AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1173190

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1173190 MtrunA17_Chr1g0152281 95.238 84 3 1 1 84 1 83 1.48e-38 123
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1173190 AT3G49780.1 45.783 83 40 4 1 82 1 79 1.10e-13 60.5

Find 38 sgRNAs with CRISPR-Local

Find 106 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCTGATTTGAATGAAGAATT+TGG 0.192068 8_1:-3397517 Msa1173190:three_prime_UTR
ACACCTGTAAATACAAAATT+AGG 0.274179 8_1:+3398160 None:intergenic
TCACCTGCATGGCTAGAAAA+AGG 0.336857 8_1:+3397185 None:intergenic
TGAAAGCTTTCTTCACCCTT+AGG 0.365213 8_1:+3397560 None:intergenic
TTAAACTCAAGCTTAATAGA+AGG 0.368922 8_1:+3398197 None:intergenic
TAGTTTAATGTTTCAACCTA+AGG 0.402258 8_1:-3397576 Msa1173190:three_prime_UTR
TGAACTCACTATGTCAAAAC+TGG 0.413207 8_1:-3398239 Msa1173190:exon
AGGTTGAAACATTAAACTAT+AGG 0.419413 8_1:+3397580 None:intergenic
CTTTGTTCGAGTTCTGTTGT+TGG 0.438286 8_1:-3397286 Msa1173190:three_prime_UTR
AACAAGAATGTTTGACAAGA+AGG 0.470793 8_1:-3397818 Msa1173190:CDS
TAGAAGGGCTAAGGTGAAGA+GGG 0.511012 8_1:+3398213 None:intergenic
AGTTTAATGTTTCAACCTAA+GGG 0.517045 8_1:-3397575 Msa1173190:three_prime_UTR
TTAGGATATTGTTTCTAGCA+AGG 0.518999 8_1:-3397892 Msa1173190:intron
TAAAGAATTAAGAATTACAA+TGG 0.519029 8_1:-3397333 Msa1173190:three_prime_UTR
TAATCAGAAATTGTGGAAGA+TGG 0.524624 8_1:-3397485 Msa1173190:three_prime_UTR
GAGAATTGTGAAGGAGTGGA+AGG 0.529911 8_1:-3397843 Msa1173190:CDS
AAAATTAGGACGGGAGGCAG+AGG 0.534908 8_1:+3398174 None:intergenic
AAATGAGAATTGTGAAGGAG+TGG 0.536266 8_1:-3397847 Msa1173190:CDS
TGTAAATACAAAATTAGGAC+GGG 0.537151 8_1:+3398165 None:intergenic
TGTTCGAGTTCTGTTGTTGG+TGG 0.538277 8_1:-3397283 Msa1173190:three_prime_UTR
TTAGAAAATGAGAATTGTGA+AGG 0.542330 8_1:-3397852 Msa1173190:CDS
TTCAAATCAGAGAAGCGTAT+GGG 0.547158 8_1:+3397529 None:intergenic
TTCAGCATAATCAGAAATTG+TGG 0.547601 8_1:-3397492 Msa1173190:three_prime_UTR
CAAGCTTAATAGAAGGGCTA+AGG 0.548012 8_1:+3398204 None:intergenic
TATTTGAATATATACATGTA+CGG 0.549368 8_1:-3397620 Msa1173190:three_prime_UTR
TAAACTCAAGCTTAATAGAA+GGG 0.552086 8_1:+3398198 None:intergenic
ATTCAAATCAGAGAAGCGTA+TGG 0.573306 8_1:+3397528 None:intergenic
ATAGAAGGGCTAAGGTGAAG+AGG 0.576004 8_1:+3398212 None:intergenic
TGTTGGTGGAAAGACCTTGT+CGG 0.582430 8_1:-3397269 Msa1173190:three_prime_UTR
TATATATCCCCTCACCTGCA+TGG 0.599144 8_1:+3397174 None:intergenic
CTGTAAATACAAAATTAGGA+CGG 0.605617 8_1:+3398164 None:intergenic
