AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0052820

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0052820 MtrunA17_Chr1g0152281 96.429 84 2 1 1 84 1 83 7.46e-54 161
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0052820 AT3G49780.1 45.783 83 40 4 1 82 1 79 8.91e-14 60.8

Find 33 sgRNAs with CRISPR-Local

Find 86 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCTGATTTGAATGAAGAATT+TGG 0.192068 1_2:-7122538 Msa0052820:three_prime_UTR
ACACCTGTAAATACAAAATT+AGG 0.274179 1_2:+7123181 None:intergenic
TGAAAGCTTTCTTCACCCTT+AGG 0.365213 1_2:+7122581 None:intergenic
TAGTTTAATGTTTCAACCTA+AGG 0.402258 1_2:-7122597 Msa0052820:three_prime_UTR
TGAACTCACTATGTCAAAAC+TGG 0.413207 1_2:-7123260 Msa0052820:exon
AGGTTGAAACATTAAACTAT+AGG 0.419413 1_2:+7122601 None:intergenic
CTTTGTTCGAGTTCTGTTGT+TGG 0.438286 1_2:-7122308 Msa0052820:three_prime_UTR
TAGAAGAGCTAAGGTGAAGA+GGG 0.441297 1_2:+7123234 None:intergenic
AACAAGAATGTTTGACAAGA+AGG 0.470793 1_2:-7122839 Msa0052820:CDS
AGTTTAATGTTTCAACCTAA+GGG 0.517045 1_2:-7122596 Msa0052820:three_prime_UTR
TTAGGATATTGTTTCTAGCA+AGG 0.518999 1_2:-7122913 Msa0052820:intron
TAAAGAATTAAGAATTACAA+TGG 0.519029 1_2:-7122355 Msa0052820:three_prime_UTR
TAATCAGAAATTGTGGAAGA+TGG 0.524624 1_2:-7122506 Msa0052820:three_prime_UTR
GAGAATTGTGAAGGAGTGGA+AGG 0.529911 1_2:-7122864 Msa0052820:CDS
AAAATTAGGACGGGAGGCAG+AGG 0.534908 1_2:+7123195 None:intergenic
ATAGAAGAGCTAAGGTGAAG+AGG 0.536160 1_2:+7123233 None:intergenic
AAATGAGAATTGTGAAGGAG+TGG 0.536266 1_2:-7122868 Msa0052820:CDS
TGTAAATACAAAATTAGGAC+GGG 0.537151 1_2:+7123186 None:intergenic
TGTTCGAGTTCTGTTGTTGG+TGG 0.538277 1_2:-7122305 Msa0052820:three_prime_UTR
TTAGAAAATGAGAATTGTGA+AGG 0.542330 1_2:-7122873 Msa0052820:CDS
TTCAAATCAGAGAAGCGTAT+GGG 0.547158 1_2:+7122550 None:intergenic
TTCAGCATAATCAGAAATTG+TGG 0.547601 1_2:-7122513 Msa0052820:three_prime_UTR
TATTTGAATATATACATGTA+CGG 0.549368 1_2:-7122641 Msa0052820:three_prime_UTR
CAAGCTTAATAGAAGAGCTA+AGG 0.557176 1_2:+7123225 None:intergenic
ATTCAAATCAGAGAAGCGTA+TGG 0.573306 1_2:+7122549 None:intergenic
TGTTGGTGGAAAGACCTTGT+CGG 0.582430 1_2:-7122291 Msa0052820:three_prime_UTR
CTGTAAATACAAAATTAGGA+CGG 0.605617 1_2:+7123185 None:intergenic
CATACTATTATTTACCGACA+AGG 0.613201 1_2:+7122277 None:intergenic
AGGTGTCTCTTCACTACATG+AGG 0.640533 1_2:-7123164 Msa0052820:intron
AAATACAAAATTAGGACGGG+AGG 0.641028 1_2:+7123189 None:intergenic
TCAAATCAGAGAAGCGTATG+GGG 0.646004 1_2:+7122551 None:intergenic
AATCAGAGAAGCGTATGGGG+TGG 0.699372 1_2:+7122554 None:intergenic
TGGCTTTAATCTCAAGTACG+AGG 0.711072 1_2:-7122486 Msa0052820:three_prime_UTR

