AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0869010


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 9 sgRNAs with CRISPR-Local

Find 110 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAGAGGTGGAAGAGCATTGT+TGG 0.392371 6_1:+2841379 Msa0869010:intron
AAGAGCATTGTTGGTTTCAG+TGG 0.499187 6_1:+2841388 Msa0869010:CDS
AAGAACATTGTTGATTTCAG+TGG 0.510674 6_1:+2842372 Msa0869010:CDS
TCTCGTCAAAACCGTGGAAG+AGG 0.517503 6_1:+2841090 Msa0869010:CDS
GAGAGAGAGTGAATCAGAAG+AGG 0.523266 6_1:-2841021 None:intergenic
AGCATTGTTGGTTTCAGTGG+AGG 0.538384 6_1:+2841391 Msa0869010:CDS
AAATCAAATATTGAAATCAA+CGG 0.594348 6_1:+2840910 None:intergenic
TTCCTCTCTCGTCAAAACCG+TGG 0.622333 6_1:+2841084 Msa0869010:CDS
AAGAATCCGAACCTCTTCCA+CGG 0.634242 6_1:-2841101 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATCAATTTACCTTTATATT+GGG - chr6_1:2841931-2841950 None:intergenic 15.0%
!! AAATCAATTTACCTTTATAT+TGG - chr6_1:2841932-2841951 None:intergenic 15.0%
!! AATAAGCTGAAAAAAATTTA+TGG + chr6_1:2842071-2842090 Msa0869010:intron 15.0%
!! AATCAATTTACCTTTATATT+GGG - chr6_1:2841931-2841950 None:intergenic 15.0%
!! AAATCAATTTACCTTTATAT+TGG - chr6_1:2841932-2841951 None:intergenic 15.0%
!! AATAAGCTGAAAAAAATTTA+TGG + chr6_1:2842071-2842090 Msa0869010:intron 15.0%
!!! ATTTTGTTGAATGTTAGTTT+GGG + chr6_1:2841436-2841455 Msa0869010:intron 20.0%
!!! ATTTTGTTGAATGTTAGTTT+GGG + chr6_1:2841436-2841455 Msa0869010:intron 20.0%
!! GATTTTGTTGAATGTTAGTT+TGG + chr6_1:2841435-2841454 Msa0869010:intron 25.0%
!! AAATTTTGTGTTTGAATGCT+AGG + chr6_1:2841471-2841490 Msa0869010:intron 25.0%
!! AATTTTGTGTTTGAATGCTA+GGG + chr6_1:2841472-2841491 Msa0869010:intron 25.0%
! ATAAGCTGAAAACAACTTAT+TGG + chr6_1:2841567-2841586 Msa0869010:intron 25.0%
!! AATTTTCTGTGTTCAGTTTT+AGG + chr6_1:2841642-2841661 Msa0869010:intron 25.0%
!!! TAAGCTATTTCTATTGTGAA+AGG + chr6_1:2841742-2841761 Msa0869010:intron 25.0%
!! AGTTATATGTTGTTTGCATA+AGG + chr6_1:2841958-2841977 Msa0869010:intron 25.0%
! ATGGTTATGATTTCTATCTT+TGG + chr6_1:2842208-2842227 Msa0869010:intron 25.0%
!! GATTTTGTTGAATGTTAGTT+TGG + chr6_1:2841435-2841454 Msa0869010:intron 25.0%
!! AAATTTTGTGTTTGAATGCT+AGG + chr6_1:2841471-2841490 Msa0869010:intron 25.0%
!! AATTTTGTGTTTGAATGCTA+GGG + chr6_1:2841472-2841491 Msa0869010:intron 25.0%
! ATAAGCTGAAAACAACTTAT+TGG + chr6_1:2841567-2841586 Msa0869010:intron 25.0%
!! AATTTTCTGTGTTCAGTTTT+AGG + chr6_1:2841642-2841661 Msa0869010:intron 25.0%
!!! TAAGCTATTTCTATTGTGAA+AGG + chr6_1:2841742-2841761 Msa0869010:intron 25.0%
!! AGTTATATGTTGTTTGCATA+AGG + chr6_1:2841958-2841977 Msa0869010:intron 25.0%
