AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene78726


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene78726.t1 MTR_5g053250 97.761 134 3 0 2 135 4 137 2.20e-90 263
MS.gene78726.t1 MTR_5g053250 81.366 161 3 1 2 135 4 164 4.12e-84 248
MS.gene78726.t1 MTR_5g053250 98.701 77 1 0 59 135 1 77 1.39e-49 157
MS.gene78726.t1 MTR_6g017105 39.130 138 79 3 1 137 1 134 7.15e-24 93.2
MS.gene78726.t1 MTR_1g100643 39.456 147 81 5 1 146 1 140 2.82e-22 89.0
MS.gene78726.t1 MTR_1g033360 38.760 129 70 4 20 146 21 142 1.26e-20 84.3
MS.gene78726.t1 MTR_1g100643 42.697 89 48 2 59 146 1 87 1.58e-14 67.4
MS.gene78726.t1 MTR_1g033390 30.894 123 80 4 14 135 9 127 1.82e-11 59.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene78726.t1 AT1G26100 62.222 135 40 1 1 135 1 124 6.61e-50 160
MS.gene78726.t1 AT5G38630 44.186 129 63 5 10 135 10 132 1.45e-25 97.4
MS.gene78726.t1 AT4G25570 39.568 139 77 4 9 146 8 140 1.30e-23 92.8
MS.gene78726.t1 AT4G25570 39.568 139 77 4 9 146 49 181 2.31e-23 92.8

