AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene051942

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene051942.t1 MTR_2g100020 87.892 223 18 4 1 223 63 276 1.25e-125 357
MS.gene051942.t1 MTR_8g017090 59.016 61 25 0 1 61 56 116 1.94e-17 79.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene051942.t1 AT1G72980 45.570 79 42 1 1 78 57 135 7.76e-16 73.9
MS.gene051942.t1 AT3G13850 43.662 71 40 0 1 71 80 150 1.39e-11 62.8

Find 35 sgRNAs with CRISPR-Local

Find 37 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCTTGTAAAGGAACATAATT+AGG 0.133443 2.2:+3063143 None:intergenic
AATCAATGAAATGAATTCTT+TGG 0.228002 2.2:-3062976 MS.gene051942:CDS
AAGAATTCATTTCATTGATT+AGG 0.332115 2.2:+3062979 None:intergenic
GCAACATGTTCATATTCAAT+TGG 0.430357 2.2:+3063231 None:intergenic
CTTGTAAAGGAACATAATTA+GGG 0.440777 2.2:+3063144 None:intergenic
TCAATCTGATATGCGTGCTA+TGG 0.454015 2.2:-3063525 MS.gene051942:CDS
CAGCAGAAGTAGTATTGATC+CGG 0.456820 2.2:-3062946 MS.gene051942:CDS
ACCGCTGTCGCCGTTGACAT+TGG 0.480229 2.2:-3063087 MS.gene051942:CDS
TAGTATTGATCCGGGGCACC+AGG 0.481958 2.2:-3062937 MS.gene051942:CDS
AATCGATAACAACCACCAAC+AGG 0.487385 2.2:+3063500 None:intergenic
CATAATAATAACGATGATGA+TGG 0.501827 2.2:-3063314 MS.gene051942:CDS
AGCAGAAGTAGTATTGATCC+GGG 0.521215 2.2:-3062945 MS.gene051942:CDS
AATTAACAAACCTGGTGCCC+CGG 0.523440 2.2:+3062927 None:intergenic
GTATTAAAATCCTCTTGTAA+AGG 0.525655 2.2:+3063131 None:intergenic
GAACGTGTTGGTGATGATCA+AGG 0.525830 2.2:-3063026 MS.gene051942:CDS
TGCAGCAGTTGCAGTTGTTG+AGG 0.538937 2.2:+3063200 None:intergenic
TCATCATTATAATGACATGC+AGG 0.554364 2.2:-3063345 MS.gene051942:CDS
ATCAATACTACTTCTGCTGT+TGG 0.557959 2.2:+3062950 None:intergenic
TAATTATGTTCCTTTACAAG+AGG 0.560978 2.2:-3063141 MS.gene051942:CDS
CACCAACTAATTAACAAACC+TGG 0.563620 2.2:+3062919 None:intergenic
TGCAGTTGTTGAGGTTGTTG+AGG 0.566132 2.2:+3063209 None:intergenic
GCTGTCGCCGTTGACATTGG+AGG 0.577848 2.2:-3063084 MS.gene051942:CDS
GACATTGGAGGGTAACAAGA+AGG 0.582425 2.2:-3063072 MS.gene051942:CDS
CTGTCGCCGTTGACATTGGA+GGG 0.585568 2.2:-3063083 MS.gene051942:CDS
CGTGCTATGGATCCTGTTGG+TGG 0.590598 2.2:-3063512 MS.gene051942:CDS
CAATATGTTGTTGATGATGT+CGG 0.594144 2.2:-3063173 MS.gene051942:CDS
TTGTTACCCTCCAATGTCAA+CGG 0.595962 2.2:+3063077 None:intergenic
GTATGATCTCTAAGATGAGG+TGG 0.598062 2.2:+3063566 None:intergenic
TCCAATGTCAACGGCGACAG+CGG 0.601203 2.2:+3063086 None:intergenic
ATAGTATGATCTCTAAGATG+AGG 0.624071 2.2:+3063563 None:intergenic
GGTAACAAGAAGGAGGAAGA+CGG 0.630879 2.2:-3063062 MS.gene051942:CDS
GAACAAGATCAAGAACGTGT+TGG 0.646768 2.2:-3063038 MS.gene051942:CDS
ATGCGTGCTATGGATCCTGT+TGG 0.652692 2.2:-3063515 MS.gene051942:CDS
ATTGGAGGGTAACAAGAAGG+AGG 0.688764 2.2:-3063069 MS.gene051942:CDS
