AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene41267


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene41267.t1 MTR_1g048720 86.885 244 32 0 1 244 1 244 1.72e-153 427
MS.gene41267.t1 MTR_1g048720 86.475 244 32 1 1 244 1 243 6.55e-151 420
MS.gene41267.t1 MTR_1g048710 83.936 249 31 2 1 249 1 240 3.14e-141 395
MS.gene41267.t1 MTR_1g048720 87.215 219 28 0 1 219 1 219 5.12e-139 389
MS.gene41267.t1 MTR_1g048720 86.758 219 28 1 1 219 1 218 1.53e-136 383
MS.gene41267.t1 MTR_1g048750 81.651 218 32 1 1 218 1 210 1.77e-126 359
MS.gene41267.t1 MTR_7g090410 58.367 245 95 6 1 241 1 242 3.71e-65 203
MS.gene41267.t1 MTR_0007s0330 30.539 167 104 5 65 228 6 163 2.46e-11 60.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene41267.t1 AT3G56970 42.570 249 132 5 1 240 1 247 1.18e-54 176
MS.gene41267.t1 AT3G56980 39.844 256 138 3 1 242 1 254 1.17e-45 153
MS.gene41267.t1 AT2G41240 37.255 255 130 7 1 242 1 238 1.33e-42 145
MS.gene41267.t1 AT2G41240 36.863 255 130 8 1 242 1 237 3.33e-40 139
MS.gene41267.t1 AT5G04150 43.169 183 96 4 60 237 78 257 3.85e-34 124
MS.gene41267.t1 AT5G04150 44.172 163 86 2 60 219 78 238 8.06e-34 122

Find 45 sgRNAs with CRISPR-Local

Find 93 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTAATTCCAGTATGTATTTA+AGG 0.091448 1.4:+34690474 None:intergenic
AGTGACCCTGAAGCTGTTTA+TGG 0.179245 1.4:+34690927 None:intergenic
TGAAGCTGTTTATGGGTTAT+TGG 0.224116 1.4:+34690935 None:intergenic
GAGCTTCTCATTTAGAATTT+CGG 0.255939 1.4:+34689216 None:intergenic
CTTCTATAATTTGCATTTCC+AGG 0.265122 1.4:-34690168 MS.gene41267:intron
TTCTGAGATCTTGATATGTT+TGG 0.287728 1.4:-34690249 MS.gene41267:CDS
TGAGAAGCTCTTATCAATAA+TGG 0.319674 1.4:-34689203 MS.gene41267:CDS
GTTTCTTCATCTCAGACCTT+TGG 0.353556 1.4:-34690200 MS.gene41267:CDS
CAGAAGAAATTGAGCATTCC+GGG 0.366600 1.4:-34690512 MS.gene41267:CDS
AAAAGTCCTTAAATACATAC+TGG 0.376466 1.4:-34690480 MS.gene41267:CDS
GCAGAAGAAATTGAGCATTC+CGG 0.378244 1.4:-34690513 MS.gene41267:intron
AATAACCCATAAACAGCTTC+AGG 0.395318 1.4:-34690933 MS.gene41267:CDS
TCTTCATCTCAGACCTTTGG+AGG 0.399420 1.4:-34690197 MS.gene41267:CDS
GTCACTGCTTGTGGACTGTA+AGG 0.403959 1.4:+34690832 None:intergenic
AGTACCATTTGATCTGAAAC+AGG 0.414053 1.4:+34690716 None:intergenic
GTGACCCTGAAGCTGTTTAT+GGG 0.414301 1.4:+34690928 None:intergenic
ATGGGTTATTGGCTCTTCAA+AGG 0.431180 1.4:+34690946 None:intergenic
