AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0734290


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0734290 MtrunA17_Chr5g0430231 91.908 346 21 4 1 342 1 343 0.0 524
Msa0734290 MtrunA17_Chr3g0105161 35.038 391 165 12 28 338 27 408 2.53e-46 162
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 28 sgRNAs with CRISPR-Local

Find 126 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACAATGAGTGTGTAGATATT+TGG 0.183054 5_1:-48050352 Msa0734290:CDS
TGGTGTAGTTGCAAGGTTAA+TGG 0.255423 5_1:-48051553 Msa0734290:CDS
AAGAGTTTGTTTAAGGAAGT+TGG 0.287665 5_1:-48051276 Msa0734290:CDS
ATTATAGTTCTTGTAGTAGT+AGG 0.296600 5_1:+48051591 None:intergenic
GGTGTAGTTGCAAGGTTAAT+GGG 0.347018 5_1:-48051552 Msa0734290:CDS
GACCATGATGTTTCTGGAAC+AGG 0.374639 5_1:-48051141 Msa0734290:intron
TCAAAATCAAAGACAGAAAC+AGG 0.400738 5_1:+48051162 None:intergenic
AGTTGCAAGGTTAATGGGAT+TGG 0.401363 5_1:-48051547 Msa0734290:CDS
CAAGCTAGTTGATGATGAAT+TGG 0.402114 5_1:-48050318 Msa0734290:CDS
TGAAGAAGAGATGAAAGTTA+AGG 0.412030 5_1:-48050423 Msa0734290:CDS
GTTAATGGGATTGGATTCAA+TGG 0.432909 5_1:-48051538 Msa0734290:CDS
ATTGAGAACAATTTGAATGA+AGG 0.436801 5_1:-48050398 Msa0734290:CDS
CTTCTTCTGGTGTAGTTGCA+AGG 0.448678 5_1:-48051560 Msa0734290:CDS
TTGTTTAAGGAAGTTGGAAA+TGG 0.464241 5_1:-48051270 Msa0734290:CDS
AGTAGAAAATTCAAGTCTAA+AGG 0.473374 5_1:-48051384 Msa0734290:CDS
TTTGTGATGTTGATATGAGT+TGG 0.497412 5_1:-48050517 Msa0734290:CDS
TTGAGAACAATTTGAATGAA+GGG 0.508268 5_1:-48050397 Msa0734290:CDS
GTGAATTGCATGAAGTAAAG+AGG 0.512937 5_1:-48050286 Msa0734290:CDS
TTGCAATGTGTAAGTGAACT+TGG 0.522297 5_1:+48051489 None:intergenic
CTAGTTGATGATGAATTGGT+TGG 0.537429 5_1:-48050314 Msa0734290:CDS
TAAAGGAAGAAGAAAAGAGA+AGG 0.540213 5_1:-48051367 Msa0734290:CDS
TTGGTGTTCAGCTTTGAAAG+TGG 0.556241 5_1:-48051414 Msa0734290:CDS
TCAAGCAAATGAAAAGCTTG+TGG 0.565993 5_1:+48051450 None:intergenic
AACATGTTGTGTTGAAGAGA+AGG 0.571785 5_1:-48051217 Msa0734290:CDS
AACCTGTTCCAGAAACATCA+TGG 0.596050 5_1:+48051139 None:intergenic
CTCAAGTTTGATGAAGATGA+TGG 0.599664 5_1:+48051744 None:intergenic
GTGTTCAGCTTTGAAAGTGG+AGG 0.622267 5_1:-48051411 Msa0734290:CDS
AAAGGAAGAAGAAAAGAGAA+GGG 0.643077 5_1:-48051366 Msa0734290:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTAATTTTATCTTCATTTTT+TGG - chr5_1:48051200-48051219 Msa0734290:CDS 10.0%
