AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0226290


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0226290 MtrunA17_Chr2g0333051 83.704 135 5 1 1 118 1 135 2.70e-68 201
Msa0226290 MtrunA17_Chr4g0003391 49.618 131 44 4 1 117 1 123 2.83e-24 89.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0226290 AT1G52565.1 41.538 130 57 4 1 118 4 126 4.06e-15 66.6
Msa0226290 AT3G15760.1 35.417 144 55 6 1 118 1 132 2.21e-13 62.4

Find 27 sgRNAs with CRISPR-Local

Find 104 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AACCCATCATTTCAAATTCT+TGG 0.173412 2_1:-76806150 Msa0226290:CDS
TACAAAGCCATTCTATTTGC+AGG 0.298881 2_1:+76805543 None:intergenic
CATCACTGGTTATTTGAGAT+TGG 0.333802 2_1:-76805267 Msa0226290:three_prime_UTR
GATAAAATACACTGCTTCAT+AGG 0.352001 2_1:+76805447 None:intergenic
TGATGGGTTAATCTTGTGTT+TGG 0.357672 2_1:+76806164 None:intergenic
TCTCCAAGAATTTGAAATGA+TGG 0.404252 2_1:+76806147 None:intergenic
ACAAATGACTTCTCTTTCAC+AGG 0.405222 2_1:-76806244 None:intergenic
TAATTAATGTAATTTAGTTA+AGG 0.407837 2_1:-76805175 Msa0226290:three_prime_UTR
ATAGAATGGCTTTGTATAAC+GGG 0.410953 2_1:-76805536 Msa0226290:CDS
GGGGACATGTTGACCACAAC+TGG 0.414179 2_1:-76805311 Msa0226290:three_prime_UTR
GATTCTCGTTGAATGAAACT+TGG 0.436395 2_1:-76805482 Msa0226290:three_prime_UTR
AATAGAATGGCTTTGTATAA+CGG 0.457196 2_1:-76805537 Msa0226290:CDS
TCAAATAACCAGTGATGAGT+TGG 0.478287 2_1:+76805273 None:intergenic
CTCCAAGAATTTGAAATGAT+GGG 0.486286 2_1:+76806148 None:intergenic
TTGAATGAAACTTGGGAAAG+AGG 0.491240 2_1:-76805474 Msa0226290:three_prime_UTR
TAGATTTGAAGAAAGTGTGA+AGG 0.513088 2_1:-76805667 Msa0226290:CDS
TGGAATTCCTGCAAATAGAA+TGG 0.533064 2_1:-76805550 Msa0226290:CDS
TTTCTCAGAGGAAAAGAAGA+GGG 0.546313 2_1:-76805727 Msa0226290:intron
CAGTTGTGTGGTTGTAGTGT+GGG 0.548424 2_1:-76805331 Msa0226290:three_prime_UTR
ATTCTCGTTGAATGAAACTT+GGG 0.558587 2_1:-76805481 Msa0226290:three_prime_UTR
CAAATGACTTCTCTTTCACA+GGG 0.565422 2_1:-76806243 Msa0226290:CDS
ATTATGATCCAACTCATCAC+TGG 0.567473 2_1:-76805281 Msa0226290:three_prime_UTR
ACAGTTGTGTGGTTGTAGTG+TGG 0.615051 2_1:-76805332 Msa0226290:three_prime_UTR
CATAATGTCAAATCCAGTTG+TGG 0.615424 2_1:+76805298 None:intergenic
ACACATACACAACAGTTGTG+TGG 0.632075 2_1:-76805343 Msa0226290:three_prime_UTR
AGTGAAACAACGAAAACTCG+TGG 0.634965 2_1:-76805570 Msa0226290:CDS
AGTTGTGTGGTTGTAGTGTG+GGG 0.706919 2_1:-76805330 Msa0226290:three_prime_UTR