GCTCTTATCAATAATGGATA+AGG 0.434619 1.4:-34689197 MS.gene41267:CDS
TCTTCCTGTTTCAGATCAAA+TGG 0.439923 1.4:-34690720 MS.gene41267:intron
TGGGTTATTGGCTCTTCAAA+GGG 0.480765 1.4:+34690947 None:intergenic
AAGAAACATTAAGTAGCAAA+AGG 0.489430 1.4:+34690216 None:intergenic
CATATCAAGATCTCAGAAAG+TGG 0.493296 1.4:+34690254 None:intergenic
CGAGGGACTAATTAAGAGAA+AGG 0.497408 1.4:-34690441 MS.gene41267:CDS
ACAAATTATTGATCTTCTTG+CGG 0.529574 1.4:+34690762 None:intergenic
CATGCCAAGGTCACTGCTTG+TGG 0.530365 1.4:+34690823 None:intergenic
TTGATATGTTTGGAAAATGA+TGG 0.537710 1.4:-34690239 MS.gene41267:CDS
AAGAAACATAGTTACAACTC+TGG 0.547575 1.4:-34690353 MS.gene41267:CDS
AGTGTAACATGAAATCTGAA+TGG 0.555088 1.4:+34690289 None:intergenic
CATCCAATTGTTGAAAACAT+AGG 0.558093 1.4:+34690971 None:intergenic
TTATCAATAATGGATAAGGA+AGG 0.562276 1.4:-34689193 MS.gene41267:CDS
CTTCATCTCAGACCTTTGGA+GGG 0.563936 1.4:-34690196 MS.gene41267:CDS
ATGATCACCTCATCTACTTG+TGG 0.565875 1.4:+34690395 None:intergenic
TCTCAGAAAGTGGAATCTTG+TGG 0.569417 1.4:+34690264 None:intergenic
ATAACCCATAAACAGCTTCA+GGG 0.574272 1.4:-34690932 MS.gene41267:CDS
CCAATTGTTGAAAACATAGG+AGG 0.582074 1.4:+34690974 None:intergenic
ATAGAAGACTCTCCCTCCAA+AGG 0.594272 1.4:+34690184 None:intergenic
AGGAAGAAGTGAACGAAGTG+AGG 0.599839 1.4:+34690736 None:intergenic
TATCAATAATGGATAAGGAA+GGG 0.600012 1.4:-34689192 MS.gene41267:CDS
CACAAGCAGTGACCTTGGCA+TGG 0.603384 1.4:-34690822 MS.gene41267:CDS
CAGTCCACAAGCAGTGACCT+TGG 0.604161 1.4:-34690827 MS.gene41267:CDS
GAATTACAGAAGCAAGTCGA+GGG 0.637852 1.4:-34690458 MS.gene41267:CDS
TCACTGCTTGTGGACTGTAA+GGG 0.641603 1.4:+34690833 None:intergenic
ACTTTCTCCACAAGTAGATG+AGG 0.642125 1.4:-34690402 MS.gene41267:CDS
CAAGCTTCTTGACCATGCCA+AGG 0.656633 1.4:+34690810 None:intergenic
GGAATTACAGAAGCAAGTCG+AGG 0.672305 1.4:-34690459 MS.gene41267:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ACATAAATATATAGAAATTT+TGG + chr1.4:34690680-34690699 None:intergenic 10.0%
!!! TAATATAATGAGTATTTTTT+TGG + chr1.4:34690840-34690859 None:intergenic 10.0%
!! AAATAATGAAACAAAAATGT+AGG - chr1.4:34690496-34690515 MS.gene41267:CDS 15.0%
!! GTGATTAATTATTTGTATAA+TGG + chr1.4:34690554-34690573 None:intergenic 15.0%
!! TTTGTCATTGTAATATTTAT+AGG + chr1.4:34690461-34690480 None:intergenic 15.0%
!!! AATTAATTAATAGTTCCTTT+TGG - chr1.4:34690859-34690878 MS.gene41267:CDS 15.0%
!!! ATTAATTAATAGTTCCTTTT+GGG - chr1.4:34690860-34690879 MS.gene41267:CDS 15.0%