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTCTAAAGACATTAATTTTT+GGG + chr1_2:7122765-7122784 None:intergenic 15.0%
!!! ATTCTAAAGACATTAATTTT+TGG + chr1_2:7122766-7122785 None:intergenic 15.0%
!!! AAAAATTAATGTCTTTAGAA+TGG - chr1_2:7122765-7122784 Msa0052820:three_prime_UTR 15.0%
!! AACAAAAACTCAATAAAATT+AGG + chr1_2:7122869-7122888 None:intergenic 15.0%
!! TATTTGAATATATACATGTA+CGG - chr1_2:7122895-7122914 Msa0052820:CDS 15.0%
!! TAAAGAATTAAGAATTACAA+TGG - chr1_2:7123181-7123200 Msa0052820:CDS 15.0%
!!! TTCTAAAGACATTAATTTTT+GGG + chr1_2:7122765-7122784 None:intergenic 15.0%
!!! ATTCTAAAGACATTAATTTT+TGG + chr1_2:7122766-7122785 None:intergenic 15.0%
!!! AAAAATTAATGTCTTTAGAA+TGG - chr1_2:7122765-7122784 Msa0052820:three_prime_UTR 15.0%
!! AACAAAAACTCAATAAAATT+AGG + chr1_2:7122869-7122888 None:intergenic 15.0%
!! TATTTGAATATATACATGTA+CGG - chr1_2:7122895-7122914 Msa0052820:CDS 15.0%
!! TAAAGAATTAAGAATTACAA+TGG - chr1_2:7123181-7123200 Msa0052820:CDS 15.0%
!! CACTAATTACTTAATTAAGA+AGG + chr1_2:7122407-7122426 None:intergenic 20.0%
!! TACCATATTTCATTTGAATT+AGG - chr1_2:7122605-7122624 Msa0052820:three_prime_UTR 20.0%
!! ATCCTAATTCAAATGAAATA+TGG + chr1_2:7122610-7122629 None:intergenic 20.0%
!! CACTAATTACTTAATTAAGA+AGG + chr1_2:7122407-7122426 None:intergenic 20.0%
!! TACCATATTTCATTTGAATT+AGG - chr1_2:7122605-7122624 Msa0052820:three_prime_UTR 20.0%
!! ATCCTAATTCAAATGAAATA+TGG + chr1_2:7122610-7122629 None:intergenic 20.0%
! TGTAAATACAAAATTAGGAC+GGG + chr1_2:7122353-7122372 None:intergenic 25.0%
! CTGTAAATACAAAATTAGGA+CGG + chr1_2:7122354-7122373 None:intergenic 25.0%
! ACACCTGTAAATACAAAATT+AGG + chr1_2:7122358-7122377 None:intergenic 25.0%
! TTAGAAAATGAGAATTGTGA+AGG - chr1_2:7122663-7122682 Msa0052820:three_prime_UTR 25.0%
! AGGTTGAAACATTAAACTAT+AGG + chr1_2:7122938-7122957 None:intergenic 25.0%
! TAGTTTAATGTTTCAACCTA+AGG - chr1_2:7122939-7122958 Msa0052820:intron 25.0%
! AGTTTAATGTTTCAACCTAA+GGG - chr1_2:7122940-7122959 Msa0052820:intron 25.0%
!! TCTGATTTGAATGAAGAATT+TGG - chr1_2:7122998-7123017 Msa0052820:intron 25.0%
! TGTAAATACAAAATTAGGAC+GGG + chr1_2:7122353-7122372 None:intergenic 25.0%
! CTGTAAATACAAAATTAGGA+CGG + chr1_2:7122354-7122373 None:intergenic 25.0%
! ACACCTGTAAATACAAAATT+AGG + chr1_2:7122358-7122377 None:intergenic 25.0%
! TTAGAAAATGAGAATTGTGA+AGG - chr1_2:7122663-7122682 Msa0052820:three_prime_UTR 25.0%
! AGGTTGAAACATTAAACTAT+AGG + chr1_2:7122938-7122957 None:intergenic 25.0%
! TAGTTTAATGTTTCAACCTA+AGG - chr1_2:7122939-7122958 Msa0052820:intron 25.0%
! AGTTTAATGTTTCAACCTAA+GGG - chr1_2:7122940-7122959 Msa0052820:intron 25.0%