TTTCTAGCCATGCAGGTGAG+GGG 0.608656 8_1:-3397181 Msa1173190:three_prime_UTR
CATACTATTATTTACCGACA+AGG 0.613201 8_1:+3397255 None:intergenic
AGGTGTCTCTTCGCTACATG+AGG 0.638518 8_1:-3398143 Msa1173190:intron
AAATACAAAATTAGGACGGG+AGG 0.641028 8_1:+3398168 None:intergenic
TCAAATCAGAGAAGCGTATG+GGG 0.646004 8_1:+3397530 None:intergenic
AATCAGAGAAGCGTATGGGG+TGG 0.699372 8_1:+3397533 None:intergenic
TGGCTTTAATCTCAAGTACG+AGG 0.711072 8_1:-3397465 Msa1173190:three_prime_UTR

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTCTAAAGACATTAATTTTT+GGG + chr8_1:3397681-3397700 None:intergenic 15.0%
!!! ATTCTAAAGACATTAATTTT+TGG + chr8_1:3397682-3397701 None:intergenic 15.0%
!!! AAAAATTAATGTCTTTAGAA+TGG - chr8_1:3397681-3397700 Msa1173190:three_prime_UTR 15.0%
!! AACAAAAACTCAATAAAATT+AGG + chr8_1:3397785-3397804 None:intergenic 15.0%
!! TATTTGAATATATACATGTA+CGG - chr8_1:3397811-3397830 Msa1173190:CDS 15.0%
!! TAAAGAATTAAGAATTACAA+TGG - chr8_1:3398098-3398117 Msa1173190:intron 15.0%
!!! TTCTAAAGACATTAATTTTT+GGG + chr8_1:3397681-3397700 None:intergenic 15.0%
!!! ATTCTAAAGACATTAATTTT+TGG + chr8_1:3397682-3397701 None:intergenic 15.0%
!!! AAAAATTAATGTCTTTAGAA+TGG - chr8_1:3397681-3397700 Msa1173190:three_prime_UTR 15.0%
!! AACAAAAACTCAATAAAATT+AGG + chr8_1:3397785-3397804 None:intergenic 15.0%
!! TATTTGAATATATACATGTA+CGG - chr8_1:3397811-3397830 Msa1173190:CDS 15.0%
!! TAAAGAATTAAGAATTACAA+TGG - chr8_1:3398098-3398117 Msa1173190:intron 15.0%
!! CACTAATTACTTAATTAAGA+AGG + chr8_1:3397323-3397342 None:intergenic 20.0%
!! TCCTAATTCAAATGAAATAT+GGG + chr8_1:3397525-3397544 None:intergenic 20.0%
!! ATCCTAATTCAAATGAAATA+TGG + chr8_1:3397526-3397545 None:intergenic 20.0%
!! CACTAATTACTTAATTAAGA+AGG + chr8_1:3397323-3397342 None:intergenic 20.0%
!! TCCTAATTCAAATGAAATAT+GGG + chr8_1:3397525-3397544 None:intergenic 20.0%
!! ATCCTAATTCAAATGAAATA+TGG + chr8_1:3397526-3397545 None:intergenic 20.0%
! TAAACTCAAGCTTAATAGAA+GGG + chr8_1:3397236-3397255 None:intergenic 25.0%
! TTAAACTCAAGCTTAATAGA+AGG + chr8_1:3397237-3397256 None:intergenic 25.0%
! TGTAAATACAAAATTAGGAC+GGG + chr8_1:3397269-3397288 None:intergenic 25.0%
! CTGTAAATACAAAATTAGGA+CGG + chr8_1:3397270-3397289 None:intergenic 25.0%
! ACACCTGTAAATACAAAATT+AGG + chr8_1:3397274-3397293 None:intergenic 25.0%
! TCCCATATTTCATTTGAATT+AGG - chr8_1:3397521-3397540 Msa1173190:three_prime_UTR 25.0%
! TTAGAAAATGAGAATTGTGA+AGG - chr8_1:3397579-3397598 Msa1173190:three_prime_UTR 25.0%
