AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0638070


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 19 sgRNAs with CRISPR-Local

Find 67 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTGAAAATGTTGAAGTTATT+TGG 0.242554 4_3:+31738605 Msa0638070:three_prime_UTR
TTTAATTATCATGTGCCTTT+TGG 0.284727 4_3:+31738538 Msa0638070:CDS
AGCTGTGCATAGAGTTGTTT+TGG 0.308338 4_3:-31738086 None:intergenic
TCTGAACTATTGTTGTTTGT+TGG 0.354497 4_3:-31738376 None:intergenic
TGGAAATTGCGACACTTAGA+AGG 0.368870 4_3:+31738429 Msa0638070:CDS
AACTCTATGCACAGCTCGGC+TGG 0.390243 4_3:+31738093 Msa0638070:five_prime_UTR
GTCAAATCATCATAAATTGC+AGG 0.439062 4_3:+31738716 Msa0638070:three_prime_UTR
TTGTTGTTTGTTGGATCTGT+TGG 0.448449 4_3:-31738367 None:intergenic
AGTGTTTATGTCTATTGTAA+TGG 0.459087 4_3:+31738641 Msa0638070:three_prime_UTR
CTTTCACACCAGAGACAATC+AGG 0.460722 4_3:-31738135 None:intergenic
TGCGACACTTAGAAGGACTA+TGG 0.475465 4_3:+31738436 Msa0638070:CDS
AATTCGCACCTGATTGTCTC+TGG 0.481903 4_3:+31738127 Msa0638070:five_prime_UTR
ACATAAACACTTAATCTAAG+AGG 0.513212 4_3:-31738629 None:intergenic
AGAATGTGTCGAGAAGGAAA+TGG 0.537490 4_3:+31738409 Msa0638070:exon
ATGTAGAGAATGTGTCGAGA+AGG 0.597119 4_3:+31738403 Msa0638070:five_prime_UTR
AAACAACTCTATGCACAGCT+CGG 0.625777 4_3:+31738089 Msa0638070:five_prime_UTR
TTACAAAGATGTCCAAACAA+AGG 0.638557 4_3:+31738173 Msa0638070:five_prime_UTR
TTAAGTTCGAGCAACTGCTG+CGG 0.651567 4_3:-31738059 None:intergenic
TAGGCTCGTAGAATTGATTG+TGG 0.686326 4_3:+31738311 Msa0638070:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTTTCAATTTTGATTTTA+GGG - chr4_3:31738017-31738036 None:intergenic 10.0%
!!! ATTTTTTCAATTTTGATTTT+AGG - chr4_3:31738018-31738037 None:intergenic 10.0%
!! AAAATCAAAATTGAAAAAAT+TGG + chr4_3:31738018-31738037 Msa0638070:five_prime_UTR 10.0%
!!! TTTTTTCAATTTTGATTTTA+GGG - chr4_3:31738017-31738036 None:intergenic 10.0%
!!! ATTTTTTCAATTTTGATTTT+AGG - chr4_3:31738018-31738037 None:intergenic 10.0%
!! AAAATCAAAATTGAAAAAAT+TGG + chr4_3:31738018-31738037 Msa0638070:five_prime_UTR 10.0%
!! AAACAAAGGAAAAAAATTAT+GGG + chr4_3:31738187-31738206 Msa0638070:five_prime_UTR 15.0%
!!! AATTTTTTTATTGTTTGTGT+AGG + chr4_3:31738292-31738311 Msa0638070:intron 15.0%
!! AAACAAAGGAAAAAAATTAT+GGG + chr4_3:31738187-31738206 Msa0638070:five_prime_UTR 15.0%
!!! AATTTTTTTATTGTTTGTGT+AGG + chr4_3:31738292-31738311 Msa0638070:intron 15.0%
!!! CATAATTTTTTTCCTTTGTT+TGG - chr4_3:31738188-31738207 None:intergenic 20.0%
!! CAAACAAAGGAAAAAAATTA+TGG + chr4_3:31738186-31738205 Msa0638070:five_prime_UTR 20.0%
!!! CATAATTTTTTTCCTTTGTT+TGG - chr4_3:31738188-31738207 None:intergenic 20.0%
!! CAAACAAAGGAAAAAAATTA+TGG + chr4_3:31738186-31738205 Msa0638070:five_prime_UTR 20.0%
