AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene05494


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene05494.t1 MTR_6g085050 97.500 160 4 0 1 160 1 160 9.24e-116 324
MS.gene05494.t1 MTR_5g054770 69.536 151 37 4 14 160 11 156 2.88e-70 209
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene05494.t1 AT1G68660 74.172 151 33 4 14 160 11 159 1.45e-74 220
MS.gene05494.t1 AT1G68660 55.629 151 31 5 14 160 11 129 1.54e-46 148

Find 29 sgRNAs with CRISPR-Local

Find 110 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATTACAGGTGATAAATATTT+TGG 0.160796 6.2:-84108128 MS.gene05494:intron
ATGCAAGAAGCACATATTAA+TGG 0.300616 6.2:-84106468 MS.gene05494:CDS
ACTGCGTAATGAAGCTTTCA+TGG 0.321586 6.2:+84108767 None:intergenic
GTTTCAAACAAGGCAAAGAT+AGG 0.391817 6.2:-84108106 MS.gene05494:CDS
GCAATATCAACTGTCATTCC+AGG 0.427583 6.2:+84106501 None:intergenic
TGCATGCAATTGAGAGGAAA+TGG 0.433575 6.2:-84106399 MS.gene05494:CDS
GAGAATCTGAATTTGACTTA+AGG 0.436402 6.2:-84107998 MS.gene05494:intron
GAGTGGATGCATTGAGTAGT+TGG 0.453547 6.2:+84108715 None:intergenic
TGGAAAAGGTGGTGGTTTGT+TGG 0.476679 6.2:-84108057 MS.gene05494:CDS
TTGTGTAGCATTACTCTGTA+TGG 0.492187 6.2:+84106576 None:intergenic
GTCAAATTCAGATTCTCGAC+CGG 0.494941 6.2:+84108004 None:intergenic
TTCCTCTCAATTGCATGCAA+TGG 0.502233 6.2:+84106403 None:intergenic
CTACTCAATGCATCCACTCC+TGG 0.512586 6.2:-84108711 MS.gene05494:intron
TTAGGTGAAATTAGAGCAAG+TGG 0.519142 6.2:+84108738 None:intergenic
ACAATGGTAGCCAGTGGAAA+AGG 0.527330 6.2:-84108071 MS.gene05494:CDS
ACTCAACAACCACCATCAGC+TGG 0.532785 6.2:+84106357 None:intergenic
AGTTCAATTGAGCCAGCTGA+TGG 0.556313 6.2:-84106369 MS.gene05494:CDS
GATGCATTGAGTAGTTGGTT+AGG 0.562303 6.2:+84108720 None:intergenic
TAGGAGTATTGTAATGACAA+TGG 0.592311 6.2:-84108087 MS.gene05494:CDS
TCAAATTCAGATTCTCGACC+GGG 0.594401 6.2:+84108005 None:intergenic
GTAGCCAGTGGAAAAGGTGG+TGG 0.601202 6.2:-84108065 MS.gene05494:CDS
GACCATTGCATGCAATTGAG+AGG 0.614338 6.2:-84106405 MS.gene05494:CDS
ATGGTAGCCAGTGGAAAAGG+TGG 0.632586 6.2:-84108068 MS.gene05494:CDS
GTGTTGATGAAAGTGATACC+TGG 0.634232 6.2:-84106519 MS.gene05494:CDS
TGTGTTATAATTACCAGGAG+TGG 0.636157 6.2:+84108698 None:intergenic
TGTAGCATTACTCTGTATGG+TGG 0.656579 6.2:+84106579 None:intergenic
ACATATTAATGGATTAGCAG+TGG 0.658551 6.2:-84106457 MS.gene05494:CDS
TCAATTGAGCCAGCTGATGG+TGG 0.665740 6.2:-84106366 MS.gene05494:CDS
