AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene31566

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene31566.t1 MTR_2g089310 88.841 233 21 2 1 228 1 233 1.59e-122 347
MS.gene31566.t1 MTR_2g011450 49.296 142 47 2 1 142 1 117 9.95e-32 112
MS.gene31566.t1 MTR_4g046640 50.847 59 29 0 5 63 36 94 1.20e-12 63.2
MS.gene31566.t1 MTR_4g008050 50.000 66 33 0 3 68 6 71 2.71e-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.gene31566.t1 AT4G27310 43.103 174 51 4 1 136 1 164 8.44e-36 126
MS.gene31566.t1 AT5G54470 45.946 185 81 4 2 186 3 168 2.41e-34 122
MS.gene31566.t1 AT3G21890 56.000 50 22 0 5 54 31 80 8.23e-11 58.2

Find 60 sgRNAs with CRISPR-Local

Find 67 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCACTTTCTTCTTGTTGCT+CGG 0.346480 2.4:+11622506 None:intergenic
CGGCGGTATAGCGATGTAAA+TGG 0.352357 2.4:-11622031 MS.gene31566:CDS
TTCTTCTTGTTGCTCGGCGC+TGG 0.356031 2.4:+11622512 None:intergenic
CTCATCTTCCTCATCGGAAT+CGG 0.374286 2.4:+11622458 None:intergenic
GTGGATGAGGTTGATTTGAT+AGG 0.378300 2.4:-11622088 MS.gene31566:CDS
TGAAGAAGATGGTGATAATC+AGG 0.403542 2.4:-11622427 MS.gene31566:CDS
CGCATCGCCGCCTTTGACGA+CGG 0.405274 2.4:+11622052 None:intergenic
CTCGGCGCTGGCACCGGCGT+TGG 0.429781 2.4:+11622524 None:intergenic
ATGCTGGGACTGCGATTCTA+AGG 0.430981 2.4:-11622709 MS.gene31566:CDS
CCACCGGCTTCGAGTTCTTC+CGG 0.435713 2.4:-11622372 MS.gene31566:CDS
CGTGGAAAGCCTCCGGTGCT+AGG 0.445561 2.4:-11622614 MS.gene31566:CDS
TTGTTGCTCGGCGCTGGCAC+CGG 0.453269 2.4:+11622518 None:intergenic
CCGACCAGGCTAGCTTATGC+TGG 0.471766 2.4:-11622725 MS.gene31566:CDS
CGGTAGCGATGAGTCGGTTA+CGG 0.474621 2.4:-11622352 MS.gene31566:CDS
CGCGTTACCGAGCCTAGCAC+CGG 0.516421 2.4:+11622602 None:intergenic
GCCAACGCTAACTCCAACGC+CGG 0.517678 2.4:-11622537 MS.gene31566:CDS
CTCGTCCTCATCTTCCTCAT+CGG 0.523137 2.4:+11622452 None:intergenic
GACTCACAGAAAGTTCTAGC+TGG 0.526494 2.4:+11622747 None:intergenic
AGTCCCAGCATAAGCTAGCC+TGG 0.526991 2.4:+11622721 None:intergenic
ACCGGCGTTGGAGTTAGCGT+TGG 0.527253 2.4:+11622536 None:intergenic
GAGGACGAGGATGAAGAAGA+TGG 0.529527 2.4:-11622438 MS.gene31566:CDS
AACTTTCTGTGAGTCCGACC+AGG 0.531925 2.4:-11622739 MS.gene31566:CDS
ACCGGAGGCTTTCCACGGCG+TGG 0.539884 2.4:+11622620 None:intergenic
TGGATGAGGTTGATTTGATA+GGG 0.541461 2.4:-11622087 MS.gene31566:CDS
