AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0427260


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0427260 MtrunA17_Chr3g0129721 51.786 112 5 1 1 63 179 290 3.86e-28 101
Msa0427260 MtrunA17_Chr4g0008561 62.162 37 14 0 4 40 176 212 3.25e-14 64.7
Msa0427260 MtrunA17_Chr8g0345801 55.000 40 18 0 1 40 169 208 3.99e-13 61.2
Msa0427260 MtrunA17_Chr3g0129701 79.310 29 6 0 13 41 14 42 1.32e-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
Msa0427260 AT1G49180.2 78.049 41 9 0 1 41 161 201 2.01e-18 77.0
Msa0427260 AT1G49180.1 78.049 41 9 0 1 41 161 201 2.25e-18 77.0
Msa0427260 AT2G37840.2 67.568 37 12 0 4 40 32 68 4.83e-15 67.8
Msa0427260 AT3G53930.1 67.568 37 12 0 4 40 177 213 4.85e-15 67.8
Msa0427260 AT3G53930.2 67.568 37 12 0 4 40 177 213 4.85e-15 67.8
Msa0427260 AT2G37840.1 67.568 37 12 0 4 40 169 205 4.85e-15 67.8
Msa0427260 AT3G61960.1 62.162 37 14 0 4 40 167 203 6.01e-13 61.6
Msa0427260 AT3G61960.2 62.162 37 14 0 4 40 167 203 7.02e-13 61.6

Find 24 sgRNAs with CRISPR-Local

Find 125 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGCAATCTCTTGTGAATATT+TGG 0.173679 3_2:+77949830 Msa0427260:three_prime_UTR
TGATTGTCATCTGTCTATCT+AGG 0.319762 3_2:+77949918 Msa0427260:three_prime_UTR
ATACCTTGTAATCATATCTA+TGG 0.338928 3_2:-77948979 None:intergenic
CTATGGAACTGAAGAACTTC+AGG 0.352912 3_2:-77948962 None:intergenic
AGGCAGACATGTGGAGTGTC+GGG 0.369853 3_2:+77949387 Msa0427260:intron
AATAAAATTCATCAAAAGAT+AGG 0.377362 3_2:-77949768 None:intergenic
ACTTCAGGAGCCATGTATAA+TGG 0.386269 3_2:-77948947 None:intergenic
ATTACTTGCTGATGACTAGT+TGG 0.451334 3_2:+77949945 Msa0427260:three_prime_UTR
TTTCTAAGAGGAAAATCGTT+GGG 0.473698 3_2:+77949799 Msa0427260:CDS
GATTGTCATCTGTCTATCTA+GGG 0.489765 3_2:+77949919 Msa0427260:three_prime_UTR
CTTGTGAATATTTGGCATTG+AGG 0.500553 3_2:+77949838 Msa0427260:three_prime_UTR
TATTTGCATAGCTTTCTAAG+AGG 0.508660 3_2:+77949787 Msa0427260:CDS
CAAGTTTAGTAGAAAGCGAT+GGG 0.510504 3_2:-77949866 None:intergenic
TTGTGGAACTCCATTATACA+TGG 0.534880 3_2:+77948937 Msa0427260:CDS
TTCACAAGAGATTGCTGTCA+AGG 0.537305 3_2:-77949823 None:intergenic
GAGTATGTTGAGACAGTTTG+TGG 0.537353 3_2:+77948920 Msa0427260:CDS
CAGGCAGACATGTGGAGTGT+CGG 0.545020 3_2:+77949386 Msa0427260:intron
CTTTCTAAGAGGAAAATCGT+TGG 0.572401 3_2:+77949798 Msa0427260:CDS
TCAAGTTTAGTAGAAAGCGA+TGG 0.574833 3_2:-77949867 None:intergenic
GTTCCATAGATATGATTACA+AGG 0.589657 3_2:+77948976 Msa0427260:CDS
GGCAGACATGTGGAGTGTCG+GGG 0.608325 3_2:+77949388 Msa0427260:intron
AATAATCACAGGCAGACATG+TGG 0.648818 3_2:+77949378 Msa0427260:intron
ATTGTCATCTGTCTATCTAG+GGG 0.650373 3_2:+77949920 Msa0427260:three_prime_UTR
AAGTTTAGTAGAAAGCGATG+GGG 0.745162 3_2:-77949865 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATAAAATTCATCAAAAGAT+AGG - chr3_2:77949771-77949790 None:intergenic 15.0%