GTAATGACAATGGTAGCCAG+TGG 0.683809 6.2:-84108077 MS.gene05494:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAAAATGAAAAAATTATTG+TGG + chr6.2:84107910-84107929 None:intergenic 10.0%
!! AATTACTAACATTTAATTAT+AGG - chr6.2:84107883-84107902 MS.gene05494:intron 10.0%
!! CCTAAAATTATAATAATAAA+GGG - chr6.2:84106773-84106792 MS.gene05494:intron 10.0%
!! TCCTAAAATTATAATAATAA+AGG - chr6.2:84106772-84106791 MS.gene05494:intron 10.0%
!!! ACTAGTAAATTATTTTATTA+TGG - chr6.2:84107630-84107649 MS.gene05494:intron 10.0%
!! ACAATAAAATATGTTATCAA+AGG + chr6.2:84108494-84108513 None:intergenic 15.0%
!! ATAGATTAAATATCAAAGAT+AGG - chr6.2:84106839-84106858 MS.gene05494:intron 15.0%
!! CATATAAAATTTGTAATTAC+AGG - chr6.2:84106981-84107000 MS.gene05494:intron 15.0%
!! TCGTTAAAAAAATTGTATTA+AGG - chr6.2:84106940-84106959 MS.gene05494:intron 15.0%
!!! CAAATTTTAAATTCAAATGT+TGG - chr6.2:84107571-84107590 MS.gene05494:intron 15.0%
!!! CCCTTTATTATTATAATTTT+AGG + chr6.2:84106776-84106795 None:intergenic 15.0%
!! AAAAAATATGGTCACTAAAT+TGG - chr6.2:84108327-84108346 MS.gene05494:intron 20.0%
!! AATAATTATCTAGTTGTTAG+AGG - chr6.2:84106546-84106565 MS.gene05494:CDS 20.0%
!! ACAAACCGATAAAAAAAATA+TGG - chr6.2:84108315-84108334 MS.gene05494:intron 20.0%
!! ACAAGGAAATACAAATAAAA+GGG + chr6.2:84108084-84108103 None:intergenic 20.0%
!! ATTGTTTCAGTATATAAACT+CGG - chr6.2:84106624-84106643 MS.gene05494:intron 20.0%
!!! AAATATTTTGGTTTCAAACA+AGG - chr6.2:84107008-84107027 MS.gene05494:intron 20.0%
!!! AAATTTGAAGCTGTTTTTTT+AGG + chr6.2:84107558-84107577 None:intergenic 20.0%
!!! AAGTTAAGAAAATCATTTTG+TGG - chr6.2:84108023-84108042 MS.gene05494:CDS 20.0%
!!! AATATTTTCTTCAATTGAGT+TGG + chr6.2:84106699-84106718 None:intergenic 20.0%
!!! AGTGACCATATTTTTTTTAT+CGG + chr6.2:84108323-84108342 None:intergenic 20.0%
!!! ATTACAGGTGATAAATATTT+TGG - chr6.2:84106996-84107015 MS.gene05494:intron 20.0%
!!! ATTTTATTGTTTTTGTCACT+AGG - chr6.2:84108504-84108523 MS.gene05494:intron 20.0%
!!! CAAAATTTTGATGTGAAATA+TGG + chr6.2:84107306-84107325 None:intergenic 20.0%
! ACATAATTAGTTGTCAAAAG+TGG - chr6.2:84107942-84107961 MS.gene05494:intron 25.0%
! ACATTAGAAGTTGAAAGATT+AGG - chr6.2:84107354-84107373 MS.gene05494:intron 25.0%
! ACGTAATCACATTAATTGAA+AGG - chr6.2:84108113-84108132 MS.gene05494:CDS 25.0%
! ACTGAACTTCAAATTATACA+AGG + chr6.2:84106579-84106598 None:intergenic 25.0%
! AGAGATCGAAAATATCAAAT+CGG - chr6.2:84108209-84108228 MS.gene05494:intron 25.0%
