AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0602250


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0602250 MtrunA17_Chr4g0029791 96.809 94 3 0 1 94 1 94 5.69e-64 188
Msa0602250 MtrunA17_Chr2g0326261 45.361 97 27 4 1 94 1 74 2.46e-11 54.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0602250 AT5G60400.3 40.449 89 51 1 6 94 5 91 1.51e-11 55.8

Find 24 sgRNAs with CRISPR-Local

Find 84 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGAGTTCCTCTCTGTCTTTC+TGG 0.075036 4_2:-45743434 Msa0602250:CDS
AAAATCAAATATGCATATTT+TGG 0.124229 4_2:-45742833 Msa0602250:three_prime_UTR
GTTTAACATGGACTGCATTT+TGG 0.222924 4_2:+45743472 None:intergenic
ACTTACTAGAATGTTAATTT+AGG 0.250075 4_2:+45742937 None:intergenic
AAAAGCTGCTTAGTTAGATT+TGG 0.304540 4_2:-45743070 Msa0602250:exon
CGAAGTTTCACCCTATTCAT+TGG 0.395651 4_2:+45742890 None:intergenic
TGATGATGATCTTGAAGATC+TGG 0.442771 4_2:-45743142 Msa0602250:CDS
TTCGTACGGACATATTTGTA+TGG 0.453259 4_2:-45742871 Msa0602250:three_prime_UTR
AGTGCATGCAAATCAAGAAA+AGG 0.472454 4_2:-45743208 Msa0602250:CDS
ACTGATGTGACCAATGAATA+GGG 0.474910 4_2:-45742900 Msa0602250:three_prime_UTR
AACTGATGTGACCAATGAAT+AGG 0.478716 4_2:-45742901 Msa0602250:three_prime_UTR
CTGTCTCTTACTTATCTCCC+AGG 0.495221 4_2:-45743102 Msa0602250:CDS
TTAAACCTTCGTGCTACTCA+TGG 0.498021 4_2:-45743455 Msa0602250:CDS
ACCGAAGAAGAAAAGATATG+AGG 0.524381 4_2:-45743242 Msa0602250:CDS
GTGCATGCAAATCAAGAAAA+GGG 0.524986 4_2:-45743207 Msa0602250:CDS
TACTCTTTGGAAAGAGCAAG+AGG 0.575505 4_2:+45743401 None:intergenic
AACATTCTAGTAAGTTCAGA+CGG 0.600784 4_2:-45742929 Msa0602250:three_prime_UTR
TTTGGAAAGAGCAAGAGGGT+TGG 0.601098 4_2:+45743406 None:intergenic
AAAAGGATGGGAAATAAAGG+AGG 0.624688 4_2:+45743523 None:intergenic
GAATAGGGTGAAACTTCGTA+CGG 0.636390 4_2:-45742885 Msa0602250:three_prime_UTR
ACTCTTTGGAAAGAGCAAGA+GGG 0.667434 4_2:+45743402 None:intergenic
AGTAGCACGAAGGTTTAACA+TGG 0.672060 4_2:+45743460 None:intergenic
GTGATTCCAGAAAGACAGAG+AGG 0.712435 4_2:+45743428 None:intergenic
GAACTCCATGAGTAGCACGA+AGG 0.732005 4_2:+45743450 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAATAAATTAATTTACTCTT+TGG + chr4_2:45743043-45743062 None:intergenic 10.0%
!! AAATAAATTAATTTACTCTT+TGG + chr4_2:45743043-45743062 None:intergenic 10.0%
!!! AAAATCAAATATGCATATTT+TGG - chr4_2:45743595-45743614 Msa0602250:five_prime_UTR 15.0%
!!! AAAATCAAATATGCATATTT+TGG - chr4_2:45743595-45743614 Msa0602250:five_prime_UTR 15.0%
!! TGATATATGTTTGAATTTGA+TGG - chr4_2:45743144-45743163 Msa0602250:CDS 20.0%
