AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0146200


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0146200 MtrunA17_Chr1g0153961 95.082 305 11 2 1 304 1 302 0.0 575
Msa0146200 MtrunA17_Chr3g0133621 49.701 334 98 14 1 303 1 295 4.37e-78 239
Msa0146200 MtrunA17_Chr4g0045231 39.130 322 152 8 1 299 1 301 1.29e-53 177
Msa0146200 MtrunA17_Chr1g0162251 37.692 260 121 10 57 302 28 260 8.81e-36 130
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0146200 AT2G15760.1 39.274 303 153 12 13 302 13 297 1.16e-29 115
Msa0146200 AT2G26530.2 34.219 301 156 10 25 300 6 289 1.89e-25 103
Msa0146200 AT2G26530.1 32.622 328 152 10 25 300 6 316 2.41e-21 92.4

Find 38 sgRNAs with CRISPR-Local

Find 106 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCCTTATAGACAAGGGATTT+TGG 0.133320 1_4:-5920752 Msa0146200:CDS
CCCAAAATCCCTTGTCTATA+AGG 0.209177 1_4:+5920751 None:intergenic
TGATGATGTTTGATCAATTA+TGG 0.230244 1_4:+5921443 None:intergenic
TTAGCTTCTTCATTAGTAAA+TGG 0.259977 1_4:+5921282 None:intergenic
TTGGGAAGGTTGTCTGGATT+TGG 0.260298 1_4:-5920733 Msa0146200:CDS
CCATCTTCTCCAAAACGTTT+TGG 0.280265 1_4:-5921537 Msa0146200:CDS
TAAAATTCACCAAAACGTTT+TGG 0.288002 1_4:+5921528 None:intergenic
TCGACGATTTATTTGATTCA+TGG 0.314817 1_4:+5921346 None:intergenic
GATGATACAAAGTTCTAGTA+TGG 0.343620 1_4:-5921610 Msa0146200:CDS
AATACAAGTGAAGAAGTTAA+AGG 0.350409 1_4:-5920907 Msa0146200:CDS
GAATCATCATCAAATAATTC+TGG 0.360745 1_4:-5921192 Msa0146200:CDS
GATTCCTCTTTGTTGCTACT+AGG 0.362236 1_4:+5921081 None:intergenic
TTCTGAATTATATAGTGAAA+TGG 0.377274 1_4:-5921475 Msa0146200:CDS
TTTCGAAGGGTTCGAGGAGA+TGG 0.388899 1_4:-5921023 Msa0146200:CDS
CCAACAAAATATTTCTTCAA+TGG 0.389000 1_4:+5920940 None:intergenic
TATAATTCAGAAAGCCTAGA+TGG 0.397292 1_4:+5921486 None:intergenic
TCAGCTGAAGAACTCTTTCA+TGG 0.412277 1_4:-5921318 Msa0146200:CDS
GAAAGCCTAGATGGACTTGA+AGG 0.448937 1_4:+5921495 None:intergenic
GTGCCCCTTCAAGTCCATCT+AGG 0.450184 1_4:-5921500 Msa0146200:CDS
GTTCGATTTCGAAGGGTTCG+AGG 0.475655 1_4:-5921029 Msa0146200:CDS
AAGATATCAAACAGTAGTAC+AGG 0.498075 1_4:-5921057 Msa0146200:CDS
AGGTCCTGGTTCGATTTCGA+AGG 0.504546 1_4:-5921037 Msa0146200:CDS
GAACCCTTCGAAATCGAACC+AGG 0.510031 1_4:+5921033 None:intergenic
AGAAGTGCTTCAGAAGGAAG+AGG 0.521434 1_4:-5920976 Msa0146200:CDS
TCAAACAGTAGTACAGGTCC+TGG 0.538921 1_4:-5921051 Msa0146200:CDS
ATTTACTAATGAAGAAGCTA+AGG 0.540876 1_4:-5921280 Msa0146200:CDS
AAAGTTCAAGATGAAAGAAG+AGG 0.559986 1_4:-5921234 Msa0146200:CDS
GGTCCTGGTTCGATTTCGAA+GGG 0.575115 1_4:-5921036 Msa0146200:CDS
