AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1134110


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1134110 MtrunA17_Chr7g0214651 77.841 176 39 0 1 176 170 345 2.28e-96 288
Msa1134110 MtrunA17_Chr7g0214571 88.312 154 17 1 1 153 119 272 4.20e-89 265
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1134110 AT2G43180.4 65.896 173 58 1 5 176 184 356 1.54e-74 232
Msa1134110 AT2G43180.2 65.896 173 58 1 5 176 184 356 1.58e-74 231
Msa1134110 AT2G43180.1 66.279 172 57 1 6 176 185 356 4.30e-74 231
Msa1134110 AT2G43180.3 66.279 172 57 1 6 176 185 356 4.88e-74 231
Msa1134110 AT1G77060.1 34.637 179 108 5 3 176 155 329 3.39e-27 105
Msa1134110 AT1G21440.2 34.637 179 108 5 3 176 153 327 6.71e-27 104
Msa1134110 AT1G21440.1 34.637 179 108 5 3 176 153 327 6.71e-27 104

Find 52 sgRNAs with CRISPR-Local

Find 84 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCAAAAGAAGGTATGCTTTC+AGG 0.165841 7_4:-538291 None:intergenic
CGTTTATCCACTTTCTTTGA+TGG 0.242085 7_4:+537795 Msa1134110:CDS
GGGTGCACTGACTGCCATTA+AGG 0.275760 7_4:+538251 Msa1134110:intron
TGGTTTCAACGACTATTATA+AGG 0.346377 7_4:+538332 Msa1134110:CDS
ACACACAAACGCACCAGTTT+AGG 0.371161 7_4:-537261 None:intergenic
AGGAACACCACCTCCCTTAA+TGG 0.372837 7_4:-538265 None:intergenic
TGCTCCTCATGTTCCTAAAC+TGG 0.383743 7_4:+537248 Msa1134110:CDS
GAAGAAATTAAGGATATTGT+TGG 0.393515 7_4:+538312 Msa1134110:CDS
TCCTTAATTTCTTCAAAAGA+AGG 0.427712 7_4:-538303 None:intergenic
GTTTATCCACTTTCTTTGAT+GGG 0.434265 7_4:+537796 Msa1134110:CDS
CGGCAAGTTTATAACCAACT+TGG 0.460557 7_4:-537774 None:intergenic
CGAGAGAGGAGGCAGTTATG+AGG 0.464342 7_4:+537034 Msa1134110:CDS
CATCAAAGAAAGTGGATAAA+CGG 0.465075 7_4:-537794 None:intergenic
GCAAATATGCTTGAAGGAGG+AGG 0.471259 7_4:+537718 Msa1134110:CDS
GGTGCACTGACTGCCATTAA+GGG 0.488259 7_4:+538252 Msa1134110:CDS
CGTGTGTGCCCACACGCTTT+CGG 0.493926 7_4:-536994 None:intergenic
GAAGGTATGCTTTCAGGAGG+AGG 0.499629 7_4:-538285 None:intergenic
TTGCAGGCAAATATGCTTGA+AGG 0.500123 7_4:+537712 Msa1134110:intron
GAAACACCCATCAAAGAAAG+TGG 0.503237 7_4:-537802 None:intergenic
CTACAATACTACAATGTCAA+AGG 0.507068 7_4:-538420 None:intergenic
TACAATACTACAATGTCAAA+GGG 0.512945 7_4:-538419 None:intergenic
TGTTTCTATACGAGCAATGC+AGG 0.515697 7_4:+537819 Msa1134110:CDS
TGTGTCTCTTGAAGAGGCAC+TGG 0.541396 7_4:+537134 Msa1134110:CDS
CCTCAGGAACTTGACCAAGT+TGG 0.544137 7_4:+537760 Msa1134110:CDS