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TAATTAATGTAATTTAGTTA+AGG - chr2_1:76806223-76806242 Msa0226290:CDS 10.0%
!! TAATTAATGTAATTTAGTTA+AGG - chr2_1:76806223-76806242 Msa0226290:CDS 10.0%
!! ATCGATATTGATATTAATTA+AGG + chr2_1:76805554-76805573 None:intergenic 15.0%
!! ATCGATATTGATATTAATTA+AGG + chr2_1:76805554-76805573 None:intergenic 15.0%
!! TCTACATACAAAATAAAGTA+AGG + chr2_1:76805358-76805377 None:intergenic 20.0%
!!! TTACTTTATTTTGTATGTAG+AGG - chr2_1:76805357-76805376 Msa0226290:three_prime_UTR 20.0%
!! ATATCGATATTGATATTGTT+AGG + chr2_1:76805474-76805493 None:intergenic 20.0%
!! TCTACATACAAAATAAAGTA+AGG + chr2_1:76805358-76805377 None:intergenic 20.0%
!!! TTACTTTATTTTGTATGTAG+AGG - chr2_1:76805357-76805376 Msa0226290:three_prime_UTR 20.0%
!! ATATCGATATTGATATTGTT+AGG + chr2_1:76805474-76805493 None:intergenic 20.0%
! ATAGTAAGAACTAAGAACTA+AGG + chr2_1:76805636-76805655 None:intergenic 25.0%
!!! AATAGAATGGCTTTGTATAA+CGG - chr2_1:76805861-76805880 Msa0226290:intron 25.0%
! TCAAAGAAAAACAAAAACAG+AGG + chr2_1:76805994-76806013 None:intergenic 25.0%
!!! TGTTTTTGTTTTTCTTTGAG+TGG - chr2_1:76805995-76806014 Msa0226290:intron 25.0%
!!! TGAATTCTAGTTTAGTTTTG+TGG - chr2_1:76806021-76806040 Msa0226290:intron 25.0%
! ATAGTAAGAACTAAGAACTA+AGG + chr2_1:76805636-76805655 None:intergenic 25.0%
!!! AATAGAATGGCTTTGTATAA+CGG - chr2_1:76805861-76805880 Msa0226290:intron 25.0%
! TCAAAGAAAAACAAAAACAG+AGG + chr2_1:76805994-76806013 None:intergenic 25.0%
!!! TGTTTTTGTTTTTCTTTGAG+TGG - chr2_1:76805995-76806014 Msa0226290:intron 25.0%
!!! TGAATTCTAGTTTAGTTTTG+TGG - chr2_1:76806021-76806040 Msa0226290:intron 25.0%
AACCCATCATTTCAAATTCT+TGG - chr2_1:76805248-76805267 Msa0226290:three_prime_UTR 30.0%
! CTCCAAGAATTTGAAATGAT+GGG + chr2_1:76805253-76805272 None:intergenic 30.0%
! TCTCCAAGAATTTGAAATGA+TGG + chr2_1:76805254-76805273 None:intergenic 30.0%
GTAAGGTTAATCAAAAGAAG+AGG + chr2_1:76805341-76805360 None:intergenic 30.0%
! TTTTCTATGACCTAACTCAA+CGG + chr2_1:76805500-76805519 None:intergenic 30.0%
!!! GTGTGTATTTTTTTTCTCAG+AGG - chr2_1:76805659-76805678 Msa0226290:CDS 30.0%
! TAGATTTGAAGAAAGTGTGA+AGG - chr2_1:76805731-76805750 Msa0226290:intron 30.0%
TAGCAAAAAAAGAGAAACAG+AGG - chr2_1:76805775-76805794 Msa0226290:intron 30.0%
!! ATAGAATGGCTTTGTATAAC+GGG - chr2_1:76805862-76805881 Msa0226290:intron 30.0%
