AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1377050


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1377050 MtrunA17_Chr1g0153961 94.754 305 12 2 1 304 1 302 2.05e-172 479
Msa1377050 MtrunA17_Chr3g0133621 49.401 334 99 14 1 303 1 295 1.91e-77 238
Msa1377050 MtrunA17_Chr4g0045231 39.441 322 151 8 1 299 1 301 2.78e-54 179
Msa1377050 MtrunA17_Chr1g0162251 37.692 260 121 10 57 302 28 260 8.90e-36 130
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1377050 AT2G15760.1 38.944 303 154 12 13 302 13 297 3.86e-29 113
Msa1377050 AT2G26530.2 33.887 301 157 10 25 300 6 289 1.85e-25 103
Msa1377050 AT2G26530.1 32.317 328 153 10 25 300 6 316 2.77e-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 tig0019847:+103437 Msa1377050:CDS
CCCAAAATCCCTTGTCTATA+AGG 0.209177 tig0019847:-103438 None:intergenic
TGATGATGTTTGATCAATTA+TGG 0.230244 tig0019847:-102746 None:intergenic
TTAGCTTCTTCATTAGTAAA+TGG 0.259977 tig0019847:-102907 None:intergenic
TTGGGAAGGTTGTCTGGATT+TGG 0.260298 tig0019847:+103456 Msa1377050:CDS
CCATCTTCTCCAAAACGTTT+TGG 0.280265 tig0019847:+102652 Msa1377050:CDS
TAAAATTCACCAAAACGTTT+TGG 0.288002 tig0019847:-102661 None:intergenic
TCGACGATTTATTTGATTCA+TGG 0.314817 tig0019847:-102843 None:intergenic
GATGATACAAAGTTCTAGTA+TGG 0.343620 tig0019847:+102579 Msa1377050:CDS
AATACAAGTGAAGAAGTTAA+AGG 0.350409 tig0019847:+103282 Msa1377050:CDS
GAATCATCATCAAATAATTC+TGG 0.360745 tig0019847:+102997 Msa1377050:CDS
GATTCCTCTTTGTTGCTACT+AGG 0.362236 tig0019847:-103108 None:intergenic
TTCTGAATTATATAGTGAAA+TGG 0.377274 tig0019847:+102714 Msa1377050:CDS
TTTCGAAGGGTTCGAGGAGA+TGG 0.388899 tig0019847:+103166 Msa1377050:CDS
CCAACAAAATATTTCTTCAA+TGG 0.389000 tig0019847:-103249 None:intergenic
TATAATTCAGAAAGCCTAGA+TGG 0.397292 tig0019847:-102703 None:intergenic
TCAGCTGAAGAACTCTTTCA+TGG 0.412277 tig0019847:+102871 Msa1377050:CDS
GAAAGCCTAGATGGACTTGA+AGG 0.448937 tig0019847:-102694 None:intergenic
GTGCCCCTTCAAGTCCATCT+AGG 0.450184 tig0019847:+102689 Msa1377050:CDS
GTTCGATTTCGAAGGGTTCG+AGG 0.475655 tig0019847:+103160 Msa1377050:CDS
AAGATATCAAACAGTAGTAC+AGG 0.498075 tig0019847:+103132 Msa1377050:CDS
AGGTCCTGGTTCGATTTCGA+AGG 0.504546 tig0019847:+103152 Msa1377050:CDS
GAACCCTTCGAAATCGAACC+AGG 0.510031 tig0019847:-103156 None:intergenic
AGAAGTGCTTCAGAAGGAAG+AGG 0.521434 tig0019847:+103213 Msa1377050:CDS
TCAAACAGTAGTACAGGTCC+TGG 0.538921 tig0019847:+103138 Msa1377050:CDS
ATTTACTAATGAAGAAGCTA+AGG 0.540876 tig0019847:+102909 Msa1377050:CDS
AAAGTTCAAGATGAAAGAAG+AGG 0.559986 tig0019847:+102955 Msa1377050:CDS
GGTCCTGGTTCGATTTCGAA+GGG 0.575115 tig0019847:+103153 Msa1377050:CDS