! ATGGTTATGATTTCTATCTT+TGG + chr6_1:2842208-2842227 Msa0869010:intron 25.0%
!!! TTTTTTTGTGTTTGATGCAG+AGG + chr6_1:2841362-2841381 Msa0869010:intron 30.0%
TTGAGTTTATCCATTAGCAT+AGG - chr6_1:2842146-2842165 None:intergenic 30.0%
!! TTTCTATCTTTGGTGTTTCA+AGG + chr6_1:2842218-2842237 Msa0869010:intron 30.0%
!!! TTTTTTTGTGTTTGATGCAG+AGG + chr6_1:2841362-2841381 Msa0869010:intron 30.0%
!! AAGAACATTGTTGATTTCAG+TGG + chr6_1:2842372-2842391 Msa0869010:CDS 30.0%
!!! TTTTTTTGTGTTTGATGCAG+AGG + chr6_1:2841362-2841381 Msa0869010:intron 30.0%
TTGAGTTTATCCATTAGCAT+AGG - chr6_1:2842146-2842165 None:intergenic 30.0%
!! TTTCTATCTTTGGTGTTTCA+AGG + chr6_1:2842218-2842237 Msa0869010:intron 30.0%
!!! TTTTTTTGTGTTTGATGCAG+AGG + chr6_1:2841362-2841381 Msa0869010:intron 30.0%
!! AAGAACATTGTTGATTTCAG+TGG + chr6_1:2842372-2842391 Msa0869010:CDS 30.0%
!!! TTTTTTCGTGTTTGATGCAG+TGG + chr6_1:2841209-2841228 Msa0869010:intron 35.0%
!!! AAGAGCATTTTCGATTTCAG+TGG + chr6_1:2841235-2841254 Msa0869010:intron 35.0%
!!! GTTCAGTTTTAGGTGATGTA+TGG + chr6_1:2841652-2841671 Msa0869010:intron 35.0%
TATATTGGGACTGTTTGGAT+TGG - chr6_1:2841917-2841936 None:intergenic 35.0%
TCCAAACAGTCCCAATATAA+AGG + chr6_1:2841918-2841937 Msa0869010:intron 35.0%
ACCTTTATATTGGGACTGTT+TGG - chr6_1:2841922-2841941 None:intergenic 35.0%
!! GCTGTTTTCATTAGCTATCT+TGG + chr6_1:2842036-2842055 Msa0869010:intron 35.0%
ACAATCCAAACAAACCCTTA+CGG + chr6_1:2842172-2842191 Msa0869010:intron 35.0%
TATATCCAAACATGCCGTAA+GGG - chr6_1:2842189-2842208 None:intergenic 35.0%
ATATATCCAAACATGCCGTA+AGG - chr6_1:2842190-2842209 None:intergenic 35.0%
TTACGGCATGTTTGGATATA+TGG + chr6_1:2842189-2842208 Msa0869010:intron 35.0%
AAAAGAAATCCTTGTGTGTG+TGG + chr6_1:2842250-2842269 Msa0869010:intron 35.0%
!!! TTTTTTCGTGTTTGATGCAG+TGG + chr6_1:2841209-2841228 Msa0869010:intron 35.0%
!!! AAGAGCATTTTCGATTTCAG+TGG + chr6_1:2841235-2841254 Msa0869010:intron 35.0%
!!! GTTCAGTTTTAGGTGATGTA+TGG + chr6_1:2841652-2841671 Msa0869010:intron 35.0%
TATATTGGGACTGTTTGGAT+TGG - chr6_1:2841917-2841936 None:intergenic 35.0%
TCCAAACAGTCCCAATATAA+AGG + chr6_1:2841918-2841937 Msa0869010:intron 35.0%
ACCTTTATATTGGGACTGTT+TGG - chr6_1:2841922-2841941 None:intergenic 35.0%
!! GCTGTTTTCATTAGCTATCT+TGG + chr6_1:2842036-2842055 Msa0869010:intron 35.0%
ACAATCCAAACAAACCCTTA+CGG + chr6_1:2842172-2842191 Msa0869010:intron 35.0%
TATATCCAAACATGCCGTAA+GGG - chr6_1:2842189-2842208 None:intergenic 35.0%
ATATATCCAAACATGCCGTA+AGG - chr6_1:2842190-2842209 None:intergenic 35.0%
TTACGGCATGTTTGGATATA+TGG + chr6_1:2842189-2842208 Msa0869010:intron 35.0%
AAAAGAAATCCTTGTGTGTG+TGG + chr6_1:2842250-2842269 Msa0869010:intron 35.0%
