AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1257510


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1257510 MtrunA17_Chr4g0056141 100.000 62 0 0 1 62 1 62 2.23e-39 123
Msa1257510 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
Msa1257510 AT2G19750.1 95.161 62 3 0 1 62 1 62 6.52e-30 100
Msa1257510 AT5G56670.1 95.161 62 3 0 1 62 1 62 6.52e-30 100
Msa1257510 AT4G29390.1 95.161 62 3 0 1 62 1 62 6.52e-30 100

Find 29 sgRNAs with CRISPR-Local

Find 98 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTGTCTTGCTTTGCAACTTT+TGG 0.146380 8_2:-58127497 None:intergenic
ACAAATAGATCAAGCATTTC+TGG 0.178726 8_2:+58127230 Msa1257510:five_prime_UTR
ATTTGTATTGGCAGGGTTAA+AGG 0.244046 8_2:-58127213 None:intergenic
GCAAATAATTTGACCTTTGC+TGG 0.248572 8_2:+58127989 Msa1257510:three_prime_UTR
CATTTCTGGTTTGAGTTTCT+AGG 0.265980 8_2:+58127244 Msa1257510:five_prime_UTR
ATTATTGCAGTTGTGGGATT+TGG 0.276718 8_2:+58127705 Msa1257510:intron
TTTGTTGTGCTAGGTAATTT+TGG 0.315592 8_2:+58127871 Msa1257510:three_prime_UTR
TATTCGACCATATGATTGTT+TGG 0.335567 8_2:+58127905 Msa1257510:three_prime_UTR
TTGCTCGTGCAGGAAAAGTT+AGG 0.368060 8_2:+58127465 Msa1257510:CDS
CTTGATCTATTTGTATTGGC+AGG 0.372214 8_2:-58127221 None:intergenic
AATGCTTGATCTATTTGTAT+TGG 0.402254 8_2:-58127225 None:intergenic
ATTTCTGGTTTGAGTTTCTA+GGG 0.428673 8_2:+58127245 Msa1257510:five_prime_UTR
TTTATTTGATTCATGAATTG+TGG 0.463970 8_2:+58127812 Msa1257510:three_prime_UTR
CGATTTGCAGCAGCAGCTCT+CGG 0.470283 8_2:-58127274 None:intergenic
TGCTCGTGCAGGAAAAGTTA+GGG 0.470658 8_2:+58127466 Msa1257510:CDS
CAAATAATTTGACCTTTGCT+GGG 0.477286 8_2:+58127990 Msa1257510:three_prime_UTR
GACAAATTCGTCTTCACCAT+GGG 0.495739 8_2:+58127322 Msa1257510:exon
AAAGTGAAGATGATGCTTAG+TGG 0.503837 8_2:+58127755 Msa1257510:exon
CATGGTTCCCTTGCTCGTGC+AGG 0.506156 8_2:+58127455 Msa1257510:CDS
AGTTACCGGCGGTGACGAAA+CGG 0.526875 8_2:-58127568 None:intergenic
TGAAATGCAGGTAAAGTGCA+TGG 0.575483 8_2:+58127437 Msa1257510:intron
TTGATCTATTTGTATTGGCA+GGG 0.577138 8_2:-58127220 None:intergenic
TGACAAATTCGTCTTCACCA+TGG 0.606303 8_2:+58127321 Msa1257510:exon
AATTACAAAATGGGTCGATG+TGG 0.607442 8_2:+58127933 Msa1257510:three_prime_UTR
GTGGGATTTGGAAAGAAGCG+TGG 0.615049 8_2:+58127717 Msa1257510:CDS
AATCGCCGTTTCGTCACCGC+CGG 0.622871 8_2:+58127563 Msa1257510:CDS
