AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene059933


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene059933.t1 MTR_4g104870 99.115 113 1 0 1 113 1 113 2.06e-82 238
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene059933.t1 AT4G24700 41.860 86 42 3 16 98 24 104 1.60e-13 63.5

Find 25 sgRNAs with CRISPR-Local

Find 56 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCCAAATCAGTTCAACTAAA+AGG 0.265894 8.1:-19715306 MS.gene059933:intron
CTTTCAACACTTCTAAATCT+TGG 0.352567 8.1:+19715592 None:intergenic
GTTTCAAGAAGGATTGAAAC+AGG 0.360068 8.1:-19715366 MS.gene059933:CDS
GTTTCAAGCTTAAACCTTGA+AGG 0.367417 8.1:+19715483 None:intergenic
ACACTTCTAAATCTTGGTTA+TGG 0.368826 8.1:+19715598 None:intergenic
TAAACAGAGCCTAACCAAAA+AGG 0.376150 8.1:-19714641 MS.gene059933:intron
GAAACTGTTACAAGCTCATA+AGG 0.391839 8.1:+19715384 None:intergenic
TGACTTTCAACACTCACTTT+GGG 0.415015 8.1:-19715409 MS.gene059933:CDS
GAAATTTCCTTCGCACTTTG+TGG 0.415079 8.1:+19714580 None:intergenic
TCCTTCGCACTTTGTGGTAG+TGG 0.419797 8.1:+19714586 None:intergenic
ATTTCAGAGGTAAGCCTTCA+AGG 0.422597 8.1:-19715497 MS.gene059933:CDS
GTGACTTTCAACACTCACTT+TGG 0.455830 8.1:-19715410 MS.gene059933:CDS
AGTGGTCGAGTGATCAAGAT+AGG 0.479619 8.1:+19714604 None:intergenic
TTCCCTAGTTGATGATGACT+TGG 0.515303 8.1:+19715455 None:intergenic
AGCTTGTAACAGTTTCAAGA+AGG 0.526241 8.1:-19715377 MS.gene059933:CDS
TAACCAAGTCATCATCAACT+AGG 0.529261 8.1:-19715458 MS.gene059933:CDS
AAACTGTTACAAGCTCATAA+GGG 0.547351 8.1:+19715385 None:intergenic
ACTCAAAGGCTTTACACTGC+CGG 0.552991 8.1:+19715542 None:intergenic
AACCAAGTCATCATCAACTA+GGG 0.574505 8.1:-19715457 MS.gene059933:CDS
TGAAAGCTGTTGCACAAGCT+TGG 0.604295 8.1:-19715575 MS.gene059933:CDS
CGCGCGTCGAATTCACTCAA+AGG 0.612095 8.1:+19715528 None:intergenic
ACCACTACCACAAAGTGCGA+AGG 0.629370 8.1:-19714587 MS.gene059933:CDS
TTTCAAGAAGGATTGAAACA+GGG 0.651798 8.1:-19715365 MS.gene059933:CDS
GCGCGTCGAAGAAATTTCAG+AGG 0.671191 8.1:-19715510 MS.gene059933:CDS
CAAGCTTGGTACAATCACTC+CGG 0.679934 8.1:-19715561 MS.gene059933:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTTTATTTTTTTTTAAAA+TGG + chr8.1:19715399-19715418 None:intergenic 0.0%
!! ATATATAAGTTATGAAAATG+AGG + chr8.1:19715319-19715338 None:intergenic 15.0%
!!! TATACTAGTTTGTTATATTA+GGG - chr8.1:19715095-19715114 MS.gene059933:intron 15.0%
!!! TTATACTAGTTTGTTATATT+AGG - chr8.1:19715094-19715113 MS.gene059933:intron 15.0%
!!! TTTTTAAAATGGAAAAGAAA+TGG + chr8.1:19715388-19715407 None:intergenic 15.0%
!! TATTAGGGAAATAGATTATT+CGG - chr8.1:19715110-19715129 MS.gene059933:intron 20.0%
!!! ATTTTTCAGTGGATAATTTA+GGG + chr8.1:19714987-19715006 None:intergenic 20.0%
!!! TTAATATAAAGTACCCTTAA+GGG - chr8.1:19715345-19715364 MS.gene059933:CDS 20.0%
! AGACACAAAAATCATCAAAT+GGG + chr8.1:19714876-19714895 None:intergenic 25.0%
! ATCGTGCGATTAAAAATAAA+CGG - chr8.1:19715163-19715182 MS.gene059933:intron 25.0%
! TATTGTCTAATTGTTTCCTA+TGG - chr8.1:19715490-19715509 MS.gene059933:CDS 25.0%
!! AGTGTTACAATATTTTCCAT+AGG + chr8.1:19715509-19715528 None:intergenic 25.0%
!! CTTAATATAAAGTACCCTTA+AGG - chr8.1:19715344-19715363 MS.gene059933:CDS 25.0%
!!! ACGAAATAACTTTCACTTTT+TGG - chr8.1:19715250-19715269 MS.gene059933:intron 25.0%
!!! CATTTTTCAGTGGATAATTT+AGG + chr8.1:19714988-19715007 None:intergenic 25.0%
!!! CTTAAGGGTACTTTATATTA+AGG + chr8.1:19715346-19715365 None:intergenic 25.0%
AAACTGTTACAAGCTCATAA+GGG + chr8.1:19714819-19714838 None:intergenic 30.0%
AAATCAAAACATTGCCCTTA+AGG + chr8.1:19715362-19715381 None:intergenic 30.0%