! ATTGATGAAATTGTGTAAGA+AGG - chr6.2:84106716-84106735 MS.gene05494:intron 25.0%
! CATTAGAAGTTGAAAGATTA+GGG - chr6.2:84107355-84107374 MS.gene05494:intron 25.0%
! CATTGTTTATGTAGTTACAT+AGG + chr6.2:84108164-84108183 None:intergenic 25.0%
! CTGAACTTCAAATTATACAA+GGG + chr6.2:84106578-84106597 None:intergenic 25.0%
! GACAAGGAAATACAAATAAA+AGG + chr6.2:84108085-84108104 None:intergenic 25.0%
! TAATGTTATCGTTAGAGTAA+TGG + chr6.2:84107340-84107359 None:intergenic 25.0%
! TCGTTAACATTAGAAATTAG+CGG - chr6.2:84108244-84108263 MS.gene05494:intron 25.0%
! TGATTAACGAGCTTAATTTA+TGG + chr6.2:84106669-84106688 None:intergenic 25.0%
! TTCTTAGTACTTTAGATTGA+AGG - chr6.2:84108366-84108385 MS.gene05494:intron 25.0%
! TTGTTTCAGTATATAAACTC+GGG - chr6.2:84106625-84106644 MS.gene05494:intron 25.0%
! TTTCAACATTGTTATACACA+TGG + chr6.2:84107843-84107862 None:intergenic 25.0%
!! TAACTGAAATACATTTTCAC+TGG + chr6.2:84106887-84106906 None:intergenic 25.0%
!!! TAGGAGTATTATAATGACTA+TGG - chr6.2:84106858-84106877 MS.gene05494:intron 25.0%
ACGAGTGTTAATATCATGTT+AGG + chr6.2:84108404-84108423 None:intergenic 30.0%
AGTACACCTCAAATTGTAAA+AGG + chr6.2:84107602-84107621 None:intergenic 30.0%
GGTCTAACTAAAATTTGACT+CGG - chr6.2:84107431-84107450 MS.gene05494:intron 30.0%
GGTTATATAAATCATTCCAG+TGG - chr6.2:84108424-84108443 MS.gene05494:intron 30.0%
GTTCAATGGGAAGAATATAA+TGG + chr6.2:84107692-84107711 None:intergenic 30.0%
TAACATGATATTAACACTCG+TGG - chr6.2:84108403-84108422 MS.gene05494:intron 30.0%
TCAGTCGAGTTAATTAAAGT+CGG - chr6.2:84106594-84106613 MS.gene05494:CDS 30.0%
TTTAACGACATTTCCTAAGT+CGG - chr6.2:84108267-84108286 MS.gene05494:intron 30.0%
! ACAATTTGAGGTGTACTTAA+GGG - chr6.2:84107605-84107624 MS.gene05494:intron 30.0%
! ACTTCACATGTTTAGTTCAA+TGG + chr6.2:84107706-84107725 None:intergenic 30.0%
! ATGCAAGAAGCACATATTAA+TGG - chr6.2:84108656-84108675 MS.gene05494:intron 30.0%
! CTTCACATGTTTAGTTCAAT+GGG + chr6.2:84107705-84107724 None:intergenic 30.0%
! GAGAATCTGAATTTGACTTA+AGG - chr6.2:84107126-84107145 MS.gene05494:intron 30.0%
! TACAATTTGAGGTGTACTTA+AGG - chr6.2:84107604-84107623 MS.gene05494:intron 30.0%
!! ACATATTAATGGATTAGCAG+TGG - chr6.2:84108667-84108686 MS.gene05494:intron 30.0%
!! TAGGAGTATTGTAATGACAA+TGG - chr6.2:84107037-84107056 MS.gene05494:intron 30.0%
ACACATGCAGAAAGATAGAT+AGG + chr6.2:84108058-84108077 None:intergenic 35.0%
ACCATAGAAAAAACAACACC+CGG - chr6.2:84107101-84107120 MS.gene05494:intron 35.0%
