AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene92201

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene92201.t1 MTR_2g066700 97.166 247 7 0 1 247 1 247 2.30e-178 489
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene92201.t1 AT1G79160 53.846 260 82 12 1 247 5 239 1.92e-70 216
MS.gene92201.t1 AT1G16500 45.775 284 92 13 1 247 1 259 2.39e-59 188

Find 46 sgRNAs with CRISPR-Local

Find 94 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTGAAGTTAGCTCTCTTGTT+AGG 0.215095 2.4:-27139929 MS.gene92201:CDS
AGCTCTCTTGTTAGGGTTCT+AGG 0.222073 2.4:-27139921 MS.gene92201:CDS
AGAATTGGATCTTGATTTAC+AGG 0.260293 2.4:-27139781 MS.gene92201:CDS
CTAAATTTGATTCATCAAAT+AGG 0.294108 2.4:+27138536 None:intergenic
TTCAATTGAATCCCAAGAAT+TGG 0.301025 2.4:-27139796 MS.gene92201:CDS
ATTCTTGAAATCGTCAATTT+CGG 0.309411 2.4:-27138395 MS.gene92201:CDS
AAATTCAAGTCTTGAAGTTT+AGG 0.312878 2.4:+27138589 None:intergenic
ATCCTAGGTTTCTTCATAGT+TGG 0.320748 2.4:+27138187 None:intergenic
GTAAATCAAGATCCAATTCT+TGG 0.341520 2.4:+27139784 None:intergenic
GATTCATCAAATAGGTTCAA+TGG 0.342241 2.4:+27138544 None:intergenic
TTTGTTCAGAAATTGGTGAT+TGG 0.359020 2.4:+27138635 None:intergenic
TTGTTCAGAAATTGGTGATT+GGG 0.387101 2.4:+27138636 None:intergenic
GGTTTCTTCATAGTTGGAAT+TGG 0.391404 2.4:+27138193 None:intergenic
GGAACATTTGATTGTGTTGA+TGG 0.395950 2.4:+27138565 None:intergenic
ATTTACAGGTTCCTAGTGGC+TGG 0.409368 2.4:-27139767 MS.gene92201:CDS
TGAAGTTAGCTCTCTTGTTA+GGG 0.424505 2.4:-27139928 MS.gene92201:CDS
ACACTTTGGTAATTGCTTGT+TGG 0.436517 2.4:+27138487 None:intergenic
CCAATGGCTGCAGGGTGTCC+TGG 0.445132 2.4:-27138280 MS.gene92201:CDS
TAAATCAAGATCCAATTCTT+GGG 0.456351 2.4:+27139785 None:intergenic
CTTGTTAGGGTTCTAGGTGG+TGG 0.457284 2.4:-27139915 MS.gene92201:CDS
ATTTCATCACCAATGGCTGC+AGG 0.458385 2.4:-27138289 MS.gene92201:CDS
AGAATAATCCTAAGTGTCCT+AGG 0.485771 2.4:-27138231 MS.gene92201:CDS
GAAATATTAAGATCAATCCT+AGG 0.490407 2.4:+27138172 None:intergenic
CAGGGAAAGTTTATATTCAA+AGG 0.491847 2.4:-27138672 MS.gene92201:CDS
GTTAGGGTTCTAGGTGGTGG+TGG 0.502792 2.4:-27139912 MS.gene92201:CDS
TGTCAAGAGTGCACACACTT+TGG 0.506113 2.4:+27138473 None:intergenic
CCAGGACACCCTGCAGCCAT+TGG 0.515852 2.4:+27138280 None:intergenic