CCCACGCCGTGGAAAGCCTC+CGG 0.541657 2.4:-11622621 MS.gene31566:CDS
CGATGAGGAAGATGAGGACG+AGG 0.544127 2.4:-11622451 MS.gene31566:CDS
CGACGAGGAACCGTCGTCAA+AGG 0.547277 2.4:-11622062 MS.gene31566:CDS
GAAGAACTCGAAGCCGGTGG+TGG 0.549423 2.4:+11622375 None:intergenic
CGTCAAAGGCGGCGATGCGG+CGG 0.550222 2.4:-11622048 MS.gene31566:CDS
AACAGCGGCGCAACCACCAC+CGG 0.553693 2.4:-11622388 MS.gene31566:CDS
CGACCAGGCTAGCTTATGCT+GGG 0.557426 2.4:-11622724 MS.gene31566:CDS
CATTCTCAGCCACACGATTG+AGG 0.570452 2.4:-11622001 None:intergenic
CGTAACCGACTCATCGCTAC+CGG 0.571656 2.4:+11622353 None:intergenic
TCAACGAAGAGAGGTGGATG+AGG 0.575020 2.4:-11622101 MS.gene31566:CDS
TTCTTCCGGTAGCGATGAGT+CGG 0.577433 2.4:-11622358 MS.gene31566:CDS
CGTTGGAGTTAGCGTTGGCG+TGG 0.586469 2.4:+11622541 None:intergenic
TCGTTGTGTGATAGATGCGC+CGG 0.591718 2.4:-11622576 MS.gene31566:CDS
AAAGCCTCCGGTGCTAGGCT+CGG 0.592338 2.4:-11622609 MS.gene31566:CDS
CCGGAGGCTTTCCACGGCGT+GGG 0.600004 2.4:+11622621 None:intergenic
CTAGCACCGGAGGCTTTCCA+CGG 0.603148 2.4:+11622615 None:intergenic
CCAGCATAAGCTAGCCTGGT+CGG 0.605872 2.4:+11622725 None:intergenic
CGAGGAACCGTCGTCAAAGG+CGG 0.613549 2.4:-11622059 MS.gene31566:CDS
CGATTCCGATGAGGAAGATG+AGG 0.619273 2.4:-11622457 MS.gene31566:CDS
CTACCGGAAGAACTCGAAGC+CGG 0.624941 2.4:+11622369 None:intergenic
GAGATTGACATGCGTGACAG+AGG 0.627483 2.4:+11622643 None:intergenic
CGTCGTCAAAGGCGGCGATG+CGG 0.629213 2.4:-11622051 MS.gene31566:CDS
CATGTCAATCTCCCACGCCG+TGG 0.644127 2.4:-11622632 MS.gene31566:CDS
GTTACCGAGCCTAGCACCGG+AGG 0.644615 2.4:+11622605 None:intergenic
ATAGTACGGCCTCAATCGTG+TGG 0.647407 2.4:+11621992 None:intergenic
CCGGAAGAACTCGAAGCCGG+TGG 0.652243 2.4:+11622372 None:intergenic
GTATAGCGATGTAAATGGAA+CGG 0.655447 2.4:-11622026 MS.gene31566:CDS
TTGTGTGATAGATGCGCCGG+CGG 0.662123 2.4:-11622573 MS.gene31566:CDS
GTGATAATCAGGTTGTGCCG+TGG 0.677277 2.4:-11622416 MS.gene31566:CDS
GAGCAACAAGAAGAAAGTGA+AGG 0.680813 2.4:-11622504 MS.gene31566:CDS
AGAAGACACCGATTCCGATG+AGG 0.691256 2.4:-11622466 MS.gene31566:CDS
TGCGCCGCTGTTGATGACCA+CGG 0.697626 2.4:+11622399 None:intergenic
TGATTTGATAGGGTGCGACG+AGG 0.704245 2.4:-11622077 MS.gene31566:CDS
TGTGCCGTGGTCATCAACAG+CGG 0.705571 2.4:-11622403 MS.gene31566:CDS
GTGCAACGATAACCACGATG+AGG 0.723607 2.4:-11622322 MS.gene31566:CDS