!!! TTAATTTTATCTTCATTTTT+TGG - chr5_1:48051200-48051219 Msa0734290:CDS 10.0%
!!! TGATTTTCTCAAATTATTAC+CGG + chr5_1:48050986-48051005 None:intergenic 20.0%
!! TTAAAATGAGACAAACAATT+AGG + chr5_1:48051298-48051317 None:intergenic 20.0%
!!! CAAATTTAAAACATGGAAAA+AGG + chr5_1:48051390-48051409 None:intergenic 20.0%
!!! TAGTTAGCAAATTTAAAACA+TGG + chr5_1:48051397-48051416 None:intergenic 20.0%
!!! TGATTTTCTCAAATTATTAC+CGG + chr5_1:48050986-48051005 None:intergenic 20.0%
!! TTAAAATGAGACAAACAATT+AGG + chr5_1:48051298-48051317 None:intergenic 20.0%
!!! CAAATTTAAAACATGGAAAA+AGG + chr5_1:48051390-48051409 None:intergenic 20.0%
!!! TAGTTAGCAAATTTAAAACA+TGG + chr5_1:48051397-48051416 None:intergenic 20.0%
!!! GTTTTACAACCATTTTTCAT+AGG - chr5_1:48050290-48050309 Msa0734290:CDS 25.0%
! TTCTCTAATCCTATGAAAAA+TGG + chr5_1:48050302-48050321 None:intergenic 25.0%
! ATTATAGTTCTTGTAGTAGT+AGG + chr5_1:48050379-48050398 None:intergenic 25.0%
! ATAATTTCTTCTTCTTCTTC+TGG - chr5_1:48050394-48050413 Msa0734290:CDS 25.0%
! AGTAGAAAATTCAAGTCTAA+AGG - chr5_1:48050583-48050602 Msa0734290:intron 25.0%
!!! TTTTGAGAAGAGTTTGTTTA+AGG - chr5_1:48050684-48050703 Msa0734290:intron 25.0%
! TTCAGTGTAATTATATGTGT+CGG - chr5_1:48051011-48051030 Msa0734290:intron 25.0%
! GTACTTCATATTTACATACA+AGG - chr5_1:48051067-48051086 Msa0734290:intron 25.0%
! GCTCATAAATCATAATAAGT+TGG - chr5_1:48051106-48051125 Msa0734290:intron 25.0%
!!! ATTATTTCTACTAGCTTTTG+AGG - chr5_1:48051135-48051154 Msa0734290:intron 25.0%
! TGTAATACATAAGCACTTAT+GGG - chr5_1:48051229-48051248 Msa0734290:CDS 25.0%
! TTAAACTGTTTATCCAAACA+TGG - chr5_1:48051272-48051291 Msa0734290:CDS 25.0%
! ATTGAGAACAATTTGAATGA+AGG - chr5_1:48051569-48051588 Msa0734290:CDS 25.0%
! TTGAGAACAATTTGAATGAA+GGG - chr5_1:48051570-48051589 Msa0734290:CDS 25.0%
!!! GTTTTACAACCATTTTTCAT+AGG - chr5_1:48050290-48050309 Msa0734290:CDS 25.0%
! TTCTCTAATCCTATGAAAAA+TGG + chr5_1:48050302-48050321 None:intergenic 25.0%
! ATTATAGTTCTTGTAGTAGT+AGG + chr5_1:48050379-48050398 None:intergenic 25.0%
! ATAATTTCTTCTTCTTCTTC+TGG - chr5_1:48050394-48050413 Msa0734290:CDS 25.0%
! AGTAGAAAATTCAAGTCTAA+AGG - chr5_1:48050583-48050602 Msa0734290:intron 25.0%
!!! TTTTGAGAAGAGTTTGTTTA+AGG - chr5_1:48050684-48050703 Msa0734290:intron 25.0%
! TTCAGTGTAATTATATGTGT+CGG - chr5_1:48051011-48051030 Msa0734290:intron 25.0%
