AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene053056

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene053056.t1 MTR_3g108460 59.341 91 28 2 39 123 173 260 7.22e-16 72.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene053056.t1 AT3G57560 61.039 77 24 1 53 123 191 267 3.23e-14 67.8

Find 32 sgRNAs with CRISPR-Local

Find 55 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTTATTTACTTTCTCTAGAT+TGG 0.241733 6.2:+899692 None:intergenic
GCGGCTCACGGTGACGGTTT+TGG 0.336339 6.2:+899794 None:intergenic
TTATTTACTTTCTCTAGATT+GGG 0.340953 6.2:+899693 None:intergenic
ATCAATGCCGATACGGTTGC+CGG 0.377368 6.2:-899390 MS.gene053056:CDS
CATCGACATCAGACATATTC+CGG 0.402871 6.2:-899457 MS.gene053056:CDS
TCAGTTGCGGTTGATGAATC+TGG 0.403778 6.2:-899426 MS.gene053056:CDS
ATTAGGATTCAAGCCATTGC+AGG 0.408001 6.2:-899829 MS.gene053056:CDS
GGAGATATAGCGGCGGCGTT+AGG 0.420822 6.2:-899369 MS.gene053056:CDS
GTATCGGCATTGATGTTATA+CGG 0.437708 6.2:+899399 None:intergenic
CGAGGTCGCAAGTGTAGATT+CGG 0.458392 6.2:-899496 MS.gene053056:intron
GAGAGCGAGAAACAAACATT+AGG 0.462236 6.2:-899846 MS.gene053056:CDS
TTTGTAGCGGCTCACGGTGA+CGG 0.475184 6.2:+899788 None:intergenic
GTGGTGGTGATTTCCTGCAA+TGG 0.503387 6.2:+899816 None:intergenic
ATTGACACTGTTGACGGATG+TGG 0.514400 6.2:-899337 MS.gene053056:CDS
TCCGGTGGTTACATCAGTTG+CGG 0.521292 6.2:-899439 MS.gene053056:CDS
TTGACACTGTTGACGGATGT+GGG 0.539102 6.2:-899336 MS.gene053056:CDS
AACTTTAGAAACATTAATTG+TGG 0.559094 6.2:+899755 None:intergenic
TTTAGAAACATTAATTGTGG+TGG 0.559824 6.2:+899758 None:intergenic
ACTTTCTCTAGATTGGGTGT+AGG 0.561222 6.2:+899699 None:intergenic
GTATAACATCAATGCCGATA+CGG 0.582195 6.2:-899397 MS.gene053056:CDS
TATATCTCCGGCAACCGTAT+CGG 0.584124 6.2:+899383 None:intergenic
GTCTGATGTCGATGAGAGAT+CGG 0.594894 6.2:+899466 None:intergenic
TAACGCCGCCGCTATATCTC+CGG 0.607844 6.2:+899371 None:intergenic
GACACTGTTGACGGATGTGG+GGG 0.614485 6.2:-899334 MS.gene053056:CDS
ACCGCAACTGATGTAACCAC+CGG 0.619911 6.2:+899438 None:intergenic
GGAGAAATTGACACTGTTGA+CGG 0.625300 6.2:-899343 MS.gene053056:CDS
ATGTTTCTAAAGTTGCAGCA+AGG 0.637176 6.2:-899746 MS.gene053056:CDS
TGACACTGTTGACGGATGTG+GGG 0.644034 6.2:-899335 MS.gene053056:CDS
TACGGTTGCCGGAGATATAG+CGG 0.647174 6.2:-899379 MS.gene053056:CDS
TATAGCGGCGGCGTTAGGTG+CGG 0.660812 6.2:-899364 MS.gene053056:CDS
CGACATCAGACATATTCCGG+TGG 0.698866 6.2:-899454 MS.gene053056:CDS
GGTTGCCGGAGATATAGCGG+CGG 0.799312 6.2:-899376 MS.gene053056:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTATTTACTTTCTCTAGATT+GGG + chr6.2:899500-899519 None:intergenic 20.0%
!!! AACTTTAGAAACATTAATTG+TGG + chr6.2:899438-899457 None:intergenic 20.0%
!!! TTTATTCCTAATTTTCTAGA+AGG + chr6.2:899574-899593 None:intergenic 20.0%
! AAACCTGATAAAAGAATAGA+AGG - chr6.2:899591-899610 MS.gene053056:intron 25.0%
! AACCTGATAAAAGAATAGAA+GGG - chr6.2:899592-899611 MS.gene053056:intron 25.0%
! GTTATTTACTTTCTCTAGAT+TGG + chr6.2:899501-899520 None:intergenic 25.0%
! TAATATCCATTCATCTCATT+TGG + chr6.2:899643-899662 None:intergenic 25.0%
! TTTAGAAACATTAATTGTGG+TGG + chr6.2:899435-899454 None:intergenic 25.0%
!! AAAACTCCTTCTAGAAAATT+AGG - chr6.2:899565-899584 MS.gene053056:intron 25.0%
!! TTTTATGCAGTGATGATTTA+TGG + chr6.2:899548-899567 None:intergenic 25.0%
GTATAACATCAATGCCGATA+CGG - chr6.2:899793-899812 MS.gene053056:CDS 35.0%
! CTCCCTTCTATTCTTTTATC+AGG + chr6.2:899597-899616 None:intergenic 35.0%
!! ATGTTTCTAAAGTTGCAGCA+AGG - chr6.2:899444-899463 MS.gene053056:CDS 35.0%
!! GTATCGGCATTGATGTTATA+CGG + chr6.2:899794-899813 None:intergenic 35.0%