GAGTTACACCTAGGACACTT+AGG 0.522057 2.4:+27138223 None:intergenic
TTCTTGGGATTCAATTGAAG+AGG 0.536073 2.4:+27139800 None:intergenic
ATTACAAGAGACTTGCTTGG+TGG 0.546683 2.4:-27139825 MS.gene92201:CDS
GAAAATGATTTCATCACCAA+TGG 0.554457 2.4:-27138296 MS.gene92201:CDS
CTGATTACAAGAGACTTGCT+TGG 0.555890 2.4:-27139828 MS.gene92201:CDS
GAACATTTGATTGTGTTGAT+GGG 0.563188 2.4:+27138566 None:intergenic
TTACAAGAGACTTGCTTGGT+GGG 0.576143 2.4:-27139824 MS.gene92201:CDS
TTTACAGGTTCCTAGTGGCT+GGG 0.577425 2.4:-27139766 MS.gene92201:CDS
AATACATACGATAAGCAACC+AGG 0.589362 2.4:+27138262 None:intergenic
GAAGAGCAACATCGAACGGT+AGG 0.589713 2.4:-27139882 MS.gene92201:CDS
CTTGATTTACAGGTTCCTAG+TGG 0.589849 2.4:-27139771 MS.gene92201:CDS
CAAAGAAGAGCAACATCGAA+CGG 0.609358 2.4:-27139886 MS.gene92201:CDS
ACGGTAGGTAATGATTCTCA+TGG 0.626022 2.4:-27139867 MS.gene92201:CDS
TTTCATCACCAATGGCTGCA+GGG 0.626120 2.4:-27138288 MS.gene92201:CDS
TTCCAACTATGAAGAAACCT+AGG 0.628247 2.4:-27138189 MS.gene92201:CDS
TTCTCATGGTGAGAAATCAA+CGG 0.650661 2.4:-27139853 MS.gene92201:CDS
TCTCTTGTTAGGGTTCTAGG+TGG 0.667514 2.4:-27139918 MS.gene92201:CDS
GGTACAATAGAGTTACACCT+AGG 0.708224 2.4:+27138214 None:intergenic
GATGATGAAGAAGAATACGA+AGG 0.712070 2.4:+27138364 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTTAAAATTCAATTTGTTT+AGG - chr2.4:27138842-27138861 MS.gene92201:intron 10.0%
!! AACTTAGATATCAAAAAATT+TGG + chr2.4:27139070-27139089 None:intergenic 15.0%
!! AAGTCTTTATGATATATTTA+TGG + chr2.4:27139150-27139169 None:intergenic 15.0%
!! AATAGAAACATAATAATTGA+AGG - chr2.4:27138781-27138800 MS.gene92201:intron 15.0%
!! AGTCTTTATGATATATTTAT+GGG + chr2.4:27139149-27139168 None:intergenic 15.0%
!! ATAGAAACATAATAATTGAA+GGG - chr2.4:27138782-27138801 MS.gene92201:intron 15.0%
!! TATCTAAGTTAATGAAAATA+TGG - chr2.4:27139080-27139099 MS.gene92201:intron 15.0%
!!! AAATTTCACTTTTTTGTTTA+TGG - chr2.4:27138477-27138496 MS.gene92201:CDS 15.0%
!!! AATTTCACTTTTTTGTTTAT+GGG - chr2.4:27138478-27138497 MS.gene92201:CDS 15.0%
!!! GAAAATATAAATTTTCTCTT+AGG - chr2.4:27138400-27138419 MS.gene92201:CDS 15.0%
!! ATTTCTGAACAAAAAAATCA+AGG - chr2.4:27139476-27139495 MS.gene92201:intron 20.0%
!! CTAAATTTGATTCATCAAAT+AGG + chr2.4:27139568-27139587 None:intergenic 20.0%
