AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1207270


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1207270 MtrunA17_Chr4g0056141 100.000 62 0 0 1 62 1 62 2.23e-39 123
Msa1207270 MtrunA17_Chr5g0399231 100.000 62 0 0 1 62 1 62 2.23e-39 123
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1207270 AT2G19750.1 95.161 62 3 0 1 62 1 62 6.52e-30 100
Msa1207270 AT5G56670.1 95.161 62 3 0 1 62 1 62 6.52e-30 100
Msa1207270 AT4G29390.1 95.161 62 3 0 1 62 1 62 6.52e-30 100

Find 29 sgRNAs with CRISPR-Local

Find 100 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTGTCTTGCTTTGCAACTTT+TGG 0.146380 8_1:-64699244 None:intergenic
ACAAATAGATCAAGCATTTC+TGG 0.178726 8_1:+64698977 Msa1207270:five_prime_UTR
ATTTGTATTGGCAGGGTTAA+AGG 0.244046 8_1:-64698960 None:intergenic
CATTTCTGGTTTGAGTTTCT+AGG 0.265980 8_1:+64698991 Msa1207270:five_prime_UTR
ATTATTGCAGTTGTGGGATT+TGG 0.276718 8_1:+64699452 Msa1207270:intron
GCAGATAATTTGACCTTTGC+TGG 0.282556 8_1:+64699748 Msa1207270:three_prime_UTR
TTTGTTGTGCTAGGTAATTT+TGG 0.315592 8_1:+64699630 Msa1207270:three_prime_UTR
TATTCGACCATATGATTGTT+TGG 0.335567 8_1:+64699664 Msa1207270:three_prime_UTR
TTGCTCGTGCAGGAAAAGTT+AGG 0.368060 8_1:+64699212 Msa1207270:CDS
CTTGATCTATTTGTATTGGC+AGG 0.372214 8_1:-64698968 None:intergenic
AATGCTTGATCTATTTGTAT+TGG 0.402254 8_1:-64698972 None:intergenic
ATTTCTGGTTTGAGTTTCTA+GGG 0.428673 8_1:+64698992 Msa1207270:five_prime_UTR
TTTATTTGATTCATGAATTG+TGG 0.463970 8_1:+64699571 Msa1207270:three_prime_UTR
CGATTTGCAGCAGCAGCTCT+CGG 0.470283 8_1:-64699021 None:intergenic
TGCTCGTGCAGGAAAAGTTA+GGG 0.470658 8_1:+64699213 Msa1207270:CDS
GACAAATTCGTCTTCACCAT+GGG 0.495739 8_1:+64699069 Msa1207270:exon
CAGATAATTTGACCTTTGCT+GGG 0.504584 8_1:+64699749 Msa1207270:three_prime_UTR
CATGGTTCCCTTGCTCGTGC+AGG 0.506156 8_1:+64699202 Msa1207270:CDS
TAAGTGAAGATGATGCTTAG+TGG 0.520375 8_1:+64699515 Msa1207270:three_prime_UTR
AGTTACCGGCGGTGACGAAA+CGG 0.526875 8_1:-64699315 None:intergenic
TGAAATGCAGGTAAAGTGCA+TGG 0.575483 8_1:+64699184 Msa1207270:intron
TTGATCTATTTGTATTGGCA+GGG 0.577138 8_1:-64698967 None:intergenic
TGACAAATTCGTCTTCACCA+TGG 0.606303 8_1:+64699068 Msa1207270:exon
GTGGGATTTGGAAAGAAGCG+TGG 0.615049 8_1:+64699464 Msa1207270:CDS
AATTACAAAATGGGTCGGTG+TGG 0.618754 8_1:+64699692 Msa1207270:three_prime_UTR
AATCGCCGTTTCGTCACCGC+CGG 0.622871 8_1:+64699310 Msa1207270:CDS