GAAGATGGAGGACTTAGATA+CGG 0.590817 tig0019847:-102637 None:intergenic
AAAGCCTAGATGGACTTGAA+GGG 0.592999 tig0019847:-102693 None:intergenic
CTTTCTTGCCTTATAGACAA+GGG 0.596379 tig0019847:+103430 Msa1377050:CDS
ACTTTCTTGCCTTATAGACA+AGG 0.596868 tig0019847:+103429 Msa1377050:CDS
TTGTTTAGAAGTGCTTCAGA+AGG 0.602019 tig0019847:+103207 Msa1377050:CDS
ACAACCTAGTAGCAACAAAG+AGG 0.606605 tig0019847:+103104 Msa1377050:CDS
AAGCCTAGATGGACTTGAAG+GGG 0.623098 tig0019847:-102692 None:intergenic
AGAAGGAAGAGGTTCAAGCA+AGG 0.639581 tig0019847:+103224 Msa1377050:CDS
GCTGAAGAACTCTTTCATGG+TGG 0.696192 tig0019847:+102874 Msa1377050:CDS
GATGATGATGATAAGCAAGG+TGG 0.748240 tig0019847:+102802 Msa1377050:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTCTGAATTATATAGTGAAA+TGG + tig0019847:102714-102733 Msa1377050:CDS 20.0%
!!! ATGTAGTTTGATTTTCTATA+AGG - tig0019847:103048-103067 None:intergenic 20.0%
!!! CATTGAAGAAATATTTTGTT+GGG + tig0019847:103250-103269 Msa1377050:CDS 20.0%
!! TTCTGAATTATATAGTGAAA+TGG + tig0019847:102714-102733 Msa1377050:CDS 20.0%
!!! ATGTAGTTTGATTTTCTATA+AGG - tig0019847:103048-103067 None:intergenic 20.0%
!!! CATTGAAGAAATATTTTGTT+GGG + tig0019847:103250-103269 Msa1377050:CDS 20.0%
!!! GATACATTCAATTTTAGTAG+TGG + tig0019847:102601-102620 Msa1377050:CDS 25.0%
!! TAAAATTCACCAAAACGTTT+TGG - tig0019847:102664-102683 None:intergenic 25.0%
!! TGATGATGTTTGATCAATTA+TGG - tig0019847:102749-102768 None:intergenic 25.0%
! TTAGCTTCTTCATTAGTAAA+TGG - tig0019847:102910-102929 None:intergenic 25.0%
! ATTTACTAATGAAGAAGCTA+AGG + tig0019847:102909-102928 Msa1377050:CDS 25.0%
! GAATCATCATCAAATAATTC+TGG + tig0019847:102997-103016 Msa1377050:CDS 25.0%
! CCAACAAAATATTTCTTCAA+TGG - tig0019847:103252-103271 None:intergenic 25.0%
!! CCATTGAAGAAATATTTTGT+TGG + tig0019847:103249-103268 Msa1377050:CDS 25.0%
! AATACAAGTGAAGAAGTTAA+AGG + tig0019847:103282-103301 Msa1377050:CDS 25.0%
!!! GATACATTCAATTTTAGTAG+TGG + tig0019847:102601-102620 Msa1377050:CDS 25.0%
!! TAAAATTCACCAAAACGTTT+TGG - tig0019847:102664-102683 None:intergenic 25.0%
!! TGATGATGTTTGATCAATTA+TGG - tig0019847:102749-102768 None:intergenic 25.0%
! TTAGCTTCTTCATTAGTAAA+TGG - tig0019847:102910-102929 None:intergenic 25.0%
! ATTTACTAATGAAGAAGCTA+AGG + tig0019847:102909-102928 Msa1377050:CDS 25.0%
! GAATCATCATCAAATAATTC+TGG + tig0019847:102997-103016 Msa1377050:CDS 25.0%
! CCAACAAAATATTTCTTCAA+TGG - tig0019847:103252-103271 None:intergenic 25.0%
!! CCATTGAAGAAATATTTTGT+TGG + tig0019847:103249-103268 Msa1377050:CDS 25.0%
! AATACAAGTGAAGAAGTTAA+AGG + tig0019847:103282-103301 Msa1377050:CDS 25.0%
! GATGATACAAAGTTCTAGTA+TGG + tig0019847:102579-102598 Msa1377050:CDS 30.0%
