AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene023820

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene023820.t1 MTR_7g076530 97.531 81 2 0 1 81 1 81 3.25e-57 170
MS.gene023820.t1 MTR_2g436800 96.296 81 3 0 1 81 1 81 5.47e-56 167
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene023820.t1 AT5G27700 86.420 81 11 0 1 81 1 81 1.70e-51 155
MS.gene023820.t1 AT3G53890 81.481 81 15 0 1 81 1 81 2.65e-49 150
MS.gene023820.t1 AT3G53890 81.481 81 15 0 1 81 1 81 2.65e-49 150

Find 15 sgRNAs with CRISPR-Local

Find 75 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGCTCTACATTCCCAGAAAA+TGG 0.339849 7.1:+26757395 MS.gene023820:CDS
TCAGCTTAACATCGGTCATT+TGG 0.359324 7.1:+26757537 MS.gene023820:CDS
GAATGTAGAGCTCGGTGATT+TGG 0.379996 7.1:-26757384 None:intergenic
CTGTGGCTTCACTCGCGCAC+AGG 0.458896 7.1:+26757603 MS.gene023820:CDS
TACTGCCAAGGATCACGCTT+CGG 0.492236 7.1:+26757513 MS.gene023820:CDS
GAAGCCACAGAGGGCAAAAG+TGG 0.538865 7.1:-26757590 None:intergenic
CTGAACCGAAGCGTGATCCT+TGG 0.542452 7.1:-26757518 None:intergenic
TGCGCGAGTGAAGCCACAGA+GGG 0.586789 7.1:-26757599 None:intergenic
AAACAGATTGATTACTGCCA+AGG 0.589977 7.1:+26757501 MS.gene023820:CDS
GATGAAAGCGGTGTCTACAA+TGG 0.621212 7.1:+26757559 MS.gene023820:CDS
TTCCAGGGAGATGCTGACAG+TGG 0.628839 7.1:+26758715 MS.gene023820:intron
ATCGGTCATTTGGATGAAAG+CGG 0.639908 7.1:+26757547 MS.gene023820:CDS
GCTTCGGTTCAGCTTAACAT+CGG 0.677252 7.1:+26757529 MS.gene023820:CDS
ACAGTGGAATTGATCGCTTG+TGG 0.696079 7.1:+26758731 MS.gene023820:CDS
GTGCGCGAGTGAAGCCACAG+AGG 0.703435 7.1:-26757600 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATATAAATCAGAATACAATA+TGG - chr7.1:26758593-26758612 None:intergenic 15.0%
!!! CAAAAAATAGCTTTTTAAAA+GGG - chr7.1:26758087-26758106 None:intergenic 15.0%
!!! CTTTTAAAAAGCTATTTTTT+GGG + chr7.1:26758086-26758105 MS.gene023820:intron 15.0%
!!! TTTTAAAAAGCTATTTTTTG+GGG + chr7.1:26758087-26758106 MS.gene023820:intron 15.0%
!! AAATAGTTCCTTAATTAAGA+TGG + chr7.1:26758032-26758051 MS.gene023820:intron 20.0%
!! ATCATGAAATCAAGTTAAAA+TGG + chr7.1:26757747-26757766 MS.gene023820:intron 20.0%
!! TTAACAAATTATTATCAACG+TGG + chr7.1:26757907-26757926 MS.gene023820:intron 20.0%
!!! CATATTGAAATATTGCTTTT+AGG + chr7.1:26758451-26758470 MS.gene023820:intron 20.0%
!!! CCAAAAAATAGCTTTTTAAA+AGG - chr7.1:26758088-26758107 None:intergenic 20.0%
!!! CCTTTTAAAAAGCTATTTTT+TGG + chr7.1:26758085-26758104 MS.gene023820:intron 20.0%
!!! TCTTAATTAAGGAACTATTT+TGG - chr7.1:26758032-26758051 None:intergenic 20.0%
!!! TTATGTCATTTTTATTTCCA+GGG + chr7.1:26758700-26758719 MS.gene023820:intron 20.0%
!!! TTTTATGAATTGCATTTCTA+AGG + chr7.1:26758664-26758683 MS.gene023820:intron 20.0%
! AGAATCAACCATCTTAATTA+AGG - chr7.1:26758043-26758062 None:intergenic 25.0%