CGCTTGTGAGCACGTCCTCG+TGG 0.625412 8_2:-58127530 None:intergenic
GCTCGTGCAGGAAAAGTTAG+GGG 0.631196 8_2:+58127467 Msa1257510:CDS
GACAAGAAGAAGCAGCCACG+AGG 0.688180 8_2:+58127515 Msa1257510:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTTTTTTTGTTCTGATTT+TGG + chr8_2:58127670-58127689 Msa1257510:intron 15.0%
!!! TTTGGTTTTTAATTACAAAA+TGG + chr8_2:58127923-58127942 Msa1257510:three_prime_UTR 15.0%
!!! TTGGTTTTTAATTACAAAAT+GGG + chr8_2:58127924-58127943 Msa1257510:three_prime_UTR 15.0%
!!! TTTTTTTTTTGTTCTGATTT+TGG + chr8_2:58127670-58127689 Msa1257510:intron 15.0%
!!! TTTGGTTTTTAATTACAAAA+TGG + chr8_2:58127923-58127942 Msa1257510:three_prime_UTR 15.0%
!!! TTGGTTTTTAATTACAAAAT+GGG + chr8_2:58127924-58127943 Msa1257510:three_prime_UTR 15.0%
!! TTTATTTGATTCATGAATTG+TGG + chr8_2:58127812-58127831 Msa1257510:three_prime_UTR 20.0%
!! TTAAAAACCAAACAATCATA+TGG - chr8_2:58127915-58127934 None:intergenic 20.0%
!! TTTATTTGATTCATGAATTG+TGG + chr8_2:58127812-58127831 Msa1257510:three_prime_UTR 20.0%
!! TTAAAAACCAAACAATCATA+TGG - chr8_2:58127915-58127934 None:intergenic 20.0%
! AATGCTTGATCTATTTGTAT+TGG - chr8_2:58127228-58127247 None:intergenic 25.0%
! TGATTCGATACCTATAAAAT+TGG + chr8_2:58127364-58127383 Msa1257510:intron 25.0%
!! GAAATCGAAACCAATTTTAT+AGG - chr8_2:58127377-58127396 None:intergenic 25.0%
! AGAAAGAATGATAAAGTTAC+CGG - chr8_2:58127585-58127604 None:intergenic 25.0%
! TATGATTATTATTGCAGTTG+TGG + chr8_2:58127698-58127717 Msa1257510:intron 25.0%
! ATGATTATTATTGCAGTTGT+GGG + chr8_2:58127699-58127718 Msa1257510:intron 25.0%
!!! TTCTTTGTTTTAAGACATTG+AGG + chr8_2:58128039-58128058 Msa1257510:three_prime_UTR 25.0%
! AATGCTTGATCTATTTGTAT+TGG - chr8_2:58127228-58127247 None:intergenic 25.0%
! TGATTCGATACCTATAAAAT+TGG + chr8_2:58127364-58127383 Msa1257510:intron 25.0%
!! GAAATCGAAACCAATTTTAT+AGG - chr8_2:58127377-58127396 None:intergenic 25.0%
! AGAAAGAATGATAAAGTTAC+CGG - chr8_2:58127585-58127604 None:intergenic 25.0%
! TATGATTATTATTGCAGTTG+TGG + chr8_2:58127698-58127717 Msa1257510:intron 25.0%
! ATGATTATTATTGCAGTTGT+GGG + chr8_2:58127699-58127718 Msa1257510:intron 25.0%
!!! TTCTTTGTTTTAAGACATTG+AGG + chr8_2:58128039-58128058 Msa1257510:three_prime_UTR 25.0%
! TTGATCTATTTGTATTGGCA+GGG - chr8_2:58127223-58127242 None:intergenic 30.0%
ACAAATAGATCAAGCATTTC+TGG + chr8_2:58127230-58127249 Msa1257510:five_prime_UTR 30.0%