AGAAGAAGCAATATAGAGAG+TGG + chr6.2:84106453-84106472 None:intergenic 35.0%
ATCAATATGACGCGACAAAT+TGG + chr6.2:84107282-84107301 None:intergenic 35.0%
ATGTCTGTCTAAGAACCTAA+CGG + chr6.2:84107504-84107523 None:intergenic 35.0%
ATTGTTATACACATGGAGGA+TGG + chr6.2:84107836-84107855 None:intergenic 35.0%
CAACATTGTTATACACATGG+AGG + chr6.2:84107840-84107859 None:intergenic 35.0%
GATTACGTGATATCATGACA+AGG + chr6.2:84108101-84108120 None:intergenic 35.0%
GTGGATGTGTTATAATTACC+AGG + chr6.2:84106434-84106453 None:intergenic 35.0%
GTTTCAAACAAGGCAAAGAT+AGG - chr6.2:84107018-84107037 MS.gene05494:intron 35.0%
TGTGTTATAATTACCAGGAG+TGG + chr6.2:84106429-84106448 None:intergenic 35.0%
TTAGGTGAAATTAGAGCAAG+TGG + chr6.2:84106389-84106408 None:intergenic 35.0%
TTCTTTCTATCCACAAGACT+CGG + chr6.2:84107478-84107497 None:intergenic 35.0%
TTGTGTAGCATTACTCTGTA+TGG + chr6.2:84108551-84108570 None:intergenic 35.0%
! ATGACGCATTGATACAAACA+CGG + chr6.2:84108462-84108481 None:intergenic 35.0%
! GTGCATCCTTTTACAATTTG+AGG - chr6.2:84107593-84107612 MS.gene05494:intron 35.0%
!! TTTGACTCGGAGAATCTTTA+AGG - chr6.2:84107444-84107463 MS.gene05494:intron 35.0%
!!! GGTGTTGTTTTTTCTATGGT+TGG + chr6.2:84107101-84107120 None:intergenic 35.0%
!!! GTTGTTTTTTCTATGGTTGG+AGG + chr6.2:84107098-84107117 None:intergenic 35.0%
ACTAACTTAGAGTCCGACTT+AGG + chr6.2:84108283-84108302 None:intergenic 40.0%
CACAGCTATTATAGCAGACA+AGG + chr6.2:84107784-84107803 None:intergenic 40.0%
CCAACATGAACGCATTACAT+TGG - chr6.2:84107410-84107429 MS.gene05494:intron 40.0%
CCAATGTAATGCGTTCATGT+TGG + chr6.2:84107413-84107432 None:intergenic 40.0%
CTTGTCTGCTATAATAGCTG+TGG - chr6.2:84107782-84107801 MS.gene05494:intron 40.0%
GATGCATTGAGTAGTTGGTT+AGG + chr6.2:84106407-84106426 None:intergenic 40.0%
GCAATATCAACTGTCATTCC+AGG + chr6.2:84108626-84108645 None:intergenic 40.0%
GTCAAATTCAGATTCTCGAC+CGG + chr6.2:84107123-84107142 None:intergenic 40.0%
TCAAATTCAGATTCTCGACC+GGG + chr6.2:84107122-84107141 None:intergenic 40.0%
TGCATGCAATTGAGAGGAAA+TGG - chr6.2:84108725-84108744 MS.gene05494:CDS 40.0%
TGTAGCATTACTCTGTATGG+TGG + chr6.2:84108548-84108567 None:intergenic 40.0%
TGTCTGTCTAAGAACCTAAC+GGG + chr6.2:84107503-84107522 None:intergenic 40.0%
TTCCTCTCAATTGCATGCAA+TGG + chr6.2:84108724-84108743 None:intergenic 40.0%
! GTGTTGATGAAAGTGATACC+TGG - chr6.2:84108605-84108624 MS.gene05494:intron 40.0%