Find 45 sgRNAs with CRISPR-Local

Find 60 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCTTTAGCTTCTGGGATATT+TGG 0.112597 5.3:+42939489 MS.gene78726:CDS
TAGCATTTCTTGTTCTCTTC+TGG 0.118815 5.3:+42939049 MS.gene78726:CDS
CAAGGGGTGGCTTTAGCTTC+TGG 0.175443 5.3:+42939480 MS.gene78726:CDS
GAATGTTTGTGCAGCAATTT+TGG 0.224729 5.3:+42939401 MS.gene78726:intron
CTTTAGCTTCTGGGATATTT+GGG 0.267158 5.3:+42939490 MS.gene78726:CDS
CTTCTGGGATATTTGGGATT+TGG 0.279862 5.3:+42939496 MS.gene78726:CDS
TCCTGTTGAGGAAGAGAATT+AGG 0.298620 5.3:-42939105 None:intergenic
ATTTCTACAGCCTTCATTCA+TGG 0.299138 5.3:+42939553 MS.gene78726:CDS
CTCTTTCTTGCGAGAGTTTG+TGG 0.301862 5.3:+42939018 MS.gene78726:CDS
AAGGGGTGGCTTTAGCTTCT+GGG 0.303519 5.3:+42939481 MS.gene78726:CDS
AGCATTTCTTGTTCTCTTCT+GGG 0.319777 5.3:+42939050 MS.gene78726:CDS
TACTACCTTCTCCACTTAAA+AGG 0.321243 5.3:-42939268 None:intergenic
CCACAATCCCATCATTTACT+TGG 0.326307 5.3:-42939527 None:intergenic
CATCCTGTGCTCATGGTCAT+TGG 0.339718 5.3:+42939239 MS.gene78726:CDS
TCTTGTTCTCTTCTGGGCTC+TGG 0.357755 5.3:+42939056 MS.gene78726:CDS
TGTATCCCTCTTTGAAGCTC+AGG 0.397102 5.3:+42939590 MS.gene78726:CDS
TCCTAATTCTCTTCCTCAAC+AGG 0.404001 5.3:+42939104 MS.gene78726:CDS
TAGATGGTTGCCTGGGTCAA+GGG 0.416984 5.3:+42939428 MS.gene78726:CDS
ACAAAATTCCAAGTAAATGA+TGG 0.437217 5.3:+42939519 MS.gene78726:CDS
TACAGCCTTCATTCATGGAT+GGG 0.445813 5.3:+42939558 MS.gene78726:CDS
ATAGATGGTTGCCTGGGTCA+AGG 0.449560 5.3:+42939427 MS.gene78726:CDS
GAAGAGAATTAGGAGTATTG+AGG 0.459271 5.3:-42939095 None:intergenic
TCGGTGCATTTATGTCTTCA+AGG 0.466772 5.3:+42939462 MS.gene78726:CDS
TTGGTGCATAGATGGTTGCC+TGG 0.471390 5.3:+42939420 MS.gene78726:CDS
GGTTCTCCATCCTGTGCTCA+TGG 0.477323 5.3:+42939232 MS.gene78726:intron
CTACAGCCTTCATTCATGGA+TGG 0.480089 5.3:+42939557 MS.gene78726:CDS
AGATGGTTGCCTGGGTCAAG+GGG 0.483244 5.3:+42939429 MS.gene78726:CDS
AAGAGCAAAGGGAGTAGTGA+GGG 0.491250 5.3:-42939000 None:intergenic
CTCTCGCAAGAAAGAGCAAA+GGG 0.500913 5.3:-42939011 None:intergenic
CGGTGCATTTATGTCTTCAA+GGG 0.507370 5.3:+42939463 MS.gene78726:CDS
CAAAATTCCAAGTAAATGAT+GGG 0.535853 5.3:+42939520 MS.gene78726:CDS
CCAAGTAAATGATGGGATTG+TGG 0.538655 5.3:+42939527 MS.gene78726:CDS
TCAAACCCATCCATGAATGA+AGG 0.539092 5.3:-42939563 None:intergenic
GCATTTATGTCTTCAAGGGG+TGG 0.549961 5.3:+42939467 MS.gene78726:CDS
TGGTGCATAGATGGTTGCCT+GGG 0.586545 5.3:+42939421 MS.gene78726:CDS
AATCCAATGACCATGAGCAC+AGG 0.602677 5.3:-42939242 None:intergenic
TACTCACCTGAGCTTCAAAG+AGG 0.613059 5.3:-42939596 None:intergenic
CAATGACCATGAGCACAGGA+TGG 0.614301 5.3:-42939238 None:intergenic
GATGGTTGCCTGGGTCAAGG+GGG 0.624454 5.3:+42939430 MS.gene78726:CDS
ACTCTCGCAAGAAAGAGCAA+AGG 0.634673 5.3:-42939012 None:intergenic
ACTCACCTGAGCTTCAAAGA+GGG 0.638153 5.3:-42939595 None:intergenic
GGTGCATTTATGTCTTCAAG+GGG 0.646132 5.3:+42939464 MS.gene78726:CDS
AAAGAGCAAAGGGAGTAGTG+AGG 0.647530 5.3:-42939001 None:intergenic
GCATAGATGAGATCCTGTTG+AGG 0.669004 5.3:-42939117 None:intergenic
GAGTAGTGAGGGAAAGACAG+TGG 0.669481 5.3:-42938989 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTGATGTAATTAAATAAAAA+GGG - chr5.3:42939173-42939192 None:intergenic 10.0%
!! TTTGATGTAATTAAATAAAA+AGG - chr5.3:42939174-42939193 None:intergenic 10.0%
!!! TTTAATTTTAATTTAATTGC+AGG + chr5.3:42939211-42939230 MS.gene78726:intron 10.0%
!! AAATATTATGTATTGGGATT+AGG + chr5.3:42939311-42939330 MS.gene78726:intron 20.0%
!! AACCCAAAAATATTATGTAT+TGG + chr5.3:42939304-42939323 MS.gene78726:intron 20.0%
!! ACCCAAAAATATTATGTATT+GGG + chr5.3:42939305-42939324 MS.gene78726:intron 20.0%
!! TAATGAAATCAAGTCATTAT+TGG + chr5.3:42939344-42939363 MS.gene78726:intron 20.0%
!!! ATCCCAATACATAATATTTT+TGG - chr5.3:42939310-42939329 None:intergenic 20.0%
!!! TCCCAATACATAATATTTTT+GGG - chr5.3:42939309-42939328 None:intergenic 20.0%
! ACAAAATTCCAAGTAAATGA+TGG + chr5.3:42939519-42939538 MS.gene78726:CDS 25.0%