TATAATTCAGAAAGCCTAGA+TGG - tig0019847:102706-102725 None:intergenic 30.0%
!!! ATGAACAACGTTGTTGTTTT+TGG - tig0019847:102773-102792 None:intergenic 30.0%
TCGACGATTTATTTGATTCA+TGG - tig0019847:102846-102865 None:intergenic 30.0%
!! TGAACTTTTTGTTGCTTCTT+AGG - tig0019847:102943-102962 None:intergenic 30.0%
AAAGTTCAAGATGAAAGAAG+AGG + tig0019847:102955-102974 Msa1377050:CDS 30.0%
AAGATATCAAACAGTAGTAC+AGG + tig0019847:103132-103151 Msa1377050:CDS 30.0%
! GATGATACAAAGTTCTAGTA+TGG + tig0019847:102579-102598 Msa1377050:CDS 30.0%
TATAATTCAGAAAGCCTAGA+TGG - tig0019847:102706-102725 None:intergenic 30.0%
!!! ATGAACAACGTTGTTGTTTT+TGG - tig0019847:102773-102792 None:intergenic 30.0%
TCGACGATTTATTTGATTCA+TGG - tig0019847:102846-102865 None:intergenic 30.0%
!! TGAACTTTTTGTTGCTTCTT+AGG - tig0019847:102943-102962 None:intergenic 30.0%
AAAGTTCAAGATGAAAGAAG+AGG + tig0019847:102955-102974 Msa1377050:CDS 30.0%
AAGATATCAAACAGTAGTAC+AGG + tig0019847:103132-103151 Msa1377050:CDS 30.0%
! GATGATGATGATGATAAGCA+AGG + tig0019847:102799-102818 Msa1377050:CDS 35.0%
!! TTGTTTAGAAGTGCTTCAGA+AGG + tig0019847:103207-103226 Msa1377050:CDS 35.0%
!! TCTGATTCGTTTTCACATCA+TGG + tig0019847:103324-103343 Msa1377050:CDS 35.0%
!! CTGATTCGTTTTCACATCAT+GGG + tig0019847:103325-103344 Msa1377050:CDS 35.0%
ACTTTCTTGCCTTATAGACA+AGG + tig0019847:103429-103448 Msa1377050:CDS 35.0%
CTTTCTTGCCTTATAGACAA+GGG + tig0019847:103430-103449 Msa1377050:CDS 35.0%
! CCTTATAGACAAGGGATTTT+GGG + tig0019847:103438-103457 Msa1377050:CDS 35.0%
! GATGATGATGATGATAAGCA+AGG + tig0019847:102799-102818 Msa1377050:CDS 35.0%
!! TTGTTTAGAAGTGCTTCAGA+AGG + tig0019847:103207-103226 Msa1377050:CDS 35.0%
!! TCTGATTCGTTTTCACATCA+TGG + tig0019847:103324-103343 Msa1377050:CDS 35.0%
!! CTGATTCGTTTTCACATCAT+GGG + tig0019847:103325-103344 Msa1377050:CDS 35.0%
ACTTTCTTGCCTTATAGACA+AGG + tig0019847:103429-103448 Msa1377050:CDS 35.0%
CTTTCTTGCCTTATAGACAA+GGG + tig0019847:103430-103449 Msa1377050:CDS 35.0%
! CCTTATAGACAAGGGATTTT+GGG + tig0019847:103438-103457 Msa1377050:CDS 35.0%
GAAGATGGAGGACTTAGATA+CGG - tig0019847:102640-102659 None:intergenic 40.0%
!!! AAACGTTTTGGAGAAGATGG+AGG - tig0019847:102652-102671 None:intergenic 40.0%
!!! CCAAAACGTTTTGGAGAAGA+TGG - tig0019847:102655-102674 None:intergenic 40.0%
! CCATCTTCTCCAAAACGTTT+TGG + tig0019847:102652-102671 Msa1377050:CDS 40.0%
! AAAGCCTAGATGGACTTGAA+GGG - tig0019847:102696-102715 None:intergenic 40.0%
! GATGATGATGATAAGCAAGG+TGG + tig0019847:102802-102821 Msa1377050:CDS 40.0%
TCAGCTGAAGAACTCTTTCA+TGG + tig0019847:102871-102890 Msa1377050:CDS 40.0%