! GTACTTCATATTTACATACA+AGG - chr5_1:48051067-48051086 Msa0734290:intron 25.0%
! GCTCATAAATCATAATAAGT+TGG - chr5_1:48051106-48051125 Msa0734290:intron 25.0%
!!! ATTATTTCTACTAGCTTTTG+AGG - chr5_1:48051135-48051154 Msa0734290:intron 25.0%
! TGTAATACATAAGCACTTAT+GGG - chr5_1:48051229-48051248 Msa0734290:CDS 25.0%
! TTAAACTGTTTATCCAAACA+TGG - chr5_1:48051272-48051291 Msa0734290:CDS 25.0%
! ATTGAGAACAATTTGAATGA+AGG - chr5_1:48051569-48051588 Msa0734290:CDS 25.0%
! TTGAGAACAATTTGAATGAA+GGG - chr5_1:48051570-48051589 Msa0734290:CDS 25.0%
! GCTTGAAAATGAGAACTTTT+TGG - chr5_1:48050534-48050553 Msa0734290:intron 30.0%
TAAAGGAAGAAGAAAAGAGA+AGG - chr5_1:48050600-48050619 Msa0734290:intron 30.0%
AAAGGAAGAAGAAAAGAGAA+GGG - chr5_1:48050601-48050620 Msa0734290:intron 30.0%
GAAGAAAAACAAGAGAGAAA+AGG - chr5_1:48050639-48050658 Msa0734290:intron 30.0%
! AAGAGTTTGTTTAAGGAAGT+TGG - chr5_1:48050691-48050710 Msa0734290:intron 30.0%
TTGTTTAAGGAAGTTGGAAA+TGG - chr5_1:48050697-48050716 Msa0734290:intron 30.0%
TCAAAATCAAAGACAGAAAC+AGG + chr5_1:48050808-48050827 None:intergenic 30.0%
CCAAACATGCATTAAATTTG+AGG + chr5_1:48050895-48050914 None:intergenic 30.0%
CCTCAAATTTAATGCATGTT+TGG - chr5_1:48050892-48050911 Msa0734290:intron 30.0%
TGAGTTTACAATATGAAGCA+CGG - chr5_1:48050926-48050945 Msa0734290:intron 30.0%
GTGTAATACATAAGCACTTA+TGG - chr5_1:48051228-48051247 Msa0734290:CDS 30.0%
CATATATAAACATGTTGCAG+AGG - chr5_1:48051421-48051440 Msa0734290:CDS 30.0%
TTTGTGATGTTGATATGAGT+TGG - chr5_1:48051450-48051469 Msa0734290:CDS 30.0%
TGAAGAAGAGATGAAAGTTA+AGG - chr5_1:48051544-48051563 Msa0734290:CDS 30.0%
ACAATGAGTGTGTAGATATT+TGG - chr5_1:48051615-48051634 Msa0734290:CDS 30.0%
! GCTTGAAAATGAGAACTTTT+TGG - chr5_1:48050534-48050553 Msa0734290:intron 30.0%
TAAAGGAAGAAGAAAAGAGA+AGG - chr5_1:48050600-48050619 Msa0734290:intron 30.0%
AAAGGAAGAAGAAAAGAGAA+GGG - chr5_1:48050601-48050620 Msa0734290:intron 30.0%
GAAGAAAAACAAGAGAGAAA+AGG - chr5_1:48050639-48050658 Msa0734290:intron 30.0%
! AAGAGTTTGTTTAAGGAAGT+TGG - chr5_1:48050691-48050710 Msa0734290:intron 30.0%
TTGTTTAAGGAAGTTGGAAA+TGG - chr5_1:48050697-48050716 Msa0734290:intron 30.0%
TCAAAATCAAAGACAGAAAC+AGG + chr5_1:48050808-48050827 None:intergenic 30.0%
CCAAACATGCATTAAATTTG+AGG + chr5_1:48050895-48050914 None:intergenic 30.0%