! CAAAATTCCAAGTAAATGAT+GGG + chr5.3:42939520-42939539 MS.gene78726:CDS 25.0%
!! ATTGGATTTATCCTTTTAAG+TGG + chr5.3:42939257-42939276 MS.gene78726:CDS 25.0%
AAAGGGAATGAAGAAAATAG+AGG - chr5.3:42939156-42939175 None:intergenic 30.0%
!! TTTATCCTTTTAAGTGGAGA+AGG + chr5.3:42939263-42939282 MS.gene78726:CDS 30.0%
AGCATTTCTTGTTCTCTTCT+GGG + chr5.3:42939050-42939069 MS.gene78726:CDS 35.0%
ATTTCTACAGCCTTCATTCA+TGG + chr5.3:42939553-42939572 MS.gene78726:CDS 35.0%
TACTACCTTCTCCACTTAAA+AGG - chr5.3:42939271-42939290 None:intergenic 35.0%
TAGCATTTCTTGTTCTCTTC+TGG + chr5.3:42939049-42939068 MS.gene78726:CDS 35.0%
! GAATGTTTGTGCAGCAATTT+TGG + chr5.3:42939401-42939420 MS.gene78726:intron 35.0%
!! CTTTAGCTTCTGGGATATTT+GGG + chr5.3:42939490-42939509 MS.gene78726:CDS 35.0%
!! GAAGAGAATTAGGAGTATTG+AGG - chr5.3:42939098-42939117 None:intergenic 35.0%
CCACAATCCCATCATTTACT+TGG - chr5.3:42939530-42939549 None:intergenic 40.0%
CGGTGCATTTATGTCTTCAA+GGG + chr5.3:42939463-42939482 MS.gene78726:CDS 40.0%
GGTGCATTTATGTCTTCAAG+GGG + chr5.3:42939464-42939483 MS.gene78726:CDS 40.0%
TACAGCCTTCATTCATGGAT+GGG + chr5.3:42939558-42939577 MS.gene78726:CDS 40.0%
TCAAACCCATCCATGAATGA+AGG - chr5.3:42939566-42939585 None:intergenic 40.0%
TCCTAATTCTCTTCCTCAAC+AGG + chr5.3:42939104-42939123 MS.gene78726:CDS 40.0%
TCCTGTTGAGGAAGAGAATT+AGG - chr5.3:42939108-42939127 None:intergenic 40.0%
TCGGTGCATTTATGTCTTCA+AGG + chr5.3:42939462-42939481 MS.gene78726:CDS 40.0%
! CCAAGTAAATGATGGGATTG+TGG + chr5.3:42939527-42939546 MS.gene78726:CDS 40.0%
!! CAGCAATTTTGGTGCATAGA+TGG + chr5.3:42939412-42939431 MS.gene78726:intron 40.0%
!! CTTCTGGGATATTTGGGATT+TGG + chr5.3:42939496-42939515 MS.gene78726:CDS 40.0%
!! GCTTTAGCTTCTGGGATATT+TGG + chr5.3:42939489-42939508 MS.gene78726:CDS 40.0%
AAAGAGCAAAGGGAGTAGTG+AGG - chr5.3:42939004-42939023 None:intergenic 45.0%
AAGAGCAAAGGGAGTAGTGA+GGG - chr5.3:42939003-42939022 None:intergenic 45.0%
AATCCAATGACCATGAGCAC+AGG - chr5.3:42939245-42939264 None:intergenic 45.0%
ACTCACCTGAGCTTCAAAGA+GGG - chr5.3:42939598-42939617 None:intergenic 45.0%
ACTCTCGCAAGAAAGAGCAA+AGG - chr5.3:42939015-42939034 None:intergenic 45.0%
CTACAGCCTTCATTCATGGA+TGG + chr5.3:42939557-42939576 MS.gene78726:CDS 45.0%
CTCTCGCAAGAAAGAGCAAA+GGG - chr5.3:42939014-42939033 None:intergenic 45.0%
CTCTTTCTTGCGAGAGTTTG+TGG + chr5.3:42939018-42939037 MS.gene78726:CDS 45.0%
GCATAGATGAGATCCTGTTG+AGG - chr5.3:42939120-42939139 None:intergenic 45.0%
GCATTTATGTCTTCAAGGGG+TGG + chr5.3:42939467-42939486 MS.gene78726:CDS 45.0%
GTCAAGGGGGTTGAAGAAAT+CGG + chr5.3:42939443-42939462 MS.gene78726:CDS 45.0%
TACTCACCTGAGCTTCAAAG+AGG - chr5.3:42939599-42939618 None:intergenic 45.0%
!! TGTATCCCTCTTTGAAGCTC+AGG + chr5.3:42939590-42939609 MS.gene78726:CDS 45.0%
ATAGATGGTTGCCTGGGTCA+AGG + chr5.3:42939427-42939446 MS.gene78726:CDS 50.0%
CAATGACCATGAGCACAGGA+TGG - chr5.3:42939241-42939260 None:intergenic 50.0%
CATCCTGTGCTCATGGTCAT+TGG + chr5.3:42939239-42939258 MS.gene78726:CDS 50.0%
GAGTAGTGAGGGAAAGACAG+TGG - chr5.3:42938992-42939011 None:intergenic 50.0%
TAGATGGTTGCCTGGGTCAA+GGG + chr5.3:42939428-42939447 MS.gene78726:CDS 50.0%
TCTTGTTCTCTTCTGGGCTC+TGG + chr5.3:42939056-42939075 MS.gene78726:CDS 50.0%
TGGTGCATAGATGGTTGCCT+GGG + chr5.3:42939421-42939440 MS.gene78726:CDS 50.0%
TTGGTGCATAGATGGTTGCC+TGG + chr5.3:42939420-42939439 MS.gene78726:CDS 50.0%
!! AAGGGGTGGCTTTAGCTTCT+GGG + chr5.3:42939481-42939500 MS.gene78726:CDS 50.0%
AGATGGTTGCCTGGGTCAAG+GGG + chr5.3:42939429-42939448 MS.gene78726:CDS 55.0%
GGTTCTCCATCCTGTGCTCA+TGG + chr5.3:42939232-42939251 MS.gene78726:intron 55.0%
TTCTTCAACCCCCTTGACCC+AGG - chr5.3:42939441-42939460 None:intergenic 55.0%
!! CAAGGGGTGGCTTTAGCTTC+TGG + chr5.3:42939480-42939499 MS.gene78726:CDS 55.0%
GATGGTTGCCTGGGTCAAGG+GGG + chr5.3:42939430-42939449 MS.gene78726:CDS 60.0%


