AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0581160

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0581160 MtrunA17_Chr7g0270601 61.272 173 21 4 1 127 282 454 1.88e-50 166
Msa0581160 MtrunA17_Chr7g0269191 69.697 99 19 3 40 127 1 99 7.92e-29 101
Msa0581160 MtrunA17_Chr7g0271391 39.167 120 63 3 18 127 504 623 3.99e-22 90.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0581160 AT3G62200.1 36.054 147 74 4 1 127 505 651 3.90e-21 88.2

Find 39 sgRNAs with CRISPR-Local

Find 114 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCTTCATTTATCGGCAATTT+TGG 0.159196 4_1:+86493829 Msa0581160:CDS
GTACATTCCCATCTGCTTAC+TGG 0.214575 4_1:+86494287 Msa0581160:three_prime_UTR
GTACATTTCAATCTGCTTAC+TGG 0.250536 4_1:+86494347 Msa0581160:three_prime_UTR
CAATTCCTTGCTTCATTTAT+CGG 0.255799 4_1:+86493820 Msa0581160:CDS
CGTGGTTCCCAGACGCAATC+TGG 0.270910 4_1:+86493785 Msa0581160:CDS
TTAGCCTCTGTAAGTGAAAA+TGG 0.275804 4_1:-86494096 None:intergenic
GGGTGATGTACTTAAGATTT+TGG 0.277803 4_1:+86494013 Msa0581160:CDS
GATGACACAGATAGTGATTC+TGG 0.347850 4_1:+86494130 Msa0581160:three_prime_UTR
AAGGTGGTTAAACGAGTCTT+TGG 0.382873 4_1:+86493706 Msa0581160:intron
ATCCTAACCCAGATTGCGTC+TGG 0.396295 4_1:-86493793 None:intergenic
TTATACCTTGTCATTCTAGA+TGG 0.412658 4_1:+86494063 Msa0581160:CDS
GAATACACTGATGAATGAAA+TGG 0.416796 4_1:+86493579 Msa0581160:CDS
CTGTAAGTGAAAATGGTAAT+CGG 0.431067 4_1:-86494089 None:intergenic
TTGTTGCAAATGAGAATCTA+TGG 0.442211 4_1:+86493746 Msa0581160:CDS
TTATAATCACAATCAAGAAA+TGG 0.466378 4_1:+86494039 Msa0581160:CDS
CCTCTACATATCTCTAACTA+CGG 0.467900 4_1:-86494213 None:intergenic
TTGCGTCTGGGAACCACGTA+AGG 0.473407 4_1:-86493780 None:intergenic
TCCCAGACGCAATCTGGGTT+AGG 0.483088 4_1:+86493791 Msa0581160:CDS
AGCAGATGGGAATGTACAAA+AGG 0.496986 4_1:-86494281 None:intergenic
TGTCTTGAAGAGCTTGTGTT+GGG 0.501883 4_1:+86493993 Msa0581160:CDS
CATTTCAATCTGCTTACTGG+TGG 0.505776 4_1:+86494350 Msa0581160:three_prime_UTR
ATTCCCATCTGCTTACTGGT+GGG 0.506945 4_1:+86494291 Msa0581160:three_prime_UTR
TGAGAATTTGCAAGGACTTG+TGG 0.513544 4_1:+86493537 Msa0581160:CDS
CATTCCCATCTGCTTACTGG+TGG 0.519665 4_1:+86494290 Msa0581160:three_prime_UTR
TTCCCATCTGCTTACTGGTG+GGG 0.524628 4_1:+86494292 Msa0581160:three_prime_UTR
GTGTCTTGAAGAGCTTGTGT+TGG 0.527052 4_1:+86493992 Msa0581160:CDS
GTGGTTCCCAGACGCAATCT+GGG 0.539558 4_1:+86493786 Msa0581160:CDS
AGTCCCCACCAGTAAGCAGA+TGG 0.550048 4_1:-86494295 None:intergenic
TCCTAACCCAGATTGCGTCT+GGG 0.566146 4_1:-86493792 None:intergenic
GAGATATGTAGAGGAATTCG+TGG 0.572067 4_1:+86494222 Msa0581160:three_prime_UTR
CCGTAGTTAGAGATATGTAG+AGG 0.580945 4_1:+86494213 Msa0581160:three_prime_UTR
TGCGTCTGGGAACCACGTAA+GGG 0.598064 4_1:-86493779 None:intergenic
