tig0006506 CDS 89735 89811 89735 ID=Msa1343760-mRNA-1:cds;Parent=Msa1343760-mRNA-1
Gene Sequence

>Msa1343760

ATGGCTGCTGCTGAATCTCCAACTTCTGTTCGTAAAGTGGTTGTTCATCTTAGAGCCACCGGTGATGCTCCTATTCTCAAACAATCCAAGTTCAAGGTACTTTTCCTTTTTAAT

Protein sequence

>Msa1343760

MAAAESPTSVRKVVVHLRATGDAPILKQSKFKVLFLFN