!! TATGATATATTTATGGGTAA+GGG + chr2.4:27139143-27139162 None:intergenic 20.0%
!! TCATAAAAATGTAACTAACT+TGG + chr2.4:27139331-27139350 None:intergenic 20.0%
!! TTATGATATATTTATGGGTA+AGG + chr2.4:27139144-27139163 None:intergenic 20.0%
!!! AATGATGATCTTTTTCTTAT+TGG + chr2.4:27139689-27139708 None:intergenic 20.0%
!!! AGAGAAAATTTATATTTTCC+CGG + chr2.4:27138399-27138418 None:intergenic 20.0%
!!! TAGTTACATTTTTATGACTA+TGG - chr2.4:27139334-27139353 MS.gene92201:intron 20.0%
!!! TCTTTTTGATTTTTTACATG+AGG - chr2.4:27138678-27138697 MS.gene92201:intron 20.0%
!!! TGATTTTTTTGTTCAGAAAT+TGG + chr2.4:27139476-27139495 None:intergenic 20.0%
!!! TGTTTGTGTTTTTTTTACAA+TGG - chr2.4:27138575-27138594 MS.gene92201:CDS 20.0%
! AAAATGTAACTAACTTGGTA+TGG + chr2.4:27139326-27139345 None:intergenic 25.0%
! AAATTCAAGTCTTGAAGTTT+AGG + chr2.4:27139515-27139534 None:intergenic 25.0%
! AAGTGTACACTATGATTAAT+AGG - chr2.4:27138449-27138468 MS.gene92201:CDS 25.0%
! ATGATATATTTATGGGTAAG+GGG + chr2.4:27139142-27139161 None:intergenic 25.0%
! ATTCTTGAAATCGTCAATTT+CGG - chr2.4:27139706-27139725 MS.gene92201:intron 25.0%
! GAAATATTAAGATCAATCCT+AGG + chr2.4:27139932-27139951 None:intergenic 25.0%
! TAAATCAAGATCCAATTCTT+GGG + chr2.4:27138319-27138338 None:intergenic 25.0%
! TTGTTTGTGTTTCATTTGTA+TGG - chr2.4:27138919-27138938 MS.gene92201:intron 25.0%
!! GAGAAAATTTATATTTTCCC+GGG + chr2.4:27138398-27138417 None:intergenic 25.0%
!!! TTTTGTTTTGCTCTTTTGAT+TGG - chr2.4:27138755-27138774 MS.gene92201:intron 25.0%
AACAAAAGGAAAATACCTGA+AGG + chr2.4:27138374-27138393 None:intergenic 30.0%
ACTTTGTTCTATCATTGCAA+AGG + chr2.4:27138888-27138907 None:intergenic 30.0%
AGAATTGGATCTTGATTTAC+AGG - chr2.4:27138320-27138339 MS.gene92201:CDS 30.0%
CAGGGAAAGTTTATATTCAA+AGG - chr2.4:27139429-27139448 MS.gene92201:intron 30.0%
GAAAATGATTTCATCACCAA+TGG - chr2.4:27139805-27139824 MS.gene92201:CDS 30.0%
GACATAAATACAGAGTACAT+AGG + chr2.4:27139011-27139030 None:intergenic 30.0%
GATTCATCAAATAGGTTCAA+TGG + chr2.4:27139560-27139579 None:intergenic 30.0%
GTAAATCAAGATCCAATTCT+TGG + chr2.4:27138320-27138339 None:intergenic 30.0%
TTCAATTGAATCCCAAGAAT+TGG - chr2.4:27138305-27138324 MS.gene92201:CDS 30.0%
! AAGCAGATGAAACAAGTTTT+AGG + chr2.4:27139592-27139611 None:intergenic 30.0%
