AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1310160


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1310160 MtrunA17_Chr8g0337271 81.579 190 35 0 1 190 1 190 1.64e-115 326
Msa1310160 MtrunA17_Chr8g0358731 34.682 173 85 4 1 173 1 145 1.66e-24 94.4
Msa1310160 MtrunA17_Chr6g0452691 27.211 147 100 2 10 149 9 155 4.38e-12 62.0
Msa1310160 MtrunA17_Chr5g0439111 27.660 141 96 4 10 148 9 145 2.77e-11 60.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1310160 AT2G19820.1 31.183 93 63 1 5 96 7 99 3.19e-13 63.9
Msa1310160 AT3G50510.1 26.957 115 83 1 1 114 3 117 2.12e-12 63.5
Msa1310160 AT3G50510.2 26.957 115 83 1 1 114 3 117 2.12e-12 63.5

Find 51 sgRNAs with CRISPR-Local

Find 102 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CATCCAAGGATGTGCTTATT+TGG 0.063042 8_4:+6681505 None:intergenic
TCAGTGTGTCATTCAAATTT+TGG 0.142179 8_4:-6681670 Msa1310160:CDS
CTGACTTAAACTTGAGTATA+TGG 0.197296 8_4:-6681389 Msa1310160:CDS
CATGACACTGATTGTGAATT+TGG 0.306396 8_4:-6681726 Msa1310160:CDS
ATCCAAGGATGTGCTTATTT+GGG 0.326625 8_4:+6681506 None:intergenic
TCTTGGACACCAATTGGAGC+TGG 0.391570 8_4:-6681532 Msa1310160:CDS
TTCATCAGCCACCATTCCCT+TGG 0.409411 8_4:+6680981 None:intergenic
TGTCCAAGAAAACCCCGATC+TGG 0.424943 8_4:+6681546 None:intergenic
TTTGGGCACCCAGCTCCAAT+TGG 0.428496 8_4:+6681523 None:intergenic
TTAATTGCATAATTCTCATC+AGG 0.430232 8_4:+6681637 None:intergenic
GGGAATGGTGGCTGATGAAA+AGG 0.430935 8_4:-6680977 Msa1310160:CDS
TGACTTAAACTTGAGTATAT+GGG 0.443514 8_4:-6681388 Msa1310160:intron
CTTGGACACCAATTGGAGCT+GGG 0.456606 8_4:-6681531 Msa1310160:CDS
CATGCCTTCTGCTCATATAT+CGG 0.462277 8_4:+6681745 None:intergenic
TTGGCGAAGTAACCCAGATC+GGG 0.470404 8_4:-6681559 Msa1310160:CDS
TGCCCAAATAAGCACATCCT+TGG 0.475102 8_4:-6681508 Msa1310160:CDS
AGCAATTTCAATTTCATCCA+AGG 0.478006 8_4:+6681491 None:intergenic
CATATACTCAAGTTTAAGTC+AGG 0.479889 8_4:+6681390 None:intergenic
CATCCTCATTACTGGTGGGT+GGG 0.488409 8_4:+6680928 None:intergenic
TCTCCTCTTTCACAAGTACA+TGG 0.497829 8_4:+6681139 None:intergenic
TCATCCTCATTACTGGTGGG+TGG 0.506726 8_4:+6680927 None:intergenic
TCCTTCTGTGAGAAGCGAAT+CGG 0.511515 8_4:+6681587 None:intergenic
TACTGAACACATGGGTGACA+TGG 0.514848 8_4:-6681191 Msa1310160:CDS
GCCGATTCGCTTCTCACAGA+AGG 0.517177 8_4:-6681588 Msa1310160:CDS
ATTCCATGTACTTGTGAAAG+AGG 0.523001 8_4:-6681142 Msa1310160:CDS
TGTACACAGTAATGCATCCA+AGG 0.526625 8_4:-6680998 Msa1310160:intron
GTCCAAGAAAACCCCGATCT+GGG 0.526848 8_4:+6681547 None:intergenic
CTGAAAGTCAGCATGCCTAC+TGG 0.528158 8_4:+6681689 None:intergenic
GTGGCTGATGAAAAGGGAAA+AGG 0.537842 8_4:-6680970 Msa1310160:CDS