!!! ATTTTAGGGTTTTTGATTTG+GGG - chr4_3:31738003-31738022 None:intergenic 25.0%
!!! GATTTTAGGGTTTTTGATTT+GGG - chr4_3:31738004-31738023 None:intergenic 25.0%
!!! TGATTTTAGGGTTTTTGATT+TGG - chr4_3:31738005-31738024 None:intergenic 25.0%
!! TTTAATTATCATGTGCCTTT+TGG + chr4_3:31738538-31738557 Msa0638070:CDS 25.0%
! GTGAAAATGTTGAAGTTATT+TGG + chr4_3:31738605-31738624 Msa0638070:three_prime_UTR 25.0%
! ACATAAACACTTAATCTAAG+AGG - chr4_3:31738632-31738651 None:intergenic 25.0%
! AGTGTTTATGTCTATTGTAA+TGG + chr4_3:31738641-31738660 Msa0638070:three_prime_UTR 25.0%
!!! ATTTTAGGGTTTTTGATTTG+GGG - chr4_3:31738003-31738022 None:intergenic 25.0%
!!! GATTTTAGGGTTTTTGATTT+GGG - chr4_3:31738004-31738023 None:intergenic 25.0%
!!! TGATTTTAGGGTTTTTGATT+TGG - chr4_3:31738005-31738024 None:intergenic 25.0%
!! TTTAATTATCATGTGCCTTT+TGG + chr4_3:31738538-31738557 Msa0638070:CDS 25.0%
! GTGAAAATGTTGAAGTTATT+TGG + chr4_3:31738605-31738624 Msa0638070:three_prime_UTR 25.0%
! ACATAAACACTTAATCTAAG+AGG - chr4_3:31738632-31738651 None:intergenic 25.0%
! AGTGTTTATGTCTATTGTAA+TGG + chr4_3:31738641-31738660 Msa0638070:three_prime_UTR 25.0%
!!! TTTTAGGGTTTTTGATTTGG+GGG - chr4_3:31738002-31738021 None:intergenic 30.0%
TTACAAAGATGTCCAAACAA+AGG + chr4_3:31738173-31738192 Msa0638070:five_prime_UTR 30.0%
!! ATGGGATTTTAGAAACTTTG+TGG + chr4_3:31738205-31738224 Msa0638070:five_prime_UTR 30.0%
!! TCTGAACTATTGTTGTTTGT+TGG - chr4_3:31738379-31738398 None:intergenic 30.0%
! ACATCAACATTTTCACCAAA+AGG - chr4_3:31738556-31738575 None:intergenic 30.0%
GTCAAATCATCATAAATTGC+AGG + chr4_3:31738716-31738735 Msa0638070:three_prime_UTR 30.0%
!!! TTTTAGGGTTTTTGATTTGG+GGG - chr4_3:31738002-31738021 None:intergenic 30.0%
TTACAAAGATGTCCAAACAA+AGG + chr4_3:31738173-31738192 Msa0638070:five_prime_UTR 30.0%
!! ATGGGATTTTAGAAACTTTG+TGG + chr4_3:31738205-31738224 Msa0638070:five_prime_UTR 30.0%
!! TCTGAACTATTGTTGTTTGT+TGG - chr4_3:31738379-31738398 None:intergenic 30.0%
! ACATCAACATTTTCACCAAA+AGG - chr4_3:31738556-31738575 None:intergenic 30.0%
GTCAAATCATCATAAATTGC+AGG + chr4_3:31738716-31738735 Msa0638070:three_prime_UTR 30.0%
!! TTGTTGTTTGTTGGATCTGT+TGG - chr4_3:31738370-31738389 None:intergenic 35.0%
!! TTGTTGTTTGTTGGATCTGT+TGG - chr4_3:31738370-31738389 None:intergenic 35.0%
! AGCTGTGCATAGAGTTGTTT+TGG - chr4_3:31738089-31738108 None:intergenic 40.0%
AAACAACTCTATGCACAGCT+CGG + chr4_3:31738089-31738108 Msa0638070:five_prime_UTR 40.0%
TAGGCTCGTAGAATTGATTG+TGG + chr4_3:31738311-31738330 Msa0638070:intron 40.0%
ATGTAGAGAATGTGTCGAGA+AGG + chr4_3:31738403-31738422 Msa0638070:five_prime_UTR 40.0%
AGAATGTGTCGAGAAGGAAA+TGG + chr4_3:31738409-31738428 Msa0638070:exon 40.0%