!!! ATTTAAAGTAATATCGAAAA+AGG + chr1.4:34689565-34689584 None:intergenic 15.0%
!!! TTTAAAGTAATATCGAAAAA+GGG + chr1.4:34689564-34689583 None:intergenic 15.0%
!!! TTTTATTAATAGTTCCTTTT+GGG - chr1.4:34690883-34690902 MS.gene41267:CDS 15.0%
!! AACTATTAATAAAACCCAAA+AGG + chr1.4:34690877-34690896 None:intergenic 20.0%
!! AAGACTTTACTCAATAATAT+TGG + chr1.4:34690059-34690078 None:intergenic 20.0%
!! ATATATAAAGAAATGAACGA+AGG + chr1.4:34689480-34689499 None:intergenic 20.0%
!! TTCGATATTACTTTAAATTG+TGG - chr1.4:34689567-34689586 MS.gene41267:intron 20.0%
!!! GTTTTATTAATAGTTCCTTT+TGG - chr1.4:34690882-34690901 MS.gene41267:CDS 20.0%
!!! TTTTGGTTTTTTTTTTGTAG+TGG + chr1.4:34690823-34690842 None:intergenic 20.0%
! AAAAGTCCTTAAATACATAC+TGG - chr1.4:34689677-34689696 MS.gene41267:intron 25.0%
! AAGAAACATTAAGTAGCAAA+AGG + chr1.4:34689944-34689963 None:intergenic 25.0%
! ACAAATTATTGATCTTCTTG+CGG + chr1.4:34689398-34689417 None:intergenic 25.0%
! GTAATTCCAGTATGTATTTA+AGG + chr1.4:34689686-34689705 None:intergenic 25.0%
! TTGATATGTTTGGAAAATGA+TGG - chr1.4:34689918-34689937 MS.gene41267:intron 25.0%
!!! TATCAATAATGGATAAGGAA+GGG - chr1.4:34690965-34690984 MS.gene41267:CDS 25.0%
!!! TTATCAATAATGGATAAGGA+AGG - chr1.4:34690964-34690983 MS.gene41267:CDS 25.0%
AAGAAACATAGTTACAACTC+TGG - chr1.4:34689804-34689823 MS.gene41267:intron 30.0%
ACAAAAAATAGCCAATGCAT+TGG + chr1.4:34690437-34690456 None:intergenic 30.0%
AGTGTAACATGAAATCTGAA+TGG + chr1.4:34689871-34689890 None:intergenic 30.0%
ATAAAGAAATGAACGAAGGA+AGG + chr1.4:34689476-34689495 None:intergenic 30.0%
ATATTTATGTGTCAGTCCAA+GGG - chr1.4:34690690-34690709 MS.gene41267:intron 30.0%
CATCCAATTGTTGAAAACAT+AGG + chr1.4:34689189-34689208 None:intergenic 30.0%
GACAATGCATAATATATGCA+AGG - chr1.4:34690778-34690797 MS.gene41267:CDS 30.0%
TAAAGAAATGAACGAAGGAA+GGG + chr1.4:34689475-34689494 None:intergenic 30.0%
TACTGTAAAATTAACACACC+TGG + chr1.4:34690010-34690029 None:intergenic 30.0%
TATATTTATGTGTCAGTCCA+AGG - chr1.4:34690689-34690708 MS.gene41267:intron 30.0%
TGAGAAGCTCTTATCAATAA+TGG - chr1.4:34690954-34690973 MS.gene41267:CDS 30.0%
TTTATCTATGACCAATGCAT+TGG - chr1.4:34690423-34690442 MS.gene41267:CDS 30.0%
! CTATGTTTTCAACAATTGGA+TGG - chr1.4:34689187-34689206 MS.gene41267:CDS 30.0%
! CTTCTATAATTTGCATTTCC+AGG - chr1.4:34689989-34690008 MS.gene41267:intron 30.0%
! GAGCTTCTCATTTAGAATTT+CGG + chr1.4:34690944-34690963 None:intergenic 30.0%
