AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0473770

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0473770 MtrunA17_Chr3g0129721 54.464 112 2 1 1 63 179 290 9.37e-31 108
Msa0473770 MtrunA17_Chr4g0008561 62.162 37 14 0 4 40 176 212 5.68e-14 64.3
Msa0473770 MtrunA17_Chr8g0345801 57.500 40 17 0 1 40 169 208 8.98e-14 63.2
Msa0473770 MtrunA17_Chr3g0129701 86.207 29 4 0 13 41 14 42 3.12e-13 58.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0473770 AT1G49180.2 80.488 41 8 0 1 41 161 201 4.89e-19 78.6
Msa0473770 AT1G49180.1 80.488 41 8 0 1 41 161 201 5.12e-19 78.6
Msa0473770 AT3G53930.1 67.568 37 12 0 4 40 177 213 8.62e-15 67.0
Msa0473770 AT3G53930.2 67.568 37 12 0 4 40 177 213 8.62e-15 67.0
Msa0473770 AT2G37840.1 67.568 37 12 0 4 40 169 205 1.17e-14 66.6
Msa0473770 AT2G37840.2 67.568 37 12 0 4 40 32 68 1.56e-14 66.2
Msa0473770 AT3G61960.1 62.162 37 14 0 4 40 167 203 1.49e-12 60.5
Msa0473770 AT3G61960.2 62.162 37 14 0 4 40 167 203 1.63e-12 60.5

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_3:+76499148 Msa0473770:three_prime_UTR
TGATTGTCATCTGTCTATCT+AGG 0.319762 3_3:+76499236 Msa0473770:three_prime_UTR
CTCTGGAACTGAAGAACTTC+AGG 0.337569 3_3:-76498281 None:intergenic
AATAAAATTCATCAAAAGAT+AGG 0.377362 3_3:-76499086 None:intergenic
AGGCAGACATGTGGAGTGTC+GGG 0.400314 3_3:+76498706 Msa0473770:intron
ATTACTTGCTGATGACTAGT+TGG 0.451334 3_3:+76499263 Msa0473770:three_prime_UTR
ATACCTTGTGATCATATCTC+TGG 0.462832 3_3:-76498298 None:intergenic
TTTCTAAGAGGAAAATCGTT+GGG 0.473698 3_3:+76499117 Msa0473770:CDS
GATTGTCATCTGTCTATCTA+GGG 0.489765 3_3:+76499237 Msa0473770:three_prime_UTR
CTTGTGAATATTTGGCATTG+AGG 0.500553 3_3:+76499156 Msa0473770:three_prime_UTR
TATTTGCATAGCTTTCTAAG+AGG 0.508660 3_3:+76499105 Msa0473770:CDS
CAAGTTTAGTAGAAAGCGAT+GGG 0.510504 3_3:-76499184 None:intergenic
TTGTGGAACTCCATCGTACA+TGG 0.531694 3_3:+76498256 Msa0473770:CDS
GAGTATGTTGAGACAGTTTG+TGG 0.534326 3_3:+76498239 Msa0473770:CDS
TTCACAAGAGATTGCTGTCA+AGG 0.537305 3_3:-76499141 None:intergenic
CAGGCAGACATGTGGAGTGT+CGG 0.549758 3_3:+76498705 Msa0473770:intron
CTTTCTAAGAGGAAAATCGT+TGG 0.572401 3_3:+76499116 Msa0473770:CDS
TCAAGTTTAGTAGAAAGCGA+TGG 0.574833 3_3:-76499185 None:intergenic
GGCAGACATGTGGAGTGTCG+GGG 0.613063 3_3:+76498707 Msa0473770:intron
AATAATTACAGGCAGACATG+TGG 0.624194 3_3:+76498697 Msa0473770:intron
ACTTCAGGAGCCATGTACGA+TGG 0.648921 3_3:-76498266 None:intergenic
ATTGTCATCTGTCTATCTAG+GGG 0.650373 3_3:+76499238 Msa0473770:three_prime_UTR
GTTCCAGAGATATGATCACA+AGG 0.686583 3_3:+76498295 Msa0473770:CDS
AAGTTTAGTAGAAAGCGATG+GGG 0.745162 3_3:-76499183 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTTACTTGATAATAATTAC+AGG + chr3_3:76498686-76498705 Msa0473770:intron 15.0%