GAAGATGGAGGACTTAGATA+CGG 0.590817 1_4:+5921552 None:intergenic
AAAGCCTAGATGGACTTGAA+GGG 0.592999 1_4:+5921496 None:intergenic
CTTTCTTGCCTTATAGACAA+GGG 0.596379 1_4:-5920759 Msa0146200:CDS
ACTTTCTTGCCTTATAGACA+AGG 0.596868 1_4:-5920760 Msa0146200:CDS
TTGTTTAGAAGTGCTTCAGA+AGG 0.602019 1_4:-5920982 Msa0146200:CDS
ACAACCTAGTAGCAACAAAG+AGG 0.606605 1_4:-5921085 Msa0146200:CDS
AAGCCTAGATGGACTTGAAG+GGG 0.623098 1_4:+5921497 None:intergenic
AGAAGGAAGAGGTTCAAGCA+AGG 0.639581 1_4:-5920965 Msa0146200:CDS
GCTGAAGAACTCTTTCATGG+TGG 0.696192 1_4:-5921315 Msa0146200:CDS
GATGATGATGATAAGCAAGG+TGG 0.748240 1_4:-5921387 Msa0146200:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTCTGAATTATATAGTGAAA+TGG - chr1_4:5920869-5920888 Msa0146200:CDS 20.0%
!!! ATGTAGTTTGATTTTCTATA+AGG + chr1_4:5921203-5921222 None:intergenic 20.0%
!!! CATTGAAGAAATATTTTGTT+GGG - chr1_4:5921405-5921424 Msa0146200:CDS 20.0%
!! TTCTGAATTATATAGTGAAA+TGG - chr1_4:5920869-5920888 Msa0146200:CDS 20.0%
!!! ATGTAGTTTGATTTTCTATA+AGG + chr1_4:5921203-5921222 None:intergenic 20.0%
!!! CATTGAAGAAATATTTTGTT+GGG - chr1_4:5921405-5921424 Msa0146200:CDS 20.0%
!!! GATACATTCAATTTTAGTAG+TGG - chr1_4:5920756-5920775 Msa0146200:CDS 25.0%
!! TAAAATTCACCAAAACGTTT+TGG + chr1_4:5920819-5920838 None:intergenic 25.0%
!! TGATGATGTTTGATCAATTA+TGG + chr1_4:5920904-5920923 None:intergenic 25.0%
! TTAGCTTCTTCATTAGTAAA+TGG + chr1_4:5921065-5921084 None:intergenic 25.0%
! ATTTACTAATGAAGAAGCTA+AGG - chr1_4:5921064-5921083 Msa0146200:CDS 25.0%
! GAATCATCATCAAATAATTC+TGG - chr1_4:5921152-5921171 Msa0146200:CDS 25.0%
! CCAACAAAATATTTCTTCAA+TGG + chr1_4:5921407-5921426 None:intergenic 25.0%
!! CCATTGAAGAAATATTTTGT+TGG - chr1_4:5921404-5921423 Msa0146200:CDS 25.0%
! AATACAAGTGAAGAAGTTAA+AGG - chr1_4:5921437-5921456 Msa0146200:CDS 25.0%
!!! GATACATTCAATTTTAGTAG+TGG - chr1_4:5920756-5920775 Msa0146200:CDS 25.0%
!! TAAAATTCACCAAAACGTTT+TGG + chr1_4:5920819-5920838 None:intergenic 25.0%
!! TGATGATGTTTGATCAATTA+TGG + chr1_4:5920904-5920923 None:intergenic 25.0%
! TTAGCTTCTTCATTAGTAAA+TGG + chr1_4:5921065-5921084 None:intergenic 25.0%
! ATTTACTAATGAAGAAGCTA+AGG - chr1_4:5921064-5921083 Msa0146200:CDS 25.0%
! GAATCATCATCAAATAATTC+TGG - chr1_4:5921152-5921171 Msa0146200:CDS 25.0%
! CCAACAAAATATTTCTTCAA+TGG + chr1_4:5921407-5921426 None:intergenic 25.0%
!! CCATTGAAGAAATATTTTGT+TGG - chr1_4:5921404-5921423 Msa0146200:CDS 25.0%
! AATACAAGTGAAGAAGTTAA+AGG - chr1_4:5921437-5921456 Msa0146200:CDS 25.0%
! GATGATACAAAGTTCTAGTA+TGG - chr1_4:5920734-5920753 Msa0146200:CDS 30.0%