GTCCCCACCAGTAAGCAGAT+GGG 0.623279 4_1:-86494294 None:intergenic
AATTGCCGATAAATGAAGCA+AGG 0.623661 4_1:-86493825 None:intergenic
AAACTACGTGAGCTTTGACA+TGG 0.629175 4_1:+86494178 Msa0581160:three_prime_UTR
TCAACACATGAGAATTTGCA+AGG 0.634115 4_1:+86493529 Msa0581160:CDS
GCGTCTGGGAACCACGTAAG+GGG 0.647796 4_1:-86493778 None:intergenic
GGAAGTGTGAACCCCTTACG+TGG 0.663822 4_1:+86493767 Msa0581160:CDS
GGCTGCCATCTAGAATGACA+AGG 0.705174 4_1:-86494068 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AACATATAATAAAAGACAAA+AGG - chr4_1:86493934-86493953 None:intergenic 15.0%
!! AACATATAATAAAAGACAAA+AGG - chr4_1:86493934-86493953 None:intergenic 15.0%
!! ATATCAAATGTCTCATATTT+GGG - chr4_1:86493652-86493671 None:intergenic 20.0%
!! AATATCAAATGTCTCATATT+TGG - chr4_1:86493653-86493672 None:intergenic 20.0%
!! AATATGAGACATTTGATATT+AGG + chr4_1:86493653-86493672 Msa0581160:intron 20.0%
!! TTATAATCACAATCAAGAAA+TGG + chr4_1:86494039-86494058 Msa0581160:CDS 20.0%
!! ATATCAAATGTCTCATATTT+GGG - chr4_1:86493652-86493671 None:intergenic 20.0%
!! AATATCAAATGTCTCATATT+TGG - chr4_1:86493653-86493672 None:intergenic 20.0%
!! AATATGAGACATTTGATATT+AGG + chr4_1:86493653-86493672 Msa0581160:intron 20.0%
!! TTATAATCACAATCAAGAAA+TGG + chr4_1:86494039-86494058 Msa0581160:CDS 20.0%
! GCAATCAATTATATTTCCTT+CGG - chr4_1:86493614-86493633 None:intergenic 25.0%
! ATAATTGATTGCATTCGTTA+TGG + chr4_1:86493622-86493641 Msa0581160:intron 25.0%
!!! TATTGTTTTTCTTAGTTCCT+TGG + chr4_1:86493874-86493893 Msa0581160:intron 25.0%
! GCAATCAATTATATTTCCTT+CGG - chr4_1:86493614-86493633 None:intergenic 25.0%
! ATAATTGATTGCATTCGTTA+TGG + chr4_1:86493622-86493641 Msa0581160:intron 25.0%
!!! TATTGTTTTTCTTAGTTCCT+TGG + chr4_1:86493874-86493893 Msa0581160:intron 25.0%
GAATACACTGATGAATGAAA+TGG + chr4_1:86493579-86493598 Msa0581160:CDS 30.0%
TCAATTATATTTCCTTCGGT+AGG - chr4_1:86493610-86493629 None:intergenic 30.0%
TGAGACATTTGATATTAGGA+AGG + chr4_1:86493657-86493676 Msa0581160:intron 30.0%
GAGACATTTGATATTAGGAA+GGG + chr4_1:86493658-86493677 Msa0581160:intron 30.0%
TTGTTGCAAATGAGAATCTA+TGG + chr4_1:86493746-86493765 Msa0581160:CDS 30.0%
CAATTCCTTGCTTCATTTAT+CGG + chr4_1:86493820-86493839 Msa0581160:CDS 30.0%
TAACAAGTAATAAAGCTCCA+AGG - chr4_1:86493894-86493913 None:intergenic 30.0%
TTATACCTTGTCATTCTAGA+TGG + chr4_1:86494063-86494082 Msa0581160:CDS 30.0%
CTGTAAGTGAAAATGGTAAT+CGG - chr4_1:86494092-86494111 None:intergenic 30.0%
! ATTACCATTTTCACTTACAG+AGG + chr4_1:86494092-86494111 Msa0581160:CDS 30.0%
GAATACACTGATGAATGAAA+TGG + chr4_1:86493579-86493598 Msa0581160:CDS 30.0%
TCAATTATATTTCCTTCGGT+AGG - chr4_1:86493610-86493629 None:intergenic 30.0%
TGAGACATTTGATATTAGGA+AGG + chr4_1:86493657-86493676 Msa0581160:intron 30.0%