! GAACATTTGATTGTGTTGAT+GGG + chr2.4:27139538-27139557 None:intergenic 30.0%
! TTGTTCAGAAATTGGTGATT+GGG + chr2.4:27139468-27139487 None:intergenic 30.0%
! TTTGTTCAGAAATTGGTGAT+TGG + chr2.4:27139469-27139488 None:intergenic 30.0%
!! TTGCATTTTAATGTAACAGC+AGG - chr2.4:27138961-27138980 MS.gene92201:intron 30.0%
!!! CAGATTTTTTATGTGGTCTA+TGG - chr2.4:27138704-27138723 MS.gene92201:intron 30.0%
!!! TTGTTTTTTTGATGCAGTCA+GGG - chr2.4:27139411-27139430 MS.gene92201:intron 30.0%
!!! TTTGTTTTTTTGATGCAGTC+AGG - chr2.4:27139410-27139429 MS.gene92201:intron 30.0%
!!! TTTTTTGTTTATGGGCTATG+TGG - chr2.4:27138486-27138505 MS.gene92201:CDS 30.0%
AATACATACGATAAGCAACC+AGG + chr2.4:27139842-27139861 None:intergenic 35.0%
AGAATAATCCTAAGTGTCCT+AGG - chr2.4:27139870-27139889 MS.gene92201:CDS 35.0%
ATATATTTATGGGTAAGGGG+CGG + chr2.4:27139139-27139158 None:intergenic 35.0%
ATCCTAGGTTTCTTCATAGT+TGG + chr2.4:27139917-27139936 None:intergenic 35.0%
GATGATGAAGAAGAATACGA+AGG + chr2.4:27139740-27139759 None:intergenic 35.0%
GATGCATAGTTCTTCAATCA+TGG - chr2.4:27138603-27138622 MS.gene92201:CDS 35.0%
GGAACATTTGATTGTGTTGA+TGG + chr2.4:27139539-27139558 None:intergenic 35.0%
GGTTTCTTCATAGTTGGAAT+TGG + chr2.4:27139911-27139930 None:intergenic 35.0%
TTCCAACTATGAAGAAACCT+AGG - chr2.4:27139912-27139931 MS.gene92201:CDS 35.0%
TTCTCATGGTGAGAAATCAA+CGG - chr2.4:27138248-27138267 MS.gene92201:CDS 35.0%
TTCTTGGGATTCAATTGAAG+AGG + chr2.4:27138304-27138323 None:intergenic 35.0%
! ACACTTTGGTAATTGCTTGT+TGG + chr2.4:27139617-27139636 None:intergenic 35.0%
! ATATTTTCCCGGGAAACAAA+AGG + chr2.4:27138388-27138407 None:intergenic 35.0%
! TGAAGTTAGCTCTCTTGTTA+GGG - chr2.4:27138173-27138192 MS.gene92201:CDS 35.0%
!! GGTATTTTCCTTTTGTTTCC+CGG - chr2.4:27138377-27138396 MS.gene92201:CDS 35.0%
!! GTATTTTCCTTTTGTTTCCC+GGG - chr2.4:27138378-27138397 MS.gene92201:CDS 35.0%
!!! GAGGAAGCAGATTTTTTATG+TGG - chr2.4:27138697-27138716 MS.gene92201:intron 35.0%
ACGGTAGGTAATGATTCTCA+TGG - chr2.4:27138234-27138253 MS.gene92201:CDS 40.0%
ATCTGATCAAAATGGCGTCA+TGG + chr2.4:27139109-27139128 None:intergenic 40.0%
CAAAGAAGAGCAACATCGAA+CGG - chr2.4:27138215-27138234 MS.gene92201:CDS 40.0%
CTTGATTTACAGGTTCCTAG+TGG - chr2.4:27138330-27138349 MS.gene92201:CDS 40.0%
