AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1210020


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 31 sgRNAs with CRISPR-Local

Find 102 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGAAACCCTAATTTAAAATT+TGG 0.114721 8_1:+68699981 None:intergenic
TAGTTACTATTGAAAATATT+TGG 0.211067 8_1:-68699498 Msa1210020:three_prime_UTR
AAATTAGGGTTTCTGAGATT+TGG 0.249611 8_1:-68699972 Msa1210020:five_prime_UTR
TTGACGTTCTCGGAAGGTTT+TGG 0.276388 8_1:+68699928 None:intergenic
AATTAGGGTTTCTGAGATTT+GGG 0.294104 8_1:-68699971 Msa1210020:five_prime_UTR
AAGAAATAAAACTATTTGTT+AGG 0.306769 8_1:-68699584 Msa1210020:exon
ACAACTCATTTGAGATGATA+AGG 0.388084 8_1:-68700063 Msa1210020:five_prime_UTR
CATAGTATCACTTGTGAGTA+TGG 0.389503 8_1:-68699413 Msa1210020:three_prime_UTR
CTCAGCAATGGGAAGATGAT+TGG 0.389575 8_1:-68699673 Msa1210020:CDS
CAACTCATTTGAGATGATAA+GGG 0.399945 8_1:-68700062 Msa1210020:five_prime_UTR
TCAGCTAAAGAGAGAGTTAG+AGG 0.407568 8_1:-68699618 Msa1210020:CDS
GAGATCAACCTTGACGTTCT+CGG 0.418361 8_1:+68699918 None:intergenic
AGACAAGGAGGAAGGGAGAG+AGG 0.431303 8_1:-68699699 Msa1210020:CDS
TGAAGACGACGACGAGTTCG+AGG 0.463513 8_1:-68699893 Msa1210020:CDS
TCAGCAATGGGAAGATGATT+GGG 0.477084 8_1:-68699672 Msa1210020:CDS
GAACGATTGTGGTTAAACTT+AGG 0.479254 8_1:-68699370 Msa1210020:three_prime_UTR
TGAGATTTGGGTTAATCCAA+TGG 0.503923 8_1:-68699959 Msa1210020:exon
GGAGAGAGGTAGCTCAGCAA+TGG 0.520450 8_1:-68699685 Msa1210020:CDS
GGTTGGGAAGACAAGGAGGA+AGG 0.522923 8_1:-68699707 Msa1210020:CDS
GAGAGAGGTAGCTCAGCAAT+GGG 0.525728 8_1:-68699684 Msa1210020:CDS
GTTGGGAAGACAAGGAGGAA+GGG 0.529450 8_1:-68699706 Msa1210020:CDS
TACACCACATCAAATTGTTG+TGG 0.549280 8_1:-68699436 Msa1210020:three_prime_UTR
ACGATAGTGATATGTCTTCG+AGG 0.550743 8_1:+68700021 None:intergenic
GTATCACTTGTGAGTATGGT+TGG 0.566274 8_1:-68699409 Msa1210020:three_prime_UTR
TCAACCTTGACGTTCTCGGA+AGG 0.583809 8_1:+68699922 None:intergenic
ACTTGCAGGTTGGGAAGACA+AGG 0.596138 8_1:-68699714 Msa1210020:intron
CAGCTAAAGAGAGAGTTAGA+GGG 0.638489 8_1:-68699617 Msa1210020:CDS
GAGGAGTTTGAAATCAACGA+AGG 0.657612 8_1:-68699874 Msa1210020:intron
TGCAGGTTGGGAAGACAAGG+AGG 0.659645 8_1:-68699711 Msa1210020:intron
AAAACCTTCCGAGAACGTCA+AGG 0.660047 8_1:-68699926 Msa1210020:CDS