! AGTGAAAAAGTAAAAGTGAA+TGG + chr7.1:26758350-26758369 MS.gene023820:intron 25.0%
! CAACTAATACTTATAATCTG+CGG + chr7.1:26758307-26758326 MS.gene023820:intron 25.0%
! TAATTCCAACGTGTTTATAA+AGG - chr7.1:26758561-26758580 None:intergenic 25.0%
! TGAAAATTGATATGTTGCAA+TGG + chr7.1:26758411-26758430 MS.gene023820:intron 25.0%
! TGTTGAAAGTTAATGAAGTT+GGG + chr7.1:26758510-26758529 MS.gene023820:intron 25.0%
! TTTAACCTTTATAAACACGT+TGG + chr7.1:26758553-26758572 MS.gene023820:intron 25.0%
! TTTAGTGTAATCATATGTGT+CGG - chr7.1:26757877-26757896 None:intergenic 25.0%
!! CAAAGTTTATACCATTTTCT+GGG - chr7.1:26757409-26757428 None:intergenic 25.0%
!! TCAAAGTTTATACCATTTTC+TGG - chr7.1:26757410-26757429 None:intergenic 25.0%
!!! GAAATTGAACTGTGTTTTTT+TGG + chr7.1:26757458-26757477 MS.gene023820:intron 25.0%
!!! GTTATGTCATTTTTATTTCC+AGG + chr7.1:26758699-26758718 MS.gene023820:intron 25.0%
!!! TCTCGTTATTTTCATTGTTA+TGG + chr7.1:26757436-26757455 MS.gene023820:intron 25.0%
GAACAACATAGTATGTTCAA+TGG - chr7.1:26758619-26758638 None:intergenic 30.0%
GTGTTGAAAGTTAATGAAGT+TGG + chr7.1:26758509-26758528 MS.gene023820:intron 30.0%
TCATAAAACCTGAATCATCA+AGG - chr7.1:26758652-26758671 None:intergenic 30.0%
! GTTGATTCTGTTTCTCATAT+TGG + chr7.1:26758054-26758073 MS.gene023820:intron 30.0%
!!! GCTATTTTTTGGGGAAAATT+TGG + chr7.1:26758096-26758115 MS.gene023820:intron 30.0%
AAACAGATTGATTACTGCCA+AGG + chr7.1:26757501-26757520 MS.gene023820:CDS 35.0%
AAGTGAACAAAGAAGGACAA+TGG + chr7.1:26758223-26758242 MS.gene023820:intron 35.0%
ACTTTCTCATACTCTTCTTG+CGG - chr7.1:26758333-26758352 None:intergenic 35.0%
ATTGTCCTTCTTTGTTCACT+TGG - chr7.1:26758224-26758243 None:intergenic 35.0%
GCACAGGTCTCTAATTAATT+TGG + chr7.1:26757619-26757638 MS.gene023820:intron 35.0%
GTTAATGAAGTTGGGAACTA+TGG + chr7.1:26758518-26758537 MS.gene023820:intron 35.0%
TGATTCCAAGTGAACAAAGA+AGG + chr7.1:26758216-26758235 MS.gene023820:intron 35.0%
TGTCCTGTATTTCATTCTGT+GGG + chr7.1:26758138-26758157 MS.gene023820:intron 35.0%
TTGTCCTGTATTTCATTCTG+TGG + chr7.1:26758137-26758156 MS.gene023820:intron 35.0%
! TTGATACACCTTGATGATTC+AGG + chr7.1:26758641-26758660 MS.gene023820:intron 35.0%
ACAACCACTTGCAAAGTTGT+GGG - chr7.1:26757981-26758000 None:intergenic 40.0%
AGCTCTACATTCCCAGAAAA+TGG + chr7.1:26757395-26757414 MS.gene023820:CDS 40.0%
ATCGGTCATTTGGATGAAAG+CGG + chr7.1:26757547-26757566 MS.gene023820:CDS 40.0%
GTCCTGTATTTCATTCTGTG+GGG + chr7.1:26758139-26758158 MS.gene023820:intron 40.0%
TCAGCTTAACATCGGTCATT+TGG + chr7.1:26757537-26757556 MS.gene023820:CDS 40.0%
TCATAGGTTGCGAGACTATT+TGG - chr7.1:26757812-26757831 None:intergenic 40.0%
TTTGCAAGTGGTTGTGTTTG+TGG + chr7.1:26757986-26758005 MS.gene023820:intron 40.0%
!! TTTTCTGGGAATGTAGAGCT+CGG - chr7.1:26757395-26757414 None:intergenic 40.0%