AGTTCCTGAGGATTAAGAAT+CGG 0.544892 7_4:-537748 None:intergenic
AACACCGATTCTTAATCCTC+AGG 0.552852 7_4:+537744 Msa1134110:CDS
GAGGAAAGTGGTTTCGAGAG+AGG 0.555242 7_4:+537020 Msa1134110:CDS
GCTCGCAGCGATGCACGCCA+AGG 0.563386 7_4:+537111 Msa1134110:CDS
CAACGACTATTATAAGGAGG+AGG 0.567646 7_4:+538338 Msa1134110:CDS
AAAGACTTAAAGCTGGTGAT+CGG 0.569588 7_4:-538378 None:intergenic
CCAAGGTGTGTCTCTTGAAG+AGG 0.571020 7_4:+537128 Msa1134110:CDS
GCACACACGCGGGAGGAAAG+TGG 0.574186 7_4:+537008 Msa1134110:CDS
GTTGATGCTAGAACTGAAAG+TGG 0.576743 7_4:+537069 Msa1134110:CDS
AAAGCGTGTGGGCACACACG+CGG 0.583026 7_4:+536997 Msa1134110:CDS
CTCTGGGAAAGACTTAAAGC+TGG 0.595684 7_4:-538385 None:intergenic
TAGATGTCACCGAAAGCGTG+TGG 0.598587 7_4:+536985 None:intergenic
TGGATCTGATATTGTGATTG+TGG 0.599115 7_4:+537089 Msa1134110:CDS
CAAATATGCTTGAAGGAGGA+GGG 0.610251 7_4:+537719 Msa1134110:CDS
TTTCAACGACTATTATAAGG+AGG 0.614707 7_4:+538335 Msa1134110:CDS
AAGCGTGTGGGCACACACGC+GGG 0.615438 7_4:+536998 Msa1134110:CDS
CGCACCAGTTTAGGAACATG+AGG 0.616260 7_4:-537252 None:intergenic
CTGACTGCCATTAAGGGAGG+TGG 0.618884 7_4:+538258 Msa1134110:CDS
CCTCTTCAAGAGACACACCT+TGG 0.622010 7_4:-537128 None:intergenic
CAGGCAAATATGCTTGAAGG+AGG 0.622900 7_4:+537715 Msa1134110:intron
GAAAGTGGTTTCGAGAGAGG+AGG 0.631931 7_4:+537023 Msa1134110:CDS
CCAACTTGGTCAAGTTCCTG+AGG 0.635636 7_4:-537760 None:intergenic
CTCTTGAAGAGGCACTGGTG+AGG 0.638629 7_4:+537139 Msa1134110:CDS
AAAGAAGGTATGCTTTCAGG+AGG 0.640179 7_4:-538288 None:intergenic
GGCAGTTATGAGGATTAAAG+CGG 0.641001 7_4:+537044 Msa1134110:CDS
CGTGTGGGCACACACGCGGG+AGG 0.651137 7_4:+537001 Msa1134110:CDS
AGATGTCACCGAAAGCGTGT+GGG 0.679949 7_4:+536986 None:intergenic
GCACTGACTGCCATTAAGGG+AGG 0.684734 7_4:+538255 Msa1134110:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTTAATTAAAGTATCACT+TGG + chr7_4:538188-538207 Msa1134110:intron 15.0%
!! ATACTAATGTTAGAAATTGT+AGG + chr7_4:537325-537344 Msa1134110:intron 20.0%
!! AAACTATAATGACATTAAGT+TGG + chr7_4:537445-537464 Msa1134110:intron 20.0%
!!! CAATATTCTAAAATGATCTA+TGG - chr7_4:537570-537589 None:intergenic 20.0%
! GAAATTGCAAATTACTAATC+AGG + chr7_4:537397-537416 Msa1134110:intron 25.0%
! TCTAGAAAACTATGTTGAAA+AGG + chr7_4:537595-537614 Msa1134110:intron 25.0%
! TGTCCTATACTATTATCAAA+GGG - chr7_4:537885-537904 None:intergenic 25.0%
! ATGTCCTATACTATTATCAA+AGG - chr7_4:537886-537905 None:intergenic 25.0%