GCAGAAGTAGTATTGATCCG+GGG 0.729367 2.2:-3062944 MS.gene051942:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATCAATGAAATGAATTCTT+TGG - chr2.2:3063534-3063553 MS.gene051942:CDS 20.0%
!!! AAGAATTCATTTCATTGATT+AGG + chr2.2:3063534-3063553 None:intergenic 20.0%
! CATAATAATAACGATGATGA+TGG - chr2.2:3063196-3063215 MS.gene051942:CDS 25.0%
! CTTGTAAAGGAACATAATTA+GGG + chr2.2:3063369-3063388 None:intergenic 25.0%
! GTATTAAAATCCTCTTGTAA+AGG + chr2.2:3063382-3063401 None:intergenic 25.0%
! TAATTATGTTCCTTTACAAG+AGG - chr2.2:3063369-3063388 MS.gene051942:CDS 25.0%
! TCTTGTAAAGGAACATAATT+AGG + chr2.2:3063370-3063389 None:intergenic 25.0%
!! TTCATTGATTAGGTCAAAAA+CGG + chr2.2:3063524-3063543 None:intergenic 25.0%
!!! ACAAGAGGATTTTAATACAT+GGG - chr2.2:3063384-3063403 MS.gene051942:CDS 25.0%
!!! TACAAGAGGATTTTAATACA+TGG - chr2.2:3063383-3063402 MS.gene051942:CDS 25.0%
GCAACATGTTCATATTCAAT+TGG + chr2.2:3063282-3063301 None:intergenic 30.0%
TCATCATTATAATGACATGC+AGG - chr2.2:3063165-3063184 MS.gene051942:CDS 30.0%
! TCATTGATTAGGTCAAAAAC+GGG + chr2.2:3063523-3063542 None:intergenic 30.0%
!! ATAGTATGATCTCTAAGATG+AGG + chr2.2:3062950-3062969 None:intergenic 30.0%
!! CAATATGTTGTTGATGATGT+CGG - chr2.2:3063337-3063356 MS.gene051942:CDS 30.0%
ATCAATACTACTTCTGCTGT+TGG + chr2.2:3063563-3063582 None:intergenic 35.0%
AATCGATAACAACCACCAAC+AGG + chr2.2:3063013-3063032 None:intergenic 40.0%
GAACAAGATCAAGAACGTGT+TGG - chr2.2:3063472-3063491 MS.gene051942:CDS 40.0%
TCAATCTGATATGCGTGCTA+TGG - chr2.2:3062985-3063004 MS.gene051942:CDS 40.0%
TTGTTACCCTCCAATGTCAA+CGG + chr2.2:3063436-3063455 None:intergenic 40.0%
!! AGCAGAAGTAGTATTGATCC+GGG - chr2.2:3063565-3063584 MS.gene051942:CDS 40.0%
!! CAGCAGAAGTAGTATTGATC+CGG - chr2.2:3063564-3063583 MS.gene051942:CDS 40.0%
!! GTATGATCTCTAAGATGAGG+TGG + chr2.2:3062947-3062966 None:intergenic 40.0%
ATTGGAGGGTAACAAGAAGG+AGG - chr2.2:3063441-3063460 MS.gene051942:CDS 45.0%
GACATTGGAGGGTAACAAGA+AGG - chr2.2:3063438-3063457 MS.gene051942:CDS 45.0%
GGTAACAAGAAGGAGGAAGA+CGG - chr2.2:3063448-3063467 MS.gene051942:CDS 45.0%
TGCAGTTGTTGAGGTTGTTG+AGG + chr2.2:3063304-3063323 None:intergenic 45.0%
!! GAACGTGTTGGTGATGATCA+AGG - chr2.2:3063484-3063503 MS.gene051942:CDS 45.0%
!! GCAGAAGTAGTATTGATCCG+GGG - chr2.2:3063566-3063585 MS.gene051942:CDS 45.0%
ATGCGTGCTATGGATCCTGT+TGG - chr2.2:3062995-3063014 MS.gene051942:CDS 50.0%
TGCAGCAGTTGCAGTTGTTG+AGG + chr2.2:3063313-3063332 None:intergenic 50.0%
CGTGCTATGGATCCTGTTGG+TGG - chr2.2:3062998-3063017 MS.gene051942:CDS 55.0%
CTGTCGCCGTTGACATTGGA+GGG - chr2.2:3063427-3063446 MS.gene051942:CDS 55.0%
TCCAATGTCAACGGCGACAG+CGG + chr2.2:3063427-3063446 None:intergenic 55.0%
!! TAGTATTGATCCGGGGCACC+AGG - chr2.2:3063573-3063592 MS.gene051942:CDS 55.0%
ACCGCTGTCGCCGTTGACAT+TGG - chr2.2:3063423-3063442 MS.gene051942:CDS 60.0%
GCTGTCGCCGTTGACATTGG+AGG - chr2.2:3063426-3063445 MS.gene051942:CDS 60.0%