!! TCTGATTTGAATGAAGAATT+TGG - chr1_2:7122998-7123017 Msa0052820:intron 25.0%
! CGTCCTAATTTTGTATTTAC+AGG - chr1_2:7122352-7122371 Msa0052820:three_prime_UTR 30.0%
TTATCTTATTCTTGTGATGC+TGG - chr1_2:7122547-7122566 Msa0052820:three_prime_UTR 30.0%
!! TTAGGATATTGTTTCTAGCA+AGG - chr1_2:7122623-7122642 Msa0052820:three_prime_UTR 30.0%
AACAAGAATGTTTGACAAGA+AGG - chr1_2:7122697-7122716 Msa0052820:three_prime_UTR 30.0%
TTCAGCATAATCAGAAATTG+TGG - chr1_2:7123023-7123042 Msa0052820:intron 30.0%
TAATCAGAAATTGTGGAAGA+TGG - chr1_2:7123030-7123049 Msa0052820:intron 30.0%
CATACTATTATTTACCGACA+AGG + chr1_2:7123262-7123281 None:intergenic 30.0%
! CGTCCTAATTTTGTATTTAC+AGG - chr1_2:7122352-7122371 Msa0052820:three_prime_UTR 30.0%
TTATCTTATTCTTGTGATGC+TGG - chr1_2:7122547-7122566 Msa0052820:three_prime_UTR 30.0%
!! TTAGGATATTGTTTCTAGCA+AGG - chr1_2:7122623-7122642 Msa0052820:three_prime_UTR 30.0%
AACAAGAATGTTTGACAAGA+AGG - chr1_2:7122697-7122716 Msa0052820:three_prime_UTR 30.0%
TTCAGCATAATCAGAAATTG+TGG - chr1_2:7123023-7123042 Msa0052820:intron 30.0%
TAATCAGAAATTGTGGAAGA+TGG - chr1_2:7123030-7123049 Msa0052820:intron 30.0%
CATACTATTATTTACCGACA+AGG + chr1_2:7123262-7123281 None:intergenic 30.0%
TGAACTCACTATGTCAAAAC+TGG - chr1_2:7122276-7122295 Msa0052820:three_prime_UTR 35.0%
CAAGCTTAATAGAAGAGCTA+AGG + chr1_2:7122314-7122333 None:intergenic 35.0%
AAATACAAAATTAGGACGGG+AGG + chr1_2:7122350-7122369 None:intergenic 35.0%
AAATGAGAATTGTGAAGGAG+TGG - chr1_2:7122668-7122687 Msa0052820:three_prime_UTR 35.0%
! TTCAAATCAGAGAAGCGTAT+GGG + chr1_2:7122989-7123008 None:intergenic 35.0%
! ATTCAAATCAGAGAAGCGTA+TGG + chr1_2:7122990-7123009 None:intergenic 35.0%
TGAACTCACTATGTCAAAAC+TGG - chr1_2:7122276-7122295 Msa0052820:three_prime_UTR 35.0%
CAAGCTTAATAGAAGAGCTA+AGG + chr1_2:7122314-7122333 None:intergenic 35.0%
AAATACAAAATTAGGACGGG+AGG + chr1_2:7122350-7122369 None:intergenic 35.0%
AAATGAGAATTGTGAAGGAG+TGG - chr1_2:7122668-7122687 Msa0052820:three_prime_UTR 35.0%
! TTCAAATCAGAGAAGCGTAT+GGG + chr1_2:7122989-7123008 None:intergenic 35.0%
! ATTCAAATCAGAGAAGCGTA+TGG + chr1_2:7122990-7123009 None:intergenic 35.0%
TAGAAGAGCTAAGGTGAAGA+GGG + chr1_2:7122305-7122324 None:intergenic 40.0%
ATAGAAGAGCTAAGGTGAAG+AGG + chr1_2:7122306-7122325 None:intergenic 40.0%
TGAAAGCTTTCTTCACCCTT+AGG + chr1_2:7122958-7122977 None:intergenic 40.0%
! TCAAATCAGAGAAGCGTATG+GGG + chr1_2:7122988-7123007 None:intergenic 40.0%
!! TGGCTTTAATCTCAAGTACG+AGG - chr1_2:7123050-7123069 Msa0052820:intron 40.0%
! CTTTGTTCGAGTTCTGTTGT+TGG - chr1_2:7123228-7123247 Msa0052820:CDS 40.0%
TAGAAGAGCTAAGGTGAAGA+GGG + chr1_2:7122305-7122324 None:intergenic 40.0%