!! AATAAAATTCATCAAAAGAT+AGG - chr3_3:76499089-76499108 None:intergenic 15.0%
!!! ATTTACTTGATAATAATTAC+AGG + chr3_3:76498686-76498705 Msa0473770:intron 15.0%
!! AATAAAATTCATCAAAAGAT+AGG - chr3_3:76499089-76499108 None:intergenic 15.0%
!! TAATATTCAATAAGTTCAAG+TGG + chr3_3:76498353-76498372 Msa0473770:intron 20.0%
!! TTATATACTATGTTGTGATA+TGG + chr3_3:76498408-76498427 Msa0473770:intron 20.0%
!! AAACAAGCAAGTAAAATTAA+AGG + chr3_3:76498437-76498456 Msa0473770:intron 20.0%
!!! TGAAAGTGTTAATGAATTTT+TGG - chr3_3:76498641-76498660 None:intergenic 20.0%
!! ACTTTCAACATTAATTAACT+TGG + chr3_3:76498654-76498673 Msa0473770:intron 20.0%
!! ATATTAAAAATGCTGATGTT+TGG + chr3_3:76498846-76498865 Msa0473770:intron 20.0%
!! TAATATTCAATAAGTTCAAG+TGG + chr3_3:76498353-76498372 Msa0473770:intron 20.0%
!! TTATATACTATGTTGTGATA+TGG + chr3_3:76498408-76498427 Msa0473770:intron 20.0%
!! AAACAAGCAAGTAAAATTAA+AGG + chr3_3:76498437-76498456 Msa0473770:intron 20.0%
!!! TGAAAGTGTTAATGAATTTT+TGG - chr3_3:76498641-76498660 None:intergenic 20.0%
!! ACTTTCAACATTAATTAACT+TGG + chr3_3:76498654-76498673 Msa0473770:intron 20.0%
!! ATATTAAAAATGCTGATGTT+TGG + chr3_3:76498846-76498865 Msa0473770:intron 20.0%
! AAATACAACAGAAATCAAGA+AGG - chr3_3:76498331-76498350 None:intergenic 25.0%
!! AAATCTGGAATAGAAACAAA+CGG - chr3_3:76498597-76498616 None:intergenic 25.0%
! TTAATATCAACAGTAATCGT+AGG - chr3_3:76498833-76498852 None:intergenic 25.0%
!!! TTTTTTCACTCAATTACTTG+TGG + chr3_3:76499010-76499029 Msa0473770:intron 25.0%
! AAATACAACAGAAATCAAGA+AGG - chr3_3:76498331-76498350 None:intergenic 25.0%
!! AAATCTGGAATAGAAACAAA+CGG - chr3_3:76498597-76498616 None:intergenic 25.0%
! TTAATATCAACAGTAATCGT+AGG - chr3_3:76498833-76498852 None:intergenic 25.0%
!!! TTTTTTCACTCAATTACTTG+TGG + chr3_3:76499010-76499029 Msa0473770:intron 25.0%
ATTTAGAAGCTCAAAAAGCA+TGG - chr3_3:76498733-76498752 None:intergenic 30.0%
!! ATGCTTTTTGAGCTTCTAAA+TGG + chr3_3:76498732-76498751 Msa0473770:CDS 30.0%
! AATGGTTATCCACCTTTTAA+TGG + chr3_3:76498750-76498769 Msa0473770:intron 30.0%
TAAAGAATCGGTTGAGAAAA+TGG - chr3_3:76498904-76498923 None:intergenic 30.0%
!! TTTTCTCAACCGATTCTTTA+TGG + chr3_3:76498904-76498923 Msa0473770:intron 30.0%
TCTTGAACAAATATCAAGAC+AGG - chr3_3:76498941-76498960 None:intergenic 30.0%
TATTTGCATAGCTTTCTAAG+AGG + chr3_3:76499105-76499124 Msa0473770:CDS 30.0%
! TTTCTAAGAGGAAAATCGTT+GGG + chr3_3:76499117-76499136 Msa0473770:CDS 30.0%
AGCAATCTCTTGTGAATATT+TGG + chr3_3:76499148-76499167 Msa0473770:three_prime_UTR 30.0%
ATTTAGAAGCTCAAAAAGCA+TGG - chr3_3:76498733-76498752 None:intergenic 30.0%
!! ATGCTTTTTGAGCTTCTAAA+TGG + chr3_3:76498732-76498751 Msa0473770:CDS 30.0%
! AATGGTTATCCACCTTTTAA+TGG + chr3_3:76498750-76498769 Msa0473770:intron 30.0%