Chromosome Type Strat End Strand Name
chr5.3 gene 42938985 42939662 42938985 ID=MS.gene78726
chr5.3 mRNA 42938985 42939662 42938985 ID=MS.gene78726.t1;Parent=MS.gene78726
chr5.3 exon 42938985 42939140 42938985 ID=MS.gene78726.t1.exon1;Parent=MS.gene78726.t1
chr5.3 CDS 42938985 42939140 42938985 ID=cds.MS.gene78726.t1;Parent=MS.gene78726.t1
chr5.3 exon 42939233 42939284 42939233 ID=MS.gene78726.t1.exon2;Parent=MS.gene78726.t1
chr5.3 CDS 42939233 42939284 42939233 ID=cds.MS.gene78726.t1;Parent=MS.gene78726.t1
chr5.3 exon 42939415 42939662 42939415 ID=MS.gene78726.t1.exon3;Parent=MS.gene78726.t1
chr5.3 CDS 42939415 42939662 42939415 ID=cds.MS.gene78726.t1;Parent=MS.gene78726.t1
Gene Sequence

>MS.gene78726

ATGGCCACTGTCTTTCCCTCACTACTCCCTTTGCTCTTTCTTGCGAGAGTTTGTGGTCTTTCAGTAGCATTTCTTGTTCTCTTCTGGGCTCTGGCTTTCAAATCTAGCTTCCTCAATACTCCTAATTCTCTTCCTCAACAGGATCTCATCTATGCAGTACATACATAACCTCTATTTTCTTCATTCCCTTTTTATTTAATTACATCAAAGAATGCATAAGCTTTATTTTAATTTTAATTTAATTGCAGGTTCTCCATCCTGTGCTCATGGTCATTGGATTTATCCTTTTAAGTGGAGAAGGTAGTACTCTAGTTTTAGCAACCCAAAAATATTATGTATTGGGATTAGGATATTTTACATAATGAAATCAAGTCATTATTGGTCAATTTGTATTTAGTTTAATTGTTTTAATGAATGAATGTTTGTGCAGCAATTTTGGTGCATAGATGGTTGCCTGGGTCAAGGGGGTTGAAGAAATCGGTGCATTTATGTCTTCAAGGGGTGGCTTTAGCTTCTGGGATATTTGGGATTTGGACAAAATTCCAAGTAAATGATGGGATTGTGGCTAATTTCTACAGCCTTCATTCATGGATGGGTTTGATTTGTGTATCCCTCTTTGAAGCTCAGGTGAGTATGCTCTATCATTTCTTTACATTTTTTAAATCAGAGACTTTCTAA

Protein sequence

>MS.gene78726.t1

MATVFPSLLPLLFLARVCGLSVAFLVLFWALAFKSSFLNTPNSLPQQDLIYAVLHPVLMVIGFILLSGEAILVHRWLPGSRGLKKSVHLCLQGVALASGIFGIWTKFQVNDGIVANFYSLHSWMGLICVSLFEAQVSMLYHFFTFFKSETF