AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene83172


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene83172.t1 MTR_4g078240 98.802 167 0 1 1 165 1 167 4.73e-116 325
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene83172.t1 AT4G03600 62.025 158 55 1 13 165 3 160 4.34e-68 204
MS.gene83172.t1 AT1G03730 64.417 163 54 2 7 165 3 165 9.95e-60 183
MS.gene83172.t1 AT4G28330 57.862 159 58 2 1 159 1 150 3.20e-44 143
MS.gene83172.t1 AT4G28340 57.823 147 61 1 13 159 5 150 1.35e-42 139

Find 28 sgRNAs with CRISPR-Local

Find 41 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGCTGCTGTTTGTGCTGTTT+TGG 0.192732 4.2:+31792678 MS.gene83172:CDS
GGTTGCTGCTTTGGTTATTA+TGG 0.210965 4.2:+31792504 MS.gene83172:CDS
TTCTCAAATCAATGCTTTCT+TGG 0.227365 4.2:+31792392 MS.gene83172:CDS
ATCTATGCATCTGTTCTTCT+TGG 0.241680 4.2:+31792457 MS.gene83172:CDS
AATTCCATGAAGAAGCTAAA+AGG 0.267312 4.2:-31792369 None:intergenic
GCTTTCTATGGTTGCTGCTT+TGG 0.287079 4.2:+31792495 MS.gene83172:CDS
AACAATAACATGTATGAATA+TGG 0.311322 4.2:-31792289 None:intergenic
AGAACAGATGCATAGATTGC+AGG 0.399836 4.2:-31792451 None:intergenic
GTTGAAGGAAGGAAGATTAC+TGG 0.414092 4.2:+31792604 MS.gene83172:CDS
TATTATGGTTCCTGCAGTTA+TGG 0.418968 4.2:+31792519 MS.gene83172:CDS
AGGAGGACTTTGGTGGTTGA+AGG 0.432920 4.2:+31792589 MS.gene83172:CDS
GAAAGCCAACAAAACAACTA+TGG 0.434853 4.2:-31792554 None:intergenic
GGACTTTGGTGGTTGAAGGA+AGG 0.465297 4.2:+31792593 MS.gene83172:CDS
TGGAAAACCTAGGAGGACTT+TGG 0.466296 4.2:+31792579 MS.gene83172:CDS
CAAGCTCAATCATCAACCTC+TGG 0.488041 4.2:+31792424 MS.gene83172:CDS
ATTCCATGAAGAAGCTAAAA+GGG 0.497710 4.2:-31792368 None:intergenic
TCAACCACCAAAGTCCTCCT+AGG 0.505379 4.2:-31792586 None:intergenic
CTAAAAGGGTACCGTAAACA+AGG 0.549968 4.2:-31792354 None:intergenic
AAAACCTAGGAGGACTTTGG+TGG 0.554975 4.2:+31792582 MS.gene83172:CDS
CTCAATCATCAACCTCTGGT+TGG 0.564957 4.2:+31792428 MS.gene83172:CDS
TGTTGTTGAATCGATGATGT+TGG 0.569323 4.2:-31792259 None:intergenic
ATCCACGTCACCATAACTGC+AGG 0.577508 4.2:-31792529 None:intergenic
TAATGAGCAAAAGAAGAACA+TGG 0.605526 4.2:+31792317 MS.gene83172:CDS
TGGCTTTCTTTGGAAAACCT+AGG 0.614419 4.2:+31792569 MS.gene83172:CDS
CTTTCTTTGGAAAACCTAGG+AGG 0.626529 4.2:+31792572 MS.gene83172:CDS
AATGAGCAAAAGAAGAACAT+GGG 0.646111 4.2:+31792318 MS.gene83172:CDS
ATAGATTGCAGGCCAACCAG+AGG 0.699263 4.2:-31792440 None:intergenic
TTCCTGCAGTTATGGTGACG+TGG 0.716496 4.2:+31792527 MS.gene83172:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AACAATAACATGTATGAATA+TGG - chr4.2:31792292-31792311 None:intergenic 20.0%
!! ATTAAGATTTTGCTGAAAGA+AGG + chr4.2:31792646-31792665 MS.gene83172:CDS 25.0%
!! TTAAGATTTTGCTGAAAGAA+GGG + chr4.2:31792647-31792666 MS.gene83172:CDS 25.0%
!!! TGTCTATTTTTCCTTGTTTA+CGG + chr4.2:31792343-31792362 MS.gene83172:CDS 25.0%
