AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene35760

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene35760.t1 MTR_2g089310 90.129 233 18 2 1 228 1 233 2.03e-122 347
MS.gene35760.t1 MTR_2g011450 48.252 143 49 2 1 143 1 118 1.16e-31 112
MS.gene35760.t1 MTR_4g046640 50.847 59 29 0 5 63 36 94 1.25e-12 63.2
MS.gene35760.t1 MTR_4g008050 50.000 66 33 0 3 68 6 71 2.80e-12 64.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene35760.t1 AT4G27310 42.690 171 56 3 1 136 1 164 4.58e-36 127
MS.gene35760.t1 AT5G54470 48.128 187 74 5 2 186 3 168 3.39e-34 122
MS.gene35760.t1 AT3G21890 56.000 50 22 0 5 54 31 80 8.32e-11 58.2

Find 62 sgRNAs with CRISPR-Local

Find 69 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCGTTTAGATCATGACTTTC+AGG 0.284332 2.1:-12766932 MS.gene35760:intron
CGGCGGTATAGCGACGTAAA+TGG 0.305299 2.1:-12766708 MS.gene35760:CDS
TTCACTTTCTTCTTGTTGCT+CGG 0.346480 2.1:+12767185 None:intergenic
TTCTTCTTGTTGCTCGGCGC+TGG 0.356031 2.1:+12767191 None:intergenic
CGCATCGCCGCCTTTGACGA+CGG 0.374944 2.1:+12766729 None:intergenic
GTGGATGAGGTTGATTTGAT+AGG 0.378300 2.1:-12766765 MS.gene35760:CDS
CTCGGCGCTGGCACCGGCGT+TGG 0.399687 2.1:+12767203 None:intergenic
GCTGGCACCGGCGTTGGCGT+TGG 0.401559 2.1:+12767209 None:intergenic
TGAAGAAGATGGTGATAATC+AGG 0.403542 2.1:-12767100 MS.gene35760:CDS
TTCCTCATCGGAATCGTAAT+CGG 0.408569 2.1:+12767137 None:intergenic
ATGCTGGGACTGCGATTCTA+AGG 0.430981 2.1:-12767382 MS.gene35760:CDS
CGTGGAAAGCCTCCGGCGCT+AGG 0.440306 2.1:-12767287 MS.gene35760:CDS
TTGTTGCTCGGCGCTGGCAC+CGG 0.453269 2.1:+12767197 None:intergenic
CCGACCAGGCTAGCTTATGC+TGG 0.471766 2.1:-12767398 MS.gene35760:CDS
CGCGTTACCGAGCCTAGCGC+CGG 0.498391 2.1:+12767275 None:intergenic
CTCGTCCTCATCTTCCTCAT+CGG 0.523137 2.1:+12767125 None:intergenic
CGACGAGGAGCCGTCGTCAA+AGG 0.525973 2.1:-12766739 MS.gene35760:CDS
CCCACGCCGTGGAAAGCCTC+CGG 0.526413 2.1:-12767294 MS.gene35760:CDS
GACTCACAGAAAGTTCTAGC+TGG 0.526494 2.1:+12767420 None:intergenic
AGTCCCAGCATAAGCTAGCC+TGG 0.526991 2.1:+12767394 None:intergenic
GAGGACGAGGATGAAGAAGA+TGG 0.529527 2.1:-12767111 MS.gene35760:CDS
AACTTTCTGTGAGTCCGACC+AGG 0.531925 2.1:-12767412 MS.gene35760:CDS
AACAGCGGCGCAACCACCGC+CGG 0.536758 2.1:-12767061 MS.gene35760:CDS
CACCGGCGTTGGCGTTGGCG+TGG 0.539822 2.1:+12767214 None:intergenic
CCGCCGGCTTCTAGTTCCTC+CGG 0.540421 2.1:-12767045 MS.gene35760:CDS