!! ACTTACTAGAATGTTAATTT+AGG + chr4_2:45743494-45743513 None:intergenic 20.0%
!!! ATGCATATTTGATTTTGATT+TGG + chr4_2:45743591-45743610 None:intergenic 20.0%
!! TGATATATGTTTGAATTTGA+TGG - chr4_2:45743144-45743163 Msa0602250:CDS 20.0%
!! ACTTACTAGAATGTTAATTT+AGG + chr4_2:45743494-45743513 None:intergenic 20.0%
!!! ATGCATATTTGATTTTGATT+TGG + chr4_2:45743591-45743610 None:intergenic 20.0%
!! TTTTCTAGGTAAAGGAAAAA+AGG + chr4_2:45742925-45742944 None:intergenic 25.0%
!!! GTTTTGTTTTTTCTAGGTAA+AGG + chr4_2:45742933-45742952 None:intergenic 25.0%
!!! TGGTTTGTTTTGTTTTTTCT+AGG + chr4_2:45742939-45742958 None:intergenic 25.0%
!! TCAAAGAAACAATGATTTTG+TGG - chr4_2:45743253-45743272 Msa0602250:CDS 25.0%
!! TCTAAATCACTTTCATTTTC+TGG - chr4_2:45743395-45743414 Msa0602250:intron 25.0%
!! TTTTCTAGGTAAAGGAAAAA+AGG + chr4_2:45742925-45742944 None:intergenic 25.0%
!!! GTTTTGTTTTTTCTAGGTAA+AGG + chr4_2:45742933-45742952 None:intergenic 25.0%
!!! TGGTTTGTTTTGTTTTTTCT+AGG + chr4_2:45742939-45742958 None:intergenic 25.0%
!! TCAAAGAAACAATGATTTTG+TGG - chr4_2:45743253-45743272 Msa0602250:CDS 25.0%
!! TCTAAATCACTTTCATTTTC+TGG - chr4_2:45743395-45743414 Msa0602250:intron 25.0%
GAAAAAAGGATGGGAAATAA+AGG + chr4_2:45742911-45742930 None:intergenic 30.0%
TAGGTAAAGGAAAAAAGGAT+GGG + chr4_2:45742920-45742939 None:intergenic 30.0%
! TCCTCATATCTTTTCTTCTT+CGG + chr4_2:45743190-45743209 None:intergenic 30.0%
! AATGATTTTGTGGAGATGAA+AGG - chr4_2:45743263-45743282 Msa0602250:intron 30.0%
AAAAGCTGCTTAGTTAGATT+TGG - chr4_2:45743358-45743377 Msa0602250:intron 30.0%
AACATTCTAGTAAGTTCAGA+CGG - chr4_2:45743499-45743518 Msa0602250:five_prime_UTR 30.0%
GAAAAAAGGATGGGAAATAA+AGG + chr4_2:45742911-45742930 None:intergenic 30.0%
TAGGTAAAGGAAAAAAGGAT+GGG + chr4_2:45742920-45742939 None:intergenic 30.0%
! TCCTCATATCTTTTCTTCTT+CGG + chr4_2:45743190-45743209 None:intergenic 30.0%
! AATGATTTTGTGGAGATGAA+AGG - chr4_2:45743263-45743282 Msa0602250:intron 30.0%
AAAAGCTGCTTAGTTAGATT+TGG - chr4_2:45743358-45743377 Msa0602250:intron 30.0%
AACATTCTAGTAAGTTCAGA+CGG - chr4_2:45743499-45743518 Msa0602250:five_prime_UTR 30.0%
AAAAGGATGGGAAATAAAGG+AGG + chr4_2:45742908-45742927 None:intergenic 35.0%
CTAGGTAAAGGAAAAAAGGA+TGG + chr4_2:45742921-45742940 None:intergenic 35.0%
!! GTTTAACATGGACTGCATTT+TGG + chr4_2:45742959-45742978 None:intergenic 35.0%
GTGAGATCATAGATCAAAAG+AGG + chr4_2:45743085-45743104 None:intergenic 35.0%
!! ATGTTTGAATTTGATGGTGC+AGG - chr4_2:45743150-45743169 Msa0602250:CDS 35.0%