CTTGGCGAAGTAACCCAGAT+CGG 0.540526 8_4:-6681560 Msa1310160:CDS
GCAACAATTTGTCTTTGATG+TGG 0.547669 8_4:+6681609 None:intergenic
TTCTCACAGAAGGAGAAGCT+TGG 0.549947 8_4:-6681578 Msa1310160:CDS
GTCTTCATCCTCATTACTGG+TGG 0.553332 8_4:+6680923 None:intergenic
GTGCAAGAAGGCATGGAAGA+AGG 0.556829 8_4:+6681420 None:intergenic
CAGTAATGCATCCAAGGGAA+TGG 0.575632 8_4:-6680992 Msa1310160:CDS
AATTTGAGTGCAAGAAGGCA+TGG 0.581783 8_4:+6681413 None:intergenic
AAATGCATCAGAGAAATACA+AGG 0.593981 8_4:-6681788 Msa1310160:CDS
TGTGCCGATATATGAGCAGA+AGG 0.598052 8_4:-6681749 Msa1310160:CDS
TAATGCATCCAAGGGAATGG+TGG 0.611462 8_4:-6680989 Msa1310160:CDS
CTTGTGAAAGAGGAGAATCA+AGG 0.617523 8_4:-6681132 Msa1310160:intron
GGAATGGTGGCTGATGAAAA+GGG 0.618900 8_4:-6680976 Msa1310160:CDS
CATGGGTGACATGGACATCA+CGG 0.621521 8_4:-6681182 Msa1310160:CDS
TCAGGAATTTGAGTGCAAGA+AGG 0.621914 8_4:+6681408 None:intergenic
TTAATAGAGTACTGAACACA+TGG 0.626411 8_4:-6681200 Msa1310160:intron
GTACACAGTAATGCATCCAA+GGG 0.631300 8_4:-6680997 Msa1310160:intron
TCTTCATCCTCATTACTGGT+GGG 0.634658 8_4:+6680924 None:intergenic
AAAGGAATTCTTAATGAACA+AGG 0.657272 8_4:-6680952 Msa1310160:CDS
TGGCGAAGTAACCCAGATCG+GGG 0.667644 8_4:-6681558 Msa1310160:CDS
ATCACGGAACAAGACATGCA+AGG 0.684891 8_4:-6681166 Msa1310160:CDS
AATGCATCAGAGAAATACAA+GGG 0.687321 8_4:-6681787 Msa1310160:CDS
TAATAGAGTACTGAACACAT+GGG 0.740993 8_4:-6681199 Msa1310160:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! TTAATTGCATAATTCTCATC+AGG + chr8_4:6681088-6681107 None:intergenic 25.0%
! TGACTTAAACTTGAGTATAT+GGG - chr8_4:6681334-6681353 Msa1310160:intron 25.0%
! TTGAAAAGAATGATAGATCT+TGG + chr8_4:6681478-6681497 None:intergenic 25.0%
! AAAGGAATTCTTAATGAACA+AGG - chr8_4:6681770-6681789 Msa1310160:CDS 25.0%
! TTAATTGCATAATTCTCATC+AGG + chr8_4:6681088-6681107 None:intergenic 25.0%
! TGACTTAAACTTGAGTATAT+GGG - chr8_4:6681334-6681353 Msa1310160:intron 25.0%
! TTGAAAAGAATGATAGATCT+TGG + chr8_4:6681478-6681497 None:intergenic 25.0%
! AAAGGAATTCTTAATGAACA+AGG - chr8_4:6681770-6681789 Msa1310160:CDS 25.0%
!! TCAGTGTGTCATTCAAATTT+TGG - chr8_4:6681052-6681071 Msa1310160:intron 30.0%
!! CAGTGTGTCATTCAAATTTT+GGG - chr8_4:6681053-6681072 Msa1310160:intron 30.0%
!! AGTGTGTCATTCAAATTTTG+GGG - chr8_4:6681054-6681073 Msa1310160:intron 30.0%
AGCAATTTCAATTTCATCCA+AGG + chr8_4:6681234-6681253 None:intergenic 30.0%
CATATACTCAAGTTTAAGTC+AGG + chr8_4:6681335-6681354 None:intergenic 30.0%
CTGACTTAAACTTGAGTATA+TGG - chr8_4:6681333-6681352 Msa1310160:intron 30.0%
!! TTAATAGAGTACTGAACACA+TGG - chr8_4:6681522-6681541 Msa1310160:CDS 30.0%
!! TAATAGAGTACTGAACACAT+GGG - chr8_4:6681523-6681542 Msa1310160:CDS 30.0%