! TGACGCATTGATACAAACAC+GGG + chr6.2:84108461-84108480 None:intergenic 40.0%
!! CGGAGAATCTTTAAGGTCTT+GGG - chr6.2:84107451-84107470 MS.gene05494:intron 40.0%
!! TCGGAGAATCTTTAAGGTCT+TGG - chr6.2:84107450-84107469 MS.gene05494:intron 40.0%
!!! ACCGGGTGTTGTTTTTTCTA+TGG + chr6.2:84107105-84107124 None:intergenic 40.0%
ACAATGGTAGCCAGTGGAAA+AGG - chr6.2:84107053-84107072 MS.gene05494:intron 45.0%
AGTTCAATTGAGCCAGCTGA+TGG - chr6.2:84108755-84108774 MS.gene05494:CDS 45.0%
GACCATTGCATGCAATTGAG+AGG - chr6.2:84108719-84108738 MS.gene05494:CDS 45.0%
GAGTGGATGCATTGAGTAGT+TGG + chr6.2:84106412-84106431 None:intergenic 45.0%
GCTATAATAGCTGTGGTCAC+TGG - chr6.2:84107789-84107808 MS.gene05494:intron 45.0%
GGATAGAAAGAATGCCCGTT+AGG - chr6.2:84107486-84107505 MS.gene05494:intron 45.0%
GTAATGACAATGGTAGCCAG+TGG - chr6.2:84107047-84107066 MS.gene05494:intron 45.0%
! TGGAAAAGGTGGTGGTTTGT+TGG - chr6.2:84107067-84107086 MS.gene05494:intron 45.0%
ACGGGCATCATATACACCAC+TGG + chr6.2:84108443-84108462 None:intergenic 50.0%
ATGGTAGCCAGTGGAAAAGG+TGG - chr6.2:84107056-84107075 MS.gene05494:intron 50.0%
CTACTCAATGCATCCACTCC+TGG - chr6.2:84106413-84106432 MS.gene05494:CDS 50.0%
TCAATTGAGCCAGCTGATGG+TGG - chr6.2:84108758-84108777 MS.gene05494:CDS 50.0%
! CAAACCACCACCTTTTCCAC+TGG + chr6.2:84107066-84107085 None:intergenic 50.0%
GTAGCCAGTGGAAAAGGTGG+TGG - chr6.2:84107059-84107078 MS.gene05494:intron 55.0%
GGTCTTGGGTCCGAGTCTTG+TGG - chr6.2:84107465-84107484 MS.gene05494:intron 60.0%


Chromosome Type Strat End Strand Name
chr6.2 gene 84106359 84108787 84106359 ID=MS.gene05494
chr6.2 mRNA 84106359 84108787 84106359 ID=MS.gene05494.t1;Parent=MS.gene05494
chr6.2 exon 84108712 84108787 84108712 ID=MS.gene05494.t1.exon1;Parent=MS.gene05494.t1
chr6.2 CDS 84108712 84108787 84108712 ID=cds.MS.gene05494.t1;Parent=MS.gene05494.t1
chr6.2 exon 84107999 84108143 84107999 ID=MS.gene05494.t1.exon2;Parent=MS.gene05494.t1
chr6.2 CDS 84107999 84108143 84107999 ID=cds.MS.gene05494.t1;Parent=MS.gene05494.t1
chr6.2 exon 84106359 84106620 84106359 ID=MS.gene05494.t1.exon3;Parent=MS.gene05494.t1
chr6.2 CDS 84106359 84106620 84106359 ID=cds.MS.gene05494.t1;Parent=MS.gene05494.t1
Gene Sequence

>MS.gene05494