CGCTTGTGAGCACGTCCTCG+TGG 0.625412 8_1:-64699277 None:intergenic
GCTCGTGCAGGAAAAGTTAG+GGG 0.631196 8_1:+64699214 Msa1207270:CDS
GACAAGAAGAAGCAGCCACG+AGG 0.688180 8_1:+64699262 Msa1207270:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTGGTTTTTAATTACAAAA+TGG + chr8_1:64699682-64699701 Msa1207270:three_prime_UTR 15.0%
!!! TTGGTTTTTAATTACAAAAT+GGG + chr8_1:64699683-64699702 Msa1207270:three_prime_UTR 15.0%
!!! TTTGGTTTTTAATTACAAAA+TGG + chr8_1:64699682-64699701 Msa1207270:three_prime_UTR 15.0%
!!! TTGGTTTTTAATTACAAAAT+GGG + chr8_1:64699683-64699702 Msa1207270:three_prime_UTR 15.0%
!!! TTTTTTTGTTGTTCTGATTT+TGG + chr8_1:64699417-64699436 Msa1207270:intron 20.0%
!! TTTATTTGATTCATGAATTG+TGG + chr8_1:64699571-64699590 Msa1207270:three_prime_UTR 20.0%
!! TTAAAAACCAAACAATCATA+TGG - chr8_1:64699674-64699693 None:intergenic 20.0%
!!! TTTTTAATTACAAAATGGGT+CGG + chr8_1:64699687-64699706 Msa1207270:three_prime_UTR 20.0%
!!! TTTTTTTGTTGTTCTGATTT+TGG + chr8_1:64699417-64699436 Msa1207270:intron 20.0%
!! TTTATTTGATTCATGAATTG+TGG + chr8_1:64699571-64699590 Msa1207270:three_prime_UTR 20.0%
!! TTAAAAACCAAACAATCATA+TGG - chr8_1:64699674-64699693 None:intergenic 20.0%
!!! TTTTTAATTACAAAATGGGT+CGG + chr8_1:64699687-64699706 Msa1207270:three_prime_UTR 20.0%
! AATGCTTGATCTATTTGTAT+TGG - chr8_1:64698975-64698994 None:intergenic 25.0%
! TGATTCGATACCTATAAAAT+TGG + chr8_1:64699111-64699130 Msa1207270:intron 25.0%
!! GAAATCGAAACCAATTTTAT+AGG - chr8_1:64699124-64699143 None:intergenic 25.0%
! AGAAAGAATGATAAAGTTAC+CGG - chr8_1:64699332-64699351 None:intergenic 25.0%
! TATGATTATTATTGCAGTTG+TGG + chr8_1:64699445-64699464 Msa1207270:intron 25.0%
! ATGATTATTATTGCAGTTGT+GGG + chr8_1:64699446-64699465 Msa1207270:intron 25.0%
!!! TTCTTTGTTTTAAGACATTG+AGG + chr8_1:64699798-64699817 Msa1207270:three_prime_UTR 25.0%
! AATGCTTGATCTATTTGTAT+TGG - chr8_1:64698975-64698994 None:intergenic 25.0%
! TGATTCGATACCTATAAAAT+TGG + chr8_1:64699111-64699130 Msa1207270:intron 25.0%
!! GAAATCGAAACCAATTTTAT+AGG - chr8_1:64699124-64699143 None:intergenic 25.0%
! AGAAAGAATGATAAAGTTAC+CGG - chr8_1:64699332-64699351 None:intergenic 25.0%
! TATGATTATTATTGCAGTTG+TGG + chr8_1:64699445-64699464 Msa1207270:intron 25.0%
! ATGATTATTATTGCAGTTGT+GGG + chr8_1:64699446-64699465 Msa1207270:intron 25.0%
!!! TTCTTTGTTTTAAGACATTG+AGG + chr8_1:64699798-64699817 Msa1207270:three_prime_UTR 25.0%
