AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0438070


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0438070 MtrunA17_Chr1g0153961 95.082 305 11 2 1 304 1 302 0.0 575
Msa0438070 MtrunA17_Chr3g0133621 49.701 334 98 14 1 303 1 295 4.37e-78 239
Msa0438070 MtrunA17_Chr4g0045231 39.130 322 152 8 1 299 1 301 1.29e-53 177
Msa0438070 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
Msa0438070 AT2G15760.1 39.274 303 153 12 13 302 13 297 1.16e-29 115
Msa0438070 AT2G26530.2 34.219 301 156 10 25 300 6 289 1.89e-25 103
Msa0438070 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 3_3:-2110027 Msa0438070:CDS
CCCAAAATCCCTTGTCTATA+AGG 0.209177 3_3:+2110026 None:intergenic
TGATGATGTTTGATCAATTA+TGG 0.230244 3_3:+2110718 None:intergenic
TTAGCTTCTTCATTAGTAAA+TGG 0.259977 3_3:+2110557 None:intergenic
TTGGGAAGGTTGTCTGGATT+TGG 0.260298 3_3:-2110008 Msa0438070:CDS
CCATCTTCTCCAAAACGTTT+TGG 0.280265 3_3:-2110812 Msa0438070:CDS
TAAAATTCACCAAAACGTTT+TGG 0.288002 3_3:+2110803 None:intergenic
TCGACGATTTATTTGATTCA+TGG 0.314817 3_3:+2110621 None:intergenic
GATGATACAAAGTTCTAGTA+TGG 0.343620 3_3:-2110885 Msa0438070:CDS
AATACAAGTGAAGAAGTTAA+AGG 0.350409 3_3:-2110182 Msa0438070:CDS
GAATCATCATCAAATAATTC+TGG 0.360745 3_3:-2110467 Msa0438070:CDS
GATTCCTCTTTGTTGCTACT+AGG 0.362236 3_3:+2110356 None:intergenic
TTCTGAATTATATAGTGAAA+TGG 0.377274 3_3:-2110750 Msa0438070:CDS
TTTCGAAGGGTTCGAGGAGA+TGG 0.388899 3_3:-2110298 Msa0438070:CDS
CCAACAAAATATTTCTTCAA+TGG 0.389000 3_3:+2110215 None:intergenic
TATAATTCAGAAAGCCTAGA+TGG 0.397292 3_3:+2110761 None:intergenic
TCAGCTGAAGAACTCTTTCA+TGG 0.412277 3_3:-2110593 Msa0438070:CDS
GAAAGCCTAGATGGACTTGA+AGG 0.448937 3_3:+2110770 None:intergenic
GTGCCCCTTCAAGTCCATCT+AGG 0.450184 3_3:-2110775 Msa0438070:CDS
GTTCGATTTCGAAGGGTTCG+AGG 0.475655 3_3:-2110304 Msa0438070:CDS
AAGATATCAAACAGTAGTAC+AGG 0.498075 3_3:-2110332 Msa0438070:CDS
AGGTCCTGGTTCGATTTCGA+AGG 0.504546 3_3:-2110312 Msa0438070:CDS
GAACCCTTCGAAATCGAACC+AGG 0.510031 3_3:+2110308 None:intergenic
AGAAGTGCTTCAGAAGGAAG+AGG 0.521434 3_3:-2110251 Msa0438070:CDS
TCAAACAGTAGTACAGGTCC+TGG 0.538921 3_3:-2110326 Msa0438070:CDS
ATTTACTAATGAAGAAGCTA+AGG 0.540876 3_3:-2110555 Msa0438070:CDS
AAAGTTCAAGATGAAAGAAG+AGG 0.559986 3_3:-2110509 Msa0438070:CDS
GGTCCTGGTTCGATTTCGAA+GGG 0.575115 3_3:-2110311 Msa0438070:CDS
GAAGATGGAGGACTTAGATA+CGG 0.590817 3_3:+2110827 None:intergenic
AAAGCCTAGATGGACTTGAA+GGG 0.592999 3_3:+2110771 None:intergenic