AATGAGCAAAAGAAGAACAT+GGG + chr4.2:31792318-31792337 MS.gene83172:CDS 30.0%
AATTCCATGAAGAAGCTAAA+AGG - chr4.2:31792372-31792391 None:intergenic 30.0%
ATTCCATGAAGAAGCTAAAA+GGG - chr4.2:31792371-31792390 None:intergenic 30.0%
TAATGAGCAAAAGAAGAACA+TGG + chr4.2:31792317-31792336 MS.gene83172:CDS 30.0%
TTCTCAAATCAATGCTTTCT+TGG + chr4.2:31792392-31792411 MS.gene83172:CDS 30.0%
!! GATAACCATAGTTGTTTTGT+TGG + chr4.2:31792549-31792568 MS.gene83172:CDS 30.0%
!! TTCTTCTTGGAACTGTTTTT+GGG + chr4.2:31792470-31792489 MS.gene83172:CDS 30.0%
!!! GGTATTTTGTTTTGGTTAGA+AGG + chr4.2:31792701-31792720 MS.gene83172:CDS 30.0%
!!! TGTTTTGGGGTATTTTGTTT+TGG + chr4.2:31792693-31792712 MS.gene83172:CDS 30.0%
ATCTATGCATCTGTTCTTCT+TGG + chr4.2:31792457-31792476 MS.gene83172:CDS 35.0%
GAAAGCCAACAAAACAACTA+TGG - chr4.2:31792557-31792576 None:intergenic 35.0%
TATTATGGTTCCTGCAGTTA+TGG + chr4.2:31792519-31792538 MS.gene83172:CDS 35.0%
TGTTGTTGAATCGATGATGT+TGG - chr4.2:31792262-31792281 None:intergenic 35.0%
! GTTCTTCTTGGAACTGTTTT+TGG + chr4.2:31792469-31792488 MS.gene83172:CDS 35.0%
!!! GTTGTTTTGTTGGCTTTCTT+TGG + chr4.2:31792559-31792578 MS.gene83172:CDS 35.0%
!!! TGTTTTTGGGTTGCTTTCTA+TGG + chr4.2:31792483-31792502 MS.gene83172:CDS 35.0%
AGAACAGATGCATAGATTGC+AGG - chr4.2:31792454-31792473 None:intergenic 40.0%
GTTGAAGGAAGGAAGATTAC+TGG + chr4.2:31792604-31792623 MS.gene83172:CDS 40.0%
! CTTTCTTTGGAAAACCTAGG+AGG + chr4.2:31792572-31792591 MS.gene83172:CDS 40.0%
! TGGCTTTCTTTGGAAAACCT+AGG + chr4.2:31792569-31792588 MS.gene83172:CDS 40.0%
!! CTAAAAGGGTACCGTAAACA+AGG - chr4.2:31792357-31792376 None:intergenic 40.0%
!! GGTTGCTGCTTTGGTTATTA+TGG + chr4.2:31792504-31792523 MS.gene83172:CDS 40.0%
!!! GTACCCTTTTAGCTTCTTCA+TGG + chr4.2:31792365-31792384 MS.gene83172:CDS 40.0%
AAAACCTAGGAGGACTTTGG+TGG + chr4.2:31792582-31792601 MS.gene83172:CDS 45.0%
CAAGCTCAATCATCAACCTC+TGG + chr4.2:31792424-31792443 MS.gene83172:CDS 45.0%
CTCAATCATCAACCTCTGGT+TGG + chr4.2:31792428-31792447 MS.gene83172:CDS 45.0%
TGGAAAACCTAGGAGGACTT+TGG + chr4.2:31792579-31792598 MS.gene83172:CDS 45.0%
! GCTTTCTATGGTTGCTGCTT+TGG + chr4.2:31792495-31792514 MS.gene83172:CDS 45.0%
!!! CTGCTGTTTGTGCTGTTTTG+GGG + chr4.2:31792680-31792699 MS.gene83172:CDS 45.0%
!!! GCTGCTGTTTGTGCTGTTTT+GGG + chr4.2:31792679-31792698 MS.gene83172:CDS 45.0%
!!! TGCTGCTGTTTGTGCTGTTT+TGG + chr4.2:31792678-31792697 MS.gene83172:CDS 45.0%
ATAGATTGCAGGCCAACCAG+AGG - chr4.2:31792443-31792462 None:intergenic 50.0%
ATCCACGTCACCATAACTGC+AGG - chr4.2:31792532-31792551 None:intergenic 50.0%
TCAACCACCAAAGTCCTCCT+AGG - chr4.2:31792589-31792608 None:intergenic 50.0%
! AGGAGGACTTTGGTGGTTGA+AGG + chr4.2:31792589-31792608 MS.gene83172:CDS 50.0%
! GGACTTTGGTGGTTGAAGGA+AGG + chr4.2:31792593-31792612 MS.gene83172:CDS 50.0%
! TTCCTGCAGTTATGGTGACG+TGG + chr4.2:31792527-31792546 MS.gene83172:CDS 50.0%