TAAAGAATCGGTTGAGAAAA+TGG - chr3_3:76498904-76498923 None:intergenic 30.0%
!! TTTTCTCAACCGATTCTTTA+TGG + chr3_3:76498904-76498923 Msa0473770:intron 30.0%
TCTTGAACAAATATCAAGAC+AGG - chr3_3:76498941-76498960 None:intergenic 30.0%
TATTTGCATAGCTTTCTAAG+AGG + chr3_3:76499105-76499124 Msa0473770:CDS 30.0%
! TTTCTAAGAGGAAAATCGTT+GGG + chr3_3:76499117-76499136 Msa0473770:CDS 30.0%
AGCAATCTCTTGTGAATATT+TGG + chr3_3:76499148-76499167 Msa0473770:three_prime_UTR 30.0%
ATACCTTGTGATCATATCTC+TGG - chr3_3:76498301-76498320 None:intergenic 35.0%
TTATTGTTGTGCACACGAAT+CGG - chr3_3:76498526-76498545 None:intergenic 35.0%
CCTAATATGACTACGAAATC+TGG - chr3_3:76498612-76498631 None:intergenic 35.0%
CCAGATTTCGTAGTCATATT+AGG + chr3_3:76498609-76498628 Msa0473770:intron 35.0%
AATAATTACAGGCAGACATG+TGG + chr3_3:76498697-76498716 Msa0473770:intron 35.0%
TTGTTTCAGCCATTAAAAGG+TGG - chr3_3:76498762-76498781 None:intergenic 35.0%
! ACGTTGTTTCAGCCATTAAA+AGG - chr3_3:76498765-76498784 None:intergenic 35.0%
! TCAACCGATTCTTTATGGAT+TGG + chr3_3:76498909-76498928 Msa0473770:intron 35.0%
GAGTCCAATCCATAAAGAAT+CGG - chr3_3:76498916-76498935 None:intergenic 35.0%
! CTTTCTAAGAGGAAAATCGT+TGG + chr3_3:76499116-76499135 Msa0473770:CDS 35.0%
CTTGTGAATATTTGGCATTG+AGG + chr3_3:76499156-76499175 Msa0473770:three_prime_UTR 35.0%
AAGTTTAGTAGAAAGCGATG+GGG - chr3_3:76499186-76499205 None:intergenic 35.0%
CAAGTTTAGTAGAAAGCGAT+GGG - chr3_3:76499187-76499206 None:intergenic 35.0%
TCAAGTTTAGTAGAAAGCGA+TGG - chr3_3:76499188-76499207 None:intergenic 35.0%
TGATTGTCATCTGTCTATCT+AGG + chr3_3:76499236-76499255 Msa0473770:three_prime_UTR 35.0%
GATTGTCATCTGTCTATCTA+GGG + chr3_3:76499237-76499256 Msa0473770:three_prime_UTR 35.0%
ATTGTCATCTGTCTATCTAG+GGG + chr3_3:76499238-76499257 Msa0473770:three_prime_UTR 35.0%
! ATTACTTGCTGATGACTAGT+TGG + chr3_3:76499263-76499282 Msa0473770:three_prime_UTR 35.0%
ATACCTTGTGATCATATCTC+TGG - chr3_3:76498301-76498320 None:intergenic 35.0%
TTATTGTTGTGCACACGAAT+CGG - chr3_3:76498526-76498545 None:intergenic 35.0%
CCTAATATGACTACGAAATC+TGG - chr3_3:76498612-76498631 None:intergenic 35.0%
CCAGATTTCGTAGTCATATT+AGG + chr3_3:76498609-76498628 Msa0473770:intron 35.0%
AATAATTACAGGCAGACATG+TGG + chr3_3:76498697-76498716 Msa0473770:intron 35.0%
TTGTTTCAGCCATTAAAAGG+TGG - chr3_3:76498762-76498781 None:intergenic 35.0%
! ACGTTGTTTCAGCCATTAAA+AGG - chr3_3:76498765-76498784 None:intergenic 35.0%
! TCAACCGATTCTTTATGGAT+TGG + chr3_3:76498909-76498928 Msa0473770:intron 35.0%
GAGTCCAATCCATAAAGAAT+CGG - chr3_3:76498916-76498935 None:intergenic 35.0%
! CTTTCTAAGAGGAAAATCGT+TGG + chr3_3:76499116-76499135 Msa0473770:CDS 35.0%
CTTGTGAATATTTGGCATTG+AGG + chr3_3:76499156-76499175 Msa0473770:three_prime_UTR 35.0%