ACTTAGAAATAACCTCATCG+TGG 0.742114 2.4:+11622310 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTTGTTGATTTTGTTTTC+AGG - chr2.4:11622631-11622650 MS.gene31566:CDS 20.0%
!!! TTGATTTTGTTTTCAGGTTA+CGG - chr2.4:11622637-11622656 MS.gene31566:CDS 25.0%
AGGTTACGGATTCAAAAAAT+TGG - chr2.4:11622651-11622670 MS.gene31566:CDS 30.0%
! TCGTTTAGATCATGATTTTC+AGG - chr2.4:11622521-11622540 MS.gene31566:CDS 30.0%
ACTTAGAAATAACCTCATCG+TGG + chr2.4:11622473-11622492 None:intergenic 35.0%
GTATAGCGATGTAAATGGAA+CGG - chr2.4:11622754-11622773 MS.gene31566:CDS 35.0%
TGAAGAAGATGGTGATAATC+AGG - chr2.4:11622353-11622372 MS.gene31566:CDS 35.0%
TTCACTTTCTTCTTGTTGCT+CGG + chr2.4:11622277-11622296 None:intergenic 35.0%
TTGGAAAAATCAACGAAGAG+AGG - chr2.4:11622670-11622689 MS.gene31566:CDS 35.0%
!! TGGATGAGGTTGATTTGATA+GGG - chr2.4:11622693-11622712 MS.gene31566:CDS 35.0%
GAAAAATCAACGAAGAGAGG+TGG - chr2.4:11622673-11622692 MS.gene31566:CDS 40.0%
GAGCAACAAGAAGAAAGTGA+AGG - chr2.4:11622276-11622295 MS.gene31566:CDS 40.0%
!! GTGGATGAGGTTGATTTGAT+AGG - chr2.4:11622692-11622711 MS.gene31566:CDS 40.0%
CAACCAAAAAGTTAGCAGCG+TGG + chr2.4:11622098-11622117 None:intergenic 45.0%
CTCATCTTCCTCATCGGAAT+CGG + chr2.4:11622325-11622344 None:intergenic 45.0%
! GACTCACAGAAAGTTCTAGC+TGG + chr2.4:11622036-11622055 None:intergenic 45.0%
AACTTTCTGTGAGTCCGACC+AGG - chr2.4:11622041-11622060 MS.gene31566:CDS 50.0%
ATGCTGGGACTGCGATTCTA+AGG - chr2.4:11622071-11622090 MS.gene31566:CDS 50.0%
CGATTCCGATGAGGAAGATG+AGG - chr2.4:11622323-11622342 MS.gene31566:CDS 50.0%
CGGCGGTATAGCGATGTAAA+TGG - chr2.4:11622749-11622768 MS.gene31566:CDS 50.0%
CTCGTCCTCATCTTCCTCAT+CGG + chr2.4:11622331-11622350 None:intergenic 50.0%
GAGATTGACATGCGTGACAG+AGG + chr2.4:11622140-11622159 None:intergenic 50.0%
GAGGACGAGGATGAAGAAGA+TGG - chr2.4:11622342-11622361 MS.gene31566:CDS 50.0%
GTGCAACGATAACCACGATG+AGG - chr2.4:11622458-11622477 MS.gene31566:CDS 50.0%
TCAACGAAGAGAGGTGGATG+AGG - chr2.4:11622679-11622698 MS.gene31566:CDS 50.0%
TCGTTGTGTGATAGATGCGC+CGG - chr2.4:11622204-11622223 MS.gene31566:intron 50.0%
TGATTTGATAGGGTGCGACG+AGG - chr2.4:11622703-11622722 MS.gene31566:CDS 50.0%
TTCTTCCGGTAGCGATGAGT+CGG - chr2.4:11622422-11622441 MS.gene31566:CDS 50.0%
! GGTCCACGCTGCTAACTTTT+TGG - chr2.4:11622092-11622111 MS.gene31566:CDS 50.0%
