AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene013633

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene013633.t1 MTR_3g090830 98.413 63 1 0 1 63 1 63 3.94e-38 120
MS.gene013633.t1 MTR_1g028610 76.271 59 12 1 7 63 4 62 2.29e-18 70.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene013633.t1 AT2G46330 63.462 52 19 0 12 63 11 62 9.80e-19 72.4
MS.gene013633.t1 AT3G61640 56.667 60 26 0 4 63 3 62 1.35e-17 69.3
MS.gene013633.t1 AT5G53250 58.182 55 23 0 9 63 9 63 2.23e-15 63.5
MS.gene013633.t1 AT5G24105 63.492 63 23 0 1 63 1 63 4.83e-11 52.4

Find 19 sgRNAs with CRISPR-Local

Find 51 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTGTTTCATGTGCTTCATTC+AGG 0.175879 3.4:-83135582 MS.gene013633:CDS
TGTTCTAATGCTTGTGGCTT+TGG 0.292333 3.4:-83134744 MS.gene013633:CDS
TTCAGGGTGGTTGCGTTCCT+TGG 0.345700 3.4:-83135565 MS.gene013633:CDS
GATAAATTAATGAATGATAT+AGG 0.396044 3.4:+83134715 None:intergenic
GAATATTTACCATCGCTTGT+AGG 0.408971 3.4:+83135481 None:intergenic
TGTTTCATGTGCTTCATTCA+GGG 0.448362 3.4:-83135581 MS.gene013633:CDS
TTACCATCGCTTGTAGGAGC+AGG 0.455603 3.4:+83135487 None:intergenic
AGGAGCAGGGGCAGGTGCAA+TGG 0.532358 3.4:+83135501 None:intergenic
TTATGCAACACTTATTTCTG+TGG 0.538882 3.4:-83135536 MS.gene013633:CDS
TACCATCGCTTGTAGGAGCA+GGG 0.542274 3.4:+83135488 None:intergenic
AAATAAGTGTTGCATAAATG+AGG 0.548157 3.4:+83135542 None:intergenic
TGCATGTGTTCTAATGCTTG+TGG 0.551000 3.4:-83134750 MS.gene013633:CDS
TCGCTTGTAGGAGCAGGGGC+AGG 0.566771 3.4:+83135493 None:intergenic
TTAGAACACATGCAATCGCT+TGG 0.574241 3.4:+83134759 None:intergenic
TGCAATCGCTTGGTCAATTG+TGG 0.581446 3.4:+83134769 None:intergenic
GTGTTGCATAAATGAGGCCA+AGG 0.582795 3.4:+83135548 None:intergenic
GCCCCTGCTCCTACAAGCGA+TGG 0.595947 3.4:-83135490 MS.gene013633:intron
ACCATCGCTTGTAGGAGCAG+GGG 0.636251 3.4:+83135489 None:intergenic
TTCATGTGCTTCATTCAGGG+TGG 0.668781 3.4:-83135578 MS.gene013633:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TATTGAAAAATAGATTAAAA+TGG + chr3.4:83134945-83134964 None:intergenic 10.0%
!! AACAAATTGAAAATCAAATA+TGG + chr3.4:83135426-83135445 None:intergenic 15.0%
!! TAATGATTATAAAACAAATG+TGG - chr3.4:83135261-83135280 MS.gene013633:intron 15.0%
!!! AATCATTTCATAAATCTTTT+TGG - chr3.4:83135136-83135155 MS.gene013633:intron 15.0%
!!! TTTATTTTCAGAGATTAAAT+TGG + chr3.4:83134982-83135001 None:intergenic 15.0%
!! AAAGTGATGAAACATTAATA+AGG + chr3.4:83134882-83134901 None:intergenic 20.0%
!! AAGTGATGAAACATTAATAA+GGG + chr3.4:83134881-83134900 None:intergenic 20.0%
!! GCTAAAAGTTAAGTAAAATT+TGG + chr3.4:83135343-83135362 None:intergenic 20.0%
!! TGAAAAATAGATTAAAATGG+AGG + chr3.4:83134942-83134961 None:intergenic 20.0%
!!! AAAACACCTTATACTTTTTA+AGG - chr3.4:83135178-83135197 MS.gene013633:intron 20.0%
!!! AATTGTTGTTTATAATATGC+AGG - chr3.4:83135513-83135532 MS.gene013633:CDS 20.0%
!!! ATTTAGCCTTAAAAAGTATA+AGG + chr3.4:83135187-83135206 None:intergenic 20.0%
! TAATATCCATATAAACGGTT+AGG - chr3.4:83135286-83135305 MS.gene013633:intron 25.0%
! TCTTTATGAGCATTATTGAT+AGG - chr3.4:83135464-83135483 MS.gene013633:intron 25.0%
! TGGACTAATATCCATATAAA+CGG - chr3.4:83135281-83135300 MS.gene013633:intron 25.0%
!! AAATAAGTGTTGCATAAATG+AGG + chr3.4:83134768-83134787 None:intergenic 25.0%