! GTTTTGTAGTTTCAACAAGT+AGG - chr1.4:34689826-34689845 MS.gene41267:intron 30.0%
! TCATTTTCAGCATCAATTTG+AGG - chr1.4:34689281-34689300 MS.gene41267:intron 30.0%
!! GCTCTTATCAATAATGGATA+AGG - chr1.4:34690960-34690979 MS.gene41267:CDS 30.0%
!! TTCTGAGATCTTGATATGTT+TGG - chr1.4:34689908-34689927 MS.gene41267:intron 30.0%
AATAACCCATAAACAGCTTC+AGG - chr1.4:34689224-34689243 MS.gene41267:CDS 35.0%
ATAACCCATAAACAGCTTCA+GGG - chr1.4:34689225-34689244 MS.gene41267:CDS 35.0%
CATAATATATGCAAGGTCTG+GGG - chr1.4:34690785-34690804 MS.gene41267:CDS 35.0%
CATATCAAGATCTCAGAAAG+TGG + chr1.4:34689906-34689925 None:intergenic 35.0%
CCAATTGTTGAAAACATAGG+AGG + chr1.4:34689186-34689205 None:intergenic 35.0%
GCATAATATATGCAAGGTCT+GGG - chr1.4:34690784-34690803 MS.gene41267:CDS 35.0%
TCTTCCTGTTTCAGATCAAA+TGG - chr1.4:34689437-34689456 MS.gene41267:intron 35.0%
TGCATAATATATGCAAGGTC+TGG - chr1.4:34690783-34690802 MS.gene41267:CDS 35.0%
! AGTACCATTTGATCTGAAAC+AGG + chr1.4:34689444-34689463 None:intergenic 35.0%
! CCTCCTATGTTTTCAACAAT+TGG - chr1.4:34689183-34689202 MS.gene41267:CDS 35.0%
! CTTGAAAACCTTGTGTTTTG+AGG - chr1.4:34689508-34689527 MS.gene41267:intron 35.0%
! TGAAGCTGTTTATGGGTTAT+TGG + chr1.4:34689225-34689244 None:intergenic 35.0%
!!! AGGACTTTTGAAATTGTTCC+CGG + chr1.4:34689666-34689685 None:intergenic 35.0%
!!! GGTTTTTTTTTTGTAGTGGC+CGG + chr1.4:34690819-34690838 None:intergenic 35.0%
!!! GTTTTTTTTTTGTAGTGGCC+GGG + chr1.4:34690818-34690837 None:intergenic 35.0%
!!! TTTTTTTTTTGTAGTGGCCG+GGG + chr1.4:34690817-34690836 None:intergenic 35.0%
ACCATACTCCTCAAAACACA+AGG + chr1.4:34689519-34689538 None:intergenic 40.0%
ACTTTCTCCACAAGTAGATG+AGG - chr1.4:34689755-34689774 MS.gene41267:intron 40.0%
ATGATCACCTCATCTACTTG+TGG + chr1.4:34689765-34689784 None:intergenic 40.0%
CAGAAGAAATTGAGCATTCC+GGG - chr1.4:34689645-34689664 MS.gene41267:intron 40.0%
CGAGGGACTAATTAAGAGAA+AGG - chr1.4:34689716-34689735 MS.gene41267:intron 40.0%
CTACCTGCAAAAAACCCAAA+AGG + chr1.4:34690900-34690919 None:intergenic 40.0%
GAATTACAGAAGCAAGTCGA+GGG - chr1.4:34689699-34689718 MS.gene41267:intron 40.0%
GCAGAAGAAATTGAGCATTC+CGG - chr1.4:34689644-34689663 MS.gene41267:intron 40.0%
GTTTCTTCATCTCAGACCTT+TGG - chr1.4:34689957-34689976 MS.gene41267:intron 40.0%
TCTCAGAAAGTGGAATCTTG+TGG + chr1.4:34689896-34689915 None:intergenic 40.0%