! TTGATCTATTTGTATTGGCA+GGG - chr8_1:64698970-64698989 None:intergenic 30.0%
ACAAATAGATCAAGCATTTC+TGG + chr8_1:64698977-64698996 Msa1207270:five_prime_UTR 30.0%
!! ATTTCTGGTTTGAGTTTCTA+GGG + chr8_1:64698992-64699011 Msa1207270:five_prime_UTR 30.0%
AATAATAATCAACTCACCCA+TGG - chr8_1:64699088-64699107 None:intergenic 30.0%
!! TGAAAGAATTTTGTTGTGCT+AGG + chr8_1:64699621-64699640 Msa1207270:three_prime_UTR 30.0%
!! TTTGTTGTGCTAGGTAATTT+TGG + chr8_1:64699630-64699649 Msa1207270:three_prime_UTR 30.0%
TATTCGACCATATGATTGTT+TGG + chr8_1:64699664-64699683 Msa1207270:three_prime_UTR 30.0%
! ATAACAAATTTTCCCAGCAA+AGG - chr8_1:64699764-64699783 None:intergenic 30.0%
! TTGATCTATTTGTATTGGCA+GGG - chr8_1:64698970-64698989 None:intergenic 30.0%
ACAAATAGATCAAGCATTTC+TGG + chr8_1:64698977-64698996 Msa1207270:five_prime_UTR 30.0%
!! ATTTCTGGTTTGAGTTTCTA+GGG + chr8_1:64698992-64699011 Msa1207270:five_prime_UTR 30.0%
AATAATAATCAACTCACCCA+TGG - chr8_1:64699088-64699107 None:intergenic 30.0%
!! TGAAAGAATTTTGTTGTGCT+AGG + chr8_1:64699621-64699640 Msa1207270:three_prime_UTR 30.0%
!! TTTGTTGTGCTAGGTAATTT+TGG + chr8_1:64699630-64699649 Msa1207270:three_prime_UTR 30.0%
TATTCGACCATATGATTGTT+TGG + chr8_1:64699664-64699683 Msa1207270:three_prime_UTR 30.0%
! ATAACAAATTTTCCCAGCAA+AGG - chr8_1:64699764-64699783 None:intergenic 30.0%
! ATTTGTATTGGCAGGGTTAA+AGG - chr8_1:64698963-64698982 None:intergenic 35.0%
! CTTGATCTATTTGTATTGGC+AGG - chr8_1:64698971-64698990 None:intergenic 35.0%
!! CATTTCTGGTTTGAGTTTCT+AGG + chr8_1:64698991-64699010 Msa1207270:five_prime_UTR 35.0%
! TGAATCGACATTTGAAATGC+AGG + chr8_1:64699172-64699191 Msa1207270:intron 35.0%
! TGTCTTGCTTTGCAACTTTT+GGG - chr8_1:64699246-64699265 None:intergenic 35.0%
! TTGTCTTGCTTTGCAACTTT+TGG - chr8_1:64699247-64699266 None:intergenic 35.0%
AAGAATGATAAAGTTACCGG+CGG - chr8_1:64699329-64699348 None:intergenic 35.0%
ATTATTGCAGTTGTGGGATT+TGG + chr8_1:64699452-64699471 Msa1207270:intron 35.0%
!! CTTCACTTTTCAGATGAGTT+AGG - chr8_1:64699491-64699510 None:intergenic 35.0%
TAAGTGAAGATGATGCTTAG+TGG + chr8_1:64699515-64699534 Msa1207270:three_prime_UTR 35.0%
CAGATAATTTGACCTTTGCT+GGG + chr8_1:64699749-64699768 Msa1207270:three_prime_UTR 35.0%
! ATTTGTATTGGCAGGGTTAA+AGG - chr8_1:64698963-64698982 None:intergenic 35.0%
! CTTGATCTATTTGTATTGGC+AGG - chr8_1:64698971-64698990 None:intergenic 35.0%