AAGTTTAGTAGAAAGCGATG+GGG - chr3_3:76499186-76499205 None:intergenic 35.0%
CAAGTTTAGTAGAAAGCGAT+GGG - chr3_3:76499187-76499206 None:intergenic 35.0%
TCAAGTTTAGTAGAAAGCGA+TGG - chr3_3:76499188-76499207 None:intergenic 35.0%
TGATTGTCATCTGTCTATCT+AGG + chr3_3:76499236-76499255 Msa0473770:three_prime_UTR 35.0%
GATTGTCATCTGTCTATCTA+GGG + chr3_3:76499237-76499256 Msa0473770:three_prime_UTR 35.0%
ATTGTCATCTGTCTATCTAG+GGG + chr3_3:76499238-76499257 Msa0473770:three_prime_UTR 35.0%
! ATTACTTGCTGATGACTAGT+TGG + chr3_3:76499263-76499282 Msa0473770:three_prime_UTR 35.0%
GAGTATGTTGAGACAGTTTG+TGG + chr3_3:76498239-76498258 Msa0473770:CDS 40.0%
GTTCCAGAGATATGATCACA+AGG + chr3_3:76498295-76498314 Msa0473770:CDS 40.0%
AGTTCAAGTGGCACATAAGA+TGG + chr3_3:76498365-76498384 Msa0473770:intron 40.0%
ATCGCTTGCGCTAAAAGAAT+TGG + chr3_3:76498462-76498481 Msa0473770:intron 40.0%
TCGCTTGCGCTAAAAGAATT+GGG + chr3_3:76498463-76498482 Msa0473770:intron 40.0%
TAATGGCTGAAACAACGTTC+AGG + chr3_3:76498767-76498786 Msa0473770:intron 40.0%
AGAAAATGGAAGACAGGTAC+GGG - chr3_3:76498890-76498909 None:intergenic 40.0%
GAGAAAATGGAAGACAGGTA+CGG - chr3_3:76498891-76498910 None:intergenic 40.0%
TTCACAAGAGATTGCTGTCA+AGG - chr3_3:76499144-76499163 None:intergenic 40.0%
ACTAGTTGGTTGTGAGTAGT+AGG + chr3_3:76499277-76499296 Msa0473770:three_prime_UTR 40.0%
GAGTATGTTGAGACAGTTTG+TGG + chr3_3:76498239-76498258 Msa0473770:CDS 40.0%
GTTCCAGAGATATGATCACA+AGG + chr3_3:76498295-76498314 Msa0473770:CDS 40.0%
AGTTCAAGTGGCACATAAGA+TGG + chr3_3:76498365-76498384 Msa0473770:intron 40.0%
ATCGCTTGCGCTAAAAGAAT+TGG + chr3_3:76498462-76498481 Msa0473770:intron 40.0%
TCGCTTGCGCTAAAAGAATT+GGG + chr3_3:76498463-76498482 Msa0473770:intron 40.0%
TAATGGCTGAAACAACGTTC+AGG + chr3_3:76498767-76498786 Msa0473770:intron 40.0%
AGAAAATGGAAGACAGGTAC+GGG - chr3_3:76498890-76498909 None:intergenic 40.0%
GAGAAAATGGAAGACAGGTA+CGG - chr3_3:76498891-76498910 None:intergenic 40.0%
TTCACAAGAGATTGCTGTCA+AGG - chr3_3:76499144-76499163 None:intergenic 40.0%
TTGTGGAACTCCATCGTACA+TGG + chr3_3:76498256-76498275 Msa0473770:CDS 45.0%
!! CTCTGGAACTGAAGAACTTC+AGG - chr3_3:76498284-76498303 None:intergenic 45.0%
CACACGAATCGGAAAATCAG+AGG - chr3_3:76498515-76498534 None:intergenic 45.0%
!! TCATTTTTCTCACGTTCCCG+TGG + chr3_3:76498556-76498575 Msa0473770:intron 45.0%
! CATTTTTCTCACGTTCCCGT+GGG + chr3_3:76498557-76498576 Msa0473770:intron 45.0%
CGGTTGAGAAAATGGAAGAC+AGG - chr3_3:76498896-76498915 None:intergenic 45.0%
GTATTTGCACCTTGTTGCAG+TGG + chr3_3:76499059-76499078 Msa0473770:intron 45.0%
TTGTGGAACTCCATCGTACA+TGG + chr3_3:76498256-76498275 Msa0473770:CDS 45.0%
!! CTCTGGAACTGAAGAACTTC+AGG - chr3_3:76498284-76498303 None:intergenic 45.0%