GGTACAATAGAGTTACACCT+AGG + chr2.4:27139890-27139909 None:intergenic 40.0%
GTGGAGCAATCTGATCAAAA+TGG + chr2.4:27139117-27139136 None:intergenic 40.0%
! ATTACAAGAGACTTGCTTGG+TGG - chr2.4:27138276-27138295 MS.gene92201:CDS 40.0%
! CTGAAGTTAGCTCTCTTGTT+AGG - chr2.4:27138172-27138191 MS.gene92201:CDS 40.0%
! CTGATTACAAGAGACTTGCT+TGG - chr2.4:27138273-27138292 MS.gene92201:CDS 40.0%
! TTACAAGAGACTTGCTTGGT+GGG - chr2.4:27138277-27138296 MS.gene92201:CDS 40.0%
ACGAAAACTCGAGTAACTGC+AGG + chr2.4:27138987-27139006 None:intergenic 45.0%
AGCTCTCTTGTTAGGGTTCT+AGG - chr2.4:27138180-27138199 MS.gene92201:CDS 45.0%
ATTTACAGGTTCCTAGTGGC+TGG - chr2.4:27138334-27138353 MS.gene92201:CDS 45.0%
ATTTCATCACCAATGGCTGC+AGG - chr2.4:27139812-27139831 MS.gene92201:CDS 45.0%
GAGTTACACCTAGGACACTT+AGG + chr2.4:27139881-27139900 None:intergenic 45.0%
GGAAAAACGTCTTGACCTTC+AGG - chr2.4:27138356-27138375 MS.gene92201:CDS 45.0%
TTTACAGGTTCCTAGTGGCT+GGG - chr2.4:27138335-27138354 MS.gene92201:CDS 45.0%
TTTCATCACCAATGGCTGCA+GGG - chr2.4:27139813-27139832 MS.gene92201:CDS 45.0%
! TGTCAAGAGTGCACACACTT+TGG + chr2.4:27139631-27139650 None:intergenic 45.0%
!! TCTCTTGTTAGGGTTCTAGG+TGG - chr2.4:27138183-27138202 MS.gene92201:CDS 45.0%
!! ACTAAATAAATAAAATTAAA+TGG + chr2.4:27139200-27139219 None:intergenic 5.0%
GAAGAGCAACATCGAACGGT+AGG - chr2.4:27138219-27138238 MS.gene92201:CDS 50.0%
TATTTATGGGTAAGGGGCGG+TGG + chr2.4:27139136-27139155 None:intergenic 50.0%
! AGACGTTTTTCCCAGCCACT+AGG + chr2.4:27138348-27138367 None:intergenic 50.0%
!! CTTGTTAGGGTTCTAGGTGG+TGG - chr2.4:27138186-27138205 MS.gene92201:CDS 50.0%
!! GTTAGGGTTCTAGGTGGTGG+TGG - chr2.4:27138189-27138208 MS.gene92201:CDS 55.0%
CCAGGACACCCTGCAGCCAT+TGG + chr2.4:27139824-27139843 None:intergenic 65.0%
! CCAATGGCTGCAGGGTGTCC+TGG - chr2.4:27139821-27139840 MS.gene92201:CDS 65.0%


Chromosome Type Strat End Strand Name
chr2.4 gene 27138165 27139958 27138165 ID=MS.gene92201
chr2.4 mRNA 27138165 27139958 27138165 ID=MS.gene92201.t1;Parent=MS.gene92201
chr2.4 exon 27139746 27139958 27139746 ID=MS.gene92201.t1.exon1;Parent=MS.gene92201.t1
chr2.4 CDS 27139746 27139958 27139746 ID=cds.MS.gene92201.t1;Parent=MS.gene92201.t1
chr2.4 exon 27138165 27138695 27138165 ID=MS.gene92201.t1.exon2;Parent=MS.gene92201.t1