ACAGTGGAATTGATCGCTTG+TGG + chr7.1:26758731-26758750 MS.gene023820:CDS 45.0%
AGCCCCACAGAATGAAATAC+AGG - chr7.1:26758144-26758163 None:intergenic 45.0%
ATAGCCCACAACTTTGCAAG+TGG + chr7.1:26757974-26757993 MS.gene023820:intron 45.0%
ATGAAGCACGGAAACAAACC+CGG - chr7.1:26757956-26757975 None:intergenic 45.0%
CACAACCACTTGCAAAGTTG+TGG - chr7.1:26757982-26758001 None:intergenic 45.0%
GATGAAAGCGGTGTCTACAA+TGG + chr7.1:26757559-26757578 MS.gene023820:CDS 45.0%
GCTTCGGTTCAGCTTAACAT+CGG + chr7.1:26757529-26757548 MS.gene023820:CDS 45.0%
GTCGATGTCTATGTCATGTC+CGG + chr7.1:26757934-26757953 MS.gene023820:intron 45.0%
TCGATGTCTATGTCATGTCC+GGG + chr7.1:26757935-26757954 MS.gene023820:intron 45.0%
! AAGTTGTGGGCTATGAAGCA+CGG - chr7.1:26757968-26757987 None:intergenic 45.0%
! GAATGTAGAGCTCGGTGATT+TGG - chr7.1:26757387-26757406 None:intergenic 45.0%
!! TTTTCCACTTTTGCCCTCTG+TGG + chr7.1:26757586-26757605 MS.gene023820:CDS 45.0%
GTCTCGCAACCTATGAAGCA+CGG + chr7.1:26757816-26757835 MS.gene023820:intron 50.0%
TACTGCCAAGGATCACGCTT+CGG + chr7.1:26757513-26757532 MS.gene023820:CDS 50.0%
TATGAAGCACGGACACTCCT+CGG + chr7.1:26757827-26757846 MS.gene023820:intron 50.0%
CTGAACCGAAGCGTGATCCT+TGG - chr7.1:26757521-26757540 None:intergenic 55.0%
GAAGCCACAGAGGGCAAAAG+TGG - chr7.1:26757593-26757612 None:intergenic 55.0%
TACCAACGCGACCTAATCCG+AGG - chr7.1:26757847-26757866 None:intergenic 55.0%
TTCCACTGTCAGCATCTCCC+TGG - chr7.1:26758720-26758739 None:intergenic 55.0%
TTCCAGGGAGATGCTGACAG+TGG + chr7.1:26758715-26758734 MS.gene023820:intron 55.0%
!! GAGGAGTGTCCGTGCTTCAT+AGG - chr7.1:26757828-26757847 None:intergenic 55.0%
GCACGGACACTCCTCGGATT+AGG + chr7.1:26757833-26757852 MS.gene023820:intron 60.0%
TGCGCGAGTGAAGCCACAGA+GGG - chr7.1:26757602-26757621 None:intergenic 60.0%
! CTCCTCGGATTAGGTCGCGT+TGG + chr7.1:26757842-26757861 MS.gene023820:intron 60.0%
CTGTGGCTTCACTCGCGCAC+AGG + chr7.1:26757603-26757622 MS.gene023820:CDS 65.0%
GTGCGCGAGTGAAGCCACAG+AGG - chr7.1:26757603-26757622 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr7.1 gene 26757367 26758783 26757367 ID=MS.gene023820
chr7.1 mRNA 26757367 26758783 26757367 ID=MS.gene023820.t1;Parent=MS.gene023820
chr7.1 exon 26757367 26757416 26757367 ID=MS.gene023820.t1.exon1;Parent=MS.gene023820.t1
chr7.1 CDS 26757367 26757416 26757367 ID=cds.MS.gene023820.t1;Parent=MS.gene023820.t1
chr7.1 exon 26757492 26757624 26757492 ID=MS.gene023820.t1.exon2;Parent=MS.gene023820.t1
chr7.1 CDS 26757492 26757624 26757492 ID=cds.MS.gene023820.t1;Parent=MS.gene023820.t1
chr7.1 exon 26758721 26758783 26758721 ID=MS.gene023820.t1.exon3;Parent=MS.gene023820.t1
chr7.1 CDS 26758721 26758783 26758721 ID=cds.MS.gene023820.t1;Parent=MS.gene023820.t1
Gene Sequence