!! ATTTCTGGTTTGAGTTTCTA+GGG + chr8_2:58127245-58127264 Msa1257510:five_prime_UTR 30.0%
AATAATAATCAACTCACCCA+TGG - chr8_2:58127341-58127360 None:intergenic 30.0%
!! TGAAAGAATTTTGTTGTGCT+AGG + chr8_2:58127862-58127881 Msa1257510:three_prime_UTR 30.0%
!! TTTGTTGTGCTAGGTAATTT+TGG + chr8_2:58127871-58127890 Msa1257510:three_prime_UTR 30.0%
TATTCGACCATATGATTGTT+TGG + chr8_2:58127905-58127924 Msa1257510:three_prime_UTR 30.0%
CAAATAATTTGACCTTTGCT+GGG + chr8_2:58127990-58128009 Msa1257510:three_prime_UTR 30.0%
! ATAACAAATTTTCCCAGCAA+AGG - chr8_2:58128005-58128024 None:intergenic 30.0%
! TTGATCTATTTGTATTGGCA+GGG - chr8_2:58127223-58127242 None:intergenic 30.0%
ACAAATAGATCAAGCATTTC+TGG + chr8_2:58127230-58127249 Msa1257510:five_prime_UTR 30.0%
!! ATTTCTGGTTTGAGTTTCTA+GGG + chr8_2:58127245-58127264 Msa1257510:five_prime_UTR 30.0%
AATAATAATCAACTCACCCA+TGG - chr8_2:58127341-58127360 None:intergenic 30.0%
!! TGAAAGAATTTTGTTGTGCT+AGG + chr8_2:58127862-58127881 Msa1257510:three_prime_UTR 30.0%
!! TTTGTTGTGCTAGGTAATTT+TGG + chr8_2:58127871-58127890 Msa1257510:three_prime_UTR 30.0%
TATTCGACCATATGATTGTT+TGG + chr8_2:58127905-58127924 Msa1257510:three_prime_UTR 30.0%
CAAATAATTTGACCTTTGCT+GGG + chr8_2:58127990-58128009 Msa1257510:three_prime_UTR 30.0%
! ATAACAAATTTTCCCAGCAA+AGG - chr8_2:58128005-58128024 None:intergenic 30.0%
! ATTTGTATTGGCAGGGTTAA+AGG - chr8_2:58127216-58127235 None:intergenic 35.0%
! CTTGATCTATTTGTATTGGC+AGG - chr8_2:58127224-58127243 None:intergenic 35.0%
!! CATTTCTGGTTTGAGTTTCT+AGG + chr8_2:58127244-58127263 Msa1257510:five_prime_UTR 35.0%
! TGAATCGACATTTGAAATGC+AGG + chr8_2:58127425-58127444 Msa1257510:intron 35.0%
! TGTCTTGCTTTGCAACTTTT+GGG - chr8_2:58127499-58127518 None:intergenic 35.0%
! TTGTCTTGCTTTGCAACTTT+TGG - chr8_2:58127500-58127519 None:intergenic 35.0%
AAGAATGATAAAGTTACCGG+CGG - chr8_2:58127582-58127601 None:intergenic 35.0%
ATTATTGCAGTTGTGGGATT+TGG + chr8_2:58127705-58127724 Msa1257510:intron 35.0%
!! CTTCACTTTTCAGATGAGTT+AGG - chr8_2:58127744-58127763 None:intergenic 35.0%
AAAGTGAAGATGATGCTTAG+TGG + chr8_2:58127755-58127774 Msa1257510:exon 35.0%
AATTACAAAATGGGTCGATG+TGG + chr8_2:58127933-58127952 Msa1257510:three_prime_UTR 35.0%
GCAAATAATTTGACCTTTGC+TGG + chr8_2:58127989-58128008 Msa1257510:three_prime_UTR 35.0%