GAGACATTTGATATTAGGAA+GGG + chr4_1:86493658-86493677 Msa0581160:intron 30.0%
TTGTTGCAAATGAGAATCTA+TGG + chr4_1:86493746-86493765 Msa0581160:CDS 30.0%
CAATTCCTTGCTTCATTTAT+CGG + chr4_1:86493820-86493839 Msa0581160:CDS 30.0%
TAACAAGTAATAAAGCTCCA+AGG - chr4_1:86493894-86493913 None:intergenic 30.0%
TTATACCTTGTCATTCTAGA+TGG + chr4_1:86494063-86494082 Msa0581160:CDS 30.0%
CTGTAAGTGAAAATGGTAAT+CGG - chr4_1:86494092-86494111 None:intergenic 30.0%
! ATTACCATTTTCACTTACAG+AGG + chr4_1:86494092-86494111 Msa0581160:CDS 30.0%
TCAACACATGAGAATTTGCA+AGG + chr4_1:86493529-86493548 Msa0581160:CDS 35.0%
AATTGCCGATAAATGAAGCA+AGG - chr4_1:86493828-86493847 None:intergenic 35.0%
! GCTTCATTTATCGGCAATTT+TGG + chr4_1:86493829-86493848 Msa0581160:CDS 35.0%
! GGGTGATGTACTTAAGATTT+TGG + chr4_1:86494013-86494032 Msa0581160:CDS 35.0%
TTAGCCTCTGTAAGTGAAAA+TGG - chr4_1:86494099-86494118 None:intergenic 35.0%
CCTCTACATATCTCTAACTA+CGG - chr4_1:86494216-86494235 None:intergenic 35.0%
GTACATTTCAATCTGCTTAC+TGG + chr4_1:86494347-86494366 Msa0581160:three_prime_UTR 35.0%
!!! CTTACTGGTGGATTTTTTGA+TGG + chr4_1:86494362-86494381 Msa0581160:three_prime_UTR 35.0%
TCAACACATGAGAATTTGCA+AGG + chr4_1:86493529-86493548 Msa0581160:CDS 35.0%
AATTGCCGATAAATGAAGCA+AGG - chr4_1:86493828-86493847 None:intergenic 35.0%
! GCTTCATTTATCGGCAATTT+TGG + chr4_1:86493829-86493848 Msa0581160:CDS 35.0%
! GGGTGATGTACTTAAGATTT+TGG + chr4_1:86494013-86494032 Msa0581160:CDS 35.0%
TTAGCCTCTGTAAGTGAAAA+TGG - chr4_1:86494099-86494118 None:intergenic 35.0%
CCTCTACATATCTCTAACTA+CGG - chr4_1:86494216-86494235 None:intergenic 35.0%
GTACATTTCAATCTGCTTAC+TGG + chr4_1:86494347-86494366 Msa0581160:three_prime_UTR 35.0%
!!! CTTACTGGTGGATTTTTTGA+TGG + chr4_1:86494362-86494381 Msa0581160:three_prime_UTR 35.0%
TGAGAATTTGCAAGGACTTG+TGG + chr4_1:86493537-86493556 Msa0581160:CDS 40.0%
! GAAATGGTTTTTCCTACCGA+AGG + chr4_1:86493595-86493614 Msa0581160:intron 40.0%
TTGTGCAATTGAGCAACAGA+AGG + chr4_1:86493687-86493706 Msa0581160:intron 40.0%
AAGGTGGTTAAACGAGTCTT+TGG + chr4_1:86493706-86493725 Msa0581160:intron 40.0%
!! CAATTTTGGCGTCTTGTAAC+AGG + chr4_1:86493843-86493862 Msa0581160:intron 40.0%
TGTCTTGAAGAGCTTGTGTT+GGG + chr4_1:86493993-86494012 Msa0581160:CDS 40.0%
GATGACACAGATAGTGATTC+TGG + chr4_1:86494130-86494149 Msa0581160:three_prime_UTR 40.0%
! AAACTACGTGAGCTTTGACA+TGG + chr4_1:86494178-86494197 Msa0581160:three_prime_UTR 40.0%
CCGTAGTTAGAGATATGTAG+AGG + chr4_1:86494213-86494232 Msa0581160:three_prime_UTR 40.0%
GAGATATGTAGAGGAATTCG+TGG + chr4_1:86494222-86494241 Msa0581160:three_prime_UTR 40.0%
AGCAGATGGGAATGTACAAA+AGG - chr4_1:86494284-86494303 None:intergenic 40.0%
CATTTCAATCTGCTTACTGG+TGG + chr4_1:86494350-86494369 Msa0581160:three_prime_UTR 40.0%