!! AATAAAATTCATCAAAAGAT+AGG - chr3_2:77949771-77949790 None:intergenic 15.0%
!! TAATATTCAATAAGTTCAAG+TGG + chr3_2:77949034-77949053 Msa0427260:intron 20.0%
!! TTATATACTATGTTGTGATA+TGG + chr3_2:77949089-77949108 Msa0427260:intron 20.0%
!! AAACAAGCAAGTAAAATTAA+AGG + chr3_2:77949118-77949137 Msa0427260:intron 20.0%
!!! TGAAAGTGTTAATGAATTTT+TGG - chr3_2:77949322-77949341 None:intergenic 20.0%
!! ACTTTCAACATTAATTAACT+TGG + chr3_2:77949335-77949354 Msa0427260:intron 20.0%
!!! ATTTACTTGATAATAATCAC+AGG + chr3_2:77949367-77949386 Msa0427260:intron 20.0%
!! ATATTAAAAATGCTGATGTT+TGG + chr3_2:77949527-77949546 Msa0427260:intron 20.0%
!! TAATATTCAATAAGTTCAAG+TGG + chr3_2:77949034-77949053 Msa0427260:intron 20.0%
!! TTATATACTATGTTGTGATA+TGG + chr3_2:77949089-77949108 Msa0427260:intron 20.0%
!! AAACAAGCAAGTAAAATTAA+AGG + chr3_2:77949118-77949137 Msa0427260:intron 20.0%
!!! TGAAAGTGTTAATGAATTTT+TGG - chr3_2:77949322-77949341 None:intergenic 20.0%
!! ACTTTCAACATTAATTAACT+TGG + chr3_2:77949335-77949354 Msa0427260:intron 20.0%
!!! ATTTACTTGATAATAATCAC+AGG + chr3_2:77949367-77949386 Msa0427260:intron 20.0%
!! ATATTAAAAATGCTGATGTT+TGG + chr3_2:77949527-77949546 Msa0427260:intron 20.0%
! ATACCTTGTAATCATATCTA+TGG - chr3_2:77948982-77949001 None:intergenic 25.0%
! AAATACAACAGAAATCAAGA+AGG - chr3_2:77949012-77949031 None:intergenic 25.0%
!! AAATCTGGAATAGAAACAAA+CGG - chr3_2:77949278-77949297 None:intergenic 25.0%
! TTAATATCAACAGTAATCGT+AGG - chr3_2:77949514-77949533 None:intergenic 25.0%
! ATACCTTGTAATCATATCTA+TGG - chr3_2:77948982-77949001 None:intergenic 25.0%
! AAATACAACAGAAATCAAGA+AGG - chr3_2:77949012-77949031 None:intergenic 25.0%
!! AAATCTGGAATAGAAACAAA+CGG - chr3_2:77949278-77949297 None:intergenic 25.0%
! TTAATATCAACAGTAATCGT+AGG - chr3_2:77949514-77949533 None:intergenic 25.0%
GTTCCATAGATATGATTACA+AGG + chr3_2:77948976-77948995 Msa0427260:CDS 30.0%
ATTTAGAAGCTCAAAAAGCA+TGG - chr3_2:77949414-77949433 None:intergenic 30.0%
!! ATGCTTTTTGAGCTTCTAAA+TGG + chr3_2:77949413-77949432 Msa0427260:CDS 30.0%
! AATGGTTATCCACCTTTTAA+TGG + chr3_2:77949431-77949450 Msa0427260:intron 30.0%
TAAAGAATCGGTTGAGAAAA+TGG - chr3_2:77949585-77949604 None:intergenic 30.0%
!! TTTTCTCAACCGATTCTTTA+TGG + chr3_2:77949585-77949604 Msa0427260:intron 30.0%
TCTTGAACAAATATCAAGAC+AGG - chr3_2:77949622-77949641 None:intergenic 30.0%
! TTTTTGCACTCAATTACTTG+TGG + chr3_2:77949692-77949711 Msa0427260:intron 30.0%
TATTTGCATAGCTTTCTAAG+AGG + chr3_2:77949787-77949806 Msa0427260:CDS 30.0%
! TTTCTAAGAGGAAAATCGTT+GGG + chr3_2:77949799-77949818 Msa0427260:CDS 30.0%
AGCAATCTCTTGTGAATATT+TGG + chr3_2:77949830-77949849 Msa0427260:three_prime_UTR 30.0%