!! TCAGTGTGTCATTCAAATTT+TGG - chr8_4:6681052-6681071 Msa1310160:intron 30.0%
!! CAGTGTGTCATTCAAATTTT+GGG - chr8_4:6681053-6681072 Msa1310160:intron 30.0%
!! AGTGTGTCATTCAAATTTTG+GGG - chr8_4:6681054-6681073 Msa1310160:intron 30.0%
AGCAATTTCAATTTCATCCA+AGG + chr8_4:6681234-6681253 None:intergenic 30.0%
CATATACTCAAGTTTAAGTC+AGG + chr8_4:6681335-6681354 None:intergenic 30.0%
CTGACTTAAACTTGAGTATA+TGG - chr8_4:6681333-6681352 Msa1310160:intron 30.0%
!! TTAATAGAGTACTGAACACA+TGG - chr8_4:6681522-6681541 Msa1310160:CDS 30.0%
!! TAATAGAGTACTGAACACAT+GGG - chr8_4:6681523-6681542 Msa1310160:CDS 30.0%
! CATGACACTGATTGTGAATT+TGG - chr8_4:6680996-6681015 Msa1310160:intron 35.0%
GCAACAATTTGTCTTTGATG+TGG + chr8_4:6681116-6681135 None:intergenic 35.0%
ATCCAAGGATGTGCTTATTT+GGG + chr8_4:6681219-6681238 None:intergenic 35.0%
ATTCCATGTACTTGTGAAAG+AGG - chr8_4:6681580-6681599 Msa1310160:CDS 35.0%
! CATGACACTGATTGTGAATT+TGG - chr8_4:6680996-6681015 Msa1310160:intron 35.0%
GCAACAATTTGTCTTTGATG+TGG + chr8_4:6681116-6681135 None:intergenic 35.0%
ATCCAAGGATGTGCTTATTT+GGG + chr8_4:6681219-6681238 None:intergenic 35.0%
ATTCCATGTACTTGTGAAAG+AGG - chr8_4:6681580-6681599 Msa1310160:CDS 35.0%
CATGCCTTCTGCTCATATAT+CGG + chr8_4:6680980-6680999 None:intergenic 40.0%
! GTCAATACTTTTCGACCAGT+AGG - chr8_4:6681018-6681037 Msa1310160:intron 40.0%
CATCCAAGGATGTGCTTATT+TGG + chr8_4:6681220-6681239 None:intergenic 40.0%
AATTTGAGTGCAAGAAGGCA+TGG + chr8_4:6681312-6681331 None:intergenic 40.0%
TCAGGAATTTGAGTGCAAGA+AGG + chr8_4:6681317-6681336 None:intergenic 40.0%
TCTCCTCTTTCACAAGTACA+TGG + chr8_4:6681586-6681605 None:intergenic 40.0%
CTTGTGAAAGAGGAGAATCA+AGG - chr8_4:6681590-6681609 Msa1310160:CDS 40.0%
TGTACACAGTAATGCATCCA+AGG - chr8_4:6681724-6681743 Msa1310160:CDS 40.0%
GTACACAGTAATGCATCCAA+GGG - chr8_4:6681725-6681744 Msa1310160:CDS 40.0%
CATGCCTTCTGCTCATATAT+CGG + chr8_4:6680980-6680999 None:intergenic 40.0%
! GTCAATACTTTTCGACCAGT+AGG - chr8_4:6681018-6681037 Msa1310160:intron 40.0%
CATCCAAGGATGTGCTTATT+TGG + chr8_4:6681220-6681239 None:intergenic 40.0%
AATTTGAGTGCAAGAAGGCA+TGG + chr8_4:6681312-6681331 None:intergenic 40.0%
TCAGGAATTTGAGTGCAAGA+AGG + chr8_4:6681317-6681336 None:intergenic 40.0%
TCTCCTCTTTCACAAGTACA+TGG + chr8_4:6681586-6681605 None:intergenic 40.0%
CTTGTGAAAGAGGAGAATCA+AGG - chr8_4:6681590-6681609 Msa1310160:CDS 40.0%
TGTACACAGTAATGCATCCA+AGG - chr8_4:6681724-6681743 Msa1310160:CDS 40.0%
GTACACAGTAATGCATCCAA+GGG - chr8_4:6681725-6681744 Msa1310160:CDS 40.0%
! TGTGCCGATATATGAGCAGA+AGG - chr8_4:6680973-6680992 Msa1310160:CDS 45.0%
TCCTTCTGTGAGAAGCGAAT+CGG + chr8_4:6681138-6681157 None:intergenic 45.0%