CCTCAAATTTAATGCATGTT+TGG - chr5_1:48050892-48050911 Msa0734290:intron 30.0%
TGAGTTTACAATATGAAGCA+CGG - chr5_1:48050926-48050945 Msa0734290:intron 30.0%
GTGTAATACATAAGCACTTA+TGG - chr5_1:48051228-48051247 Msa0734290:CDS 30.0%
CATATATAAACATGTTGCAG+AGG - chr5_1:48051421-48051440 Msa0734290:CDS 30.0%
TTTGTGATGTTGATATGAGT+TGG - chr5_1:48051450-48051469 Msa0734290:CDS 30.0%
TGAAGAAGAGATGAAAGTTA+AGG - chr5_1:48051544-48051563 Msa0734290:CDS 30.0%
ACAATGAGTGTGTAGATATT+TGG - chr5_1:48051615-48051634 Msa0734290:CDS 30.0%
CTCAAGTTTGATGAAGATGA+TGG + chr5_1:48050226-48050245 None:intergenic 35.0%
GTTAATGGGATTGGATTCAA+TGG - chr5_1:48050429-48050448 Msa0734290:CDS 35.0%
TTGCAATGTGTAAGTGAACT+TGG + chr5_1:48050481-48050500 None:intergenic 35.0%
TCAAGCAAATGAAAAGCTTG+TGG + chr5_1:48050520-48050539 None:intergenic 35.0%
AACATGTTGTGTTGAAGAGA+AGG - chr5_1:48050750-48050769 Msa0734290:intron 35.0%
!! GATTTTGACCATGATGTTTC+TGG - chr5_1:48050820-48050839 Msa0734290:intron 35.0%
! GTAATTATATGTGTCGGTGT+CGG - chr5_1:48051017-48051036 Msa0734290:intron 35.0%
ACAAACAATTAGGCCATGTT+TGG + chr5_1:48051288-48051307 None:intergenic 35.0%
AAGGGTCAAAGAAAAAAGAG+AGG - chr5_1:48051588-48051607 Msa0734290:CDS 35.0%
!! CAAGCTAGTTGATGATGAAT+TGG - chr5_1:48051649-48051668 Msa0734290:CDS 35.0%
!! CTAGTTGATGATGAATTGGT+TGG - chr5_1:48051653-48051672 Msa0734290:CDS 35.0%
GTGAATTGCATGAAGTAAAG+AGG - chr5_1:48051681-48051700 Msa0734290:CDS 35.0%
CTCAAGTTTGATGAAGATGA+TGG + chr5_1:48050226-48050245 None:intergenic 35.0%
GTTAATGGGATTGGATTCAA+TGG - chr5_1:48050429-48050448 Msa0734290:CDS 35.0%
TTGCAATGTGTAAGTGAACT+TGG + chr5_1:48050481-48050500 None:intergenic 35.0%
TCAAGCAAATGAAAAGCTTG+TGG + chr5_1:48050520-48050539 None:intergenic 35.0%
AACATGTTGTGTTGAAGAGA+AGG - chr5_1:48050750-48050769 Msa0734290:intron 35.0%
!! GATTTTGACCATGATGTTTC+TGG - chr5_1:48050820-48050839 Msa0734290:intron 35.0%
! GTAATTATATGTGTCGGTGT+CGG - chr5_1:48051017-48051036 Msa0734290:intron 35.0%
ACAAACAATTAGGCCATGTT+TGG + chr5_1:48051288-48051307 None:intergenic 35.0%
AAGGGTCAAAGAAAAAAGAG+AGG - chr5_1:48051588-48051607 Msa0734290:CDS 35.0%
!! CAAGCTAGTTGATGATGAAT+TGG - chr5_1:48051649-48051668 Msa0734290:CDS 35.0%
!! CTAGTTGATGATGAATTGGT+TGG - chr5_1:48051653-48051672 Msa0734290:CDS 35.0%
GTGAATTGCATGAAGTAAAG+AGG - chr5_1:48051681-48051700 Msa0734290:CDS 35.0%