TGAGAATTTGCAAGGACTTG+TGG + chr4_1:86493537-86493556 Msa0581160:CDS 40.0%
! GAAATGGTTTTTCCTACCGA+AGG + chr4_1:86493595-86493614 Msa0581160:intron 40.0%
TTGTGCAATTGAGCAACAGA+AGG + chr4_1:86493687-86493706 Msa0581160:intron 40.0%
AAGGTGGTTAAACGAGTCTT+TGG + chr4_1:86493706-86493725 Msa0581160:intron 40.0%
!! CAATTTTGGCGTCTTGTAAC+AGG + chr4_1:86493843-86493862 Msa0581160:intron 40.0%
TGTCTTGAAGAGCTTGTGTT+GGG + chr4_1:86493993-86494012 Msa0581160:CDS 40.0%
GATGACACAGATAGTGATTC+TGG + chr4_1:86494130-86494149 Msa0581160:three_prime_UTR 40.0%
! AAACTACGTGAGCTTTGACA+TGG + chr4_1:86494178-86494197 Msa0581160:three_prime_UTR 40.0%
CCGTAGTTAGAGATATGTAG+AGG + chr4_1:86494213-86494232 Msa0581160:three_prime_UTR 40.0%
GAGATATGTAGAGGAATTCG+TGG + chr4_1:86494222-86494241 Msa0581160:three_prime_UTR 40.0%
AGCAGATGGGAATGTACAAA+AGG - chr4_1:86494284-86494303 None:intergenic 40.0%
CATTTCAATCTGCTTACTGG+TGG + chr4_1:86494350-86494369 Msa0581160:three_prime_UTR 40.0%
TGCAATTGAGCAACAGAAGG+TGG + chr4_1:86493690-86493709 Msa0581160:intron 45.0%
GTGTCTTGAAGAGCTTGTGT+TGG + chr4_1:86493992-86494011 Msa0581160:CDS 45.0%
GTACATTCCCATCTGCTTAC+TGG + chr4_1:86494287-86494306 Msa0581160:three_prime_UTR 45.0%
ATTCCCATCTGCTTACTGGT+GGG + chr4_1:86494291-86494310 Msa0581160:three_prime_UTR 45.0%
! TACTGGTGGGGACTTTTTGT+TGG + chr4_1:86494304-86494323 Msa0581160:three_prime_UTR 45.0%
TGCAATTGAGCAACAGAAGG+TGG + chr4_1:86493690-86493709 Msa0581160:intron 45.0%
GTGTCTTGAAGAGCTTGTGT+TGG + chr4_1:86493992-86494011 Msa0581160:CDS 45.0%
GTACATTCCCATCTGCTTAC+TGG + chr4_1:86494287-86494306 Msa0581160:three_prime_UTR 45.0%
ATTCCCATCTGCTTACTGGT+GGG + chr4_1:86494291-86494310 Msa0581160:three_prime_UTR 45.0%
! TACTGGTGGGGACTTTTTGT+TGG + chr4_1:86494304-86494323 Msa0581160:three_prime_UTR 45.0%
TCCTAACCCAGATTGCGTCT+GGG - chr4_1:86493795-86493814 None:intergenic 50.0%
ATCCTAACCCAGATTGCGTC+TGG - chr4_1:86493796-86493815 None:intergenic 50.0%
! GGCTGCCATCTAGAATGACA+AGG - chr4_1:86494071-86494090 None:intergenic 50.0%
CATTCCCATCTGCTTACTGG+TGG + chr4_1:86494290-86494309 Msa0581160:three_prime_UTR 50.0%
TTCCCATCTGCTTACTGGTG+GGG + chr4_1:86494292-86494311 Msa0581160:three_prime_UTR 50.0%
TCCTAACCCAGATTGCGTCT+GGG - chr4_1:86493795-86493814 None:intergenic 50.0%
ATCCTAACCCAGATTGCGTC+TGG - chr4_1:86493796-86493815 None:intergenic 50.0%
! GGCTGCCATCTAGAATGACA+AGG - chr4_1:86494071-86494090 None:intergenic 50.0%
CATTCCCATCTGCTTACTGG+TGG + chr4_1:86494290-86494309 Msa0581160:three_prime_UTR 50.0%
TTCCCATCTGCTTACTGGTG+GGG + chr4_1:86494292-86494311 Msa0581160:three_prime_UTR 50.0%
! GGAAGTGTGAACCCCTTACG+TGG + chr4_1:86493767-86493786 Msa0581160:CDS 55.0%
TGCGTCTGGGAACCACGTAA+GGG - chr4_1:86493782-86493801 None:intergenic 55.0%