! AGGTTGAAACATTAAACTAT+AGG + chr8_1:3397854-3397873 None:intergenic 25.0%
! TAGTTTAATGTTTCAACCTA+AGG - chr8_1:3397855-3397874 Msa1173190:CDS 25.0%
! AGTTTAATGTTTCAACCTAA+GGG - chr8_1:3397856-3397875 Msa1173190:CDS 25.0%
!! TCTGATTTGAATGAAGAATT+TGG - chr8_1:3397914-3397933 Msa1173190:intron 25.0%
! TAAACTCAAGCTTAATAGAA+GGG + chr8_1:3397236-3397255 None:intergenic 25.0%
! TTAAACTCAAGCTTAATAGA+AGG + chr8_1:3397237-3397256 None:intergenic 25.0%
! TGTAAATACAAAATTAGGAC+GGG + chr8_1:3397269-3397288 None:intergenic 25.0%
! CTGTAAATACAAAATTAGGA+CGG + chr8_1:3397270-3397289 None:intergenic 25.0%
! ACACCTGTAAATACAAAATT+AGG + chr8_1:3397274-3397293 None:intergenic 25.0%
! TCCCATATTTCATTTGAATT+AGG - chr8_1:3397521-3397540 Msa1173190:three_prime_UTR 25.0%
! TTAGAAAATGAGAATTGTGA+AGG - chr8_1:3397579-3397598 Msa1173190:three_prime_UTR 25.0%
! AGGTTGAAACATTAAACTAT+AGG + chr8_1:3397854-3397873 None:intergenic 25.0%
! TAGTTTAATGTTTCAACCTA+AGG - chr8_1:3397855-3397874 Msa1173190:CDS 25.0%
! AGTTTAATGTTTCAACCTAA+GGG - chr8_1:3397856-3397875 Msa1173190:CDS 25.0%
!! TCTGATTTGAATGAAGAATT+TGG - chr8_1:3397914-3397933 Msa1173190:intron 25.0%
! CGTCCTAATTTTGTATTTAC+AGG - chr8_1:3397268-3397287 Msa1173190:three_prime_UTR 30.0%
TTATCTTATTCTTGTGATGC+TGG - chr8_1:3397463-3397482 Msa1173190:three_prime_UTR 30.0%
!! TTAGGATATTGTTTCTAGCA+AGG - chr8_1:3397539-3397558 Msa1173190:three_prime_UTR 30.0%
! TTTTCTAAGTCTACAGTACT+TGG + chr8_1:3397567-3397586 None:intergenic 30.0%
AACAAGAATGTTTGACAAGA+AGG - chr8_1:3397613-3397632 Msa1173190:three_prime_UTR 30.0%
TTCAGCATAATCAGAAATTG+TGG - chr8_1:3397939-3397958 Msa1173190:intron 30.0%
TAATCAGAAATTGTGGAAGA+TGG - chr8_1:3397946-3397965 Msa1173190:intron 30.0%
CATACTATTATTTACCGACA+AGG + chr8_1:3398179-3398198 None:intergenic 30.0%
! CGTCCTAATTTTGTATTTAC+AGG - chr8_1:3397268-3397287 Msa1173190:three_prime_UTR 30.0%
TTATCTTATTCTTGTGATGC+TGG - chr8_1:3397463-3397482 Msa1173190:three_prime_UTR 30.0%
!! TTAGGATATTGTTTCTAGCA+AGG - chr8_1:3397539-3397558 Msa1173190:three_prime_UTR 30.0%
! TTTTCTAAGTCTACAGTACT+TGG + chr8_1:3397567-3397586 None:intergenic 30.0%
AACAAGAATGTTTGACAAGA+AGG - chr8_1:3397613-3397632 Msa1173190:three_prime_UTR 30.0%
TTCAGCATAATCAGAAATTG+TGG - chr8_1:3397939-3397958 Msa1173190:intron 30.0%
TAATCAGAAATTGTGGAAGA+TGG - chr8_1:3397946-3397965 Msa1173190:intron 30.0%
CATACTATTATTTACCGACA+AGG + chr8_1:3398179-3398198 None:intergenic 30.0%
TGAACTCACTATGTCAAAAC+TGG - chr8_1:3397192-3397211 Msa1173190:three_prime_UTR 35.0%