!! GTGGTTGATGAAACTTATGT+GGG + chr6.2:899523-899542 None:intergenic 35.0%
!! TGTGGTTGATGAAACTTATG+TGG + chr6.2:899524-899543 None:intergenic 35.0%
!!! TGGTGGTGATTTTTTTGTAG+CGG + chr6.2:899418-899437 None:intergenic 35.0%
AAAGAGACCTAATTCCTCCT+AGG - chr6.2:899662-899681 MS.gene053056:intron 40.0%
AAGAGACCTAATTCCTCCTA+GGG - chr6.2:899663-899682 MS.gene053056:intron 40.0%
ACTTTCTCTAGATTGGGTGT+AGG + chr6.2:899494-899513 None:intergenic 40.0%
ATTAGGATTCAAGCCATTGC+AGG - chr6.2:899361-899380 MS.gene053056:CDS 40.0%
CATCGACATCAGACATATTC+CGG - chr6.2:899733-899752 MS.gene053056:CDS 40.0%
GACAGACCAAATGAGATGAA+TGG - chr6.2:899634-899653 MS.gene053056:intron 40.0%
GAGAGCGAGAAACAAACATT+AGG - chr6.2:899344-899363 MS.gene053056:CDS 40.0%
GCAGTGATGATTTATGGTTG+TGG + chr6.2:899542-899561 None:intergenic 40.0%
GGAGAAATTGACACTGTTGA+CGG - chr6.2:899847-899866 MS.gene053056:CDS 40.0%
!!! GATTTTTTTGTAGCGGCTCA+CGG + chr6.2:899411-899430 None:intergenic 40.0%
GATGAACCCTAGGAGGAATT+AGG + chr6.2:899672-899691 None:intergenic 45.0%
GTCTGATGTCGATGAGAGAT+CGG + chr6.2:899727-899746 None:intergenic 45.0%
TATATCTCCGGCAACCGTAT+CGG + chr6.2:899810-899829 None:intergenic 45.0%
! ATTGACACTGTTGACGGATG+TGG - chr6.2:899853-899872 MS.gene053056:CDS 45.0%
! TTGACACTGTTGACGGATGT+GGG - chr6.2:899854-899873 MS.gene053056:CDS 45.0%
!! TCAGTTGCGGTTGATGAATC+TGG - chr6.2:899764-899783 MS.gene053056:CDS 45.0%
ACCGCAACTGATGTAACCAC+CGG + chr6.2:899755-899774 None:intergenic 50.0%
ATCAATGCCGATACGGTTGC+CGG - chr6.2:899800-899819 MS.gene053056:CDS 50.0%
CGACATCAGACATATTCCGG+TGG - chr6.2:899736-899755 MS.gene053056:CDS 50.0%
CGAGGTCGCAAGTGTAGATT+CGG - chr6.2:899694-899713 MS.gene053056:intron 50.0%
TACGGTTGCCGGAGATATAG+CGG - chr6.2:899811-899830 MS.gene053056:CDS 50.0%
TCCGGTGGTTACATCAGTTG+CGG - chr6.2:899751-899770 MS.gene053056:CDS 50.0%
! GTGGTGGTGATTTCCTGCAA+TGG + chr6.2:899377-899396 None:intergenic 50.0%
! TGACACTGTTGACGGATGTG+GGG - chr6.2:899855-899874 MS.gene053056:CDS 50.0%
CCTCCTAGGGTTCATCAACG+AGG - chr6.2:899676-899695 MS.gene053056:intron 55.0%
TAACGCCGCCGCTATATCTC+CGG + chr6.2:899822-899841 None:intergenic 55.0%
TTTGTAGCGGCTCACGGTGA+CGG + chr6.2:899405-899424 None:intergenic 55.0%
! CCTCGTTGATGAACCCTAGG+AGG + chr6.2:899679-899698 None:intergenic 55.0%
! CGACCTCGTTGATGAACCCT+AGG + chr6.2:899682-899701 None:intergenic 55.0%
! GACACTGTTGACGGATGTGG+GGG - chr6.2:899856-899875 MS.gene053056:CDS 55.0%
GGAGATATAGCGGCGGCGTT+AGG - chr6.2:899821-899840 MS.gene053056:CDS 60.0%
GGTTGCCGGAGATATAGCGG+CGG - chr6.2:899814-899833 MS.gene053056:CDS 60.0%
TATAGCGGCGGCGTTAGGTG+CGG - chr6.2:899826-899845 MS.gene053056:CDS 60.0%
! ACTGTTGACGGATGTGGGGG+CGG - chr6.2:899859-899878 MS.gene053056:CDS 60.0%
!! CACGGTGACGGTTTTGGTGG+TGG + chr6.2:899393-899412 None:intergenic 60.0%
!! GCTCACGGTGACGGTTTTGG+TGG + chr6.2:899396-899415 None:intergenic 60.0%
ACGGATGTGGGGGCGGATAG+TGG - chr6.2:899866-899885 MS.gene053056:CDS 65.0%
!! GCGGCTCACGGTGACGGTTT+TGG + chr6.2:899399-899418 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr6.2 gene 899320 899892 899320 ID=MS.gene053056
chr6.2 mRNA 899320 899892 899320 ID=MS.gene053056.t1;Parent=MS.gene053056
chr6.2 exon 899701 899892 899701 ID=MS.gene053056.t1.exon1;Parent=MS.gene053056.t1
chr6.2 CDS 899701 899892 899701 ID=cds.MS.gene053056.t1;Parent=MS.gene053056.t1
chr6.2 exon 899320 899514 899320 ID=MS.gene053056.t1.exon2;Parent=MS.gene053056.t1
chr6.2 CDS 899320 899514 899320 ID=cds.MS.gene053056.t1;Parent=MS.gene053056.t1
Gene Sequence