!! TTTGTATAACGGGATTTTGA+GGG - chr2_1:76805872-76805891 Msa0226290:intron 30.0%
ATTCTCGTTGAATGAAACTT+GGG - chr2_1:76805917-76805936 Msa0226290:intron 30.0%
GATAAAATACACTGCTTCAT+AGG + chr2_1:76805954-76805973 None:intergenic 30.0%
!!! TCTAGTTTAGTTTTGTGGTA+AGG - chr2_1:76806026-76806045 Msa0226290:intron 30.0%
!!! CTAGTTTAGTTTTGTGGTAA+GGG - chr2_1:76806027-76806046 Msa0226290:intron 30.0%
AACCCATCATTTCAAATTCT+TGG - chr2_1:76805248-76805267 Msa0226290:three_prime_UTR 30.0%
! CTCCAAGAATTTGAAATGAT+GGG + chr2_1:76805253-76805272 None:intergenic 30.0%
! TCTCCAAGAATTTGAAATGA+TGG + chr2_1:76805254-76805273 None:intergenic 30.0%
GTAAGGTTAATCAAAAGAAG+AGG + chr2_1:76805341-76805360 None:intergenic 30.0%
! TTTTCTATGACCTAACTCAA+CGG + chr2_1:76805500-76805519 None:intergenic 30.0%
!!! GTGTGTATTTTTTTTCTCAG+AGG - chr2_1:76805659-76805678 Msa0226290:CDS 30.0%
! TAGATTTGAAGAAAGTGTGA+AGG - chr2_1:76805731-76805750 Msa0226290:intron 30.0%
TAGCAAAAAAAGAGAAACAG+AGG - chr2_1:76805775-76805794 Msa0226290:intron 30.0%
!! ATAGAATGGCTTTGTATAAC+GGG - chr2_1:76805862-76805881 Msa0226290:intron 30.0%
!! TTTGTATAACGGGATTTTGA+GGG - chr2_1:76805872-76805891 Msa0226290:intron 30.0%
ATTCTCGTTGAATGAAACTT+GGG - chr2_1:76805917-76805936 Msa0226290:intron 30.0%
GATAAAATACACTGCTTCAT+AGG + chr2_1:76805954-76805973 None:intergenic 30.0%
!!! TCTAGTTTAGTTTTGTGGTA+AGG - chr2_1:76806026-76806045 Msa0226290:intron 30.0%
!!! CTAGTTTAGTTTTGTGGTAA+GGG - chr2_1:76806027-76806046 Msa0226290:intron 30.0%
GGAAAAAGCTAGATAAAGCA+TGG + chr2_1:76805216-76805235 None:intergenic 35.0%
!! TGATGGGTTAATCTTGTGTT+TGG + chr2_1:76805237-76805256 None:intergenic 35.0%
AGGTTAATCAAAAGAAGAGG+TGG + chr2_1:76805338-76805357 None:intergenic 35.0%
GTTGTTCTTGACAAAGTGTA+AGG + chr2_1:76805530-76805549 None:intergenic 35.0%
TCGATATTGTCAGTTAAGCT+AGG - chr2_1:76805569-76805588 Msa0226290:CDS 35.0%
! TTTTCTCAGAGGAAAAGAAG+AGG - chr2_1:76805670-76805689 Msa0226290:CDS 35.0%
TTTCTCAGAGGAAAAGAAGA+GGG - chr2_1:76805671-76805690 Msa0226290:CDS 35.0%
TGGAATTCCTGCAAATAGAA+TGG - chr2_1:76805848-76805867 Msa0226290:intron 35.0%
TACAAAGCCATTCTATTTGC+AGG + chr2_1:76805858-76805877 None:intergenic 35.0%
!! CTTTGTATAACGGGATTTTG+AGG - chr2_1:76805871-76805890 Msa0226290:intron 35.0%
GATTCTCGTTGAATGAAACT+TGG - chr2_1:76805916-76805935 Msa0226290:intron 35.0%
TTGAATGAAACTTGGGAAAG+AGG - chr2_1:76805924-76805943 Msa0226290:intron 35.0%