TATGCCACAACAATTTGATG+TGG 0.714011 8_1:+68699432 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTTTTCCAAATTTTAAATT+AGG - chr8_1:68699419-68699438 Msa1210020:three_prime_UTR 10.0%
!!! TTTTTCCAAATTTTAAATTA+GGG - chr8_1:68699420-68699439 Msa1210020:three_prime_UTR 10.0%
!!! ATTTTTCCAAATTTTAAATT+AGG - chr8_1:68699419-68699438 Msa1210020:three_prime_UTR 10.0%
!!! TTTTTCCAAATTTTAAATTA+GGG - chr8_1:68699420-68699439 Msa1210020:three_prime_UTR 10.0%
!! AAGAAATAAAACTATTTGTT+AGG - chr8_1:68699822-68699841 Msa1210020:intron 15.0%
!!! AAATATTTTCAATAGTAACT+AGG + chr8_1:68699909-68699928 None:intergenic 15.0%
!! TAGTTACTATTGAAAATATT+TGG - chr8_1:68699908-68699927 Msa1210020:CDS 15.0%
!! AAGAAATAAAACTATTTGTT+AGG - chr8_1:68699822-68699841 Msa1210020:intron 15.0%
!!! AAATATTTTCAATAGTAACT+AGG + chr8_1:68699909-68699928 None:intergenic 15.0%
!! TAGTTACTATTGAAAATATT+TGG - chr8_1:68699908-68699927 Msa1210020:CDS 15.0%
!!! AGAAACCCTAATTTAAAATT+TGG + chr8_1:68699428-68699447 None:intergenic 20.0%
!!! AGTTTTTGAATGTTTTCATT+TGG - chr8_1:68699934-68699953 Msa1210020:CDS 20.0%
!!! AGAAACCCTAATTTAAAATT+TGG + chr8_1:68699428-68699447 None:intergenic 20.0%
!!! AGTTTTTGAATGTTTTCATT+TGG - chr8_1:68699934-68699953 Msa1210020:CDS 20.0%
! TACTAACATGAATTCAAATC+TGG + chr8_1:68699639-68699658 None:intergenic 25.0%
!! TTTTGCATCAAGAAATTTTG+TGG + chr8_1:68699871-68699890 None:intergenic 25.0%
!! TGAATGTTTTCATTTGGATT+TGG - chr8_1:68699940-68699959 Msa1210020:CDS 25.0%
!!! TTTTTTTCTATGAACGATTG+TGG - chr8_1:68700025-68700044 Msa1210020:five_prime_UTR 25.0%
! TACTAACATGAATTCAAATC+TGG + chr8_1:68699639-68699658 None:intergenic 25.0%
!! TTTTGCATCAAGAAATTTTG+TGG + chr8_1:68699871-68699890 None:intergenic 25.0%
!! TGAATGTTTTCATTTGGATT+TGG - chr8_1:68699940-68699959 Msa1210020:CDS 25.0%
!!! TTTTTTTCTATGAACGATTG+TGG - chr8_1:68700025-68700044 Msa1210020:five_prime_UTR 25.0%
! ACAACTCATTTGAGATGATA+AGG - chr8_1:68699343-68699362 Msa1210020:three_prime_UTR 30.0%
! CAACTCATTTGAGATGATAA+GGG - chr8_1:68699344-68699363 Msa1210020:three_prime_UTR 30.0%
!! AAATTAGGGTTTCTGAGATT+TGG - chr8_1:68699434-68699453 Msa1210020:three_prime_UTR 30.0%
!! AATTAGGGTTTCTGAGATTT+GGG - chr8_1:68699435-68699454 Msa1210020:three_prime_UTR 30.0%
AAATTGATTGCAACAACGAT+TGG + chr8_1:68699596-68699615 None:intergenic 30.0%
!!! TTGTTAGGTATTTTAGCTCT+AGG - chr8_1:68699837-68699856 Msa1210020:intron 30.0%