!! CATTTCTGGTTTGAGTTTCT+AGG + chr8_1:64698991-64699010 Msa1207270:five_prime_UTR 35.0%
! TGAATCGACATTTGAAATGC+AGG + chr8_1:64699172-64699191 Msa1207270:intron 35.0%
! TGTCTTGCTTTGCAACTTTT+GGG - chr8_1:64699246-64699265 None:intergenic 35.0%
! TTGTCTTGCTTTGCAACTTT+TGG - chr8_1:64699247-64699266 None:intergenic 35.0%
AAGAATGATAAAGTTACCGG+CGG - chr8_1:64699329-64699348 None:intergenic 35.0%
ATTATTGCAGTTGTGGGATT+TGG + chr8_1:64699452-64699471 Msa1207270:intron 35.0%
!! CTTCACTTTTCAGATGAGTT+AGG - chr8_1:64699491-64699510 None:intergenic 35.0%
TAAGTGAAGATGATGCTTAG+TGG + chr8_1:64699515-64699534 Msa1207270:three_prime_UTR 35.0%
CAGATAATTTGACCTTTGCT+GGG + chr8_1:64699749-64699768 Msa1207270:three_prime_UTR 35.0%
TGACAAATTCGTCTTCACCA+TGG + chr8_1:64699068-64699087 Msa1207270:exon 40.0%
GACAAATTCGTCTTCACCAT+GGG + chr8_1:64699069-64699088 Msa1207270:exon 40.0%
TGAAATGCAGGTAAAGTGCA+TGG + chr8_1:64699184-64699203 Msa1207270:intron 40.0%
! GTCTTGCTTTGCAACTTTTG+GGG - chr8_1:64699245-64699264 None:intergenic 40.0%
AATTACAAAATGGGTCGGTG+TGG + chr8_1:64699692-64699711 Msa1207270:three_prime_UTR 40.0%
GCAGATAATTTGACCTTTGC+TGG + chr8_1:64699748-64699767 Msa1207270:three_prime_UTR 40.0%
TGACAAATTCGTCTTCACCA+TGG + chr8_1:64699068-64699087 Msa1207270:exon 40.0%
GACAAATTCGTCTTCACCAT+GGG + chr8_1:64699069-64699088 Msa1207270:exon 40.0%
TGAAATGCAGGTAAAGTGCA+TGG + chr8_1:64699184-64699203 Msa1207270:intron 40.0%
! GTCTTGCTTTGCAACTTTTG+GGG - chr8_1:64699245-64699264 None:intergenic 40.0%
AATTACAAAATGGGTCGGTG+TGG + chr8_1:64699692-64699711 Msa1207270:three_prime_UTR 40.0%
GCAGATAATTTGACCTTTGC+TGG + chr8_1:64699748-64699767 Msa1207270:three_prime_UTR 40.0%
! AACTTTTCCTGCACGAGCAA+GGG - chr8_1:64699212-64699231 None:intergenic 45.0%
! TAACTTTTCCTGCACGAGCA+AGG - chr8_1:64699213-64699232 None:intergenic 45.0%
TTGCTCGTGCAGGAAAAGTT+AGG + chr8_1:64699212-64699231 Msa1207270:CDS 45.0%
TGCTCGTGCAGGAAAAGTTA+GGG + chr8_1:64699213-64699232 Msa1207270:CDS 45.0%
! AACTTTTCCTGCACGAGCAA+GGG - chr8_1:64699212-64699231 None:intergenic 45.0%
! TAACTTTTCCTGCACGAGCA+AGG - chr8_1:64699213-64699232 None:intergenic 45.0%
TTGCTCGTGCAGGAAAAGTT+AGG + chr8_1:64699212-64699231 Msa1207270:CDS 45.0%
TGCTCGTGCAGGAAAAGTTA+GGG + chr8_1:64699213-64699232 Msa1207270:CDS 45.0%
GCTCGTGCAGGAAAAGTTAG+GGG + chr8_1:64699214-64699233 Msa1207270:CDS 50.0%
GTGGGATTTGGAAAGAAGCG+TGG + chr8_1:64699464-64699483 Msa1207270:CDS 50.0%