Chromosome Type Strat End Strand Name
chr4.2 gene 31792238 31792735 31792238 ID=MS.gene83172
chr4.2 mRNA 31792238 31792735 31792238 ID=MS.gene83172.t1;Parent=MS.gene83172
chr4.2 exon 31792238 31792735 31792238 ID=MS.gene83172.t1.exon1;Parent=MS.gene83172.t1
chr4.2 CDS 31792238 31792735 31792238 ID=cds.MS.gene83172.t1;Parent=MS.gene83172.t1
Gene Sequence

>MS.gene83172

ATGGCAAAATTAGAAGAAGAACCAACATCATCGATTCAACAACAACAAGCACCATATTCATACATGTTATTGTTGAACATAATGAGCAAAAGAAGAACATGGGCATGTCTATTTTTCCTTGTTTACGGTACCCTTTTAGCTTCTTCATGGAATTTTCTCAAATCAATGCTTTCTTGGTACAATTTACAAGCTCAATCATCAACCTCTGGTTGGCCTGCAATCTATGCATCTGTTCTTCTTGGAACTGTTTTTGGGTTGCTTTCTATGGTTGCTGCTTTGGTTATTATGGTTCCTGCAGTTATGGTGACGTGGATAACCATAGTTGTTTTGTTGGCTTTCTTTGGAAAACCTAGGAGGACTTTGGTGGTTGAAGGAAGGAAGATTACTGGTGAAATTTTCAGTTTTGTTATTAAGATTTTGCTGAAAGAAGGGAATGTTGTTGCTGCTGTTTGTGCTGTTTTGGGGTATTTTGTTTTGGTTAGAAGGAATAGTGAATGA

Protein sequence

>MS.gene83172.t1

MAKLEEEPTSSIQQQQAPYSYMLLLNIMSKRRTWACLFFLVYGTLLASSWNFLKSMLSWYNLQAQSSTSGWPAIYASVLLGTVFGLLSMVAALVIMVPAVMVTWITIVVLLAFFGKPRRTLVVEGRKITGEIFSFVIKILLKEGNVVAAVCAVLGYFVLVRRNSE