TGGATGAGGTTGATTTGATA+GGG 0.541461 2.1:-12766764 MS.gene35760:CDS
GCCGGAGGCTTTCCACGGCG+TGG 0.543692 2.1:+12767293 None:intergenic
CGATGAGGAAGATGAGGACG+AGG 0.544127 2.1:-12767124 MS.gene35760:CDS
TTCCTCCGGTAGCGAAGAGT+CGG 0.547879 2.1:-12767031 MS.gene35760:CDS
CGTCAAAGGCGGCGATGCGG+CGG 0.550222 2.1:-12766725 MS.gene35760:CDS
AAAGCCTCCGGCGCTAGGCT+CGG 0.551924 2.1:-12767282 MS.gene35760:CDS
CTCCACGCCAACGCCAACGC+CGG 0.553166 2.1:-12767216 MS.gene35760:CDS
CGACCAGGCTAGCTTATGCT+GGG 0.557426 2.1:-12767397 MS.gene35760:CDS
GTTACCGAGCCTAGCGCCGG+AGG 0.559866 2.1:+12767278 None:intergenic
CCGGAGGCTTTCCACGGCGT+GGG 0.569147 2.1:+12767294 None:intergenic
CATTCTCAGCCACACGATTG+AGG 0.570452 2.1:-12766678 None:intergenic
CTAGCGCCGGAGGCTTTCCA+CGG 0.572274 2.1:+12767288 None:intergenic
CGTAACCGACTCTTCGCTAC+CGG 0.573854 2.1:+12767026 None:intergenic
TCAACGAAGAGAGGTGGATG+AGG 0.575020 2.1:-12766778 MS.gene35760:CDS
CTACCGGAGGAACTAGAAGC+CGG 0.582394 2.1:+12767042 None:intergenic
CGAGGAGCCGTCGTCAAAGG+CGG 0.588865 2.1:-12766736 MS.gene35760:CDS
TCGTTGTGTGATAGATGCGC+CGG 0.591718 2.1:-12767249 MS.gene35760:CDS
CGTCGTCAAAGGCGGCGATG+CGG 0.596754 2.1:-12766728 MS.gene35760:CDS
GAGGAACTAGAAGCCGGCGG+TGG 0.598599 2.1:+12767048 None:intergenic
CCAGCATAAGCTAGCCTGGT+CGG 0.605872 2.1:+12767398 None:intergenic
CGGTAGCGAAGAGTCGGTTA+CGG 0.606860 2.1:-12767025 MS.gene35760:CDS
CGATTCCGATGAGGAAGATG+AGG 0.616964 2.1:-12767130 MS.gene35760:CDS
GAGATTGACATGCGTGACAG+AGG 0.627483 2.1:+12767316 None:intergenic
GTATAGCGACGTAAATGGAA+CGG 0.632422 2.1:-12766703 MS.gene35760:CDS
AACCGACTCTTCGCTACCGG+AGG 0.640395 2.1:+12767029 None:intergenic
CATGTCAATCTCCCACGCCG+TGG 0.644127 2.1:-12767305 MS.gene35760:CDS
ATAGTACGGCCTCAATCGTG+TGG 0.647407 2.1:+12766669 None:intergenic
TTGTGTGATAGATGCGCCGG+CGG 0.662123 2.1:-12767246 MS.gene35760:CDS
GTGATAATCAGGTTGTGCCG+TGG 0.677277 2.1:-12767089 MS.gene35760:CDS
GAGCAACAAGAAGAAAGTGA+AGG 0.680813 2.1:-12767183 MS.gene35760:CDS
CACCGATTACGATTCCGATG+AGG 0.696165 2.1:-12767139 MS.gene35760:CDS
TGCGCCGCTGTTGATGACCA+CGG 0.697626 2.1:+12767072 None:intergenic
CCGGAGGAACTAGAAGCCGG+CGG 0.699075 2.1:+12767045 None:intergenic
TGATTTGATAGGGTGCGACG+AGG 0.702783 2.1:-12766754 MS.gene35760:CDS
TGTGCCGTGGTCATCAACAG+CGG 0.705571 2.1:-12767076 MS.gene35760:CDS