!! ATTCAAAAATAGGTTGAGAT+GGG - chr7_4:538167-538186 None:intergenic 25.0%
!! TATTCAAAAATAGGTTGAGA+TGG - chr7_4:538168-538187 None:intergenic 25.0%
!!! ACCTTCTTTTGAAGAAATTA+AGG + chr7_4:538302-538321 Msa1134110:CDS 25.0%
! TCCTTAATTTCTTCAAAAGA+AGG - chr7_4:538306-538325 None:intergenic 25.0%
! GAAGAAATTAAGGATATTGT+TGG + chr7_4:538312-538331 Msa1134110:CDS 25.0%
!!! GTTTGTTTTATAGATGCACT+TGG + chr7_4:537192-537211 Msa1134110:CDS 30.0%
ACTATTATCATTTGCATCTC+TGG - chr7_4:537508-537527 None:intergenic 30.0%
!! CAAGTTAGTCTTGAAATTGA+AGG - chr7_4:537622-537641 None:intergenic 30.0%
CATCAAAGAAAGTGGATAAA+CGG - chr7_4:537797-537816 None:intergenic 30.0%
GTTTATCCACTTTCTTTGAT+GGG + chr7_4:537796-537815 Msa1134110:CDS 30.0%
! GTTCCCTTTGATAATAGTAT+AGG + chr7_4:537879-537898 Msa1134110:intron 30.0%
! AAAATGGTGTTTTGCAAGAA+AGG - chr7_4:537974-537993 None:intergenic 30.0%
! CTTTGGATCAAAGACATTTT+TGG + chr7_4:538061-538080 Msa1134110:intron 30.0%
TGGTTTCAACGACTATTATA+AGG + chr7_4:538332-538351 Msa1134110:CDS 30.0%
TTTCAACGACTATTATAAGG+AGG + chr7_4:538335-538354 Msa1134110:CDS 30.0%
TGGATCTGATATTGTGATTG+TGG + chr7_4:537089-537108 Msa1134110:CDS 35.0%
! GTTTTTGCAAATACCAACAG+AGG - chr7_4:537429-537448 None:intergenic 35.0%
TCGTCTTTATGAATGTTTGC+AGG + chr7_4:537696-537715 Msa1134110:intron 35.0%
AGTTCCTGAGGATTAAGAAT+CGG - chr7_4:537751-537770 None:intergenic 35.0%
CGTTTATCCACTTTCTTTGA+TGG + chr7_4:537795-537814 Msa1134110:CDS 35.0%
ATGTCTTTGATCCAAAGTGT+AGG - chr7_4:538058-538077 None:intergenic 35.0%
!!! ACATTTTTGGTGTAGTTGAC+TGG + chr7_4:538074-538093 Msa1134110:intron 35.0%
! TCAAAAGAAGGTATGCTTTC+AGG - chr7_4:538294-538313 None:intergenic 35.0%
AAAGACTTAAAGCTGGTGAT+CGG - chr7_4:538381-538400 None:intergenic 35.0%
GGCAGTTATGAGGATTAAAG+CGG + chr7_4:537044-537063 Msa1134110:CDS 40.0%
GTTGATGCTAGAACTGAAAG+TGG + chr7_4:537069-537088 Msa1134110:CDS 40.0%
! GGTGAGGACAAAACTTTTTG+CGG + chr7_4:537155-537174 Msa1134110:CDS 40.0%
! ACAAAACTTTTTGCGGATGC+TGG + chr7_4:537162-537181 Msa1134110:CDS 40.0%
! AATCAGGTTAGTTCCTCTGT+TGG + chr7_4:537413-537432 Msa1134110:intron 40.0%
GATCAAGTTCGTCTACATGT+CGG - chr7_4:537533-537552 None:intergenic 40.0%
TTGCAGGCAAATATGCTTGA+AGG + chr7_4:537712-537731 Msa1134110:intron 40.0%
CAAATATGCTTGAAGGAGGA+GGG + chr7_4:537719-537738 Msa1134110:CDS 40.0%