>MS.gene023820

ATGCAGAACGAAGAAGGCCAAATCACCGAGCTCTACATTCCCAGAAAATGGTATAAACTTTGATTATAATCTCGTTATTTTCATTGTTATGGAAATTGAACTGTGTTTTTTTGGATTTGTTTCAGTTCTGCTACAAACAGATTGATTACTGCCAAGGATCACGCTTCGGTTCAGCTTAACATCGGTCATTTGGATGAAAGCGGTGTCTACAATGGTCAATTTTCCACTTTTGCCCTCTGTGGCTTCACTCGCGCACAGGTCTCTAATTAATTTGGATTTAATTGTTAATTTGCTGTGTTTTATATTCAATACTAGTATTTGTTATGTATGAACATAATTTTAATTAGCTTTAGTCTCTGTTTGAGTAAACAACATAAATGATCATGAAATCAAGTTAAAATGGTTTTCATATATTAGCTATATGCTCTTTTCATAAGCTTTTCCAAATAGTCTCGCAACCTATGAAGCACGGACACTCCTCGGATTAGGTCGCGTTGGTATTTGACACCGACACATATGATTACACTAAATTATGTCATTTTAACAAATTATTATCAACGTGGACTTGTCGATGTCTATGTCATGTCCGGGTTTGTTTCCGTGCTTCATAGCCCACAACTTTGCAAGTGGTTGTGTTTGTGGATAAATTCTAATAACTCATTCCAAAATAGTTCCTTAATTAAGATGGTTGATTCTGTTTCTCATATTGGTATTTTACCCTTTTAAAAAGCTATTTTTTGGGGAAAATTTGGTTTTATTTTTTGTTTTAATTGTCCTGTATTTCATTCTGTGGGGCTTCTATTAGTTTAGATTGTATTTTTTTAGTCGATAGATTACAACATATTAATGTGATTCCAAGTGAACAAAGAAGGACAATGGCTGATAGAATTGTCAAGAATTTCATTGCATGAATTCTGAGTAAATTTGAACTGATAGTATACAACTAATACTTATAATCTGCGGCCGCAAGAAGAGTATGAGAAAGTGAAAAAGTAAAAGTGAATGGAACTAACATTGTCAACTTTTGTAAGAAAAAAACGTAACTGAAAATTGATATGTTGCAATGGTTTTTGTTCTTTAGAAACATATTGAAATATTGCTTTTAGGTTGTGTGACTGAATCATGATATGTTTATTAATGCTGTGTTGAAAGTTAATGAAGTTGGGAACTATGGTTGAAAAAAATATTTAACCTTTATAAACACGTTGGAATTACTCTCTGTACCATATTGTATTCTGATTTATATCAGCCATTGAACATACTATGTTGTTCTCTTGATACACCTTGATGATTCAGGTTTTATGAATTGCATTTCTAAGGTGCTGATTTCATGTTATGTCATTTTTATTTCCAGGGAGATGCTGACAGTGGAATTGATCGCTTGTGGCAGAAAAAGAAAGCTGAAATTAAGCAATAG
Protein sequence

>MS.gene023820.t1

MQNEEGQITELYIPRKCSATNRLITAKDHASVQLNIGHLDESGVYNGQFSTFALCGFTRAQGDADSGIDRLWQKKKAEIKQ