ATAGAAGAGCTAAGGTGAAG+AGG + chr1_2:7122306-7122325 None:intergenic 40.0%
TGAAAGCTTTCTTCACCCTT+AGG + chr1_2:7122958-7122977 None:intergenic 40.0%
! TCAAATCAGAGAAGCGTATG+GGG + chr1_2:7122988-7123007 None:intergenic 40.0%
!! TGGCTTTAATCTCAAGTACG+AGG - chr1_2:7123050-7123069 Msa0052820:intron 40.0%
! CTTTGTTCGAGTTCTGTTGT+TGG - chr1_2:7123228-7123247 Msa0052820:CDS 40.0%
AGGTGTCTCTTCACTACATG+AGG - chr1_2:7122372-7122391 Msa0052820:three_prime_UTR 45.0%
GAGAATTGTGAAGGAGTGGA+AGG - chr1_2:7122672-7122691 Msa0052820:three_prime_UTR 45.0%
! TGTTCGAGTTCTGTTGTTGG+TGG - chr1_2:7123231-7123250 Msa0052820:CDS 45.0%
! TGTTGGTGGAAAGACCTTGT+CGG - chr1_2:7123245-7123264 Msa0052820:CDS 45.0%
AGGTGTCTCTTCACTACATG+AGG - chr1_2:7122372-7122391 Msa0052820:three_prime_UTR 45.0%
GAGAATTGTGAAGGAGTGGA+AGG - chr1_2:7122672-7122691 Msa0052820:three_prime_UTR 45.0%
! TGTTCGAGTTCTGTTGTTGG+TGG - chr1_2:7123231-7123250 Msa0052820:CDS 45.0%
! TGTTGGTGGAAAGACCTTGT+CGG - chr1_2:7123245-7123264 Msa0052820:CDS 45.0%
!! AATAAAATATTTAATTAACA+TGG + chr1_2:7122527-7122546 None:intergenic 5.0%
!! AATAAAATATTTAATTAACA+TGG + chr1_2:7122527-7122546 None:intergenic 5.0%
AAAATTAGGACGGGAGGCAG+AGG + chr1_2:7122344-7122363 None:intergenic 50.0%
! AATCAGAGAAGCGTATGGGG+TGG + chr1_2:7122985-7123004 None:intergenic 50.0%
AAAATTAGGACGGGAGGCAG+AGG + chr1_2:7122344-7122363 None:intergenic 50.0%
! AATCAGAGAAGCGTATGGGG+TGG + chr1_2:7122985-7123004 None:intergenic 50.0%
Chromosome Type Strat End Strand Name
chr1_2 gene 7122243 7123315 7122243 ID=Msa0052820;Name=Msa0052820
chr1_2 mRNA 7122243 7123315 7122243 ID=Msa0052820-mRNA-1;Parent=Msa0052820;Name=Msa0052820-mRNA-1;_AED=0.02;_eAED=0.02;_QI=43|1|1|1|1|1|2|542|84
chr1_2 exon 7122243 7122931 7122243 ID=Msa0052820-mRNA-1:exon:2417;Parent=Msa0052820-mRNA-1
chr1_2 exon 7123165 7123315 7123165 ID=Msa0052820-mRNA-1:exon:2416;Parent=Msa0052820-mRNA-1
chr1_2 five_prime_UTR 7123273 7123315 7123273 ID=Msa0052820-mRNA-1:five_prime_utr;Parent=Msa0052820-mRNA-1
chr1_2 CDS 7123165 7123272 7123165 ID=Msa0052820-mRNA-1:cds;Parent=Msa0052820-mRNA-1
chr1_2 CDS 7122785 7122931 7122785 ID=Msa0052820-mRNA-1:cds;Parent=Msa0052820-mRNA-1
chr1_2 three_prime_UTR 7122243 7122784 7122243 ID=Msa0052820-mRNA-1:three_prime_utr;Parent=Msa0052820-mRNA-1
Gene Sequence

>Msa0052820

ATGTCAAAACTGGTCACCCTCTTCACCTTAGCTCTTCTATTAAGCTTGAGTTTAACCTCTGCCTCCCGTCCTAATTTTGTATTTACAGGTGTCTCTTCACTACATGAGGATATTGTTTCTAGCAAGGCATCAAGTACTGTAGACTTAGAAAATGAGAATTGTGAAGGAGTGGAAGGAGAACAAGAATGTTTGACAAGAAGGACTCTAGCTGCACATCTCGATTATATCTACACTCAGCATAAACCCAAAAATTAA
Protein sequence

>Msa0052820

MSKLVTLFTLALLLSLSLTSASRPNFVFTGVSSLHEDIVSSKASSTVDLENENCEGVEGEQECLTRRTLAAHLDYIYTQHKPKN*