! GTGATAATCAGGTTGTGCCG+TGG - chr2.4:11622364-11622383 MS.gene31566:CDS 50.0%
!! AGAAGACACCGATTCCGATG+AGG - chr2.4:11622314-11622333 MS.gene31566:CDS 50.0%
AGTCCCAGCATAAGCTAGCC+TGG + chr2.4:11622062-11622081 None:intergenic 55.0%
CGATGAGGAAGATGAGGACG+AGG - chr2.4:11622329-11622348 MS.gene31566:CDS 55.0%
CGGTAGCGATGAGTCGGTTA+CGG - chr2.4:11622428-11622447 MS.gene31566:CDS 55.0%
CTACCGGAAGAACTCGAAGC+CGG + chr2.4:11622414-11622433 None:intergenic 55.0%
TGTGCCGTGGTCATCAACAG+CGG - chr2.4:11622377-11622396 MS.gene31566:CDS 55.0%
TTCTTCTTGTTGCTCGGCGC+TGG + chr2.4:11622271-11622290 None:intergenic 55.0%
TTGTGTGATAGATGCGCCGG+CGG - chr2.4:11622207-11622226 MS.gene31566:intron 55.0%
! CCAGCATAAGCTAGCCTGGT+CGG + chr2.4:11622058-11622077 None:intergenic 55.0%
! CGTAACCGACTCATCGCTAC+CGG + chr2.4:11622430-11622449 None:intergenic 55.0%
!! CGACCAGGCTAGCTTATGCT+GGG - chr2.4:11622056-11622075 MS.gene31566:CDS 55.0%
CATGTCAATCTCCCACGCCG+TGG - chr2.4:11622148-11622167 MS.gene31566:intron 60.0%
CGACGAGGAACCGTCGTCAA+AGG - chr2.4:11622718-11622737 MS.gene31566:CDS 60.0%
CGAGGAACCGTCGTCAAAGG+CGG - chr2.4:11622721-11622740 MS.gene31566:CDS 60.0%
GAAGAACTCGAAGCCGGTGG+TGG + chr2.4:11622408-11622427 None:intergenic 60.0%
GCCAACGCTAACTCCAACGC+CGG - chr2.4:11622243-11622262 MS.gene31566:intron 60.0%
! AAAGCCTCCGGTGCTAGGCT+CGG - chr2.4:11622171-11622190 MS.gene31566:intron 60.0%
! ACCGGCGTTGGAGTTAGCGT+TGG + chr2.4:11622247-11622266 None:intergenic 60.0%
! CTAGCACCGGAGGCTTTCCA+CGG + chr2.4:11622168-11622187 None:intergenic 60.0%
! GGCGTGGAGTTTTCTTCCGC+CGG + chr2.4:11622226-11622245 None:intergenic 60.0%
!! CCACCGGCTTCGAGTTCTTC+CGG - chr2.4:11622408-11622427 MS.gene31566:CDS 60.0%
!! CCGACCAGGCTAGCTTATGC+TGG - chr2.4:11622055-11622074 MS.gene31566:CDS 60.0%
!! CGTTGGAGTTAGCGTTGGCG+TGG + chr2.4:11622242-11622261 None:intergenic 60.0%
!! TGCGCCGCTGTTGATGACCA+CGG + chr2.4:11622384-11622403 None:intergenic 60.0%
AACAGCGGCGCAACCACCAC+CGG - chr2.4:11622392-11622411 MS.gene31566:CDS 65.0%
CCGGAAGAACTCGAAGCCGG+TGG + chr2.4:11622411-11622430 None:intergenic 65.0%
CGCATCGCCGCCTTTGACGA+CGG + chr2.4:11622731-11622750 None:intergenic 65.0%
CGCGTTACCGAGCCTAGCAC+CGG + chr2.4:11622181-11622200 None:intergenic 65.0%