TTCTCACAGAAGGAGAAGCT+TGG - chr8_4:6681144-6681163 Msa1310160:CDS 45.0%
! GGGTTTTCTTGGACACCAAT+TGG - chr8_4:6681184-6681203 Msa1310160:CDS 45.0%
TGCCCAAATAAGCACATCCT+TGG - chr8_4:6681214-6681233 Msa1310160:intron 45.0%
TACTGAACACATGGGTGACA+TGG - chr8_4:6681531-6681550 Msa1310160:CDS 45.0%
ATCACGGAACAAGACATGCA+AGG - chr8_4:6681556-6681575 Msa1310160:CDS 45.0%
CAGTAATGCATCCAAGGGAA+TGG - chr8_4:6681730-6681749 Msa1310160:CDS 45.0%
TAATGCATCCAAGGGAATGG+TGG - chr8_4:6681733-6681752 Msa1310160:CDS 45.0%
GGAATGGTGGCTGATGAAAA+GGG - chr8_4:6681746-6681765 Msa1310160:CDS 45.0%
GTGGCTGATGAAAAGGGAAA+AGG - chr8_4:6681752-6681771 Msa1310160:CDS 45.0%
! TGTGCCGATATATGAGCAGA+AGG - chr8_4:6680973-6680992 Msa1310160:CDS 45.0%
TCCTTCTGTGAGAAGCGAAT+CGG + chr8_4:6681138-6681157 None:intergenic 45.0%
TTCTCACAGAAGGAGAAGCT+TGG - chr8_4:6681144-6681163 Msa1310160:CDS 45.0%
! GGGTTTTCTTGGACACCAAT+TGG - chr8_4:6681184-6681203 Msa1310160:CDS 45.0%
TGCCCAAATAAGCACATCCT+TGG - chr8_4:6681214-6681233 Msa1310160:intron 45.0%
TACTGAACACATGGGTGACA+TGG - chr8_4:6681531-6681550 Msa1310160:CDS 45.0%
ATCACGGAACAAGACATGCA+AGG - chr8_4:6681556-6681575 Msa1310160:CDS 45.0%
CAGTAATGCATCCAAGGGAA+TGG - chr8_4:6681730-6681749 Msa1310160:CDS 45.0%
TAATGCATCCAAGGGAATGG+TGG - chr8_4:6681733-6681752 Msa1310160:CDS 45.0%
GGAATGGTGGCTGATGAAAA+GGG - chr8_4:6681746-6681765 Msa1310160:CDS 45.0%
GTGGCTGATGAAAAGGGAAA+AGG - chr8_4:6681752-6681771 Msa1310160:CDS 45.0%
CTGAAAGTCAGCATGCCTAC+TGG + chr8_4:6681036-6681055 None:intergenic 50.0%
CTTGGCGAAGTAACCCAGAT+CGG - chr8_4:6681162-6681181 Msa1310160:CDS 50.0%
TTGGCGAAGTAACCCAGATC+GGG - chr8_4:6681163-6681182 Msa1310160:CDS 50.0%
! AACCCAGATCGGGGTTTTCT+TGG - chr8_4:6681173-6681192 Msa1310160:CDS 50.0%
GTCCAAGAAAACCCCGATCT+GGG + chr8_4:6681178-6681197 None:intergenic 50.0%
TGTCCAAGAAAACCCCGATC+TGG + chr8_4:6681179-6681198 None:intergenic 50.0%
TCTTGGACACCAATTGGAGC+TGG - chr8_4:6681190-6681209 Msa1310160:CDS 50.0%
CTTGGACACCAATTGGAGCT+GGG - chr8_4:6681191-6681210 Msa1310160:CDS 50.0%
! GTGCAAGAAGGCATGGAAGA+AGG + chr8_4:6681305-6681324 None:intergenic 50.0%
CATGGGTGACATGGACATCA+CGG - chr8_4:6681540-6681559 Msa1310160:CDS 50.0%
TTCATCAGCCACCATTCCCT+TGG + chr8_4:6681744-6681763 None:intergenic 50.0%
GGGAATGGTGGCTGATGAAA+AGG - chr8_4:6681745-6681764 Msa1310160:CDS 50.0%
CTGAAAGTCAGCATGCCTAC+TGG + chr8_4:6681036-6681055 None:intergenic 50.0%
CTTGGCGAAGTAACCCAGAT+CGG - chr8_4:6681162-6681181 Msa1310160:CDS 50.0%
TTGGCGAAGTAACCCAGATC+GGG - chr8_4:6681163-6681182 Msa1310160:CDS 50.0%
! AACCCAGATCGGGGTTTTCT+TGG - chr8_4:6681173-6681192 Msa1310160:CDS 50.0%