chr2.4 CDS 27138165 27138695 27138165 ID=cds.MS.gene92201.t1;Parent=MS.gene92201.t1
Gene Sequence

>MS.gene92201

ATGGCTACTGAAGTTAGCTCTCTTGTTAGGGTTCTAGGTGGTGGTGGATACAAAGAAGAGCAACATCGAACGGTAGGTAATGATTCTCATGGTGAGAAATCAACGGCTCTGATTACAAGAGACTTGCTTGGTGGGTCCTCTTCAATTGAATCCCAAGAATTGGATCTTGATTTACAGGTTCCTAGTGGCTGGGAAAAACGTCTTGACCTTCAGGTATTTTCCTTTTGTTTCCCGGGAAAATATAAATTTTCTCTTAGGTTTTAAAAAAATAAAAGATGAAAAAAAAGTGTACACTATGATTAATAGGAATTGAAATTTCACTTTTTTGTTTATGGGCTATGTGGAAATTGAATCATCGTACTTTGTTGTGTTTTTCTTTATATTTTAAATGAGTTTTAATGATTTTGTTCTGTTTGTGTTTTTTTTACAATGGTTTATGATGCATAGTTCTTCAATCATGGTATTTTGTTTTGTTTTGTTTTATTGATTTATAATATTTATAGCTATAATTTATCTTTTTGATTTTTTACATGAGGAAGCAGATTTTTTATGTGGTCTATGGAATGCTTGATTAAGAAGTTTTGTGATTTTTTTGTTTTGCTCTTTTGATTGGTTGAATAGAAACATAATAATTGAAGGGTTTTTATTTTTTTATCATTTTTTTTCAAATAAAACAAATTTAAAATTCAATTTGTTTAGGATTTTTTTAAGCTCTTAATTCCTTTGCAATGATAGAACAAAGTTAGAATTCAATTTGTTTGTGTTTCATTTGTATGGTGTTATGTGTGTTAAACTTTTGCATTTTAATGTAACAGCAGGCCTGCAGTTACTCGAGTTTTCGTTCCTATGTACTCTGTATTTATGTCTCATAAATTTATCATAAAGTTTGAATTTAAAGTCTTCCAAATTTTTTGATATCTAAGTTAATGAAAATATGGCATCCATGACGCCATTTTGATCAGATTGCTCCACCGCCCCTTACCCATAAATATATCATAAAGACTTCATAACTAATTACATTCTGTGACATCACCATTTAATTTTATTTATTTAGTCACATATTTGATTTCTCAAATCATAAATTAAATCATGTAGATTTCTATGTTTAATAGTATTAAAAATATCACTGAGTAAAAAAAAATATTTTAAAGATCATAACCATACCAAGTTAGTTACATTTTTATGACTATGGTATAGTACTAGTAGTTAATTTGTTAATTTTTTTACTATTTTTCTTAATTGAATTTTGTTTTTTTGATGCAGTCAGGGAAAGTTTATATTCAAAGGTGTAACACATTAACCCAATCACCAATTTCTGAACAAAAAAATCAAGGAAAATCAACAACACCTAAACTTCAAGACTTGAATTTCCCATCAACACAATCAAATGTTCCATTGAACCTATTTGATGAATCAAATTTAGACCTAAAACTTGTTTCATCTGCTTTACCAACAAGCAATTACCAAAGTGTGTGCACTCTTGACAAAGTGAAATCAGCACTTGAAAGAGCTGAAAAAGAACCAATAAGAAAAAGATCATCATTCTTGAAATCGTCAATTTCGGCAACATCGCCTTCGTATTCTTCTTCATCATCGTCGATAAGAGAACAAAATCATCAAGAAGAAGAAAGTGATCAAGAGAAAATGATTTCATCACCAATGGCTGCAGGGTGTCCTGGTTGCTTATCGTATGTATTGATTATGAAGAATAATCCTAAGTGTCCTAGGTGTAACTCTATTGTACCAATTCCAACTATGAAGAAACCTAGGATTGATCTTAATATTTCAATTTAA
Protein sequence

>MS.gene92201.t1

MATEVSSLVRVLGGGGYKEEQHRTVGNDSHGEKSTALITRDLLGGSSSIESQELDLDLQVPSGWEKRLDLQSGKVYIQRCNTLTQSPISEQKNQGKSTTPKLQDLNFPSTQSNVPLNLFDESNLDLKLVSSALPTSNYQSVCTLDKVKSALERAEKEPIRKRSSFLKSSISATSPSYSSSSSSIREQNHQEEESDQEKMISSPMAAGCPGCLSYVLIMKNNPKCPRCNSIVPIPTMKKPRIDLNISI