GTTCCATAGATATGATTACA+AGG + chr3_2:77948976-77948995 Msa0427260:CDS 30.0%
ATTTAGAAGCTCAAAAAGCA+TGG - chr3_2:77949414-77949433 None:intergenic 30.0%
!! ATGCTTTTTGAGCTTCTAAA+TGG + chr3_2:77949413-77949432 Msa0427260:CDS 30.0%
! AATGGTTATCCACCTTTTAA+TGG + chr3_2:77949431-77949450 Msa0427260:intron 30.0%
TAAAGAATCGGTTGAGAAAA+TGG - chr3_2:77949585-77949604 None:intergenic 30.0%
!! TTTTCTCAACCGATTCTTTA+TGG + chr3_2:77949585-77949604 Msa0427260:intron 30.0%
TCTTGAACAAATATCAAGAC+AGG - chr3_2:77949622-77949641 None:intergenic 30.0%
! TTTTTGCACTCAATTACTTG+TGG + chr3_2:77949692-77949711 Msa0427260:intron 30.0%
TATTTGCATAGCTTTCTAAG+AGG + chr3_2:77949787-77949806 Msa0427260:CDS 30.0%
! TTTCTAAGAGGAAAATCGTT+GGG + chr3_2:77949799-77949818 Msa0427260:CDS 30.0%
AGCAATCTCTTGTGAATATT+TGG + chr3_2:77949830-77949849 Msa0427260:three_prime_UTR 30.0%
TTGTGGAACTCCATTATACA+TGG + chr3_2:77948937-77948956 Msa0427260:CDS 35.0%
TTATTGTTGTGCACACGAAT+CGG - chr3_2:77949207-77949226 None:intergenic 35.0%
CCTAATATGACTACGAAATC+TGG - chr3_2:77949293-77949312 None:intergenic 35.0%
CCAGATTTCGTAGTCATATT+AGG + chr3_2:77949290-77949309 Msa0427260:intron 35.0%
TTGTTTCAGCCATTAAAAGG+TGG - chr3_2:77949443-77949462 None:intergenic 35.0%
! ACGTTGTTTCAGCCATTAAA+AGG - chr3_2:77949446-77949465 None:intergenic 35.0%
! TCAACCGATTCTTTATGGAT+TGG + chr3_2:77949590-77949609 Msa0427260:intron 35.0%
GAGTCCAATCCATAAAGAAT+CGG - chr3_2:77949597-77949616 None:intergenic 35.0%
! CTTTCTAAGAGGAAAATCGT+TGG + chr3_2:77949798-77949817 Msa0427260:CDS 35.0%
CTTGTGAATATTTGGCATTG+AGG + chr3_2:77949838-77949857 Msa0427260:three_prime_UTR 35.0%
AAGTTTAGTAGAAAGCGATG+GGG - chr3_2:77949868-77949887 None:intergenic 35.0%
CAAGTTTAGTAGAAAGCGAT+GGG - chr3_2:77949869-77949888 None:intergenic 35.0%
TCAAGTTTAGTAGAAAGCGA+TGG - chr3_2:77949870-77949889 None:intergenic 35.0%
TGATTGTCATCTGTCTATCT+AGG + chr3_2:77949918-77949937 Msa0427260:three_prime_UTR 35.0%
GATTGTCATCTGTCTATCTA+GGG + chr3_2:77949919-77949938 Msa0427260:three_prime_UTR 35.0%
ATTGTCATCTGTCTATCTAG+GGG + chr3_2:77949920-77949939 Msa0427260:three_prime_UTR 35.0%
! ATTACTTGCTGATGACTAGT+TGG + chr3_2:77949945-77949964 Msa0427260:three_prime_UTR 35.0%
TTGTGGAACTCCATTATACA+TGG + chr3_2:77948937-77948956 Msa0427260:CDS 35.0%
TTATTGTTGTGCACACGAAT+CGG - chr3_2:77949207-77949226 None:intergenic 35.0%
CCTAATATGACTACGAAATC+TGG - chr3_2:77949293-77949312 None:intergenic 35.0%
CCAGATTTCGTAGTCATATT+AGG + chr3_2:77949290-77949309 Msa0427260:intron 35.0%
TTGTTTCAGCCATTAAAAGG+TGG - chr3_2:77949443-77949462 None:intergenic 35.0%
! ACGTTGTTTCAGCCATTAAA+AGG - chr3_2:77949446-77949465 None:intergenic 35.0%
! TCAACCGATTCTTTATGGAT+TGG + chr3_2:77949590-77949609 Msa0427260:intron 35.0%