!! AACACCGATTCTTAATCCTC+AGG + chr7_4:537744-537763 Msa1134110:CDS 40.0%
CGGCAAGTTTATAACCAACT+TGG - chr7_4:537777-537796 None:intergenic 40.0%
GAAACACCCATCAAAGAAAG+TGG - chr7_4:537805-537824 None:intergenic 40.0%
! TGTTTCTATACGAGCAATGC+AGG + chr7_4:537819-537838 Msa1134110:CDS 40.0%
AAGTTACAGCACCTACACTT+TGG + chr7_4:538044-538063 Msa1134110:intron 40.0%
TGTAGTTGACTGGAGATTAG+TGG + chr7_4:538084-538103 Msa1134110:intron 40.0%
CTGCTATGACTGAATTTGCA+GGG + chr7_4:538231-538250 Msa1134110:intron 40.0%
! AAAGAAGGTATGCTTTCAGG+AGG - chr7_4:538291-538310 None:intergenic 40.0%
CAACGACTATTATAAGGAGG+AGG + chr7_4:538338-538357 Msa1134110:CDS 40.0%
!!! AAGGGTTTTGTTCACTCTCT+GGG - chr7_4:538404-538423 None:intergenic 40.0%
!!! AAAGGGTTTTGTTCACTCTC+TGG - chr7_4:538405-538424 None:intergenic 40.0%
TGCTCCTCATGTTCCTAAAC+TGG + chr7_4:537248-537267 Msa1134110:CDS 45.0%
ACACACAAACGCACCAGTTT+AGG - chr7_4:537264-537283 None:intergenic 45.0%
CAGGCAAATATGCTTGAAGG+AGG + chr7_4:537715-537734 Msa1134110:intron 45.0%
GCAAATATGCTTGAAGGAGG+AGG + chr7_4:537718-537737 Msa1134110:CDS 45.0%
ACAAGAGTTCAACACAACCC+TGG - chr7_4:538007-538026 None:intergenic 45.0%
GCTGCTATGACTGAATTTGC+AGG + chr7_4:538230-538249 Msa1134110:intron 45.0%
! CTCTGGGAAAGACTTAAAGC+TGG - chr7_4:538388-538407 None:intergenic 45.0%
!! AATTAAAAATATTCAAAAAT+AGG - chr7_4:538177-538196 None:intergenic 5.0%
GAGGAAAGTGGTTTCGAGAG+AGG + chr7_4:537020-537039 Msa1134110:CDS 50.0%
GAAAGTGGTTTCGAGAGAGG+AGG + chr7_4:537023-537042 Msa1134110:CDS 50.0%
CCTCTTCAAGAGACACACCT+TGG - chr7_4:537131-537150 None:intergenic 50.0%
CCAAGGTGTGTCTCTTGAAG+AGG + chr7_4:537128-537147 Msa1134110:CDS 50.0%
! TGTGTCTCTTGAAGAGGCAC+TGG + chr7_4:537134-537153 Msa1134110:CDS 50.0%
CGCACCAGTTTAGGAACATG+AGG - chr7_4:537255-537274 None:intergenic 50.0%
CCAACTTGGTCAAGTTCCTG+AGG - chr7_4:537763-537782 None:intergenic 50.0%
CCTCAGGAACTTGACCAAGT+TGG + chr7_4:537760-537779 Msa1134110:CDS 50.0%
! ACCATTTTAAGCGCGACACC+AGG + chr7_4:537986-538005 Msa1134110:intron 50.0%
! CCATTTTAAGCGCGACACCA+GGG + chr7_4:537987-538006 Msa1134110:intron 50.0%
!! GGTGCACTGACTGCCATTAA+GGG + chr7_4:538252-538271 Msa1134110:CDS 50.0%
AGGAACACCACCTCCCTTAA+TGG - chr7_4:538268-538287 None:intergenic 50.0%
! GAAGGTATGCTTTCAGGAGG+AGG - chr7_4:538288-538307 None:intergenic 50.0%
CGAGAGAGGAGGCAGTTATG+AGG + chr7_4:537034-537053 Msa1134110:CDS 55.0%