CACACGAATCGGAAAATCAG+AGG - chr3_3:76498515-76498534 None:intergenic 45.0%
!! TCATTTTTCTCACGTTCCCG+TGG + chr3_3:76498556-76498575 Msa0473770:intron 45.0%
! CATTTTTCTCACGTTCCCGT+GGG + chr3_3:76498557-76498576 Msa0473770:intron 45.0%
CGGTTGAGAAAATGGAAGAC+AGG - chr3_3:76498896-76498915 None:intergenic 45.0%
GTATTTGCACCTTGTTGCAG+TGG + chr3_3:76499059-76499078 Msa0473770:intron 45.0%
ACTTCAGGAGCCATGTACGA+TGG - chr3_3:76498269-76498288 None:intergenic 50.0%
! GTAACAAGTCTGAGACCCAC+GGG - chr3_3:76498575-76498594 None:intergenic 50.0%
! GGTAACAAGTCTGAGACCCA+CGG - chr3_3:76498576-76498595 None:intergenic 50.0%
ACTTCAGGAGCCATGTACGA+TGG - chr3_3:76498269-76498288 None:intergenic 50.0%
! GTAACAAGTCTGAGACCCAC+GGG - chr3_3:76498575-76498594 None:intergenic 50.0%
! GGTAACAAGTCTGAGACCCA+CGG - chr3_3:76498576-76498595 None:intergenic 50.0%
CAGGCAGACATGTGGAGTGT+CGG + chr3_3:76498705-76498724 Msa0473770:intron 55.0%
! AGGCAGACATGTGGAGTGTC+GGG + chr3_3:76498706-76498725 Msa0473770:intron 55.0%
ATAGGCGCACCACTGCAACA+AGG - chr3_3:76499071-76499090 None:intergenic 55.0%
CAGGCAGACATGTGGAGTGT+CGG + chr3_3:76498705-76498724 Msa0473770:intron 55.0%
! AGGCAGACATGTGGAGTGTC+GGG + chr3_3:76498706-76498725 Msa0473770:intron 55.0%
ATAGGCGCACCACTGCAACA+AGG - chr3_3:76499071-76499090 None:intergenic 55.0%
!! GGCAGACATGTGGAGTGTCG+GGG + chr3_3:76498707-76498726 Msa0473770:intron 60.0%
!! GGCAGACATGTGGAGTGTCG+GGG + chr3_3:76498707-76498726 Msa0473770:intron 60.0%
Chromosome Type Strat End Strand Name
chr3_3 gene 76498239 76499298 76498239 ID=Msa0473770;Name=Msa0473770
chr3_3 mRNA 76498239 76499298 76498239 ID=Msa0473770-mRNA-1;Parent=Msa0473770;Name=Msa0473770-mRNA-1;_AED=0.35;_eAED=0.35;_QI=0|0|0.33|1|0.5|0|3|152|63
chr3_3 exon 76498239 76498316 76498239 ID=Msa0473770-mRNA-1:exon:20063;Parent=Msa0473770-mRNA-1
chr3_3 exon 76498708 76498753 76498708 ID=Msa0473770-mRNA-1:exon:20064;Parent=Msa0473770-mRNA-1
chr3_3 exon 76499079 76499298 76499079 ID=Msa0473770-mRNA-1:exon:20065;Parent=Msa0473770-mRNA-1
chr3_3 CDS 76498239 76498316 76498239 ID=Msa0473770-mRNA-1:cds;Parent=Msa0473770-mRNA-1
chr3_3 CDS 76498708 76498753 76498708 ID=Msa0473770-mRNA-1:cds;Parent=Msa0473770-mRNA-1
chr3_3 CDS 76499079 76499146 76499079 ID=Msa0473770-mRNA-1:cds;Parent=Msa0473770-mRNA-1
chr3_3 three_prime_UTR 76499147 76499298 76499147 ID=Msa0473770-mRNA-1:three_prime_utr;Parent=Msa0473770-mRNA-1
Gene Sequence

>Msa0473770

GAGTATGTTGAGACAGTTTGTGGAACTCCATCGTACATGGCTCCTGAAGTTCTTCAGTTCCAGAGATATGATCACAAGGCAGACATGTGGAGTGTCGGGGCCATGCTTTTTGAGCTTCTAAATGTGGTGCGCCTATCTTTTGATGAATTTTATTTGCATAGCTTTCTAAGAGGAAAATCGTTGGGACCTTGA
Protein sequence

>Msa0473770

EYVETVCGTPSYMAPEVLQFQRYDHKADMWSVGAMLFELLNVVRLSFDEFYLHSFLRGKSLGP*