GAGTCCAATCCATAAAGAAT+CGG - chr3_2:77949597-77949616 None:intergenic 35.0%
! CTTTCTAAGAGGAAAATCGT+TGG + chr3_2:77949798-77949817 Msa0427260:CDS 35.0%
CTTGTGAATATTTGGCATTG+AGG + chr3_2:77949838-77949857 Msa0427260:three_prime_UTR 35.0%
AAGTTTAGTAGAAAGCGATG+GGG - chr3_2:77949868-77949887 None:intergenic 35.0%
CAAGTTTAGTAGAAAGCGAT+GGG - chr3_2:77949869-77949888 None:intergenic 35.0%
TCAAGTTTAGTAGAAAGCGA+TGG - chr3_2:77949870-77949889 None:intergenic 35.0%
TGATTGTCATCTGTCTATCT+AGG + chr3_2:77949918-77949937 Msa0427260:three_prime_UTR 35.0%
GATTGTCATCTGTCTATCTA+GGG + chr3_2:77949919-77949938 Msa0427260:three_prime_UTR 35.0%
ATTGTCATCTGTCTATCTAG+GGG + chr3_2:77949920-77949939 Msa0427260:three_prime_UTR 35.0%
! ATTACTTGCTGATGACTAGT+TGG + chr3_2:77949945-77949964 Msa0427260:three_prime_UTR 35.0%
GAGTATGTTGAGACAGTTTG+TGG + chr3_2:77948920-77948939 Msa0427260:CDS 40.0%
ACTTCAGGAGCCATGTATAA+TGG - chr3_2:77948950-77948969 None:intergenic 40.0%
CTATGGAACTGAAGAACTTC+AGG - chr3_2:77948965-77948984 None:intergenic 40.0%
AGTTCAAGTGGCACATAAGA+TGG + chr3_2:77949046-77949065 Msa0427260:intron 40.0%
ATCGCTTGCGCTAAAAGAAT+TGG + chr3_2:77949143-77949162 Msa0427260:intron 40.0%
TCGCTTGCGCTAAAAGAATT+GGG + chr3_2:77949144-77949163 Msa0427260:intron 40.0%
CACACGAATCGGAAAATCAA+AGG - chr3_2:77949196-77949215 None:intergenic 40.0%
!! TCATTTTTCTCATGTTCCCG+TGG + chr3_2:77949237-77949256 Msa0427260:intron 40.0%
! CATTTTTCTCATGTTCCCGT+GGG + chr3_2:77949238-77949257 Msa0427260:intron 40.0%
AATAATCACAGGCAGACATG+TGG + chr3_2:77949378-77949397 Msa0427260:intron 40.0%
TAATGGCTGAAACAACGTTC+AGG + chr3_2:77949448-77949467 Msa0427260:intron 40.0%
AGAAAATGGAAGACAGGTAC+GGG - chr3_2:77949571-77949590 None:intergenic 40.0%
GAGAAAATGGAAGACAGGTA+CGG - chr3_2:77949572-77949591 None:intergenic 40.0%
TTCACAAGAGATTGCTGTCA+AGG - chr3_2:77949826-77949845 None:intergenic 40.0%
ACTAGTTGGTTGTGAGTAGT+AGG + chr3_2:77949959-77949978 Msa0427260:three_prime_UTR 40.0%
GAGTATGTTGAGACAGTTTG+TGG + chr3_2:77948920-77948939 Msa0427260:CDS 40.0%
ACTTCAGGAGCCATGTATAA+TGG - chr3_2:77948950-77948969 None:intergenic 40.0%
CTATGGAACTGAAGAACTTC+AGG - chr3_2:77948965-77948984 None:intergenic 40.0%
AGTTCAAGTGGCACATAAGA+TGG + chr3_2:77949046-77949065 Msa0427260:intron 40.0%
ATCGCTTGCGCTAAAAGAAT+TGG + chr3_2:77949143-77949162 Msa0427260:intron 40.0%
TCGCTTGCGCTAAAAGAATT+GGG + chr3_2:77949144-77949163 Msa0427260:intron 40.0%
CACACGAATCGGAAAATCAA+AGG - chr3_2:77949196-77949215 None:intergenic 40.0%
!! TCATTTTTCTCATGTTCCCG+TGG + chr3_2:77949237-77949256 Msa0427260:intron 40.0%
! CATTTTTCTCATGTTCCCGT+GGG + chr3_2:77949238-77949257 Msa0427260:intron 40.0%
AATAATCACAGGCAGACATG+TGG + chr3_2:77949378-77949397 Msa0427260:intron 40.0%
TAATGGCTGAAACAACGTTC+AGG + chr3_2:77949448-77949467 Msa0427260:intron 40.0%