AAATACAAAATTAGGACGGG+AGG + chr8_1:3397266-3397285 None:intergenic 35.0%
AAATGAGAATTGTGAAGGAG+TGG - chr8_1:3397584-3397603 Msa1173190:three_prime_UTR 35.0%
! TTCAAATCAGAGAAGCGTAT+GGG + chr8_1:3397905-3397924 None:intergenic 35.0%
! ATTCAAATCAGAGAAGCGTA+TGG + chr8_1:3397906-3397925 None:intergenic 35.0%
TGAACTCACTATGTCAAAAC+TGG - chr8_1:3397192-3397211 Msa1173190:three_prime_UTR 35.0%
AAATACAAAATTAGGACGGG+AGG + chr8_1:3397266-3397285 None:intergenic 35.0%
AAATGAGAATTGTGAAGGAG+TGG - chr8_1:3397584-3397603 Msa1173190:three_prime_UTR 35.0%
! TTCAAATCAGAGAAGCGTAT+GGG + chr8_1:3397905-3397924 None:intergenic 35.0%
! ATTCAAATCAGAGAAGCGTA+TGG + chr8_1:3397906-3397925 None:intergenic 35.0%
CAAGCTTAATAGAAGGGCTA+AGG + chr8_1:3397230-3397249 None:intergenic 40.0%
TGAAAGCTTTCTTCACCCTT+AGG + chr8_1:3397874-3397893 None:intergenic 40.0%
! TCAAATCAGAGAAGCGTATG+GGG + chr8_1:3397904-3397923 None:intergenic 40.0%
!! TGGCTTTAATCTCAAGTACG+AGG - chr8_1:3397966-3397985 Msa1173190:intron 40.0%
! CTTTGTTCGAGTTCTGTTGT+TGG - chr8_1:3398145-3398164 Msa1173190:CDS 40.0%
CAAGCTTAATAGAAGGGCTA+AGG + chr8_1:3397230-3397249 None:intergenic 40.0%
TGAAAGCTTTCTTCACCCTT+AGG + chr8_1:3397874-3397893 None:intergenic 40.0%
! TCAAATCAGAGAAGCGTATG+GGG + chr8_1:3397904-3397923 None:intergenic 40.0%
!! TGGCTTTAATCTCAAGTACG+AGG - chr8_1:3397966-3397985 Msa1173190:intron 40.0%
! CTTTGTTCGAGTTCTGTTGT+TGG - chr8_1:3398145-3398164 Msa1173190:CDS 40.0%
TAGAAGGGCTAAGGTGAAGA+GGG + chr8_1:3397221-3397240 None:intergenic 45.0%
ATAGAAGGGCTAAGGTGAAG+AGG + chr8_1:3397222-3397241 None:intergenic 45.0%
GAGAATTGTGAAGGAGTGGA+AGG - chr8_1:3397588-3397607 Msa1173190:three_prime_UTR 45.0%
! TGTTCGAGTTCTGTTGTTGG+TGG - chr8_1:3398148-3398167 Msa1173190:CDS 45.0%
! TGTTGGTGGAAAGACCTTGT+CGG - chr8_1:3398162-3398181 Msa1173190:CDS 45.0%
!! GATCCTTTTTCTAGCCATGC+AGG - chr8_1:3398243-3398262 Msa1173190:exon 45.0%
TCACCTGCATGGCTAGAAAA+AGG + chr8_1:3398249-3398268 None:intergenic 45.0%
!! TTTTTCTAGCCATGCAGGTG+AGG - chr8_1:3398248-3398267 Msa1173190:exon 45.0%
!! TTTTCTAGCCATGCAGGTGA+GGG - chr8_1:3398249-3398268 Msa1173190:exon 45.0%
TATATATCCCCTCACCTGCA+TGG + chr8_1:3398260-3398279 None:intergenic 45.0%
TAGAAGGGCTAAGGTGAAGA+GGG + chr8_1:3397221-3397240 None:intergenic 45.0%
ATAGAAGGGCTAAGGTGAAG+AGG + chr8_1:3397222-3397241 None:intergenic 45.0%
GAGAATTGTGAAGGAGTGGA+AGG - chr8_1:3397588-3397607 Msa1173190:three_prime_UTR 45.0%
! TGTTCGAGTTCTGTTGTTGG+TGG - chr8_1:3398148-3398167 Msa1173190:CDS 45.0%