TATAATTCAGAAAGCCTAGA+TGG + chr1_4:5920861-5920880 None:intergenic 30.0%
!!! ATGAACAACGTTGTTGTTTT+TGG + chr1_4:5920928-5920947 None:intergenic 30.0%
TCGACGATTTATTTGATTCA+TGG + chr1_4:5921001-5921020 None:intergenic 30.0%
!! TGAACTTTTTGTTGCTTCTT+AGG + chr1_4:5921098-5921117 None:intergenic 30.0%
AAAGTTCAAGATGAAAGAAG+AGG - chr1_4:5921110-5921129 Msa0146200:CDS 30.0%
AAGATATCAAACAGTAGTAC+AGG - chr1_4:5921287-5921306 Msa0146200:CDS 30.0%
! GATGATACAAAGTTCTAGTA+TGG - chr1_4:5920734-5920753 Msa0146200:CDS 30.0%
TATAATTCAGAAAGCCTAGA+TGG + chr1_4:5920861-5920880 None:intergenic 30.0%
!!! ATGAACAACGTTGTTGTTTT+TGG + chr1_4:5920928-5920947 None:intergenic 30.0%
TCGACGATTTATTTGATTCA+TGG + chr1_4:5921001-5921020 None:intergenic 30.0%
!! TGAACTTTTTGTTGCTTCTT+AGG + chr1_4:5921098-5921117 None:intergenic 30.0%
AAAGTTCAAGATGAAAGAAG+AGG - chr1_4:5921110-5921129 Msa0146200:CDS 30.0%
AAGATATCAAACAGTAGTAC+AGG - chr1_4:5921287-5921306 Msa0146200:CDS 30.0%
! GATGATGATGATGATAAGCA+AGG - chr1_4:5920954-5920973 Msa0146200:CDS 35.0%
!! TTGTTTAGAAGTGCTTCAGA+AGG - chr1_4:5921362-5921381 Msa0146200:CDS 35.0%
!! TCTGATTCGTTTTCACATCA+TGG - chr1_4:5921479-5921498 Msa0146200:CDS 35.0%
!! CTGATTCGTTTTCACATCAT+GGG - chr1_4:5921480-5921499 Msa0146200:CDS 35.0%
ACTTTCTTGCCTTATAGACA+AGG - chr1_4:5921584-5921603 Msa0146200:CDS 35.0%
CTTTCTTGCCTTATAGACAA+GGG - chr1_4:5921585-5921604 Msa0146200:CDS 35.0%
! CCTTATAGACAAGGGATTTT+GGG - chr1_4:5921593-5921612 Msa0146200:CDS 35.0%
! GATGATGATGATGATAAGCA+AGG - chr1_4:5920954-5920973 Msa0146200:CDS 35.0%
!! TTGTTTAGAAGTGCTTCAGA+AGG - chr1_4:5921362-5921381 Msa0146200:CDS 35.0%
!! TCTGATTCGTTTTCACATCA+TGG - chr1_4:5921479-5921498 Msa0146200:CDS 35.0%
!! CTGATTCGTTTTCACATCAT+GGG - chr1_4:5921480-5921499 Msa0146200:CDS 35.0%
ACTTTCTTGCCTTATAGACA+AGG - chr1_4:5921584-5921603 Msa0146200:CDS 35.0%
CTTTCTTGCCTTATAGACAA+GGG - chr1_4:5921585-5921604 Msa0146200:CDS 35.0%
! CCTTATAGACAAGGGATTTT+GGG - chr1_4:5921593-5921612 Msa0146200:CDS 35.0%
GAAGATGGAGGACTTAGATA+CGG + chr1_4:5920795-5920814 None:intergenic 40.0%
!!! AAACGTTTTGGAGAAGATGG+AGG + chr1_4:5920807-5920826 None:intergenic 40.0%
!!! CCAAAACGTTTTGGAGAAGA+TGG + chr1_4:5920810-5920829 None:intergenic 40.0%
! CCATCTTCTCCAAAACGTTT+TGG - chr1_4:5920807-5920826 Msa0146200:CDS 40.0%
! AAAGCCTAGATGGACTTGAA+GGG + chr1_4:5920851-5920870 None:intergenic 40.0%
! GATGATGATGATAAGCAAGG+TGG - chr1_4:5920957-5920976 Msa0146200:CDS 40.0%
TCAGCTGAAGAACTCTTTCA+TGG - chr1_4:5921026-5921045 Msa0146200:CDS 40.0%
ACAACCTAGTAGCAACAAAG+AGG - chr1_4:5921259-5921278 Msa0146200:CDS 40.0%