AATCAAAACATTGCCCTTAA+GGG + chr8.1:19715361-19715380 None:intergenic 30.0%
ACACTTCTAAATCTTGGTTA+TGG + chr8.1:19714606-19714625 None:intergenic 30.0%
AGTTCAACTAAAAGGTAAGA+GGG - chr8.1:19714903-19714922 MS.gene059933:intron 30.0%
CTTTCAACACTTCTAAATCT+TGG + chr8.1:19714612-19714631 None:intergenic 30.0%
GAGACACAAAAATCATCAAA+TGG + chr8.1:19714877-19714896 None:intergenic 30.0%
TCCAAATCAGTTCAACTAAA+AGG - chr8.1:19714895-19714914 MS.gene059933:intron 30.0%
TGTTCAATAACATGTCTTCT+AGG - chr8.1:19714950-19714969 MS.gene059933:intron 30.0%
TTTCAAGAAGGATTGAAACA+GGG - chr8.1:19714836-19714855 MS.gene059933:intron 30.0%
! AAGTTATTTCGTCTATCCAA+TGG + chr8.1:19715242-19715261 None:intergenic 30.0%
!! ACCTTTTAGTTGAACTGATT+TGG + chr8.1:19714899-19714918 None:intergenic 30.0%
!! CATGTACTATCATTTTTCAG+TGG + chr8.1:19714998-19715017 None:intergenic 30.0%
AACCAAGTCATCATCAACTA+GGG - chr8.1:19714744-19714763 MS.gene059933:intron 35.0%
ACTGCATAAATCAGAACCAT+TGG - chr8.1:19715223-19715242 MS.gene059933:intron 35.0%
AGCTTGTAACAGTTTCAAGA+AGG - chr8.1:19714824-19714843 MS.gene059933:intron 35.0%
CAGTTCAACTAAAAGGTAAG+AGG - chr8.1:19714902-19714921 MS.gene059933:intron 35.0%
GAAACTGTTACAAGCTCATA+AGG + chr8.1:19714820-19714839 None:intergenic 35.0%
GTTTCAAGAAGGATTGAAAC+AGG - chr8.1:19714835-19714854 MS.gene059933:intron 35.0%
GTTTCAAGCTTAAACCTTGA+AGG + chr8.1:19714721-19714740 None:intergenic 35.0%
TAAACAGAGCCTAACCAAAA+AGG - chr8.1:19715560-19715579 MS.gene059933:CDS 35.0%
TAACCAAGTCATCATCAACT+AGG - chr8.1:19714743-19714762 MS.gene059933:intron 35.0%
TGACTTTCAACACTCACTTT+GGG - chr8.1:19714792-19714811 MS.gene059933:intron 35.0%
!!! TTTTCGATGCCTTTTTGGTT+AGG + chr8.1:19715572-19715591 None:intergenic 35.0%
ATTTCAGAGGTAAGCCTTCA+AGG - chr8.1:19714704-19714723 MS.gene059933:intron 40.0%
GAAATTTCCTTCGCACTTTG+TGG + chr8.1:19715624-19715643 None:intergenic 40.0%
GGGAGAGTAAGAATAGTCTT+AGG - chr8.1:19714923-19714942 MS.gene059933:intron 40.0%
GTGACTTTCAACACTCACTT+TGG - chr8.1:19714791-19714810 MS.gene059933:intron 40.0%
TTTAGAAAGCAGTCAAGCGA+AGG + chr8.1:19715544-19715563 None:intergenic 40.0%
! CCATGTTTTCGATGCCTTTT+TGG + chr8.1:19715577-19715596 None:intergenic 40.0%
!! CCAAAAAGGCATCGAAAACA+TGG - chr8.1:19715574-19715593 MS.gene059933:CDS 40.0%
!! TTCCCTAGTTGATGATGACT+TGG + chr8.1:19714749-19714768 None:intergenic 40.0%
ACTCAAAGGCTTTACACTGC+CGG + chr8.1:19714662-19714681 None:intergenic 45.0%
AGTGGTCGAGTGATCAAGAT+AGG + chr8.1:19715600-19715619 None:intergenic 45.0%
CAAGCTTGGTACAATCACTC+CGG - chr8.1:19714640-19714659 MS.gene059933:intron 45.0%
TGAAAGCTGTTGCACAAGCT+TGG - chr8.1:19714626-19714645 MS.gene059933:CDS 45.0%
ACCACTACCACAAAGTGCGA+AGG - chr8.1:19715614-19715633 MS.gene059933:CDS 50.0%
GCGCGTCGAAGAAATTTCAG+AGG - chr8.1:19714691-19714710 MS.gene059933:intron 50.0%
TCCTTCGCACTTTGTGGTAG+TGG + chr8.1:19715618-19715637 None:intergenic 50.0%
CGCGCGTCGAATTCACTCAA+AGG + chr8.1:19714676-19714695 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr8.1 gene 19714577 19715646 19714577 ID=MS.gene059933
chr8.1 mRNA 19714577 19715646 19714577 ID=MS.gene059933.t1;Parent=MS.gene059933
chr8.1 exon 19715307 19715646 19715307 ID=MS.gene059933.t1.exon1;Parent=MS.gene059933.t1
chr8.1 CDS 19715307 19715646 19715307 ID=cds.MS.gene059933.t1;Parent=MS.gene059933.t1
chr8.1 exon 19714577 19714656 19714577 ID=MS.gene059933.t1.exon2;Parent=MS.gene059933.t1
chr8.1 CDS 19714577 19714656 19714577 ID=cds.MS.gene059933.t1;Parent=MS.gene059933.t1
Gene Sequence