! ACAACTCATTTGAGATGATA+AGG - chr8_1:68699343-68699362 Msa1210020:three_prime_UTR 30.0%
! CAACTCATTTGAGATGATAA+GGG - chr8_1:68699344-68699363 Msa1210020:three_prime_UTR 30.0%
!! AAATTAGGGTTTCTGAGATT+TGG - chr8_1:68699434-68699453 Msa1210020:three_prime_UTR 30.0%
!! AATTAGGGTTTCTGAGATTT+GGG - chr8_1:68699435-68699454 Msa1210020:three_prime_UTR 30.0%
AAATTGATTGCAACAACGAT+TGG + chr8_1:68699596-68699615 None:intergenic 30.0%
!!! TTGTTAGGTATTTTAGCTCT+AGG - chr8_1:68699837-68699856 Msa1210020:intron 30.0%
! TGAGATTTGGGTTAATCCAA+TGG - chr8_1:68699447-68699466 Msa1210020:three_prime_UTR 35.0%
AACAACGATTGGAATGAAGA+GGG + chr8_1:68699585-68699604 None:intergenic 35.0%
! TGCAATCTTATGTAACTTGC+AGG - chr8_1:68699678-68699697 Msa1210020:CDS 35.0%
! ATCTTATGTAACTTGCAGGT+TGG - chr8_1:68699682-68699701 Msa1210020:CDS 35.0%
! TCTTATGTAACTTGCAGGTT+GGG - chr8_1:68699683-68699702 Msa1210020:CDS 35.0%
TACACCACATCAAATTGTTG+TGG - chr8_1:68699970-68699989 Msa1210020:five_prime_UTR 35.0%
TATGCCACAACAATTTGATG+TGG + chr8_1:68699977-68699996 None:intergenic 35.0%
CATAGTATCACTTGTGAGTA+TGG - chr8_1:68699993-68700012 Msa1210020:five_prime_UTR 35.0%
GAACGATTGTGGTTAAACTT+AGG - chr8_1:68700036-68700055 Msa1210020:five_prime_UTR 35.0%
! TGAGATTTGGGTTAATCCAA+TGG - chr8_1:68699447-68699466 Msa1210020:three_prime_UTR 35.0%
AACAACGATTGGAATGAAGA+GGG + chr8_1:68699585-68699604 None:intergenic 35.0%
! TGCAATCTTATGTAACTTGC+AGG - chr8_1:68699678-68699697 Msa1210020:CDS 35.0%
! ATCTTATGTAACTTGCAGGT+TGG - chr8_1:68699682-68699701 Msa1210020:CDS 35.0%
! TCTTATGTAACTTGCAGGTT+GGG - chr8_1:68699683-68699702 Msa1210020:CDS 35.0%
TACACCACATCAAATTGTTG+TGG - chr8_1:68699970-68699989 Msa1210020:five_prime_UTR 35.0%
TATGCCACAACAATTTGATG+TGG + chr8_1:68699977-68699996 None:intergenic 35.0%
CATAGTATCACTTGTGAGTA+TGG - chr8_1:68699993-68700012 Msa1210020:five_prime_UTR 35.0%
GAACGATTGTGGTTAAACTT+AGG - chr8_1:68700036-68700055 Msa1210020:five_prime_UTR 35.0%
ACGATAGTGATATGTCTTCG+AGG + chr8_1:68699388-68699407 None:intergenic 40.0%
! GAGGAGTTTGAAATCAACGA+AGG - chr8_1:68699532-68699551 Msa1210020:three_prime_UTR 40.0%
AATGAAGAGGGGTTAAAGGT+TGG + chr8_1:68699573-68699592 None:intergenic 40.0%
TTGGAATGAAGAGGGGTTAA+AGG + chr8_1:68699577-68699596 None:intergenic 40.0%
ACAACGATTGGAATGAAGAG+GGG + chr8_1:68699584-68699603 None:intergenic 40.0%