! GAAAAAGGGCGTACACAATT+AGG + chr1.4:34689550-34689569 None:intergenic 40.0%
! TGAGCTTATCTCAGTTGGTA+TGG - chr1.4:34690756-34690775 MS.gene41267:CDS 40.0%
!! ATGGGTTATTGGCTCTTCAA+AGG + chr1.4:34689214-34689233 None:intergenic 40.0%
!! TGGGTTATTGGCTCTTCAAA+GGG + chr1.4:34689213-34689232 None:intergenic 40.0%
!!! ACCTTGTGTTTTGAGGAGTA+TGG - chr1.4:34689515-34689534 MS.gene41267:intron 40.0%
!!! GTTCCTTTTGGGTTTTTTGC+AGG - chr1.4:34690894-34690913 MS.gene41267:CDS 40.0%
AGGAAGAAGTGAACGAAGTG+AGG + chr1.4:34689424-34689443 None:intergenic 45.0%
AGTGACCCTGAAGCTGTTTA+TGG + chr1.4:34689233-34689252 None:intergenic 45.0%
ATAGAAGACTCTCCCTCCAA+AGG + chr1.4:34689976-34689995 None:intergenic 45.0%
CTTCATCTCAGACCTTTGGA+GGG - chr1.4:34689961-34689980 MS.gene41267:intron 45.0%
GGAATTACAGAAGCAAGTCG+AGG - chr1.4:34689698-34689717 MS.gene41267:intron 45.0%
GTGACCCTGAAGCTGTTTAT+GGG + chr1.4:34689232-34689251 None:intergenic 45.0%
TCTTCATCTCAGACCTTTGG+AGG - chr1.4:34689960-34689979 MS.gene41267:intron 45.0%
! TCACTGCTTGTGGACTGTAA+GGG + chr1.4:34689327-34689346 None:intergenic 45.0%
!!! TTTTTTTAAAGAAAAAATAT+TGG - chr1.4:34690627-34690646 MS.gene41267:intron 5.0%
AGTACTCCTCATCTCTCCCT+TGG + chr1.4:34690709-34690728 None:intergenic 50.0%
CAAGCTTCTTGACCATGCCA+AGG + chr1.4:34689350-34689369 None:intergenic 50.0%
CCAACTGAGATAAGCTCACG+AGG + chr1.4:34690754-34690773 None:intergenic 50.0%
CCTCGTGAGCTTATCTCAGT+TGG - chr1.4:34690751-34690770 MS.gene41267:CDS 50.0%
! GTCACTGCTTGTGGACTGTA+AGG + chr1.4:34689328-34689347 None:intergenic 50.0%
CACAAGCAGTGACCTTGGCA+TGG - chr1.4:34689335-34689354 MS.gene41267:intron 55.0%
CAGTCCACAAGCAGTGACCT+TGG - chr1.4:34689330-34689349 MS.gene41267:intron 55.0%
CATGCCAAGGTCACTGCTTG+TGG + chr1.4:34689337-34689356 None:intergenic 55.0%
GTCAGTCCAAGGGAGAGATG+AGG - chr1.4:34690700-34690719 MS.gene41267:intron 55.0%
! AAGGTCTGGGGTTCAAACCC+CGG - chr1.4:34690797-34690816 MS.gene41267:CDS 55.0%


Chromosome Type Strat End Strand Name
chr1.4 gene 34689168 34691011 34689168 ID=MS.gene41267
chr1.4 mRNA 34689168 34691011 34689168 ID=MS.gene41267.t1;Parent=MS.gene41267
chr1.4 exon 34690721 34691011 34690721 ID=MS.gene41267.t1.exon1;Parent=MS.gene41267.t1
chr1.4 CDS 34690721 34691011 34690721 ID=cds.MS.gene41267.t1;Parent=MS.gene41267.t1
chr1.4 exon 34690169 34690531 34690169 ID=MS.gene41267.t1.exon2;Parent=MS.gene41267.t1
chr1.4 CDS 34690169 34690531 34690169 ID=cds.MS.gene41267.t1;Parent=MS.gene41267.t1