AGAAAATGGAAGACAGGTAC+GGG - chr3_2:77949571-77949590 None:intergenic 40.0%
GAGAAAATGGAAGACAGGTA+CGG - chr3_2:77949572-77949591 None:intergenic 40.0%
TTCACAAGAGATTGCTGTCA+AGG - chr3_2:77949826-77949845 None:intergenic 40.0%
CGGTTGAGAAAATGGAAGAC+AGG - chr3_2:77949577-77949596 None:intergenic 45.0%
GTATTTGCACCTTGTTGCAG+TGG + chr3_2:77949741-77949760 Msa0427260:intron 45.0%
CGGTTGAGAAAATGGAAGAC+AGG - chr3_2:77949577-77949596 None:intergenic 45.0%
GTATTTGCACCTTGTTGCAG+TGG + chr3_2:77949741-77949760 Msa0427260:intron 45.0%
! GTAACAAGTCTGAGACCCAC+GGG - chr3_2:77949256-77949275 None:intergenic 50.0%
! GGTAACAAGTCTGAGACCCA+CGG - chr3_2:77949257-77949276 None:intergenic 50.0%
! GTAACAAGTCTGAGACCCAC+GGG - chr3_2:77949256-77949275 None:intergenic 50.0%
! GGTAACAAGTCTGAGACCCA+CGG - chr3_2:77949257-77949276 None:intergenic 50.0%
CAGGCAGACATGTGGAGTGT+CGG + chr3_2:77949386-77949405 Msa0427260:intron 55.0%
! AGGCAGACATGTGGAGTGTC+GGG + chr3_2:77949387-77949406 Msa0427260:intron 55.0%
ATAGGCGCACCACTGCAACA+AGG - chr3_2:77949753-77949772 None:intergenic 55.0%
CAGGCAGACATGTGGAGTGT+CGG + chr3_2:77949386-77949405 Msa0427260:intron 55.0%
! AGGCAGACATGTGGAGTGTC+GGG + chr3_2:77949387-77949406 Msa0427260:intron 55.0%
ATAGGCGCACCACTGCAACA+AGG - chr3_2:77949753-77949772 None:intergenic 55.0%
!! GGCAGACATGTGGAGTGTCG+GGG + chr3_2:77949388-77949407 Msa0427260:intron 60.0%
!! GGCAGACATGTGGAGTGTCG+GGG + chr3_2:77949388-77949407 Msa0427260:intron 60.0%
Chromosome Type Strat End Strand Name
chr3_2 gene 77948920 77949980 77948920 ID=Msa0427260;Name=Msa0427260
chr3_2 mRNA 77948920 77949980 77948920 ID=Msa0427260-mRNA-1;Parent=Msa0427260;Name=Msa0427260-mRNA-1;_AED=0.44;_eAED=0.44;_QI=0|0|0.33|1|0|0|3|152|63
chr3_2 exon 77948920 77948997 77948920 ID=Msa0427260-mRNA-1:exon:20423;Parent=Msa0427260-mRNA-1
chr3_2 exon 77949389 77949434 77949389 ID=Msa0427260-mRNA-1:exon:20424;Parent=Msa0427260-mRNA-1
chr3_2 exon 77949761 77949980 77949761 ID=Msa0427260-mRNA-1:exon:20425;Parent=Msa0427260-mRNA-1
chr3_2 CDS 77948920 77948997 77948920 ID=Msa0427260-mRNA-1:cds;Parent=Msa0427260-mRNA-1
chr3_2 CDS 77949389 77949434 77949389 ID=Msa0427260-mRNA-1:cds;Parent=Msa0427260-mRNA-1
chr3_2 CDS 77949761 77949828 77949761 ID=Msa0427260-mRNA-1:cds;Parent=Msa0427260-mRNA-1
chr3_2 three_prime_UTR 77949829 77949980 77949829 ID=Msa0427260-mRNA-1:three_prime_utr;Parent=Msa0427260-mRNA-1
Gene Sequence

>Msa0427260

GAGTATGTTGAGACAGTTTGTGGAACTCCATTATACATGGCTCCTGAAGTTCTTCAGTTCCATAGATATGATTACAAGGCAGACATGTGGAGTGTCGGGGCCATGCTTTTTGAGCTTCTAAATGTGGTGCGCCTATCTTTTGATGAATTTTATTTGCATAGCTTTCTAAGAGGAAAATCGTTGGGACCTTGA

Protein sequence

>Msa0427260

EYVETVCGTPLYMAPEVLQFHRYDYKADMWSVGAMLFELLNVVRLSFDEFYLHSFLRGKSLGP*