Chromosome Type Strat End Strand Name
chr2.2 gene 3062929 3063603 3062929 ID=MS.gene051942
chr2.2 mRNA 3062929 3063603 3062929 ID=MS.gene051942.t1;Parent=MS.gene051942
chr2.2 exon 3062929 3063603 3062929 ID=MS.gene051942.t1.exon1;Parent=MS.gene051942.t1
chr2.2 CDS 3062929 3063603 3062929 ID=cds.MS.gene051942.t1;Parent=MS.gene051942.t1
Gene Sequence

>MS.gene051942

ATGATCAAGAATGTTCCACCTCATCTTAGAGATCATACTATGAGTTCTATTATTTTTCAATCTGATATGCGTGCTATGGATCCTGTTGGTGGTTGTTATCGATTCATTCAACAGCTTCAATCTCAATATGAATTTTATCAAGCTGAGCTTCATCTTACACGTCAACAAATTGCTATTTGTAAAGCTTCACAATCACAACATCAACAACAACAACAACTTGCTGCTGCTGTTAATCATCATCATTATAATGACATGCAGGTCATTAATCATAATAATAACGATGATGATGGTCATAACGATGCTGCTTTGAATATTATTAATCATTTTAATCAGCATCATTTTGTTGATGACCAATTGAATATGAACATGTTGCCTCAACAACCTCAACAACTGCAACTGCTGCAGCAGCAATATGTTGTTGATGATGTCGGTATTAACCCTAATTATGTTCCTTTACAAGAGGATTTTAATACATGGGCGAACAATATTAATATACCGCTGTCGCCGTTGACATTGGAGGGTAACAAGAAGGAGGAAGACGGTGAACAAGATCAAGAACGTGTTGGTGATGATCAAGGAAGTGATCAGAAACCCGTTTTTGACCTAATCAATGAAATGAATTCTTTGGATACCAACAGCAGAAGTAGTATTGATCCGGGGCACCAGGTTTGTTAA
Protein sequence

>MS.gene051942.t1

MIKNVPPHLRDHTMSSIIFQSDMRAMDPVGGCYRFIQQLQSQYEFYQAELHLTRQQIAICKASQSQHQQQQQLAAAVNHHHYNDMQVINHNNNDDDGHNDAALNIINHFNQHHFVDDQLNMNMLPQQPQQLQLLQQQYVVDDVGINPNYVPLQEDFNTWANNINIPLSPLTLEGNKKEEDGEQDQERVGDDQGSDQKPVFDLINEMNSLDTNSRSSIDPGHQVC