chr1.4 exon 34689168 34689263 34689168 ID=MS.gene41267.t1.exon3;Parent=MS.gene41267.t1
chr1.4 CDS 34689168 34689263 34689168 ID=cds.MS.gene41267.t1;Parent=MS.gene41267.t1
Gene Sequence

>MS.gene41267

ATGTCAGCGATATCTCCTCCTATGTTTTCAACAATTGGATGGCCCTTTGAAGAGCCAATAACCCATAAACAGCTTCAGGGTCACTTCTACAAAGACAGTACTGATCAATTATTTCATTTTCAGCATCAATTTGAGGCAGAAATTAATTCAACAGATCCCTTACAGTCCACAAGCAGTGACCTTGGCATGGTCAAGAAGCTTGTTCATAATGCTAGTGAACGCGATCGCCGCAAGAAGATCAATAATTTGTATTCCTCACTTCGTTCACTTCTTCCTGTTTCAGATCAAATGGTACTTAATTAATCCCTTCCTTCGTTCATTTCTTTATATATATTTTAATCTTGAAAACCTTGTGTTTTGAGGAGTATGGTTGCAATTTCCTAATTGTGTACGCCCTTTTTCGATATTACTTTAAATTGTGGTTGCATATCTCTTTTTAGAACTATTGTATTAGTATTAATTTATACATACATGTTGCAGAAGAAATTGAGCATTCCGGGAACAATTTCAAAAGTCCTTAAATACATACTGGAATTACAGAAGCAAGTCGAGGGACTAATTAAGAGAAAGGATGAGATCTTATTGAGACTTTCTCCACAAGTAGATGAGGTGATCATGAACAAAGAATCTCAAAAGAAGAAACATAGTTACAACTCTGGTTTTGTAGTTTCAACAAGTAGGCTCAATGATAGTGAAATTACCATTCAGATTTCATGTTACACTGTCCACAAGATTCCACTTTCTGAGATCTTGATATGTTTGGAAAATGATGGCCTTTTGCTACTTAATGTTTCTTCATCTCAGACCTTTGGAGGGAGAGTCTTCTATAATTTGCATTTCCAGGTGTGTTAATTTTACAGTAATTAGTTTATTTTCAAAATAGTTTGTCCAATATTATTGAGTAAAGTCTTCTTTTAAGAAAATTATATATATTTTTTAAAATTACAAGACTAGTTTGATAAATATGCAGTGATAAATTTATATTTTATACTTTTTGTATCTTAATTCGAAAATTGATTATGAAAATCATAAATTGTGAAATACGATTAGAATTATATTAAAAAAAATTGTAATCATTAAATATTTTAAGAATATTATCTTAAAAAAATATGTTTATTTAAGAATTAATGACACAAAAATGTAAAAAGAAAATGAAAACAATCTTTTATTATTTTAACTCATCATACAAATAATTAATTAAACAAGAAGAAATTATGAAAAAAACTGTATTTTAAAAGAAAAAATATTGAAAATATTTATCTATGACCAATGCATTGGCTATTTTTTGTGCCTATAAATATTACAATGACAAAATATGTTTAAGTAATAAATAATGAAACAAAAATGTAGGAAAATATGAAAACACTCGTTTATTATTTTAAACCATTATACAAATAATTAATCACACGAGAAGAAAATAAAAAAAACTTTTTTTTTTGACGTACATTAAAAAAAATATTTTTTTTAAAGAAAAAATATTGGAAATATTTATTGATAACAAAATGATCTCCAAAATTTCTATATATTTATGTGTCAGTCCAAGGGAGAGATGAGGAGTACTTTATACTCATTATATTGATTGTCCTCGTGAGCTTATCTCAGTTGGTATGGACAATGCATAATATATGCAAGGTCTGGGGTTCAAACCCCGGCCACTACAAAAAAAAAACCAAAAAAATACTCATTATATTAATTAATTAATAGTTCCTTTTGGGTTTTATTAATAGTTCCTTTTGGGTTTTTTGCAGGTAGATAAAACACAAAGATTAGAATCCGAAATTCTAAATGAGAAGCTCTTATCAATAATGGATAAGGAAGGGATATTTGAAGTCAACAAAGATTAG

Protein sequence

>MS.gene41267.t1

MSAISPPMFSTIGWPFEEPITHKQLQGHFYKDSTDQLFHFQHQFEAEINSTDPLQSTSSDLGMVKKLVHNASERDRRKKINNLYSSLRSLLPVSDQMKKLSIPGTISKVLKYILELQKQVEGLIKRKDEILLRLSPQVDEVIMNKESQKKKHSYNSGFVVSTSRLNDSEITIQISCYTVHKIPLSEILICLENDGLLLLNVSSSQTFGGRVFYNLHFQVDKTQRLESEILNEKLLSIMDKEGIFEVNKD