ATGAAAGCTTCATTACGCAGTGCTACTCCACTTGCTCTAATTTCACCTAACCAACTACTCAATGCATCCACTCCTGGTAATTATAACACATCCACTCTCTATATTGCTTCTTCTCACTTTCTTAAATTCAAAACTACTTTGCTTTGTTGATTAATTTCACAAACATCACAAGTTTTATATTTTATTTAATAATTATCTAGTTGTTAGAGGAAAAGTCCCTTGTATAATTTGAAGTTCAGTCGAGTTAATTAAAGTCGGACTAAAGATTGTTTCAGTATATAAACTCGGGTTATTTCAAACACTTTGACCATAAATTAAGCTCGTTAATCAATTGAGTCCAACTCAATTGAAGAAAATATTGATGAAATTGTGTAAGAAGGATATAACTAGTTGTTTTATATTTATGATATTTTTCCTAAAATTATAATAATAAAGGGATATAGAACGTATGCTCGTTAAGATATTTGAGCTCTAATTTTAATAGATTAAATATCAAAGATAGGAGTATTATAATGACTATGGTAGCCAGTGAAAATGTATTTCAGTTAAGACATTTCAGCTCTAATTTTAATAGACATTTCTCGTTAAAAAAATTGTATTAAGGTTCAAATGTTAATTGATACATATAAAATTTGTAATTACAGGTGATAAATATTTTGGTTTCAAACAAGGCAAAGATAGGAGTATTGTAATGACAATGGTAGCCAGTGGAAAAGGTGGTGGTTTGTTGGACAAGCCTCCAACCATAGAAAAAACAACACCCGGTCGAGAATCTGAATTTGACTTAAGGTAATACGAAAAAAGTTATCTTATTTGAACATCAAAATACAGAATGTGATACTATATATATTTATCTTTATTTTTTTTTCTTACTTTTTATCTTATGTAACTTACACTCATATCAAAAGTATGCATAAATACCAATTTGTCGCGTCATATTGATACCATATTTCACATCAAAATTTTGATGTCAAAGTACCATTACTCTAACGATAACATTAGAAGTTGAAAGATTAGGGTAGTAAACATTACTTTAAATCGTCTCAAATTACCAACATGAACGCATTACATTGGTCTAACTAAAATTTGACTCGGAGAATCTTTAAGGTCTTGGGTCCGAGTCTTGTGGATAGAAAGAATGCCCGTTAGGTTCTTAGACAGACATTAATCATCGACAAGCTAATAGATACTTCACACCTAAAAAAACAGCTTCAAATTTTAAATTCAAATGTTGGTGCATCCTTTTACAATTTGAGGTGTACTTAAGGGACACTAGTAAATTATTTTATTATGGACTTATATTGATAACATGAGCTATATAGTTCACATTCCATTATATTCTTCCCATTGAACTAAACATGTGAAGTTAATAGAACTGATTAAAGTAGATTGAAAAACATGCTGATCTTTATATTCAAGTTTCCTTGTCTGCTATAATAGCTGTGGTCACTGGTTATTTCAATTGCTAATGATTCCATCCTCCATGTGTATAACAATGTTGAAAATCAGTCTTTGTGCTTTCACAATTACTAACATTTAATTATAGGTCCACAATAATTTTTTCATTTTTTTAGATAACTAAGACATAATTAGTTGTCAAAAGTGGATATATGAATGAATGATTTCTTTTACTTCATGTGTCTTTGAAAAGAAGTGTAACTATGAAGTTAAGAAAATCATTTTGTGGAAGCTCATTCCTATCTATCTTTCTGCATGTGTAGTCCCTTTTATTTGTATTTCCTTGTCATGATATCACGTAATCACATTAATTGAAAGGCAAAATGAGTAGTCAAAACTGAAAACCTATGTAACTACATAAACAATGTCATGTCATATATAGCGAGCGATTTAGAGATCGAAAATATCAAATCGGTCGTTAAATCGATCGTTAACATTAGAAATTAGCGGTTTAACGACATTTCCTAAGTCGGACTCTAAGTTAGTCAAAAATCATTTACAAACCGATAAAAAAAATATGGTCACTAAATTGGTCGTCTAATAGCGATCTTCTTAGTACTTTAGATTGAAGGCGTGTTCTAGTGCCTAACATGATATTAACACTCGTGGTTATATAAATCATTCCAGTGGTGTATATGATGCCCGTGTTTGTATCAATGCGTCATAGTTCAAAACCTTTGATAACATATTTTATTGTTTTTGTCACTAGGAAATCAAAAAAGACATCTCCACCATACAGAGTAATGCTACACAATGACAACTATAACAAAAGAGAATATGTTGTGCAAGTGTTGATGAAAGTGATACCTGGAATGACAGTTGATATTGCAGTTAACGTCATGCAAGAAGCACATATTAATGGATTAGCAGTGGTCATTATTTGTGCTCAAGTTGATGCTGAAGACCATTGCATGCAATTGAGAGGAAATGGTCTTTTAAGTTCAATTGAGCCAGCTGATGGTGGTTGTTGA

Protein sequence

>MS.gene05494.t1

MKASLRSATPLALISPNQLLNASTPGDKYFGFKQGKDRSIVMTMVASGKGGGLLDKPPTIEKTTPGRESEFDLRKSKKTSPPYRVMLHNDNYNKREYVVQVLMKVIPGMTVDIAVNVMQEAHINGLAVVIICAQVDAEDHCMQLRGNGLLSSIEPADGGC