ACAACCTAGTAGCAACAAAG+AGG + tig0019847:103104-103123 Msa1377050:CDS 40.0%
GATTCCTCTTTGTTGCTACT+AGG - tig0019847:103111-103130 None:intergenic 40.0%
ACATCATGGGTCGAGAAAAA+AGG + tig0019847:103338-103357 Msa1377050:CDS 40.0%
! GCCTTATAGACAAGGGATTT+TGG + tig0019847:103437-103456 Msa1377050:CDS 40.0%
CCCAAAATCCCTTGTCTATA+AGG - tig0019847:103441-103460 None:intergenic 40.0%
!! ATAGACAAGGGATTTTGGGA+AGG + tig0019847:103442-103461 Msa1377050:CDS 40.0%
GAAGATGGAGGACTTAGATA+CGG - tig0019847:102640-102659 None:intergenic 40.0%
!!! AAACGTTTTGGAGAAGATGG+AGG - tig0019847:102652-102671 None:intergenic 40.0%
!!! CCAAAACGTTTTGGAGAAGA+TGG - tig0019847:102655-102674 None:intergenic 40.0%
! CCATCTTCTCCAAAACGTTT+TGG + tig0019847:102652-102671 Msa1377050:CDS 40.0%
! AAAGCCTAGATGGACTTGAA+GGG - tig0019847:102696-102715 None:intergenic 40.0%
! GATGATGATGATAAGCAAGG+TGG + tig0019847:102802-102821 Msa1377050:CDS 40.0%
TCAGCTGAAGAACTCTTTCA+TGG + tig0019847:102871-102890 Msa1377050:CDS 40.0%
ACAACCTAGTAGCAACAAAG+AGG + tig0019847:103104-103123 Msa1377050:CDS 40.0%
GATTCCTCTTTGTTGCTACT+AGG - tig0019847:103111-103130 None:intergenic 40.0%
ACATCATGGGTCGAGAAAAA+AGG + tig0019847:103338-103357 Msa1377050:CDS 40.0%
! GCCTTATAGACAAGGGATTT+TGG + tig0019847:103437-103456 Msa1377050:CDS 40.0%
CCCAAAATCCCTTGTCTATA+AGG - tig0019847:103441-103460 None:intergenic 40.0%
!! ATAGACAAGGGATTTTGGGA+AGG + tig0019847:103442-103461 Msa1377050:CDS 40.0%
! AAGCCTAGATGGACTTGAAG+GGG - tig0019847:102695-102714 None:intergenic 45.0%
! GAAAGCCTAGATGGACTTGA+AGG - tig0019847:102697-102716 None:intergenic 45.0%
GCTGAAGAACTCTTTCATGG+TGG + tig0019847:102874-102893 Msa1377050:CDS 45.0%
TCAAACAGTAGTACAGGTCC+TGG + tig0019847:103138-103157 Msa1377050:CDS 45.0%
!! AGAAGTGCTTCAGAAGGAAG+AGG + tig0019847:103213-103232 Msa1377050:CDS 45.0%
AGAAGGAAGAGGTTCAAGCA+AGG + tig0019847:103224-103243 Msa1377050:CDS 45.0%
TTGGGAAGGTTGTCTGGATT+TGG + tig0019847:103456-103475 Msa1377050:CDS 45.0%
! AAGCCTAGATGGACTTGAAG+GGG - tig0019847:102695-102714 None:intergenic 45.0%
! GAAAGCCTAGATGGACTTGA+AGG - tig0019847:102697-102716 None:intergenic 45.0%
GCTGAAGAACTCTTTCATGG+TGG + tig0019847:102874-102893 Msa1377050:CDS 45.0%
TCAAACAGTAGTACAGGTCC+TGG + tig0019847:103138-103157 Msa1377050:CDS 45.0%
!! AGAAGTGCTTCAGAAGGAAG+AGG + tig0019847:103213-103232 Msa1377050:CDS 45.0%
AGAAGGAAGAGGTTCAAGCA+AGG + tig0019847:103224-103243 Msa1377050:CDS 45.0%
TTGGGAAGGTTGTCTGGATT+TGG + tig0019847:103456-103475 Msa1377050:CDS 45.0%
! AGGTCCTGGTTCGATTTCGA+AGG + tig0019847:103152-103171 Msa1377050:CDS 50.0%
! GGTCCTGGTTCGATTTCGAA+GGG + tig0019847:103153-103172 Msa1377050:CDS 50.0%