!! CTCTTGAAGAGGCACTGGTG+AGG + chr7_4:537139-537158 Msa1134110:CDS 55.0%
!! CCCTGGTGTCGCGCTTAAAA+TGG - chr7_4:537990-538009 None:intergenic 55.0%
!! GGGTGCACTGACTGCCATTA+AGG + chr7_4:538251-538270 Msa1134110:intron 55.0%
!! GCACTGACTGCCATTAAGGG+AGG + chr7_4:538255-538274 Msa1134110:CDS 55.0%
CTGACTGCCATTAAGGGAGG+TGG + chr7_4:538258-538277 Msa1134110:CDS 55.0%
CGTGTGTGCCCACACGCTTT+CGG - chr7_4:536997-537016 None:intergenic 60.0%
AAAGCGTGTGGGCACACACG+CGG + chr7_4:536997-537016 Msa1134110:CDS 60.0%
AAGCGTGTGGGCACACACGC+GGG + chr7_4:536998-537017 Msa1134110:CDS 65.0%
GCACACACGCGGGAGGAAAG+TGG + chr7_4:537008-537027 Msa1134110:CDS 65.0%
GCTCGCAGCGATGCACGCCA+AGG + chr7_4:537111-537130 Msa1134110:CDS 70.0%
CGTGTGGGCACACACGCGGG+AGG + chr7_4:537001-537020 Msa1134110:CDS 75.0%
Chromosome Type Strat End Strand Name
chr7_4 gene 536988 538434 536988 ID=Msa1134110;Name=Msa1134110
chr7_4 mRNA 536988 538434 536988 ID=Msa1134110-mRNA-1;Parent=Msa1134110;Name=Msa1134110-mRNA-1;_AED=0.33;_eAED=0.38;_QI=0|0|0|0.66|1|1|3|0|195
chr7_4 exon 536988 537269 536988 ID=Msa1134110-mRNA-1:exon:182;Parent=Msa1134110-mRNA-1
chr7_4 exon 537718 537840 537718 ID=Msa1134110-mRNA-1:exon:183;Parent=Msa1134110-mRNA-1
chr7_4 exon 538252 538434 538252 ID=Msa1134110-mRNA-1:exon:184;Parent=Msa1134110-mRNA-1
chr7_4 CDS 536988 537269 536988 ID=Msa1134110-mRNA-1:cds;Parent=Msa1134110-mRNA-1
chr7_4 CDS 537718 537840 537718 ID=Msa1134110-mRNA-1:cds;Parent=Msa1134110-mRNA-1
chr7_4 CDS 538252 538434 538252 ID=Msa1134110-mRNA-1:cds;Parent=Msa1134110-mRNA-1
Gene Sequence

>Msa1134110

ATGTCACCGAAAGCGTGTGGGCACACACGCGGGAGGAAAGTGGTTTCGAGAGAGGAGGCAGTTATGAGGATTAAAGCGGCAGTTGATGCTAGAACTGAAAGTGGATCTGATATTGTGATTGTGGCTCGCAGCGATGCACGCCAAGGTGTGTCTCTTGAAGAGGCACTGGTGAGGACAAAACTTTTTGCGGATGCTGGAGCTGATGTTTGTTTTATAGATGCACTTGGTTCTGTTGAAGAGATGAAAGCTTTTTGTCAAGTTGCTCCTCATGTTCCTAAACTGGCAAATATGCTTGAAGGAGGAGGGAAAACACCGATTCTTAATCCTCAGGAACTTGACCAAGTTGGTTATAAACTTGCCGTTTATCCACTTTCTTTGATGGGTGTTTCTATACGAGCAATGCAGGGTGCACTGACTGCCATTAAGGGAGGTGGTGTTCCTCCTCCTGAAAGCATACCTTCTTTTGAAGAAATTAAGGATATTGTTGGTTTCAACGACTATTATAAGGAGGAGGAGCGTTATGCTACAAAACCGATCACCAGCTTTAAGTCTTTCCCAGAGAGTGAACAAAACCCTTTGACATTGTAG

Protein sequence

>Msa1134110

MSPKACGHTRGRKVVSREEAVMRIKAAVDARTESGSDIVIVARSDARQGVSLEEALVRTKLFADAGADVCFIDALGSVEEMKAFCQVAPHVPKLANMLEGGGKTPILNPQELDQVGYKLAVYPLSLMGVSIRAMQGALTAIKGGGVPPPESIPSFEEIKDIVGFNDYYKEEERYATKPITSFKSFPESEQNPLTL*