! ATTTGTATTGGCAGGGTTAA+AGG - chr8_2:58127216-58127235 None:intergenic 35.0%
! CTTGATCTATTTGTATTGGC+AGG - chr8_2:58127224-58127243 None:intergenic 35.0%
!! CATTTCTGGTTTGAGTTTCT+AGG + chr8_2:58127244-58127263 Msa1257510:five_prime_UTR 35.0%
! TGAATCGACATTTGAAATGC+AGG + chr8_2:58127425-58127444 Msa1257510:intron 35.0%
! TGTCTTGCTTTGCAACTTTT+GGG - chr8_2:58127499-58127518 None:intergenic 35.0%
! TTGTCTTGCTTTGCAACTTT+TGG - chr8_2:58127500-58127519 None:intergenic 35.0%
AAGAATGATAAAGTTACCGG+CGG - chr8_2:58127582-58127601 None:intergenic 35.0%
ATTATTGCAGTTGTGGGATT+TGG + chr8_2:58127705-58127724 Msa1257510:intron 35.0%
!! CTTCACTTTTCAGATGAGTT+AGG - chr8_2:58127744-58127763 None:intergenic 35.0%
AAAGTGAAGATGATGCTTAG+TGG + chr8_2:58127755-58127774 Msa1257510:exon 35.0%
AATTACAAAATGGGTCGATG+TGG + chr8_2:58127933-58127952 Msa1257510:three_prime_UTR 35.0%
GCAAATAATTTGACCTTTGC+TGG + chr8_2:58127989-58128008 Msa1257510:three_prime_UTR 35.0%
TGACAAATTCGTCTTCACCA+TGG + chr8_2:58127321-58127340 Msa1257510:exon 40.0%
GACAAATTCGTCTTCACCAT+GGG + chr8_2:58127322-58127341 Msa1257510:exon 40.0%
TGAAATGCAGGTAAAGTGCA+TGG + chr8_2:58127437-58127456 Msa1257510:intron 40.0%
! GTCTTGCTTTGCAACTTTTG+GGG - chr8_2:58127498-58127517 None:intergenic 40.0%
TGACAAATTCGTCTTCACCA+TGG + chr8_2:58127321-58127340 Msa1257510:exon 40.0%
GACAAATTCGTCTTCACCAT+GGG + chr8_2:58127322-58127341 Msa1257510:exon 40.0%
TGAAATGCAGGTAAAGTGCA+TGG + chr8_2:58127437-58127456 Msa1257510:intron 40.0%
! GTCTTGCTTTGCAACTTTTG+GGG - chr8_2:58127498-58127517 None:intergenic 40.0%
! AACTTTTCCTGCACGAGCAA+GGG - chr8_2:58127465-58127484 None:intergenic 45.0%
! TAACTTTTCCTGCACGAGCA+AGG - chr8_2:58127466-58127485 None:intergenic 45.0%
TTGCTCGTGCAGGAAAAGTT+AGG + chr8_2:58127465-58127484 Msa1257510:CDS 45.0%
TGCTCGTGCAGGAAAAGTTA+GGG + chr8_2:58127466-58127485 Msa1257510:CDS 45.0%
! AACTTTTCCTGCACGAGCAA+GGG - chr8_2:58127465-58127484 None:intergenic 45.0%
! TAACTTTTCCTGCACGAGCA+AGG - chr8_2:58127466-58127485 None:intergenic 45.0%
TTGCTCGTGCAGGAAAAGTT+AGG + chr8_2:58127465-58127484 Msa1257510:CDS 45.0%
TGCTCGTGCAGGAAAAGTTA+GGG + chr8_2:58127466-58127485 Msa1257510:CDS 45.0%
GCTCGTGCAGGAAAAGTTAG+GGG + chr8_2:58127467-58127486 Msa1257510:CDS 50.0%
GTGGGATTTGGAAAGAAGCG+TGG + chr8_2:58127717-58127736 Msa1257510:CDS 50.0%
GCTCGTGCAGGAAAAGTTAG+GGG + chr8_2:58127467-58127486 Msa1257510:CDS 50.0%