GTGCAACGATAACCACGATG+AGG 0.723607 2.1:-12766995 MS.gene35760:CDS
ACTTAGAAATAACCTCATCG+TGG 0.742114 2.1:+12766983 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATCAACAAAAATTAACAAA+AGG + chr2.1:12767296-12767315 None:intergenic 15.0%
!!! TTTTTGTTGATTTTGTTTTC+AGG - chr2.1:12767304-12767323 MS.gene35760:CDS 20.0%
!!! TTGATTTTGTTTTCAGGTTA+CGG - chr2.1:12767310-12767329 MS.gene35760:CDS 25.0%
AGGTTACGGATTCAAAAAAT+TGG - chr2.1:12767324-12767343 MS.gene35760:CDS 30.0%
ACTTAGAAATAACCTCATCG+TGG + chr2.1:12767150-12767169 None:intergenic 35.0%
TCGTTTAGATCATGACTTTC+AGG - chr2.1:12767198-12767217 MS.gene35760:CDS 35.0%
TGAAGAAGATGGTGATAATC+AGG - chr2.1:12767030-12767049 MS.gene35760:CDS 35.0%
TTCACTTTCTTCTTGTTGCT+CGG + chr2.1:12766948-12766967 None:intergenic 35.0%
TTGGAAAAATCAACGAAGAG+AGG - chr2.1:12767343-12767362 MS.gene35760:CDS 35.0%
!! TGGATGAGGTTGATTTGATA+GGG - chr2.1:12767366-12767385 MS.gene35760:CDS 35.0%
GAAAAATCAACGAAGAGAGG+TGG - chr2.1:12767346-12767365 MS.gene35760:CDS 40.0%
GAGCAACAAGAAGAAAGTGA+AGG - chr2.1:12766947-12766966 MS.gene35760:CDS 40.0%
GTATAGCGACGTAAATGGAA+CGG - chr2.1:12767427-12767446 MS.gene35760:CDS 40.0%
TTCCTCATCGGAATCGTAAT+CGG + chr2.1:12766996-12767015 None:intergenic 40.0%
!! GTGGATGAGGTTGATTTGAT+AGG - chr2.1:12767365-12767384 MS.gene35760:CDS 40.0%
CAACCAAAAAGTTAGCAGCG+TGG + chr2.1:12766775-12766794 None:intergenic 45.0%
! GACTCACAGAAAGTTCTAGC+TGG + chr2.1:12766713-12766732 None:intergenic 45.0%
AACTTTCTGTGAGTCCGACC+AGG - chr2.1:12766718-12766737 MS.gene35760:CDS 50.0%
ATGCTGGGACTGCGATTCTA+AGG - chr2.1:12766748-12766767 MS.gene35760:CDS 50.0%
CGATTCCGATGAGGAAGATG+AGG - chr2.1:12767000-12767019 MS.gene35760:CDS 50.0%
CTCGTCCTCATCTTCCTCAT+CGG + chr2.1:12767008-12767027 None:intergenic 50.0%
GAGATTGACATGCGTGACAG+AGG + chr2.1:12766817-12766836 None:intergenic 50.0%
GAGGACGAGGATGAAGAAGA+TGG - chr2.1:12767019-12767038 MS.gene35760:CDS 50.0%
GTGCAACGATAACCACGATG+AGG - chr2.1:12767135-12767154 MS.gene35760:CDS 50.0%
TCAACGAAGAGAGGTGGATG+AGG - chr2.1:12767352-12767371 MS.gene35760:CDS 50.0%
TCGTTGTGTGATAGATGCGC+CGG - chr2.1:12766881-12766900 MS.gene35760:intron 50.0%
TGATTTGATAGGGTGCGACG+AGG - chr2.1:12767376-12767395 MS.gene35760:CDS 50.0%
! CACCGATTACGATTCCGATG+AGG - chr2.1:12766991-12767010 MS.gene35760:CDS 50.0%
! GGTCCACGCTGCTAACTTTT+TGG - chr2.1:12766769-12766788 MS.gene35760:CDS 50.0%