TTGCGTCTGGGAACCACGTA+AGG - chr4_1:86493783-86493802 None:intergenic 55.0%
GTGGTTCCCAGACGCAATCT+GGG + chr4_1:86493786-86493805 Msa0581160:CDS 55.0%
TCCCAGACGCAATCTGGGTT+AGG + chr4_1:86493791-86493810 Msa0581160:CDS 55.0%
GTCCCCACCAGTAAGCAGAT+GGG - chr4_1:86494297-86494316 None:intergenic 55.0%
AGTCCCCACCAGTAAGCAGA+TGG - chr4_1:86494298-86494317 None:intergenic 55.0%
! GGAAGTGTGAACCCCTTACG+TGG + chr4_1:86493767-86493786 Msa0581160:CDS 55.0%
TGCGTCTGGGAACCACGTAA+GGG - chr4_1:86493782-86493801 None:intergenic 55.0%
TTGCGTCTGGGAACCACGTA+AGG - chr4_1:86493783-86493802 None:intergenic 55.0%
GTGGTTCCCAGACGCAATCT+GGG + chr4_1:86493786-86493805 Msa0581160:CDS 55.0%
TCCCAGACGCAATCTGGGTT+AGG + chr4_1:86493791-86493810 Msa0581160:CDS 55.0%
GTCCCCACCAGTAAGCAGAT+GGG - chr4_1:86494297-86494316 None:intergenic 55.0%
AGTCCCCACCAGTAAGCAGA+TGG - chr4_1:86494298-86494317 None:intergenic 55.0%
GCGTCTGGGAACCACGTAAG+GGG - chr4_1:86493781-86493800 None:intergenic 60.0%
CGTGGTTCCCAGACGCAATC+TGG + chr4_1:86493785-86493804 Msa0581160:CDS 60.0%
GCGTCTGGGAACCACGTAAG+GGG - chr4_1:86493781-86493800 None:intergenic 60.0%
CGTGGTTCCCAGACGCAATC+TGG + chr4_1:86493785-86493804 Msa0581160:CDS 60.0%
Chromosome Type Strat End Strand Name
chr4_1 gene 86493508 86494399 86493508 ID=Msa0581160;Name=Msa0581160
chr4_1 mRNA 86493508 86494399 86493508 ID=Msa0581160-mRNA-1;Parent=Msa0581160;Name=Msa0581160-mRNA-1;_AED=0.13;_eAED=0.18;_QI=0|0|0.33|1|0.5|0.33|3|281|132
chr4_1 exon 86493508 86493600 86493508 ID=Msa0581160-mRNA-1:exon:31992;Parent=Msa0581160-mRNA-1
chr4_1 exon 86493709 86493857 86493709 ID=Msa0581160-mRNA-1:exon:31993;Parent=Msa0581160-mRNA-1
chr4_1 exon 86493962 86494399 86493962 ID=Msa0581160-mRNA-1:exon:31994;Parent=Msa0581160-mRNA-1
chr4_1 CDS 86493508 86493600 86493508 ID=Msa0581160-mRNA-1:cds;Parent=Msa0581160-mRNA-1
chr4_1 CDS 86493709 86493857 86493709 ID=Msa0581160-mRNA-1:cds;Parent=Msa0581160-mRNA-1
chr4_1 CDS 86493962 86494118 86493962 ID=Msa0581160-mRNA-1:cds;Parent=Msa0581160-mRNA-1
chr4_1 three_prime_UTR 86494119 86494399 86494119 ID=Msa0581160-mRNA-1:three_prime_utr;Parent=Msa0581160-mRNA-1
Gene Sequence

>Msa0581160

TTAGAGACTTTGAAAACAATATCAACACATGAGAATTTGCAAGGACTTGTGGATATTATTCTAGTCACTTCGAATACACTGATGAATGAAATGGTGGTTAAACGAGTCTTTGGCACATTACGTTTGTATGTTGTTGCAAATGAGAATCTATGGAAGTGTGAACCCCTTACGTGGTTCCCAGACGCAATCTGGGTTAGGATAGAGCAATTCCTTGCTTCATTTATCGGCAATTTTGGCGTCTTATATGAAGCTTCATTAATTCTAAAGAGATTGTGTCTTGAAGAGCTTGTGTTGGGTGATGTACTTAAGATTTTGGAGATTATAATCACAATCAAGAAATGGATTATACCTTGTCATTCTAGATGGCAGCCGATTACCATTTTCACTTACAGAGGCTAA
Protein sequence

>Msa0581160

LETLKTISTHENLQGLVDIILVTSNTLMNEMVVKRVFGTLRLYVVANENLWKCEPLTWFPDAIWVRIEQFLASFIGNFGVLYEASLILKRLCLEELVLGDVLKILEIIITIKKWIIPCHSRWQPITIFTYRG*