GTCCAAGAAAACCCCGATCT+GGG + chr8_4:6681178-6681197 None:intergenic 50.0%
TGTCCAAGAAAACCCCGATC+TGG + chr8_4:6681179-6681198 None:intergenic 50.0%
TCTTGGACACCAATTGGAGC+TGG - chr8_4:6681190-6681209 Msa1310160:CDS 50.0%
CTTGGACACCAATTGGAGCT+GGG - chr8_4:6681191-6681210 Msa1310160:CDS 50.0%
! GTGCAAGAAGGCATGGAAGA+AGG + chr8_4:6681305-6681324 None:intergenic 50.0%
CATGGGTGACATGGACATCA+CGG - chr8_4:6681540-6681559 Msa1310160:CDS 50.0%
TTCATCAGCCACCATTCCCT+TGG + chr8_4:6681744-6681763 None:intergenic 50.0%
GGGAATGGTGGCTGATGAAA+AGG - chr8_4:6681745-6681764 Msa1310160:CDS 50.0%
!! GCCGATTCGCTTCTCACAGA+AGG - chr8_4:6681134-6681153 Msa1310160:CDS 55.0%
TGGCGAAGTAACCCAGATCG+GGG - chr8_4:6681164-6681183 Msa1310160:CDS 55.0%
TTTGGGCACCCAGCTCCAAT+TGG + chr8_4:6681202-6681221 None:intergenic 55.0%
!! GCCGATTCGCTTCTCACAGA+AGG - chr8_4:6681134-6681153 Msa1310160:CDS 55.0%
TGGCGAAGTAACCCAGATCG+GGG - chr8_4:6681164-6681183 Msa1310160:CDS 55.0%
TTTGGGCACCCAGCTCCAAT+TGG + chr8_4:6681202-6681221 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr8_4 gene 6680936 6681808 6680936 ID=Msa1310160;Name=Msa1310160
chr8_4 mRNA 6680936 6681808 6680936 ID=Msa1310160-mRNA-1;Parent=Msa1310160;Name=Msa1310160-mRNA-1;_AED=0.01;_eAED=0.01;_QI=0|0|0|1|1|1|3|0|192
chr8_4 exon 6681389 6681808 6681389 ID=Msa1310160-mRNA-1:exon:2250;Parent=Msa1310160-mRNA-1
chr8_4 exon 6681133 6681215 6681133 ID=Msa1310160-mRNA-1:exon:2249;Parent=Msa1310160-mRNA-1
chr8_4 exon 6680936 6681011 6680936 ID=Msa1310160-mRNA-1:exon:2248;Parent=Msa1310160-mRNA-1
chr8_4 CDS 6681389 6681808 6681389 ID=Msa1310160-mRNA-1:cds;Parent=Msa1310160-mRNA-1
chr8_4 CDS 6681133 6681215 6681133 ID=Msa1310160-mRNA-1:cds;Parent=Msa1310160-mRNA-1
chr8_4 CDS 6680936 6681011 6680936 ID=Msa1310160-mRNA-1:cds;Parent=Msa1310160-mRNA-1
Gene Sequence

>Msa1310160

ATGCATCAGAGAAATACAAGGGCTATTACATGTCTTTTGTGCCGATATATGAGCAGAAGGCATGACACTGATTGTGAATTTGGTCAATACTTTTCGACCAGTAGGCATGCTGACTTTCAGTGTGTCATTCAAATTTTGGGGTTAAGTCGCCTGATGAGAATTATGCAATTAATAGAACCACATCAAAGACAAATTGTTGCCGATTCGCTTCTCACAGAAGGAGAAGCTTGGCGAAGTAACCCAGATCGGGGTTTTCTTGGACACCAATTGGAGCTGGGTGCCCAAATAAGCACATCCTTGGATGAAATTGAAATTGCTAGAAGACTTTTAGCTTTTTGCATTGATAATGCAAATTCAAACAATGCACCTTCTTCCATGCCTTCTTGCACTCAAATTCCTGACTTAAACTTGAGTATATGGAGTACTGAACACATGGGTGACATGGACATCACGGAACAAGACATGCAAGGTATTCCATGTACTTGTGAAAGAGGAGAATCAAGTAATGCATCCAAGGGAATGGTGGCTGATGAAAAGGGAAAAGGAATTCTTAATGAACAAGGACCCACCCACCAGTAA

Protein sequence

>Msa1310160

MHQRNTRAITCLLCRYMSRRHDTDCEFGQYFSTSRHADFQCVIQILGLSRLMRIMQLIEPHQRQIVADSLLTEGEAWRSNPDRGFLGHQLELGAQISTSLDEIEIARRLLAFCIDNANSNNAPSSMPSCTQIPDLNLSIWSTEHMGDMDITEQDMQGIPCTCERGESSNASKGMVADEKGKGILNEQGPTHQ*