! GTGATAATCAGGTTGTGCCG+TGG - chr2.1:12767041-12767060 MS.gene35760:CDS 50.0%
AGTCCCAGCATAAGCTAGCC+TGG + chr2.1:12766739-12766758 None:intergenic 55.0%
CGATGAGGAAGATGAGGACG+AGG - chr2.1:12767006-12767025 MS.gene35760:CDS 55.0%
CGGCGGTATAGCGACGTAAA+TGG - chr2.1:12767422-12767441 MS.gene35760:CDS 55.0%
CGGTAGCGAAGAGTCGGTTA+CGG - chr2.1:12767105-12767124 MS.gene35760:CDS 55.0%
CTACCGGAGGAACTAGAAGC+CGG + chr2.1:12767091-12767110 None:intergenic 55.0%
TGTGCCGTGGTCATCAACAG+CGG - chr2.1:12767054-12767073 MS.gene35760:CDS 55.0%
TTCCTCCGGTAGCGAAGAGT+CGG - chr2.1:12767099-12767118 MS.gene35760:CDS 55.0%
TTCTTCTTGTTGCTCGGCGC+TGG + chr2.1:12766942-12766961 None:intergenic 55.0%
TTGTGTGATAGATGCGCCGG+CGG - chr2.1:12766884-12766903 MS.gene35760:intron 55.0%
! CCAGCATAAGCTAGCCTGGT+CGG + chr2.1:12766735-12766754 None:intergenic 55.0%
! CGTAACCGACTCTTCGCTAC+CGG + chr2.1:12767107-12767126 None:intergenic 55.0%
!! CGACCAGGCTAGCTTATGCT+GGG - chr2.1:12766733-12766752 MS.gene35760:CDS 55.0%
CATGTCAATCTCCCACGCCG+TGG - chr2.1:12766825-12766844 MS.gene35760:intron 60.0%
! AACCGACTCTTCGCTACCGG+AGG + chr2.1:12767104-12767123 None:intergenic 60.0%
! GGCGTGGAGTTTTCTTCCGC+CGG + chr2.1:12766903-12766922 None:intergenic 60.0%
!! CCGACCAGGCTAGCTTATGC+TGG - chr2.1:12766732-12766751 MS.gene35760:CDS 60.0%
!! TGCGCCGCTGTTGATGACCA+CGG + chr2.1:12767061-12767080 None:intergenic 60.0%
AAAGCCTCCGGCGCTAGGCT+CGG - chr2.1:12766848-12766867 MS.gene35760:intron 65.0%
CCGGAGGAACTAGAAGCCGG+CGG + chr2.1:12767088-12767107 None:intergenic 65.0%
CGACGAGGAGCCGTCGTCAA+AGG - chr2.1:12767391-12767410 MS.gene35760:CDS 65.0%
CGAGGAGCCGTCGTCAAAGG+CGG - chr2.1:12767394-12767413 MS.gene35760:CDS 65.0%
CGCATCGCCGCCTTTGACGA+CGG + chr2.1:12767404-12767423 None:intergenic 65.0%
CGTCGTCAAAGGCGGCGATG+CGG - chr2.1:12767402-12767421 MS.gene35760:CDS 65.0%
GAGGAACTAGAAGCCGGCGG+TGG + chr2.1:12767085-12767104 None:intergenic 65.0%
! CTAGCGCCGGAGGCTTTCCA+CGG + chr2.1:12766845-12766864 None:intergenic 65.0%
!! CCGCCGGCTTCTAGTTCCTC+CGG - chr2.1:12767085-12767104 MS.gene35760:CDS 65.0%
!! TTGTTGCTCGGCGCTGGCAC+CGG + chr2.1:12766936-12766955 None:intergenic 65.0%
AACAGCGGCGCAACCACCGC+CGG - chr2.1:12767069-12767088 MS.gene35760:CDS 70.0%
CCCACGCCGTGGAAAGCCTC+CGG - chr2.1:12766836-12766855 MS.gene35760:intron 70.0%
CCGGAGGCTTTCCACGGCGT+GGG + chr2.1:12766839-12766858 None:intergenic 70.0%