>MS.gene053056

ATGAACAAAAAACTCGAAACATATGAGAGCGAGAAACAAACATTAGGATTCAAGCCATTGCAGGAAATCACCACCACCAAAACCGTCACCGTGAGCCGCTACAAAAAAATCACCACCACAATTAATGTTTCTAAAGTTGCAGCAAGGCTTTCTTCTCTGCAGCAATCTCGACCTACACCCAATCTAGAGAAAGTAAATAACCCACATAAGTTTCATCAACCACAACCATAAATCATCACTGCATAAAAACTCCTTCTAGAAAATTAGGAATAAACCTGATAAAAGAATAGAAGGGAGAATCAAGAAGATGAATTGACAGACCAAATGAGATGAATGGATATTAAAGAGACCTAATTCCTCCTAGGGTTCATCAACGAGGTCGCAAGTGTAGATTCGGCTGTTCACCGATCTCTCATCGACATCAGACATATTCCGGTGGTTACATCAGTTGCGGTTGATGAATCTGGACAGCCGTATAACATCAATGCCGATACGGTTGCCGGAGATATAGCGGCGGCGTTAGGTGCGGAGAAATTGACACTGTTGACGGATGTGGGGGCGGATAGTGGATGA
Protein sequence

>MS.gene053056.t1

MNKKLETYESEKQTLGFKPLQEITTTKTVTVSRYKKITTTINVSKVAARLSSLQQSRPTPNLEKVASVDSAVHRSLIDIRHIPVVTSVAVDESGQPYNINADTVAGDIAAALGAEKLTLLTDVGADSG