GAACCCTTCGAAATCGAACC+AGG - tig0019847:103159-103178 None:intergenic 50.0%
GTTCGATTTCGAAGGGTTCG+AGG + tig0019847:103160-103179 Msa1377050:CDS 50.0%
TTTCGAAGGGTTCGAGGAGA+TGG + tig0019847:103166-103185 Msa1377050:CDS 50.0%
!! GGGATTTTGGGAAGGTTGTC+TGG + tig0019847:103450-103469 Msa1377050:CDS 50.0%
! AGGTCCTGGTTCGATTTCGA+AGG + tig0019847:103152-103171 Msa1377050:CDS 50.0%
! GGTCCTGGTTCGATTTCGAA+GGG + tig0019847:103153-103172 Msa1377050:CDS 50.0%
GAACCCTTCGAAATCGAACC+AGG - tig0019847:103159-103178 None:intergenic 50.0%
GTTCGATTTCGAAGGGTTCG+AGG + tig0019847:103160-103179 Msa1377050:CDS 50.0%
TTTCGAAGGGTTCGAGGAGA+TGG + tig0019847:103166-103185 Msa1377050:CDS 50.0%
!! GGGATTTTGGGAAGGTTGTC+TGG + tig0019847:103450-103469 Msa1377050:CDS 50.0%
GTGCCCCTTCAAGTCCATCT+AGG + tig0019847:102689-102708 Msa1377050:CDS 55.0%
GTGCCCCTTCAAGTCCATCT+AGG + tig0019847:102689-102708 Msa1377050:CDS 55.0%
Chromosome Type Strat End Strand Name
tig0019847 gene 102571 103485 102571 ID=Msa1377050;Name=Msa1377050
tig0019847 mRNA 102571 103485 102571 ID=Msa1377050-mRNA-1;Parent=Msa1377050;Name=Msa1377050-mRNA-1;_AED=0.00;_eAED=0.01;_QI=0|-1|0|1|-1|1|1|0|304
tig0019847 exon 102571 103485 102571 ID=Msa1377050-mRNA-1:exon:5401;Parent=Msa1377050-mRNA-1
tig0019847 CDS 102571 103485 102571 ID=Msa1377050-mRNA-1:cds;Parent=Msa1377050-mRNA-1
Gene Sequence

>Msa1377050

ATGGAAGTGATGATACAAAGTTCTAGTATGGATACATTCAATTTTAGTAGTGGAACAATGAGTTCACCGTATCTAAGTCCTCCATCTTCTCCAAAACGTTTTGGTGAATTTTACTTAAGTGCCCCTTCAAGTCCATCTAGGCTTTCTGAATTATATAGTGAAATGGATTACTTGTCCATAATTGATCAAACATCATCAACCAAAAACAACAACGTTGTTCATGAAGATGATGATGATGATGATAAGCAAGGTGGTTTTGCTTTCTTTGTTAACCATGAATCAAATAAATCGTCGACACGTTCAGCTGAAGAACTCTTTCATGGTGGCAAAATCAAACCATTTACTAATGAAGAAGCTAAGGTTGTTGTACCTAAGAAGCAACAAAAAGTTCAAGATGAAAGAAGAGGAAGAGACAGAGAGAGAATAGAATCATCATCAAATAATTCTGGTAGAAGAAGTTCAAGATCACATTCTCCTTATAGAAAATCAAACTACATATCAGAATTAGAAGATCAAAACTCTCAAAAACAGAAACAACCTAGTAGCAACAAAGAGGAATCAAAGATATCAAACAGTAGTACAGGTCCTGGTTCGATTTCGAAGGGTTCGAGGAGATGGAAATTGAGTGATCTATTGTTGTTTAGAAGTGCTTCAGAAGGAAGAGGTTCAAGCAAGGATCCATTGAAGAAATATTTTGTTGGGTATAAGAAGAATACAAGTGAAGAAGTTAAAGGTTCAAGCAGCTTTAGATCTTCTGATTCGTTTTCACATCATGGGTCGAGAAAAAAGGCTCAAGTTTCAGCTCATGAAATGCATTATGCTATGAAGAAAGCTGAGTCACAAGATATGAAGAAGAGAACTTTCTTGCCTTATAGACAAGGGATTTTGGGAAGGTTGTCTGGATTTGGACTCTAG

Protein sequence

>Msa1377050

MEVMIQSSSMDTFNFSSGTMSSPYLSPPSSPKRFGEFYLSAPSSPSRLSELYSEMDYLSIIDQTSSTKNNNVVHEDDDDDDKQGGFAFFVNHESNKSSTRSAEELFHGGKIKPFTNEEAKVVVPKKQQKVQDERRGRDRERIESSSNNSGRRSSRSHSPYRKSNYISELEDQNSQKQKQPSSNKEESKISNSSTGPGSISKGSRRWKLSDLLLFRSASEGRGSSKDPLKKYFVGYKKNTSEEVKGSSSFRSSDSFSHHGSRKKAQVSAHEMHYAMKKAESQDMKKRTFLPYRQGILGRLSGFGL*