!! ATCAAATATGGAGATGTTTT+TGG + chr3.4:83135414-83135433 None:intergenic 25.0%
!! GATTAAATTGGTGATTCATT+TGG + chr3.4:83134970-83134989 None:intergenic 25.0%
!!! AAACTCACATATATTTTGAG+AGG + chr3.4:83135219-83135238 None:intergenic 25.0%
!!! CTTTCAATCACATTAGTTTT+CGG + chr3.4:83135107-83135126 None:intergenic 25.0%
GCTCATAAAGAATAATAGCA+TGG + chr3.4:83135455-83135474 None:intergenic 30.0%
!! TTATGCAACACTTATTTCTG+TGG - chr3.4:83134771-83134790 MS.gene013633:CDS 30.0%
GAATATTTACCATCGCTTGT+AGG + chr3.4:83134829-83134848 None:intergenic 35.0%
GTTCTTCCTAACCGTTTATA+TGG + chr3.4:83135295-83135314 None:intergenic 35.0%
TGTTTCATGTGCTTCATTCA+GGG - chr3.4:83134726-83134745 MS.gene013633:CDS 35.0%
AAGATTGTTCCTACAAACCC+AGG + chr3.4:83135317-83135336 None:intergenic 40.0%
ATAAACGGTTAGGAAGAACC+TGG - chr3.4:83135296-83135315 MS.gene013633:intron 40.0%
CTGTTTCATGTGCTTCATTC+AGG - chr3.4:83134725-83134744 MS.gene013633:CDS 40.0%
TAAACGGTTAGGAAGAACCT+GGG - chr3.4:83135297-83135316 MS.gene013633:intron 40.0%
TCCCATTCCCTAGAACTAAA+GGG - chr3.4:83135382-83135401 MS.gene013633:intron 40.0%
TGCATGTGTTCTAATGCTTG+TGG - chr3.4:83135557-83135576 MS.gene013633:CDS 40.0%
TGTTCTAATGCTTGTGGCTT+TGG - chr3.4:83135563-83135582 MS.gene013633:CDS 40.0%
TTAGAACACATGCAATCGCT+TGG + chr3.4:83135551-83135570 None:intergenic 40.0%
!! AACCCTTTAGTTCTAGGGAA+TGG + chr3.4:83135387-83135406 None:intergenic 40.0%
!! ACCCTTTAGTTCTAGGGAAT+GGG + chr3.4:83135386-83135405 None:intergenic 40.0%
GTCCCATTCCCTAGAACTAA+AGG - chr3.4:83135381-83135400 MS.gene013633:intron 45.0%
GTGTTGCATAAATGAGGCCA+AGG + chr3.4:83134762-83134781 None:intergenic 45.0%
TAGGAAGAACCTGGGTTTGT+AGG - chr3.4:83135305-83135324 MS.gene013633:intron 45.0%
TCCCTAGAACTAAAGGGTTG+TGG - chr3.4:83135388-83135407 MS.gene013633:intron 45.0%
TGCAATCGCTTGGTCAATTG+TGG + chr3.4:83135541-83135560 None:intergenic 45.0%
TTCATGTGCTTCATTCAGGG+TGG - chr3.4:83134729-83134748 MS.gene013633:CDS 45.0%
!! GCCACAACCCTTTAGTTCTA+GGG + chr3.4:83135392-83135411 None:intergenic 45.0%
!! TAGTTCTAGGGAATGGGACA+TGG + chr3.4:83135380-83135399 None:intergenic 45.0%
TACCATCGCTTGTAGGAGCA+GGG + chr3.4:83134822-83134841 None:intergenic 50.0%
TTACCATCGCTTGTAGGAGC+AGG + chr3.4:83134823-83134842 None:intergenic 50.0%
!! GGCCACAACCCTTTAGTTCT+AGG + chr3.4:83135393-83135412 None:intergenic 50.0%
ACCATCGCTTGTAGGAGCAG+GGG + chr3.4:83134821-83134840 None:intergenic 55.0%
TTCAGGGTGGTTGCGTTCCT+TGG - chr3.4:83134742-83134761 MS.gene013633:CDS 55.0%
AGGAGCAGGGGCAGGTGCAA+TGG + chr3.4:83134809-83134828 None:intergenic 65.0%
GCCCCTGCTCCTACAAGCGA+TGG - chr3.4:83134817-83134836 MS.gene013633:intron 65.0%
TCGCTTGTAGGAGCAGGGGC+AGG + chr3.4:83134817-83134836 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr3.4 gene 83134721 83135608 83134721 ID=MS.gene013633
chr3.4 mRNA 83134721 83135608 83134721 ID=MS.gene013633.t1;Parent=MS.gene013633
chr3.4 exon 83135491 83135608 83135491 ID=MS.gene013633.t1.exon1;Parent=MS.gene013633.t1
chr3.4 CDS 83135491 83135608 83135491 ID=cds.MS.gene013633.t1;Parent=MS.gene013633.t1
chr3.4 exon 83134721 83134794 83134721 ID=MS.gene013633.t1.exon2;Parent=MS.gene013633.t1
chr3.4 CDS 83134721 83134794 83134721 ID=cds.MS.gene013633.t1;Parent=MS.gene013633.t1
Gene Sequence