GCTCGTGCAGGAAAAGTTAG+GGG + chr8_1:64699214-64699233 Msa1207270:CDS 50.0%
GTGGGATTTGGAAAGAAGCG+TGG + chr8_1:64699464-64699483 Msa1207270:CDS 50.0%
CGATTTGCAGCAGCAGCTCT+CGG - chr8_1:64699024-64699043 None:intergenic 55.0%
GACAAGAAGAAGCAGCCACG+AGG + chr8_1:64699262-64699281 Msa1207270:CDS 55.0%
AGTTACCGGCGGTGACGAAA+CGG - chr8_1:64699318-64699337 None:intergenic 55.0%
CGATTTGCAGCAGCAGCTCT+CGG - chr8_1:64699024-64699043 None:intergenic 55.0%
GACAAGAAGAAGCAGCCACG+AGG + chr8_1:64699262-64699281 Msa1207270:CDS 55.0%
AGTTACCGGCGGTGACGAAA+CGG - chr8_1:64699318-64699337 None:intergenic 55.0%
CATGGTTCCCTTGCTCGTGC+AGG + chr8_1:64699202-64699221 Msa1207270:CDS 60.0%
AATCGCCGTTTCGTCACCGC+CGG + chr8_1:64699310-64699329 Msa1207270:CDS 60.0%
CATGGTTCCCTTGCTCGTGC+AGG + chr8_1:64699202-64699221 Msa1207270:CDS 60.0%
AATCGCCGTTTCGTCACCGC+CGG + chr8_1:64699310-64699329 Msa1207270:CDS 60.0%
CGCTTGTGAGCACGTCCTCG+TGG - chr8_1:64699280-64699299 None:intergenic 65.0%
CGCTTGTGAGCACGTCCTCG+TGG - chr8_1:64699280-64699299 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
chr8_1 gene 64698957 64699852 64698957 ID=Msa1207270;Name=Msa1207270
chr8_1 mRNA 64698957 64699852 64698957 ID=Msa1207270-mRNA-1;Parent=Msa1207270;Name=Msa1207270-mRNA-1;_AED=0.01;_eAED=0.01;_QI=130|1|1|1|1|1|3|344|62
chr8_1 exon 64698957 64699090 64698957 ID=Msa1207270-mRNA-1:exon:21173;Parent=Msa1207270-mRNA-1
chr8_1 exon 64699194 64699331 64699194 ID=Msa1207270-mRNA-1:exon:21174;Parent=Msa1207270-mRNA-1
chr8_1 exon 64699462 64699852 64699462 ID=Msa1207270-mRNA-1:exon:21175;Parent=Msa1207270-mRNA-1
chr8_1 five_prime_UTR 64698957 64699086 64698957 ID=Msa1207270-mRNA-1:five_prime_utr;Parent=Msa1207270-mRNA-1
chr8_1 CDS 64699087 64699090 64699087 ID=Msa1207270-mRNA-1:cds;Parent=Msa1207270-mRNA-1
chr8_1 CDS 64699194 64699331 64699194 ID=Msa1207270-mRNA-1:cds;Parent=Msa1207270-mRNA-1
chr8_1 CDS 64699462 64699508 64699462 ID=Msa1207270-mRNA-1:cds;Parent=Msa1207270-mRNA-1
chr8_1 three_prime_UTR 64699509 64699852 64699509 ID=Msa1207270-mRNA-1:three_prime_utr;Parent=Msa1207270-mRNA-1
Gene Sequence

>Msa1207270

ATGGGTAAAGTGCATGGTTCCCTTGCTCGTGCAGGAAAAGTTAGGGGACAAACCCCAAAAGTTGCAAAGCAAGACAAGAAGAAGCAGCCACGAGGACGTGCTCACAAGCGTATGCAATACAATCGCCGTTTCGTCACCGCCGTTGTGGGATTTGGAAAGAAGCGTGGACCTAACTCATCTGAAAAGTGA

Protein sequence

>Msa1207270

MGKVHGSLARAGKVRGQTPKVAKQDKKKQPRGRAHKRMQYNRRFVTAVVGFGKKRGPNSSEK*