CGCGTTACCGAGCCTAGCGC+CGG + chr2.1:12766858-12766877 None:intergenic 70.0%
CGTCAAAGGCGGCGATGCGG+CGG - chr2.1:12767405-12767424 MS.gene35760:CDS 70.0%
CGTGGAAAGCCTCCGGCGCT+AGG - chr2.1:12766843-12766862 MS.gene35760:intron 70.0%
CTCCACGCCAACGCCAACGC+CGG - chr2.1:12766914-12766933 MS.gene35760:intron 70.0%
! GTTACCGAGCCTAGCGCCGG+AGG + chr2.1:12766855-12766874 None:intergenic 70.0%
GCCGGAGGCTTTCCACGGCG+TGG + chr2.1:12766840-12766859 None:intergenic 75.0%
!! CACCGGCGTTGGCGTTGGCG+TGG + chr2.1:12766919-12766938 None:intergenic 75.0%
!! GCTGGCACCGGCGTTGGCGT+TGG + chr2.1:12766924-12766943 None:intergenic 75.0%
!!! CTCGGCGCTGGCACCGGCGT+TGG + chr2.1:12766930-12766949 None:intergenic 80.0%


Chromosome Type Strat End Strand Name
chr2.1 gene 12766680 12767472 12766680 ID=MS.gene35760
chr2.1 mRNA 12766680 12767472 12766680 ID=MS.gene35760.t1;Parent=MS.gene35760
chr2.1 exon 12766933 12767472 12766933 ID=MS.gene35760.t1.exon1;Parent=MS.gene35760.t1
chr2.1 CDS 12766933 12767472 12766933 ID=cds.MS.gene35760.t1;Parent=MS.gene35760.t1
chr2.1 exon 12766680 12766826 12766680 ID=MS.gene35760.t1.exon2;Parent=MS.gene35760.t1
chr2.1 CDS 12766680 12766826 12766680 ID=cds.MS.gene35760.t1;Parent=MS.gene35760.t1
Gene Sequence

>MS.gene35760

ATGAAAAAGAACTGCGAACTCTGCAAGCTTCCAGCTAGAACTTTCTGTGAGTCCGACCAGGCTAGCTTATGCTGGGACTGCGATTCTAAGGTCCACGCTGCTAACTTTTTGGTTGAGAGACACATGAGAACTCTCCTCTGTCACGCATGTCAATCTCCCACGCCGTGGAAAGCCTCCGGCGCTAGGCTCGGTAACGCGCTTTCGTTGTGTGATAGATGCGCCGGCGGAAGAAAACTCCACGCCAACGCCAACGCCGGTGCCAGCGCCGAGCAACAAGAAGAAAGTGAAGGTGACAATGACAATGAAGAAGACACCGATTACGATTCCGATGAGGAAGATGAGGACGAGGATGAAGAAGATGGTGATAATCAGGTTGTGCCGTGGTCATCAACAGCGGCGCAACCACCGCCGGCTTCTAGTTCCTCCGGTAGCGAAGAGTCGGTTACGGTTAGCAAGTGCAACGATAACCACGATGAGGTTATTTCTAAGTTAGTTACAACGATTTCTTTGAAACGACGTCGTTTAGATCATGACTTTCAGGTAGTTAATTATTATTTTCTGTTGTAAATTAAATTACTTATTTTCTTCTGCATCTGAGTTTTCATTTTTTTATCCTTTTGTTAATTTTTGTTGATTTTGTTTTCAGGTTACGGATTCAAAAAATTGGAAAAATCAACGAAGAGAGGTGGATGAGGTTGATTTGATAGGGTGCGACGAGGAGCCGTCGTCAAAGGCGGCGATGCGGCGGTATAGCGACGTAAATGGAACGGAGCATTCTCAGCCACACGATTGA
Protein sequence

>MS.gene35760.t1

MKKNCELCKLPARTFCESDQASLCWDCDSKVHAANFLVERHMRTLLCHACQSPTPWKASGARLGNALSLCDRCAGGRKLHANANAGASAEQQEESEGDNDNEEDTDYDSDEEDEDEDEEDGDNQVVPWSSTAAQPPPASSSSGSEESVTVSKCNDNHDEVISKLVTTISLKRRRLDHDFQVTDSKNWKNQRREVDEVDLIGCDEEPSSKAAMRRYSDVNGTEHSQPHD