! TTCAGTGGAGATTTTCACGA+AGG + chr6_1:2841250-2841269 Msa0869010:intron 40.0%
TTCACGAAGGTAGAAATTCG+TGG + chr6_1:2841263-2841282 Msa0869010:intron 40.0%
! TTTTGTGTTTGATGCAGAGG+TGG + chr6_1:2841365-2841384 Msa0869010:intron 40.0%
!! AAGAGCATTGTTGGTTTCAG+TGG + chr6_1:2841388-2841407 Msa0869010:CDS 40.0%
! GGGTTTAGTGTTTTGTGTTG+TGG + chr6_1:2841492-2841511 Msa0869010:intron 40.0%
TCCATTAGCATAGGTTGTGT+GGG - chr6_1:2842137-2842156 None:intergenic 40.0%
ATCCATTAGCATAGGTTGTG+TGG - chr6_1:2842138-2842157 None:intergenic 40.0%
! TTTTGTGTTTGATGCAGAGG+TGG + chr6_1:2841365-2841384 Msa0869010:intron 40.0%
!! TTCAGTGGAGATTTTGACGA+AGG + chr6_1:2842387-2842406 Msa0869010:CDS 40.0%
! TTCAGTGGAGATTTTCACGA+AGG + chr6_1:2841250-2841269 Msa0869010:intron 40.0%
TTCACGAAGGTAGAAATTCG+TGG + chr6_1:2841263-2841282 Msa0869010:intron 40.0%
! TTTTGTGTTTGATGCAGAGG+TGG + chr6_1:2841365-2841384 Msa0869010:intron 40.0%
!! AAGAGCATTGTTGGTTTCAG+TGG + chr6_1:2841388-2841407 Msa0869010:CDS 40.0%
! GGGTTTAGTGTTTTGTGTTG+TGG + chr6_1:2841492-2841511 Msa0869010:intron 40.0%
TCCATTAGCATAGGTTGTGT+GGG - chr6_1:2842137-2842156 None:intergenic 40.0%
ATCCATTAGCATAGGTTGTG+TGG - chr6_1:2842138-2842157 None:intergenic 40.0%
! TTTTGTGTTTGATGCAGAGG+TGG + chr6_1:2841365-2841384 Msa0869010:intron 40.0%
!! TTCAGTGGAGATTTTGACGA+AGG + chr6_1:2842387-2842406 Msa0869010:CDS 40.0%
GAGAGAGAGTGAATCAGAAG+AGG - chr6_1:2841024-2841043 None:intergenic 45.0%
TCAAAACCGTGGAAGAGGTT+CGG + chr6_1:2841095-2841114 Msa0869010:intron 45.0%
AAGAATCCGAACCTCTTCCA+CGG - chr6_1:2841104-2841123 None:intergenic 45.0%
!! AGCATTGTTGGTTTCAGTGG+AGG + chr6_1:2841391-2841410 Msa0869010:CDS 45.0%
!! TTCAGTGGAGGTTTTGACGA+AGG + chr6_1:2841403-2841422 Msa0869010:CDS 45.0%
TAGGTTGTGTGGGACTGTTT+AGG - chr6_1:2842127-2842146 None:intergenic 45.0%
TCCCACACAACCTATGCTAA+TGG + chr6_1:2842133-2842152 Msa0869010:intron 45.0%
! ACATGCCGTAAGGGTTTGTT+TGG - chr6_1:2842180-2842199 None:intergenic 45.0%
ACAAACCCTTACGGCATGTT+TGG + chr6_1:2842181-2842200 Msa0869010:intron 45.0%
AAATCCTTGTGTGTGTGGCA+TGG + chr6_1:2842255-2842274 Msa0869010:intron 45.0%
AATCCTTGTGTGTGTGGCAT+GGG + chr6_1:2842256-2842275 Msa0869010:intron 45.0%
GAGAGAGAGTGAATCAGAAG+AGG - chr6_1:2841024-2841043 None:intergenic 45.0%
TCAAAACCGTGGAAGAGGTT+CGG + chr6_1:2841095-2841114 Msa0869010:intron 45.0%
AAGAATCCGAACCTCTTCCA+CGG - chr6_1:2841104-2841123 None:intergenic 45.0%
!! AGCATTGTTGGTTTCAGTGG+AGG + chr6_1:2841391-2841410 Msa0869010:CDS 45.0%
!! TTCAGTGGAGGTTTTGACGA+AGG + chr6_1:2841403-2841422 Msa0869010:CDS 45.0%
TAGGTTGTGTGGGACTGTTT+AGG - chr6_1:2842127-2842146 None:intergenic 45.0%