CATAATGTCAAATCCAGTTG+TGG + chr2_1:76806103-76806122 None:intergenic 35.0%
ATTATGATCCAACTCATCAC+TGG - chr2_1:76806117-76806136 Msa0226290:intron 35.0%
TCAAATAACCAGTGATGAGT+TGG + chr2_1:76806128-76806147 None:intergenic 35.0%
! CATCACTGGTTATTTGAGAT+TGG - chr2_1:76806131-76806150 Msa0226290:intron 35.0%
GGAAAAAGCTAGATAAAGCA+TGG + chr2_1:76805216-76805235 None:intergenic 35.0%
!! TGATGGGTTAATCTTGTGTT+TGG + chr2_1:76805237-76805256 None:intergenic 35.0%
AGGTTAATCAAAAGAAGAGG+TGG + chr2_1:76805338-76805357 None:intergenic 35.0%
GTTGTTCTTGACAAAGTGTA+AGG + chr2_1:76805530-76805549 None:intergenic 35.0%
TCGATATTGTCAGTTAAGCT+AGG - chr2_1:76805569-76805588 Msa0226290:CDS 35.0%
! TTTTCTCAGAGGAAAAGAAG+AGG - chr2_1:76805670-76805689 Msa0226290:CDS 35.0%
TTTCTCAGAGGAAAAGAAGA+GGG - chr2_1:76805671-76805690 Msa0226290:CDS 35.0%
TGGAATTCCTGCAAATAGAA+TGG - chr2_1:76805848-76805867 Msa0226290:intron 35.0%
TACAAAGCCATTCTATTTGC+AGG + chr2_1:76805858-76805877 None:intergenic 35.0%
!! CTTTGTATAACGGGATTTTG+AGG - chr2_1:76805871-76805890 Msa0226290:intron 35.0%
GATTCTCGTTGAATGAAACT+TGG - chr2_1:76805916-76805935 Msa0226290:intron 35.0%
TTGAATGAAACTTGGGAAAG+AGG - chr2_1:76805924-76805943 Msa0226290:intron 35.0%
CATAATGTCAAATCCAGTTG+TGG + chr2_1:76806103-76806122 None:intergenic 35.0%
ATTATGATCCAACTCATCAC+TGG - chr2_1:76806117-76806136 Msa0226290:intron 35.0%
TCAAATAACCAGTGATGAGT+TGG + chr2_1:76806128-76806147 None:intergenic 35.0%
! CATCACTGGTTATTTGAGAT+TGG - chr2_1:76806131-76806150 Msa0226290:intron 35.0%
TTACGCTCATGCTTGTATTC+AGG - chr2_1:76805305-76805324 Msa0226290:three_prime_UTR 40.0%
TCGATATTGTCCGTTGAGTT+AGG - chr2_1:76805487-76805506 Msa0226290:exon 40.0%
AGTGAAACAACGAAAACTCG+TGG - chr2_1:76805828-76805847 Msa0226290:intron 40.0%
ACACATACACAACAGTTGTG+TGG - chr2_1:76806055-76806074 Msa0226290:intron 40.0%
TTACGCTCATGCTTGTATTC+AGG - chr2_1:76805305-76805324 Msa0226290:three_prime_UTR 40.0%
TCGATATTGTCCGTTGAGTT+AGG - chr2_1:76805487-76805506 Msa0226290:exon 40.0%
AGTGAAACAACGAAAACTCG+TGG - chr2_1:76805828-76805847 Msa0226290:intron 40.0%
ACACATACACAACAGTTGTG+TGG - chr2_1:76806055-76806074 Msa0226290:intron 40.0%
TCTTGGAGATCACGTTTCTC+AGG - chr2_1:76805265-76805284 Msa0226290:three_prime_UTR 45.0%
TGTGGTACAGAGTTCGAACT+CGG - chr2_1:76805434-76805453 Msa0226290:three_prime_UTR 45.0%