GATTCCTCTTTGTTGCTACT+AGG + chr1_4:5921266-5921285 None:intergenic 40.0%
ACATCATGGGTCGAGAAAAA+AGG - chr1_4:5921493-5921512 Msa0146200:CDS 40.0%
! GCCTTATAGACAAGGGATTT+TGG - chr1_4:5921592-5921611 Msa0146200:CDS 40.0%
CCCAAAATCCCTTGTCTATA+AGG + chr1_4:5921596-5921615 None:intergenic 40.0%
!! ATAGACAAGGGATTTTGGGA+AGG - chr1_4:5921597-5921616 Msa0146200:CDS 40.0%
GAAGATGGAGGACTTAGATA+CGG + chr1_4:5920795-5920814 None:intergenic 40.0%
!!! AAACGTTTTGGAGAAGATGG+AGG + chr1_4:5920807-5920826 None:intergenic 40.0%
!!! CCAAAACGTTTTGGAGAAGA+TGG + chr1_4:5920810-5920829 None:intergenic 40.0%
! CCATCTTCTCCAAAACGTTT+TGG - chr1_4:5920807-5920826 Msa0146200:CDS 40.0%
! AAAGCCTAGATGGACTTGAA+GGG + chr1_4:5920851-5920870 None:intergenic 40.0%
! GATGATGATGATAAGCAAGG+TGG - chr1_4:5920957-5920976 Msa0146200:CDS 40.0%
TCAGCTGAAGAACTCTTTCA+TGG - chr1_4:5921026-5921045 Msa0146200:CDS 40.0%
ACAACCTAGTAGCAACAAAG+AGG - chr1_4:5921259-5921278 Msa0146200:CDS 40.0%
GATTCCTCTTTGTTGCTACT+AGG + chr1_4:5921266-5921285 None:intergenic 40.0%
ACATCATGGGTCGAGAAAAA+AGG - chr1_4:5921493-5921512 Msa0146200:CDS 40.0%
! GCCTTATAGACAAGGGATTT+TGG - chr1_4:5921592-5921611 Msa0146200:CDS 40.0%
CCCAAAATCCCTTGTCTATA+AGG + chr1_4:5921596-5921615 None:intergenic 40.0%
!! ATAGACAAGGGATTTTGGGA+AGG - chr1_4:5921597-5921616 Msa0146200:CDS 40.0%
! AAGCCTAGATGGACTTGAAG+GGG + chr1_4:5920850-5920869 None:intergenic 45.0%
! GAAAGCCTAGATGGACTTGA+AGG + chr1_4:5920852-5920871 None:intergenic 45.0%
GCTGAAGAACTCTTTCATGG+TGG - chr1_4:5921029-5921048 Msa0146200:CDS 45.0%
TCAAACAGTAGTACAGGTCC+TGG - chr1_4:5921293-5921312 Msa0146200:CDS 45.0%
!! AGAAGTGCTTCAGAAGGAAG+AGG - chr1_4:5921368-5921387 Msa0146200:CDS 45.0%
AGAAGGAAGAGGTTCAAGCA+AGG - chr1_4:5921379-5921398 Msa0146200:CDS 45.0%
TTGGGAAGGTTGTCTGGATT+TGG - chr1_4:5921611-5921630 Msa0146200:CDS 45.0%
! AAGCCTAGATGGACTTGAAG+GGG + chr1_4:5920850-5920869 None:intergenic 45.0%
! GAAAGCCTAGATGGACTTGA+AGG + chr1_4:5920852-5920871 None:intergenic 45.0%
GCTGAAGAACTCTTTCATGG+TGG - chr1_4:5921029-5921048 Msa0146200:CDS 45.0%
TCAAACAGTAGTACAGGTCC+TGG - chr1_4:5921293-5921312 Msa0146200:CDS 45.0%
!! AGAAGTGCTTCAGAAGGAAG+AGG - chr1_4:5921368-5921387 Msa0146200:CDS 45.0%
AGAAGGAAGAGGTTCAAGCA+AGG - chr1_4:5921379-5921398 Msa0146200:CDS 45.0%
TTGGGAAGGTTGTCTGGATT+TGG - chr1_4:5921611-5921630 Msa0146200:CDS 45.0%
! AGGTCCTGGTTCGATTTCGA+AGG - chr1_4:5921307-5921326 Msa0146200:CDS 50.0%
! GGTCCTGGTTCGATTTCGAA+GGG - chr1_4:5921308-5921327 Msa0146200:CDS 50.0%
GAACCCTTCGAAATCGAACC+AGG + chr1_4:5921314-5921333 None:intergenic 50.0%