! AGCTCAAAAACTGTTGCTTC+AGG - chr5_1:48050265-48050284 Msa0734290:CDS 40.0%
! GCTCAAAAACTGTTGCTTCA+GGG - chr5_1:48050266-48050285 Msa0734290:CDS 40.0%
TGGTGTAGTTGCAAGGTTAA+TGG - chr5_1:48050414-48050433 Msa0734290:CDS 40.0%
GGTGTAGTTGCAAGGTTAAT+GGG - chr5_1:48050415-48050434 Msa0734290:CDS 40.0%
AGTTGCAAGGTTAATGGGAT+TGG - chr5_1:48050420-48050439 Msa0734290:CDS 40.0%
!! TTGGTGTTCAGCTTTGAAAG+TGG - chr5_1:48050553-48050572 Msa0734290:intron 40.0%
AACCTGTTCCAGAAACATCA+TGG + chr5_1:48050831-48050850 None:intergenic 40.0%
TACAATATGAAGCACGGATG+TGG - chr5_1:48050932-48050951 Msa0734290:intron 40.0%
TATGAAGTACGAACACTCCT+CGG + chr5_1:48051057-48051076 None:intergenic 40.0%
!!! AGCTTGTCATTTTCAAGCAC+TGG + chr5_1:48051491-48051510 None:intergenic 40.0%
! AGCTCAAAAACTGTTGCTTC+AGG - chr5_1:48050265-48050284 Msa0734290:CDS 40.0%
! GCTCAAAAACTGTTGCTTCA+GGG - chr5_1:48050266-48050285 Msa0734290:CDS 40.0%
TGGTGTAGTTGCAAGGTTAA+TGG - chr5_1:48050414-48050433 Msa0734290:CDS 40.0%
GGTGTAGTTGCAAGGTTAAT+GGG - chr5_1:48050415-48050434 Msa0734290:CDS 40.0%
AGTTGCAAGGTTAATGGGAT+TGG - chr5_1:48050420-48050439 Msa0734290:CDS 40.0%
!! TTGGTGTTCAGCTTTGAAAG+TGG - chr5_1:48050553-48050572 Msa0734290:intron 40.0%
AACCTGTTCCAGAAACATCA+TGG + chr5_1:48050831-48050850 None:intergenic 40.0%
TACAATATGAAGCACGGATG+TGG - chr5_1:48050932-48050951 Msa0734290:intron 40.0%
TATGAAGTACGAACACTCCT+CGG + chr5_1:48051057-48051076 None:intergenic 40.0%
!!! AGCTTGTCATTTTCAAGCAC+TGG + chr5_1:48051491-48051510 None:intergenic 40.0%
CTTCTTCTGGTGTAGTTGCA+AGG - chr5_1:48050407-48050426 Msa0734290:CDS 45.0%
!! GTGTTCAGCTTTGAAAGTGG+AGG - chr5_1:48050556-48050575 Msa0734290:intron 45.0%
!! GACCATGATGTTTCTGGAAC+AGG - chr5_1:48050826-48050845 Msa0734290:intron 45.0%
CTTCTTCTGGTGTAGTTGCA+AGG - chr5_1:48050407-48050426 Msa0734290:CDS 45.0%
!! GTGTTCAGCTTTGAAAGTGG+AGG - chr5_1:48050556-48050575 Msa0734290:intron 45.0%
!! GACCATGATGTTTCTGGAAC+AGG - chr5_1:48050826-48050845 Msa0734290:intron 45.0%
GTACGAACACTCCTCGGATT+AGG + chr5_1:48051051-48051070 None:intergenic 50.0%
GTACGAACACTCCTCGGATT+AGG + chr5_1:48051051-48051070 None:intergenic 50.0%
GGACACTAACACGTCGACAC+CGG - chr5_1:48050964-48050983 Msa0734290:intron 55.0%
GGACACTAACACGTCGACAC+CGG - chr5_1:48050964-48050983 Msa0734290:intron 55.0%
GCACGGATGTGGACACGACA+CGG - chr5_1:48050943-48050962 Msa0734290:intron 60.0%