GTGGGATTTGGAAAGAAGCG+TGG + chr8_2:58127717-58127736 Msa1257510:CDS 50.0%
CGATTTGCAGCAGCAGCTCT+CGG - chr8_2:58127277-58127296 None:intergenic 55.0%
GACAAGAAGAAGCAGCCACG+AGG + chr8_2:58127515-58127534 Msa1257510:CDS 55.0%
AGTTACCGGCGGTGACGAAA+CGG - chr8_2:58127571-58127590 None:intergenic 55.0%
CGATTTGCAGCAGCAGCTCT+CGG - chr8_2:58127277-58127296 None:intergenic 55.0%
GACAAGAAGAAGCAGCCACG+AGG + chr8_2:58127515-58127534 Msa1257510:CDS 55.0%
AGTTACCGGCGGTGACGAAA+CGG - chr8_2:58127571-58127590 None:intergenic 55.0%
CATGGTTCCCTTGCTCGTGC+AGG + chr8_2:58127455-58127474 Msa1257510:CDS 60.0%
AATCGCCGTTTCGTCACCGC+CGG + chr8_2:58127563-58127582 Msa1257510:CDS 60.0%
CATGGTTCCCTTGCTCGTGC+AGG + chr8_2:58127455-58127474 Msa1257510:CDS 60.0%
AATCGCCGTTTCGTCACCGC+CGG + chr8_2:58127563-58127582 Msa1257510:CDS 60.0%
CGCTTGTGAGCACGTCCTCG+TGG - chr8_2:58127533-58127552 None:intergenic 65.0%
CGCTTGTGAGCACGTCCTCG+TGG - chr8_2:58127533-58127552 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
chr8_2 gene 58127210 58128093 58127210 ID=Msa1257510;Name=Msa1257510
chr8_2 mRNA 58127210 58128093 58127210 ID=Msa1257510-mRNA-1;Parent=Msa1257510;Name=Msa1257510-mRNA-1;_AED=0.01;_eAED=0.01;_QI=130|1|1|1|1|1|3|332|62
chr8_2 exon 58127210 58127343 58127210 ID=Msa1257510-mRNA-1:exon:17970;Parent=Msa1257510-mRNA-1
chr8_2 exon 58127447 58127584 58127447 ID=Msa1257510-mRNA-1:exon:17971;Parent=Msa1257510-mRNA-1
chr8_2 exon 58127715 58128093 58127715 ID=Msa1257510-mRNA-1:exon:17972;Parent=Msa1257510-mRNA-1
chr8_2 five_prime_UTR 58127210 58127339 58127210 ID=Msa1257510-mRNA-1:five_prime_utr;Parent=Msa1257510-mRNA-1
chr8_2 CDS 58127340 58127343 58127340 ID=Msa1257510-mRNA-1:cds;Parent=Msa1257510-mRNA-1
chr8_2 CDS 58127447 58127584 58127447 ID=Msa1257510-mRNA-1:cds;Parent=Msa1257510-mRNA-1
chr8_2 CDS 58127715 58127761 58127715 ID=Msa1257510-mRNA-1:cds;Parent=Msa1257510-mRNA-1
chr8_2 three_prime_UTR 58127762 58128093 58127762 ID=Msa1257510-mRNA-1:three_prime_utr;Parent=Msa1257510-mRNA-1
Gene Sequence

>Msa1257510

ATGGGTAAAGTGCATGGTTCCCTTGCTCGTGCAGGAAAAGTTAGGGGACAAACCCCAAAAGTTGCAAAGCAAGACAAGAAGAAGCAGCCACGAGGACGTGCTCACAAGCGTATGCAATACAATCGCCGTTTCGTCACCGCCGTTGTGGGATTTGGAAAGAAGCGTGGACCTAACTCATCTGAAAAGTGA

Protein sequence

>Msa1257510

MGKVHGSLARAGKVRGQTPKVAKQDKKKQPRGRAHKRMQYNRRFVTAVVGFGKKRGPNSSEK*