CAACAACGATTGGAATGAAG+AGG + chr8_1:68699586-68699605 None:intergenic 40.0%
TCAGCAATGGGAAGATGATT+GGG - chr8_1:68699734-68699753 Msa1210020:intron 40.0%
TCAGCTAAAGAGAGAGTTAG+AGG - chr8_1:68699788-68699807 Msa1210020:intron 40.0%
CAGCTAAAGAGAGAGTTAGA+GGG - chr8_1:68699789-68699808 Msa1210020:intron 40.0%
GTATCACTTGTGAGTATGGT+TGG - chr8_1:68699997-68700016 Msa1210020:five_prime_UTR 40.0%
ACGATAGTGATATGTCTTCG+AGG + chr8_1:68699388-68699407 None:intergenic 40.0%
! GAGGAGTTTGAAATCAACGA+AGG - chr8_1:68699532-68699551 Msa1210020:three_prime_UTR 40.0%
AATGAAGAGGGGTTAAAGGT+TGG + chr8_1:68699573-68699592 None:intergenic 40.0%
TTGGAATGAAGAGGGGTTAA+AGG + chr8_1:68699577-68699596 None:intergenic 40.0%
ACAACGATTGGAATGAAGAG+GGG + chr8_1:68699584-68699603 None:intergenic 40.0%
CAACAACGATTGGAATGAAG+AGG + chr8_1:68699586-68699605 None:intergenic 40.0%
TCAGCAATGGGAAGATGATT+GGG - chr8_1:68699734-68699753 Msa1210020:intron 40.0%
TCAGCTAAAGAGAGAGTTAG+AGG - chr8_1:68699788-68699807 Msa1210020:intron 40.0%
CAGCTAAAGAGAGAGTTAGA+GGG - chr8_1:68699789-68699808 Msa1210020:intron 40.0%
GTATCACTTGTGAGTATGGT+TGG - chr8_1:68699997-68700016 Msa1210020:five_prime_UTR 40.0%
! TTGACGTTCTCGGAAGGTTT+TGG + chr8_1:68699481-68699500 None:intergenic 45.0%
AAAACCTTCCGAGAACGTCA+AGG - chr8_1:68699480-68699499 Msa1210020:three_prime_UTR 45.0%
GAGATCAACCTTGACGTTCT+CGG + chr8_1:68699491-68699510 None:intergenic 45.0%
CTCAGCAATGGGAAGATGAT+TGG - chr8_1:68699733-68699752 Msa1210020:intron 45.0%
! TTGACGTTCTCGGAAGGTTT+TGG + chr8_1:68699481-68699500 None:intergenic 45.0%
AAAACCTTCCGAGAACGTCA+AGG - chr8_1:68699480-68699499 Msa1210020:three_prime_UTR 45.0%
GAGATCAACCTTGACGTTCT+CGG + chr8_1:68699491-68699510 None:intergenic 45.0%
CTCAGCAATGGGAAGATGAT+TGG - chr8_1:68699733-68699752 Msa1210020:intron 45.0%
!!! GTTCTCGGAAGGTTTTGGCT+CGG + chr8_1:68699476-68699495 None:intergenic 50.0%
TCAACCTTGACGTTCTCGGA+AGG + chr8_1:68699487-68699506 None:intergenic 50.0%
! ACTTGCAGGTTGGGAAGACA+AGG - chr8_1:68699692-68699711 Msa1210020:CDS 50.0%
GTTGGGAAGACAAGGAGGAA+GGG - chr8_1:68699700-68699719 Msa1210020:CDS 50.0%
GAGAGAGGTAGCTCAGCAAT+GGG - chr8_1:68699722-68699741 Msa1210020:intron 50.0%
!!! GTTCTCGGAAGGTTTTGGCT+CGG + chr8_1:68699476-68699495 None:intergenic 50.0%
TCAACCTTGACGTTCTCGGA+AGG + chr8_1:68699487-68699506 None:intergenic 50.0%