GCACGGATGTGGACACGACA+CGG - chr5_1:48050943-48050962 Msa0734290:intron 60.0%
CGGACACGACGCCTAATCCG+AGG - chr5_1:48051037-48051056 Msa0734290:intron 65.0%
CGGACACGACGCCTAATCCG+AGG - chr5_1:48051037-48051056 Msa0734290:intron 65.0%
Chromosome Type Strat End Strand Name
chr5_1 gene 48050184 48051805 48050184 ID=Msa0734290;Name=Msa0734290
chr5_1 mRNA 48050184 48051805 48050184 ID=Msa0734290-mRNA-1;Parent=Msa0734290;Name=Msa0734290-mRNA-1;_AED=0.01;_eAED=0.01;_QI=0|1|0|1|1|1|2|0|342
chr5_1 exon 48051142 48051805 48051142 ID=Msa0734290-mRNA-1:exon:13767;Parent=Msa0734290-mRNA-1
chr5_1 exon 48050184 48050548 48050184 ID=Msa0734290-mRNA-1:exon:13766;Parent=Msa0734290-mRNA-1
chr5_1 CDS 48051142 48051805 48051142 ID=Msa0734290-mRNA-1:cds;Parent=Msa0734290-mRNA-1
chr5_1 CDS 48050184 48050548 48050184 ID=Msa0734290-mRNA-1:cds;Parent=Msa0734290-mRNA-1
Gene Sequence

>Msa0734290

ATGAAGCTCTTAACATTATCTTATTCATCATCATCATCACCATCATCTTCATCAAACTTGAGCTTTGACTCAACATTTTGCAGCTCAAAAACTGTTGCTTCAGGGTGTTTTACAACCATTTTTCATAGGATTAGAGAATTTCATTCAAAGTTCATTGTAAGTGAAAAAGTTCAAAAATTGAAGACTAACACTCCTACTACTACAAGAACTATAATTTCTTCTTCTTCTTCTGGTGTAGTTGCAAGGTTAATGGGATTGGATTCAATGGAAGAAGAGAAAGTTTCTGAATCAAAACCAAGTTCACTTACACATTGCAAGTCATTGAACTATGTGCCACAAGCTTTTCATTTGCTTGAAAATGAGAACTTTTTGGTGTTCAGCTTTGAAAGTGGAGGTGAGAGTAGAAAATTCAAGTCTAAAGGAAGAAGAAAAGAGAAGGGTCGTGTTGAATTGAAGAAGAAAAACAAGAGAGAAAAGGTGAATGATGATGATGAATTTCATTTTGAGAAGAGTTTGTTTAAGGAAGTTGGAAATGGTGAGAAAGTGAAGAAGAGAAAGAAAGAAAAAACATGTTGTGTTGAAGAGAAGGTTGAAAGTGAATGTAGTTCAGAAGATTATAGTCCTGTTTCTGTCTTTGATTTTGACCATGATGTTTCTGGAACAGAGGAAGATCTTTGTGATGTTGATATGAGTTGGAGAAGAAAATTGTCACCAGTGCTTGAAAATGACAAGCTATTTATTCTACATTCTGATAGTAACTTAATAAATGAAGAAGAGATGAAAGTTAAGGAAATTGAGAACAATTTGAATGAAGGGTCAAAGAAAAAAGAGAGGCATAACAATGAGTGTGTAGATATTTGGATTAAAATTTGCAAGCTAGTTGATGATGAATTGGTTGGATCAAGTGAATTGCATGAAGTAAAGAGGAAACAAAATGATTTAGAAAATATAAGTGCTGATTTTGAGTTAGAGATTTTAGATAAATTGTTAGATGAAGTTATAGATCAATTTGTTAGTAGTTGTTTGTAA

Protein sequence

>Msa0734290

MKLLTLSYSSSSSPSSSSNLSFDSTFCSSKTVASGCFTTIFHRIREFHSKFIVSEKVQKLKTNTPTTTRTIISSSSSGVVARLMGLDSMEEEKVSESKPSSLTHCKSLNYVPQAFHLLENENFLVFSFESGGESRKFKSKGRRKEKGRVELKKKNKREKVNDDDEFHFEKSLFKEVGNGEKVKKRKKEKTCCVEEKVESECSSEDYSPVSVFDFDHDVSGTEEDLCDVDMSWRRKLSPVLENDKLFILHSDSNLINEEEMKVKEIENNLNEGSKKKERHNNECVDIWIKICKLVDDELVGSSELHEVKRKQNDLENISADFELEILDKLLDEVIDQFVSSCL*