GTTCGATTTCGAAGGGTTCG+AGG - chr1_4:5921315-5921334 Msa0146200:CDS 50.0%
TTTCGAAGGGTTCGAGGAGA+TGG - chr1_4:5921321-5921340 Msa0146200:CDS 50.0%
!! GGGATTTTGGGAAGGTTGTC+TGG - chr1_4:5921605-5921624 Msa0146200:CDS 50.0%
! AGGTCCTGGTTCGATTTCGA+AGG - chr1_4:5921307-5921326 Msa0146200:CDS 50.0%
! GGTCCTGGTTCGATTTCGAA+GGG - chr1_4:5921308-5921327 Msa0146200:CDS 50.0%
GAACCCTTCGAAATCGAACC+AGG + chr1_4:5921314-5921333 None:intergenic 50.0%
GTTCGATTTCGAAGGGTTCG+AGG - chr1_4:5921315-5921334 Msa0146200:CDS 50.0%
TTTCGAAGGGTTCGAGGAGA+TGG - chr1_4:5921321-5921340 Msa0146200:CDS 50.0%
!! GGGATTTTGGGAAGGTTGTC+TGG - chr1_4:5921605-5921624 Msa0146200:CDS 50.0%
GTGCCCCTTCAAGTCCATCT+AGG - chr1_4:5920844-5920863 Msa0146200:CDS 55.0%
GTGCCCCTTCAAGTCCATCT+AGG - chr1_4:5920844-5920863 Msa0146200:CDS 55.0%
Chromosome Type Strat End Strand Name
chr1_4 gene 5920726 5921640 5920726 ID=Msa0146200;Name=Msa0146200
chr1_4 mRNA 5920726 5921640 5920726 ID=Msa0146200-mRNA-1;Parent=Msa0146200;Name=Msa0146200-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|304
chr1_4 exon 5920726 5921640 5920726 ID=Msa0146200-mRNA-1:exon:2545;Parent=Msa0146200-mRNA-1
chr1_4 CDS 5920726 5921640 5920726 ID=Msa0146200-mRNA-1:cds;Parent=Msa0146200-mRNA-1
Gene Sequence

>Msa0146200

ATGGAAGTGATGATACAAAGTTCTAGTATGGATACATTCAATTTTAGTAGTGGAACAATGAGTTCACCGTATCTAAGTCCTCCATCTTCTCCAAAACGTTTTGGTGAATTTTACTTAAGTGCCCCTTCAAGTCCATCTAGGCTTTCTGAATTATATAGTGAAATGGATTACTTGTCCATAATTGATCAAACATCATCAACCAAAAACAACAACGTTGTTCATGAAGATGATGATGATGATGATAAGCAAGGTGGTTTTGCTTTCTTTGTTAACCATGAATCAAATAAATCGTCGACACGTTCAGCTGAAGAACTCTTTCATGGTGGCAAAATCAAACCATTTACTAATGAAGAAGCTAAGGTTGTTGTACCTAAGAAGCAACAAAAAGTTCAAGATGAAAGAAGAGGAAGAGACAGAGAGAGAATAGAATCATCATCAAATAATTCTGGTAGAAGAAGTTCAAGATCACATTCTCCTTATAGAAAATCAAACTACATATCAGAATTAGAAGAACAAAACTCTCAAAAACAGAAACAACCTAGTAGCAACAAAGAGGAATCAAAGATATCAAACAGTAGTACAGGTCCTGGTTCGATTTCGAAGGGTTCGAGGAGATGGAAATTGAGTGATCTATTGTTGTTTAGAAGTGCTTCAGAAGGAAGAGGTTCAAGCAAGGATCCATTGAAGAAATATTTTGTTGGGTATAAGAAGAATACAAGTGAAGAAGTTAAAGGTTCAAGCAGCTTTAGATCTTCTGATTCGTTTTCACATCATGGGTCGAGAAAAAAGGCTCAAGTTTCAGCTCATGAAATGCATTATGCTATGAAGAAAGCTGAGTCACAAGATATGAAGAAGAGAACTTTCTTGCCTTATAGACAAGGGATTTTGGGAAGGTTGTCTGGATTTGGACTCTAG

Protein sequence

>Msa0146200

MEVMIQSSSMDTFNFSSGTMSSPYLSPPSSPKRFGEFYLSAPSSPSRLSELYSEMDYLSIIDQTSSTKNNNVVHEDDDDDDKQGGFAFFVNHESNKSSTRSAEELFHGGKIKPFTNEEAKVVVPKKQQKVQDERRGRDRERIESSSNNSGRRSSRSHSPYRKSNYISELEEQNSQKQKQPSSNKEESKISNSSTGPGSISKGSRRWKLSDLLLFRSASEGRGSSKDPLKKYFVGYKKNTSEEVKGSSSFRSSDSFSHHGSRKKAQVSAHEMHYAMKKAESQDMKKRTFLPYRQGILGRLSGFGL*