! ACTTGCAGGTTGGGAAGACA+AGG - chr8_1:68699692-68699711 Msa1210020:CDS 50.0%
GTTGGGAAGACAAGGAGGAA+GGG - chr8_1:68699700-68699719 Msa1210020:CDS 50.0%
GAGAGAGGTAGCTCAGCAAT+GGG - chr8_1:68699722-68699741 Msa1210020:intron 50.0%
!!! GGTTTTGGCTCGGTTGCCAT+TGG + chr8_1:68699466-68699485 None:intergenic 55.0%
TGAAGACGACGACGAGTTCG+AGG - chr8_1:68699513-68699532 Msa1210020:three_prime_UTR 55.0%
! TGCAGGTTGGGAAGACAAGG+AGG - chr8_1:68699695-68699714 Msa1210020:CDS 55.0%
GGTTGGGAAGACAAGGAGGA+AGG - chr8_1:68699699-68699718 Msa1210020:CDS 55.0%
AGACAAGGAGGAAGGGAGAG+AGG - chr8_1:68699707-68699726 Msa1210020:CDS 55.0%
GGAGAGAGGTAGCTCAGCAA+TGG - chr8_1:68699721-68699740 Msa1210020:intron 55.0%
!!! GGTTTTGGCTCGGTTGCCAT+TGG + chr8_1:68699466-68699485 None:intergenic 55.0%
TGAAGACGACGACGAGTTCG+AGG - chr8_1:68699513-68699532 Msa1210020:three_prime_UTR 55.0%
! TGCAGGTTGGGAAGACAAGG+AGG - chr8_1:68699695-68699714 Msa1210020:CDS 55.0%
GGTTGGGAAGACAAGGAGGA+AGG - chr8_1:68699699-68699718 Msa1210020:CDS 55.0%
AGACAAGGAGGAAGGGAGAG+AGG - chr8_1:68699707-68699726 Msa1210020:CDS 55.0%
GGAGAGAGGTAGCTCAGCAA+TGG - chr8_1:68699721-68699740 Msa1210020:intron 55.0%
Chromosome Type Strat End Strand Name
chr8_1 gene 68699341 68700087 68699341 ID=Msa1210020;Name=Msa1210020
chr8_1 mRNA 68699341 68700087 68699341 ID=Msa1210020-mRNA-1;Parent=Msa1210020;Name=Msa1210020-mRNA-1;_AED=0.00;_eAED=0.00;_QI=125|1|1|1|1|1|2|257|72
chr8_1 exon 68699341 68699728 68699341 ID=Msa1210020-mRNA-1:exon:22902;Parent=Msa1210020-mRNA-1
chr8_1 exon 68699875 68700087 68699875 ID=Msa1210020-mRNA-1:exon:22901;Parent=Msa1210020-mRNA-1
chr8_1 five_prime_UTR 68699963 68700087 68699963 ID=Msa1210020-mRNA-1:five_prime_utr;Parent=Msa1210020-mRNA-1
chr8_1 CDS 68699875 68699962 68699875 ID=Msa1210020-mRNA-1:cds;Parent=Msa1210020-mRNA-1
chr8_1 CDS 68699598 68699728 68699598 ID=Msa1210020-mRNA-1:cds;Parent=Msa1210020-mRNA-1
chr8_1 three_prime_UTR 68699341 68699597 68699341 ID=Msa1210020-mRNA-1:three_prime_utr;Parent=Msa1210020-mRNA-1
Gene Sequence

>Msa1210020

ATGGCAACCGAGCCAAAACCTTCCGAGAACGTCAAGGTTGATCTCTTTGAAGACGACGACGAGTTCGAGGAGTTTGAAATCAACGAAGGTTGGGAAGACAAGGAGGAAGGGAGAGAGGTAGCTCAGCAATGGGAAGATGATTGGGATGATGATGATGTTAGTGATGATTTCTCTCTTCAGCTAAAGAGAGAGTTAGAGGGCAATGCTGAGAAGAAATAA

Protein sequence

>Msa1210020

MATEPKPSENVKVDLFEDDDEFEEFEINEGWEDKEEGREVAQQWEDDWDDDDVSDDFSLQLKRELEGNAEKK*