TCCCACACAACCTATGCTAA+TGG + chr6_1:2842133-2842152 Msa0869010:intron 45.0%
! ACATGCCGTAAGGGTTTGTT+TGG - chr6_1:2842180-2842199 None:intergenic 45.0%
ACAAACCCTTACGGCATGTT+TGG + chr6_1:2842181-2842200 Msa0869010:intron 45.0%
AAATCCTTGTGTGTGTGGCA+TGG + chr6_1:2842255-2842274 Msa0869010:intron 45.0%
AATCCTTGTGTGTGTGGCAT+GGG + chr6_1:2842256-2842275 Msa0869010:intron 45.0%
TTCCTCTCTCGTCAAAACCG+TGG + chr6_1:2841084-2841103 Msa0869010:CDS 50.0%
!! TTCCACGGTTTTGACGAGAG+AGG - chr6_1:2841089-2841108 None:intergenic 50.0%
TCTCGTCAAAACCGTGGAAG+AGG + chr6_1:2841090-2841109 Msa0869010:CDS 50.0%
!! CAGAGGTGGAAGAGCATTGT+TGG + chr6_1:2841379-2841398 Msa0869010:intron 50.0%
ATCCTTGTGTGTGTGGCATG+GGG + chr6_1:2842257-2842276 Msa0869010:intron 50.0%
TTCCTCTCTCGTCAAAACCG+TGG + chr6_1:2841084-2841103 Msa0869010:CDS 50.0%
!! TTCCACGGTTTTGACGAGAG+AGG - chr6_1:2841089-2841108 None:intergenic 50.0%
TCTCGTCAAAACCGTGGAAG+AGG + chr6_1:2841090-2841109 Msa0869010:CDS 50.0%
!! CAGAGGTGGAAGAGCATTGT+TGG + chr6_1:2841379-2841398 Msa0869010:intron 50.0%
ATCCTTGTGTGTGTGGCATG+GGG + chr6_1:2842257-2842276 Msa0869010:intron 50.0%
AGCCCCATGCCACACACACA+AGG - chr6_1:2842262-2842281 None:intergenic 60.0%
AGCCCCATGCCACACACACA+AGG - chr6_1:2842262-2842281 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr6_1 gene 2840924 2842431 2840924 ID=Msa0869010;Name=Msa0869010
chr6_1 mRNA 2840924 2842431 2840924 ID=Msa0869010-mRNA-1;Parent=Msa0869010;Name=Msa0869010-mRNA-1;_AED=0.14;_eAED=0.14;_QI=0|0.5|0.66|1|1|1|3|12|94
chr6_1 exon 2840924 2841111 2840924 ID=Msa0869010-mRNA-1:exon:894;Parent=Msa0869010-mRNA-1
chr6_1 exon 2841382 2841424 2841382 ID=Msa0869010-mRNA-1:exon:895;Parent=Msa0869010-mRNA-1
chr6_1 exon 2842366 2842431 2842366 ID=Msa0869010-mRNA-1:exon:896;Parent=Msa0869010-mRNA-1
chr6_1 CDS 2840924 2841111 2840924 ID=Msa0869010-mRNA-1:cds;Parent=Msa0869010-mRNA-1
chr6_1 CDS 2841382 2841424 2841382 ID=Msa0869010-mRNA-1:cds;Parent=Msa0869010-mRNA-1
chr6_1 CDS 2842366 2842419 2842366 ID=Msa0869010-mRNA-1:cds;Parent=Msa0869010-mRNA-1
chr6_1 three_prime_UTR 2842420 2842431 2842420 ID=Msa0869010-mRNA-1:three_prime_utr;Parent=Msa0869010-mRNA-1
Gene Sequence

>Msa0869010

AATCAACGGTTCAGATCTCTCTATCTCAGCGAGTGTGTGAACGTTGCTGAGTTCACTCAGCGCGTGAACAAAACTCGTTCTTCTTCGTCGTCTTCTTCCTCTTCTGATTCACTCTCTCTCATTCTTCGTTTTCTTCTTCGTTTTCTTCTTCATTTTCATCTTCCTCTCTCGTCAAAACCGTGGAAGAGAGGTGGAAGAGCATTGTTGGTTTCAGTGGAGGTTTTGACGAAGAGGTGGAAGAACATTGTTGATTTCAGTGGAGATTTTGACGAAGGTAGAATTTAG

Protein sequence

>Msa0869010

NQRFRSLYLSECVNVAEFTQRVNKTRSSSSSSSSSDSLSLILRFLLRFLLHFHLPLSSKPWKRGGRALLVSVEVLTKRWKNIVDFSGDFDEGRI*