TGGAAATTGCGACACTTAGA+AGG + chr4_3:31738429-31738448 Msa0638070:CDS 40.0%
TCATAAATTGCAGGATGAGC+TGG + chr4_3:31738725-31738744 Msa0638070:three_prime_UTR 40.0%
! AGCTGTGCATAGAGTTGTTT+TGG - chr4_3:31738089-31738108 None:intergenic 40.0%
AAACAACTCTATGCACAGCT+CGG + chr4_3:31738089-31738108 Msa0638070:five_prime_UTR 40.0%
TAGGCTCGTAGAATTGATTG+TGG + chr4_3:31738311-31738330 Msa0638070:intron 40.0%
ATGTAGAGAATGTGTCGAGA+AGG + chr4_3:31738403-31738422 Msa0638070:five_prime_UTR 40.0%
AGAATGTGTCGAGAAGGAAA+TGG + chr4_3:31738409-31738428 Msa0638070:exon 40.0%
TGGAAATTGCGACACTTAGA+AGG + chr4_3:31738429-31738448 Msa0638070:CDS 40.0%
TTAAGTTCGAGCAACTGCTG+CGG - chr4_3:31738062-31738081 None:intergenic 45.0%
AATTCGCACCTGATTGTCTC+TGG + chr4_3:31738127-31738146 Msa0638070:five_prime_UTR 45.0%
CTTTCACACCAGAGACAATC+AGG - chr4_3:31738138-31738157 None:intergenic 45.0%
!!! GTGGCTGCAGTTTTTTTGAC+TGG + chr4_3:31738330-31738349 Msa0638070:five_prime_UTR 45.0%
TGCGACACTTAGAAGGACTA+TGG + chr4_3:31738436-31738455 Msa0638070:CDS 45.0%
TTAAGTTCGAGCAACTGCTG+CGG - chr4_3:31738062-31738081 None:intergenic 45.0%
AATTCGCACCTGATTGTCTC+TGG + chr4_3:31738127-31738146 Msa0638070:five_prime_UTR 45.0%
CTTTCACACCAGAGACAATC+AGG - chr4_3:31738138-31738157 None:intergenic 45.0%
!!! GTGGCTGCAGTTTTTTTGAC+TGG + chr4_3:31738330-31738349 Msa0638070:five_prime_UTR 45.0%
TGCGACACTTAGAAGGACTA+TGG + chr4_3:31738436-31738455 Msa0638070:CDS 45.0%
AACTCTATGCACAGCTCGGC+TGG + chr4_3:31738093-31738112 Msa0638070:five_prime_UTR 55.0%
AACTCTATGCACAGCTCGGC+TGG + chr4_3:31738093-31738112 Msa0638070:five_prime_UTR 55.0%
Chromosome Type Strat End Strand Name
chr4_3 gene 31737964 31738746 31737964 ID=Msa0638070;Name=Msa0638070
chr4_3 mRNA 31737964 31738746 31737964 ID=Msa0638070-mRNA-1;Parent=Msa0638070;Name=Msa0638070-mRNA-1;_AED=0.00;_eAED=0.00;_QI=377|1|1|1|0|0.5|2|169|49
chr4_3 exon 31737964 31738226 31737964 ID=Msa0638070-mRNA-1:exon:7445;Parent=Msa0638070-mRNA-1
chr4_3 exon 31738314 31738746 31738314 ID=Msa0638070-mRNA-1:exon:7446;Parent=Msa0638070-mRNA-1
chr4_3 five_prime_UTR 31737964 31738226 31737964 ID=Msa0638070-mRNA-1:five_prime_utr;Parent=Msa0638070-mRNA-1
chr4_3 five_prime_UTR 31738314 31738427 31738314 ID=Msa0638070-mRNA-1:five_prime_utr;Parent=Msa0638070-mRNA-1
chr4_3 CDS 31738428 31738577 31738428 ID=Msa0638070-mRNA-1:cds;Parent=Msa0638070-mRNA-1
chr4_3 three_prime_UTR 31738578 31738746 31738578 ID=Msa0638070-mRNA-1:three_prime_utr;Parent=Msa0638070-mRNA-1
Gene Sequence

>Msa0638070

ATGGAAATTGCGACACTTAGAAGGACTATGGTGAAGATGCATCGTGATGAGAAAGCTATGAAGAACATGAAGCTTGTTCTTGTTATTTGTTTAGTTTTAAGTGCAATTTGTTTAATTATCATGTGCCTTTTGGTGAAAATGTTGATGTAG

Protein sequence

>Msa0638070

MEIATLRRTMVKMHRDEKAMKNMKLVLVICLVLSAICLIIMCLLVKMLM*