! TGTTGGTGGAAAGACCTTGT+CGG - chr8_1:3398162-3398181 Msa1173190:CDS 45.0%
!! GATCCTTTTTCTAGCCATGC+AGG - chr8_1:3398243-3398262 Msa1173190:exon 45.0%
TCACCTGCATGGCTAGAAAA+AGG + chr8_1:3398249-3398268 None:intergenic 45.0%
!! TTTTTCTAGCCATGCAGGTG+AGG - chr8_1:3398248-3398267 Msa1173190:exon 45.0%
!! TTTTCTAGCCATGCAGGTGA+GGG - chr8_1:3398249-3398268 Msa1173190:exon 45.0%
TATATATCCCCTCACCTGCA+TGG + chr8_1:3398260-3398279 None:intergenic 45.0%
!! AATAAAATATTTAATTAACA+TGG + chr8_1:3397443-3397462 None:intergenic 5.0%
!! AATAAAATATTTAATTAACA+TGG + chr8_1:3397443-3397462 None:intergenic 5.0%
AAAATTAGGACGGGAGGCAG+AGG + chr8_1:3397260-3397279 None:intergenic 50.0%
AGGTGTCTCTTCGCTACATG+AGG - chr8_1:3397288-3397307 Msa1173190:three_prime_UTR 50.0%
! AATCAGAGAAGCGTATGGGG+TGG + chr8_1:3397901-3397920 None:intergenic 50.0%
! TTTCTAGCCATGCAGGTGAG+GGG - chr8_1:3398250-3398269 Msa1173190:exon 50.0%
AAAATTAGGACGGGAGGCAG+AGG + chr8_1:3397260-3397279 None:intergenic 50.0%
AGGTGTCTCTTCGCTACATG+AGG - chr8_1:3397288-3397307 Msa1173190:three_prime_UTR 50.0%
! AATCAGAGAAGCGTATGGGG+TGG + chr8_1:3397901-3397920 None:intergenic 50.0%
! TTTCTAGCCATGCAGGTGAG+GGG - chr8_1:3398250-3398269 Msa1173190:exon 50.0%
Chromosome Type Strat End Strand Name
chr8_1 gene 3397159 3398294 3397159 ID=Msa1173190;Name=Msa1173190
chr8_1 mRNA 3397159 3398294 3397159 ID=Msa1173190-mRNA-1;Parent=Msa1173190;Name=Msa1173190-mRNA-1;_AED=0.02;_eAED=0.02;_QI=43|1|1|1|1|1|2|605|84
chr8_1 exon 3397159 3397910 3397159 ID=Msa1173190-mRNA-1:exon:1251;Parent=Msa1173190-mRNA-1
chr8_1 exon 3398144 3398294 3398144 ID=Msa1173190-mRNA-1:exon:1250;Parent=Msa1173190-mRNA-1
chr8_1 five_prime_UTR 3398252 3398294 3398252 ID=Msa1173190-mRNA-1:five_prime_utr;Parent=Msa1173190-mRNA-1
chr8_1 CDS 3398144 3398251 3398144 ID=Msa1173190-mRNA-1:cds;Parent=Msa1173190-mRNA-1
chr8_1 CDS 3397764 3397910 3397764 ID=Msa1173190-mRNA-1:cds;Parent=Msa1173190-mRNA-1
chr8_1 three_prime_UTR 3397159 3397763 3397159 ID=Msa1173190-mRNA-1:three_prime_utr;Parent=Msa1173190-mRNA-1
Gene Sequence

>Msa1173190

ATGTCAAAACTGGTCACCCTCTTCACCTTAGCCCTTCTATTAAGCTTGAGTTTAACCTCTGCCTCCCGTCCTAATTTTGTATTTACAGGTGTCTCTTCGCTACATGAGGATATTGTTTCTAGCAAGGCACCAAGTACTGTAGACTTAGAAAATGAGAATTGTGAAGGAGTGGAAGGAGAACAAGAATGTTTGACAAGAAGGACTCTAGCTGCACATCTCGATTATATCTACACTCAGCATAAACCCAAAAATTAA
Protein sequence

>Msa1173190

MSKLVTLFTLALLLSLSLTSASRPNFVFTGVSSLHEDIVSSKAPSTVDLENENCEGVEGEQECLTRRTLAAHLDYIYTQHKPKN*