CGTCGTCAAAGGCGGCGATG+CGG - chr2.4:11622729-11622748 MS.gene31566:CDS 65.0%
CGTGGAAAGCCTCCGGTGCT+AGG - chr2.4:11622166-11622185 MS.gene31566:intron 65.0%
! GTTACCGAGCCTAGCACCGG+AGG + chr2.4:11622178-11622197 None:intergenic 65.0%
!! TTGTTGCTCGGCGCTGGCAC+CGG + chr2.4:11622265-11622284 None:intergenic 65.0%
ACCGGAGGCTTTCCACGGCG+TGG + chr2.4:11622163-11622182 None:intergenic 70.0%
CCCACGCCGTGGAAAGCCTC+CGG - chr2.4:11622159-11622178 MS.gene31566:intron 70.0%
CCGGAGGCTTTCCACGGCGT+GGG + chr2.4:11622162-11622181 None:intergenic 70.0%
CGTCAAAGGCGGCGATGCGG+CGG - chr2.4:11622732-11622751 MS.gene31566:CDS 70.0%
!!! CTCGGCGCTGGCACCGGCGT+TGG + chr2.4:11622259-11622278 None:intergenic 80.0%


Chromosome Type Strat End Strand Name
chr2.4 gene 11622003 11622799 11622003 ID=MS.gene31566
chr2.4 mRNA 11622003 11622799 11622003 ID=MS.gene31566.t1;Parent=MS.gene31566
chr2.4 exon 11622260 11622799 11622260 ID=MS.gene31566.t1.exon1;Parent=MS.gene31566.t1
chr2.4 CDS 11622260 11622799 11622260 ID=cds.MS.gene31566.t1;Parent=MS.gene31566.t1
chr2.4 exon 11622003 11622149 11622003 ID=MS.gene31566.t1.exon2;Parent=MS.gene31566.t1
chr2.4 CDS 11622003 11622149 11622003 ID=cds.MS.gene31566.t1;Parent=MS.gene31566.t1
Gene Sequence

>MS.gene31566

ATGAAAAAGAACTGCGAACTCTGCAAGCTTCCAGCTAGAACTTTCTGTGAGTCCGACCAGGCTAGCTTATGCTGGGACTGCGATTCTAAGGTCCACGCTGCTAACTTTTTGGTTGAGAGACACATGAGAACTCTCCTCTGTCACGCATGTCAATCTCCCACGCCGTGGAAAGCCTCCGGTGCTAGGCTCGGTAACGCGCTTTCGTTGTGTGATAGATGCGCCGGCGGAAGAAAACTCCACGCCAACGCTAACTCCAACGCCGGTGCCAGCGCCGAGCAACAAGAAGAAAGTGAAGGTGACAATGACAATGAAGAAGACACCGATTCCGATGAGGAAGATGAGGACGAGGATGAAGAAGATGGTGATAATCAGGTTGTGCCGTGGTCATCAACAGCGGCGCAACCACCACCGGCTTCGAGTTCTTCCGGTAGCGATGAGTCGGTTACGGTTAGCAAGTGCAACGATAACCACGATGAGGTTATTTCTAAGTTAGTTACAACGATTTCTTTGAAACGACGTCGTTTAGATCATGATTTTCAGGTAGTTAATTATTATTTTCTGTTGTAAATTAAATTACTTATTTTCTTCTGCATCTGAGTTTTCAATTTTTTCATTATTCTTTTGTTAATTTTTGTTGATTTTGTTTTCAGGTTACGGATTCAAAAAATTGGAAAAATCAACGAAGAGAGGTGGATGAGGTTGATTTGATAGGGTGCGACGAGGAACCGTCGTCAAAGGCGGCGATGCGGCGGTATAGCGATGTAAATGGAACGGAGCATTCTCAGCCACACGATTGA
Protein sequence

>MS.gene31566.t1

MKKNCELCKLPARTFCESDQASLCWDCDSKVHAANFLVERHMRTLLCHACQSPTPWKASGARLGNALSLCDRCAGGRKLHANANSNAGASAEQQEESEGDNDNEEDTDSDEEDEDEDEEDGDNQVVPWSSTAAQPPPASSSSGSDESVTVSKCNDNHDEVISKLVTTISLKRRRLDHDFQVTDSKNWKNQRREVDEVDLIGCDEEPSSKAAMRRYSDVNGTEHSQPHD