ACCGAAGAAGAAAAGATATG+AGG - chr4_2:45743186-45743205 Msa0602250:CDS 35.0%
AGTGCATGCAAATCAAGAAA+AGG - chr4_2:45743220-45743239 Msa0602250:CDS 35.0%
GTGCATGCAAATCAAGAAAA+GGG - chr4_2:45743221-45743240 Msa0602250:CDS 35.0%
! TGATGATGATCTTGAAGATC+TGG - chr4_2:45743286-45743305 Msa0602250:intron 35.0%
AACTGATGTGACCAATGAAT+AGG - chr4_2:45743527-45743546 Msa0602250:five_prime_UTR 35.0%
ACTGATGTGACCAATGAATA+GGG - chr4_2:45743528-45743547 Msa0602250:five_prime_UTR 35.0%
TTCGTACGGACATATTTGTA+TGG - chr4_2:45743557-45743576 Msa0602250:five_prime_UTR 35.0%
AAAAGGATGGGAAATAAAGG+AGG + chr4_2:45742908-45742927 None:intergenic 35.0%
CTAGGTAAAGGAAAAAAGGA+TGG + chr4_2:45742921-45742940 None:intergenic 35.0%
!! GTTTAACATGGACTGCATTT+TGG + chr4_2:45742959-45742978 None:intergenic 35.0%
GTGAGATCATAGATCAAAAG+AGG + chr4_2:45743085-45743104 None:intergenic 35.0%
!! ATGTTTGAATTTGATGGTGC+AGG - chr4_2:45743150-45743169 Msa0602250:CDS 35.0%
ACCGAAGAAGAAAAGATATG+AGG - chr4_2:45743186-45743205 Msa0602250:CDS 35.0%
AGTGCATGCAAATCAAGAAA+AGG - chr4_2:45743220-45743239 Msa0602250:CDS 35.0%
GTGCATGCAAATCAAGAAAA+GGG - chr4_2:45743221-45743240 Msa0602250:CDS 35.0%
! TGATGATGATCTTGAAGATC+TGG - chr4_2:45743286-45743305 Msa0602250:intron 35.0%
AACTGATGTGACCAATGAAT+AGG - chr4_2:45743527-45743546 Msa0602250:five_prime_UTR 35.0%
ACTGATGTGACCAATGAATA+GGG - chr4_2:45743528-45743547 Msa0602250:five_prime_UTR 35.0%
TTCGTACGGACATATTTGTA+TGG - chr4_2:45743557-45743576 Msa0602250:five_prime_UTR 35.0%
AGTAGCACGAAGGTTTAACA+TGG + chr4_2:45742971-45742990 None:intergenic 40.0%
! TTAAACCTTCGTGCTACTCA+TGG - chr4_2:45742973-45742992 Msa0602250:three_prime_UTR 40.0%
! ACTCTTTGGAAAGAGCAAGA+GGG + chr4_2:45743029-45743048 None:intergenic 40.0%
! TACTCTTTGGAAAGAGCAAG+AGG + chr4_2:45743030-45743049 None:intergenic 40.0%
!! TTGAATTTGATGGTGCAGGA+TGG - chr4_2:45743154-45743173 Msa0602250:CDS 40.0%
! CAGCTTTTGCTGATAAACCT+GGG + chr4_2:45743346-45743365 None:intergenic 40.0%
CGAAGTTTCACCCTATTCAT+TGG + chr4_2:45743541-45743560 None:intergenic 40.0%
GAATAGGGTGAAACTTCGTA+CGG - chr4_2:45743543-45743562 Msa0602250:five_prime_UTR 40.0%
AGTAGCACGAAGGTTTAACA+TGG + chr4_2:45742971-45742990 None:intergenic 40.0%
! TTAAACCTTCGTGCTACTCA+TGG - chr4_2:45742973-45742992 Msa0602250:three_prime_UTR 40.0%
! ACTCTTTGGAAAGAGCAAGA+GGG + chr4_2:45743029-45743048 None:intergenic 40.0%
! TACTCTTTGGAAAGAGCAAG+AGG + chr4_2:45743030-45743049 None:intergenic 40.0%
!! TTGAATTTGATGGTGCAGGA+TGG - chr4_2:45743154-45743173 Msa0602250:CDS 40.0%