>MS.gene059933

ATGAAGAAGAAGCAGCATCATGAAAACCATAACCAAGATTTAGAAGTGTTGAAAGCTGTTGCACAAGCTTGGTACAATCACTCCGGCAGTGTAAAGCCTTTGAGTGAATTCGACGCGCGTCGAAGAAATTTCAGAGGTAAGCCTTCAAGGTTTAAGCTTGAAACATTAACCAAGTCATCATCAACTAGGGAAACAAACTCTTCAACTTATTATTGTGACTTTCAACACTCACTTTGGGACCCTTATGAGCTTGTAACAGTTTCAAGAAGGATTGAAACAGGGTTAGCTTTAGATAACCCATTTGATGATTTTTGTGTCTCCAAATCAGTTCAACTAAAAGGTAAGAGGGAGAGTAAGAATAGTCTTAGGAATCTGTTCAATAACATGTCTTCTAGGCGATTTAATCTCCCTAAATTATCCACTGAAAAATGATAGTACATGATTTTCTTCTTTTATCTCAAGAGTCATCTTAATTAATTCTTATTTTTGTTCAATACGTATTAGATATCAATAATAGTTATACTAGTTTGTTATATTAGGGAAATAGATTATTCGGAGTTATTGCGTCAAACAGTAACTACTGTCGATCGTGCGATTAAAAATAAACGGTTGTGATTGAACTAAGTTTGATTATTTGTCAAATTACACTGCATAAATCAGAACCATTGGATAGACGAAATAACTTTCACTTTTTGGTAGATAGACGAAATAACAATAGTCATTAAAAAGAGTCACTTCACCTCATTTTCATAACTTATATATAAAACCTTAATATAAAGTACCCTTAAGGGCAATGTTTTGATTTTCACCATTTCTTTTCCATTTTAAAAAAAAATAAAAAAAATAAAAACATGTATCACTTGCATCATATTGTCAAAAATAAAAAAAATAAAAACATGTATCACTTGTATCATATTGTCTAATTGTTTCCTATGGAAAATATTGTAACACTCGTAGCAGTATACCTTCGCTTGACTGCTTTCTAAACAGAGCCTAACCAAAAAGGCATCGAAAACATGGCCTATCTTGATCACTCGACCACTACCACAAAGTGCGAAGGAAATTTCTAA

Protein sequence

>MS.gene059933.t1

MKKKQHHENHNQDLEVLKAVAQAWYNHSGSVKPLSEFDARRRNFRGKPSRFKLETLTKSSSTRETNSSTYYCDFQHSLWDPYELVTVSRRIETGLALDNPFDDFCVSKSVQLKEPNQKGIENMAYLDHSTTTTKCEGNF