>MS.gene013633

ATGGCTGTTTCATGTGCTTCATTCAGGGTGGTTGCGTTCCTTGGCCTCATTTATGCAACACTTATTTCTGTGGCTTGTTCACAATCCATTGCACCTGCCCCTGCTCCTACAAGCGATGGTAAATATTCTTAATTTTCTCTATTTTAATTTTTAGATACCCTTATTAATGTTTCATCACTTTTTTTACAATTAATATGTTCATATAACAAATATGATATCCTCCATTTTAATCTATTTTTCAATAAACCAAATGAATCACCAATTTAATCTCTGAAAATAAATGACTGATAATTTAGTTTTTAAAATTATTAATGAATTTGAAATTCTTCAATCATATAGCTAGTCATTTTGCATTAATCAATTCGCTACATAAAATAAATTGTCCGAAAACTAATGTGATTGAAAGAAGAAAAAAAATCATTTCATAAATCTTTTTGGAATTTTGTTATTTCTAATAAAAACACCTTATACTTTTTAAGGCTAAATTATTGACTACCTCTCAAAATATATGTGAGTTTCTTGACTGATAAAATAGAGTTCTAATGATTATAAAACAAATGTGGACTAATATCCATATAAACGGTTAGGAAGAACCTGGGTTTGTAGGAACAATCTTTAACCAAATTTTACTTAACTTTTAGCTATATTATGTATCGCCATGTCCCATTCCCTAGAACTAAAGGGTTGTGGCCAAAAACATCTCCATATTTGATTTTCAATTTGTTATTTTTCCATGCTATTATTCTTTATGAGCATTATTGATAGGAGAATGTGTAGTGAATATTGCTAATGAATTGTTGTTTATAATATGCAGGCACCACAATTGACCAAGCGATTGCATGTGTTCTAATGCTTGTGGCTTTGGTGTTGACCTATATCATTCATTAA
Protein sequence

>MS.gene013633.t1

MAVSCASFRVVAFLGLIYATLISVACSQSIAPAPAPTSDGTTIDQAIACVLMLVALVLTYIIH