! CAGCTTTTGCTGATAAACCT+GGG + chr4_2:45743346-45743365 None:intergenic 40.0%
CGAAGTTTCACCCTATTCAT+TGG + chr4_2:45743541-45743560 None:intergenic 40.0%
GAATAGGGTGAAACTTCGTA+CGG - chr4_2:45743543-45743562 Msa0602250:five_prime_UTR 40.0%
GTGATTCCAGAAAGACAGAG+AGG + chr4_2:45743003-45743022 None:intergenic 45.0%
TTTGGAAAGAGCAAGAGGGT+TGG + chr4_2:45743025-45743044 None:intergenic 45.0%
CTGTCTCTTACTTATCTCCC+AGG - chr4_2:45743326-45743345 Msa0602250:intron 45.0%
! GCAGCTTTTGCTGATAAACC+TGG + chr4_2:45743347-45743366 None:intergenic 45.0%
GTGATTCCAGAAAGACAGAG+AGG + chr4_2:45743003-45743022 None:intergenic 45.0%
TTTGGAAAGAGCAAGAGGGT+TGG + chr4_2:45743025-45743044 None:intergenic 45.0%
CTGTCTCTTACTTATCTCCC+AGG - chr4_2:45743326-45743345 Msa0602250:intron 45.0%
! GCAGCTTTTGCTGATAAACC+TGG + chr4_2:45743347-45743366 None:intergenic 45.0%
GAACTCCATGAGTAGCACGA+AGG + chr4_2:45742981-45743000 None:intergenic 50.0%
GGAGTTCCTCTCTGTCTTTC+TGG - chr4_2:45742994-45743013 Msa0602250:three_prime_UTR 50.0%
GAACTCCATGAGTAGCACGA+AGG + chr4_2:45742981-45743000 None:intergenic 50.0%
GGAGTTCCTCTCTGTCTTTC+TGG - chr4_2:45742994-45743013 Msa0602250:three_prime_UTR 50.0%
Chromosome Type Strat End Strand Name
chr4_2 gene 45742831 45743619 45742831 ID=Msa0602250;Name=Msa0602250
chr4_2 mRNA 45742831 45743619 45742831 ID=Msa0602250-mRNA-1;Parent=Msa0602250;Name=Msa0602250-mRNA-1;_AED=0.00;_eAED=0.00;_QI=130|1|1|1|1|1|2|249|94
chr4_2 exon 45742831 45743278 45742831 ID=Msa0602250-mRNA-1:exon:10271;Parent=Msa0602250-mRNA-1
chr4_2 exon 45743404 45743619 45743404 ID=Msa0602250-mRNA-1:exon:10270;Parent=Msa0602250-mRNA-1
chr4_2 five_prime_UTR 45743490 45743619 45743490 ID=Msa0602250-mRNA-1:five_prime_utr;Parent=Msa0602250-mRNA-1
chr4_2 CDS 45743404 45743489 45743404 ID=Msa0602250-mRNA-1:cds;Parent=Msa0602250-mRNA-1
chr4_2 CDS 45743080 45743278 45743080 ID=Msa0602250-mRNA-1:cds;Parent=Msa0602250-mRNA-1
chr4_2 three_prime_UTR 45742831 45743079 45742831 ID=Msa0602250-mRNA-1:three_prime_utr;Parent=Msa0602250-mRNA-1
Gene Sequence

>Msa0602250

ATGCAGTCCATGTTAAACCTTCGTGCTACTCATGGAGTTCCTCTCTGTCTTTCTGGAATCACCAACCCTCTTGCTCTTTCCAAAGAGATGGCAGATCACGACCGAAGAAGAAAAGATATGAGGAAGCAAAGATCAGTGCATGCAAATCAAGAAAAGGGTGCACAAAGTCAAAGAAACAATGATTTTGTGGAGATGAAAGGTGATGATGATCTTGAAGATCTGGATGAAATCTTGCATCAACTGTCTCTTACTTATCTCCCAGGTTTATCAGCAAAAGCTGCTTAG

Protein sequence

>Msa0602250

MQSMLNLRATHGVPLCLSGITNPLALSKEMADHDRRRKDMRKQRSVHANQEKGAQSQRNNDFVEMKGDDDLEDLDEILHQLSLTYLPGLSAKAA*