!! TTTTGAGGGATCGTGTGCAT+AGG - chr2_1:76805886-76805905 Msa0226290:intron 45.0%
ACAGTTGTGTGGTTGTAGTG+TGG - chr2_1:76806066-76806085 Msa0226290:intron 45.0%
CAGTTGTGTGGTTGTAGTGT+GGG - chr2_1:76806067-76806086 Msa0226290:intron 45.0%
AGTTGTGTGGTTGTAGTGTG+GGG - chr2_1:76806068-76806087 Msa0226290:intron 45.0%
TCTTGGAGATCACGTTTCTC+AGG - chr2_1:76805265-76805284 Msa0226290:three_prime_UTR 45.0%
TGTGGTACAGAGTTCGAACT+CGG - chr2_1:76805434-76805453 Msa0226290:three_prime_UTR 45.0%
!! TTTTGAGGGATCGTGTGCAT+AGG - chr2_1:76805886-76805905 Msa0226290:intron 45.0%
ACAGTTGTGTGGTTGTAGTG+TGG - chr2_1:76806066-76806085 Msa0226290:intron 45.0%
CAGTTGTGTGGTTGTAGTGT+GGG - chr2_1:76806067-76806086 Msa0226290:intron 45.0%
AGTTGTGTGGTTGTAGTGTG+GGG - chr2_1:76806068-76806087 Msa0226290:intron 45.0%
CGAACTCACACACAACTGTG+TGG - chr2_1:76805416-76805435 Msa0226290:three_prime_UTR 50.0%
CGAACTCACACACAACTGTG+TGG - chr2_1:76805416-76805435 Msa0226290:three_prime_UTR 50.0%
GGGGACATGTTGACCACAAC+TGG - chr2_1:76806087-76806106 Msa0226290:intron 55.0%
GGGGACATGTTGACCACAAC+TGG - chr2_1:76806087-76806106 Msa0226290:intron 55.0%
Chromosome Type Strat End Strand Name
chr2_1 gene 76805158 76806262 76805158 ID=Msa0226290;Name=Msa0226290
chr2_1 mRNA 76805158 76806262 76805158 ID=Msa0226290-mRNA-1;Parent=Msa0226290;Name=Msa0226290-mRNA-1;_AED=0.13;_eAED=0.13;_QI=0|0|0|1|0|0|2|345|118
chr2_1 exon 76805158 76805739 76805158 ID=Msa0226290-mRNA-1:exon:23270;Parent=Msa0226290-mRNA-1
chr2_1 exon 76806143 76806262 76806143 ID=Msa0226290-mRNA-1:exon:23269;Parent=Msa0226290-mRNA-1
chr2_1 CDS 76806143 76806262 76806143 ID=Msa0226290-mRNA-1:cds;Parent=Msa0226290-mRNA-1
chr2_1 CDS 76805503 76805739 76805503 ID=Msa0226290-mRNA-1:cds;Parent=Msa0226290-mRNA-1
chr2_1 three_prime_UTR 76805158 76805502 76805158 ID=Msa0226290-mRNA-1:three_prime_utr;Parent=Msa0226290-mRNA-1
Gene Sequence

>Msa0226290

ATGACTTCTCTTTCACAGGGTCTTGTGTTCACTACAGCTATGCTTGTATCAAGCACCATGCTTTATCTAGCTTTTTCCAAACACAAGATTAACCCATCATTTCAAATTCTTGGAGATCACGAAAAGAAGAGGGAGAGAAAGATGAATACAAAGAAAAATAAAAAGAAAGTTAGATTTGAAGAAAGTGTGAAGGAAGTAAGAGAAAAGAGTGAGATAGCAAAAAAAGAGAAACAGAGGAAACGAAACAGAGTACATAGCAACTGCAGAAGTGAAACAACGAAAACTCGTGGAATTCCTGCAAATAGAATGGCTTTGTATAACGGGATTTTGAGGGATCGTGTGCATAGGATTGAGTGA

Protein sequence

>Msa0226290

MTSLSQGLVFTTAMLVSSTMLYLAFSKHKINPSFQILGDHEKKRERKMNTKKNKKKVRFEESVKEVREKSEIAKKEKQRKRNRVHSNCRSETTKTRGIPANRMALYNGILRDRVHRIE*