CTTTCTTGCCTTATAGACAA+GGG 0.596379 3_3:-2110034 Msa0438070:CDS
ACTTTCTTGCCTTATAGACA+AGG 0.596868 3_3:-2110035 Msa0438070:CDS
TTGTTTAGAAGTGCTTCAGA+AGG 0.602019 3_3:-2110257 Msa0438070:CDS
ACAACCTAGTAGCAACAAAG+AGG 0.606605 3_3:-2110360 Msa0438070:CDS
AAGCCTAGATGGACTTGAAG+GGG 0.623098 3_3:+2110772 None:intergenic
AGAAGGAAGAGGTTCAAGCA+AGG 0.639581 3_3:-2110240 Msa0438070:CDS
GCTGAAGAACTCTTTCATGG+TGG 0.696192 3_3:-2110590 Msa0438070:CDS
GATGATGATGATAAGCAAGG+TGG 0.748240 3_3:-2110662 Msa0438070:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTCTGAATTATATAGTGAAA+TGG - chr3_3:2110144-2110163 Msa0438070:CDS 20.0%
!!! ATGTAGTTTGATTTTCTATA+AGG + chr3_3:2110478-2110497 None:intergenic 20.0%
!!! CATTGAAGAAATATTTTGTT+GGG - chr3_3:2110680-2110699 Msa0438070:CDS 20.0%
!! TTCTGAATTATATAGTGAAA+TGG - chr3_3:2110144-2110163 Msa0438070:CDS 20.0%
!!! ATGTAGTTTGATTTTCTATA+AGG + chr3_3:2110478-2110497 None:intergenic 20.0%
!!! CATTGAAGAAATATTTTGTT+GGG - chr3_3:2110680-2110699 Msa0438070:CDS 20.0%
!!! GATACATTCAATTTTAGTAG+TGG - chr3_3:2110031-2110050 Msa0438070:CDS 25.0%
!! TAAAATTCACCAAAACGTTT+TGG + chr3_3:2110094-2110113 None:intergenic 25.0%
!! TGATGATGTTTGATCAATTA+TGG + chr3_3:2110179-2110198 None:intergenic 25.0%
! TTAGCTTCTTCATTAGTAAA+TGG + chr3_3:2110340-2110359 None:intergenic 25.0%
! ATTTACTAATGAAGAAGCTA+AGG - chr3_3:2110339-2110358 Msa0438070:CDS 25.0%
! GAATCATCATCAAATAATTC+TGG - chr3_3:2110427-2110446 Msa0438070:CDS 25.0%
! CCAACAAAATATTTCTTCAA+TGG + chr3_3:2110682-2110701 None:intergenic 25.0%
!! CCATTGAAGAAATATTTTGT+TGG - chr3_3:2110679-2110698 Msa0438070:CDS 25.0%
! AATACAAGTGAAGAAGTTAA+AGG - chr3_3:2110712-2110731 Msa0438070:CDS 25.0%
!!! GATACATTCAATTTTAGTAG+TGG - chr3_3:2110031-2110050 Msa0438070:CDS 25.0%
!! TAAAATTCACCAAAACGTTT+TGG + chr3_3:2110094-2110113 None:intergenic 25.0%
!! TGATGATGTTTGATCAATTA+TGG + chr3_3:2110179-2110198 None:intergenic 25.0%
! TTAGCTTCTTCATTAGTAAA+TGG + chr3_3:2110340-2110359 None:intergenic 25.0%
! ATTTACTAATGAAGAAGCTA+AGG - chr3_3:2110339-2110358 Msa0438070:CDS 25.0%
! GAATCATCATCAAATAATTC+TGG - chr3_3:2110427-2110446 Msa0438070:CDS 25.0%
! CCAACAAAATATTTCTTCAA+TGG + chr3_3:2110682-2110701 None:intergenic 25.0%
!! CCATTGAAGAAATATTTTGT+TGG - chr3_3:2110679-2110698 Msa0438070:CDS 25.0%
! AATACAAGTGAAGAAGTTAA+AGG - chr3_3:2110712-2110731 Msa0438070:CDS 25.0%
! GATGATACAAAGTTCTAGTA+TGG - chr3_3:2110009-2110028 Msa0438070:CDS 30.0%
TATAATTCAGAAAGCCTAGA+TGG + chr3_3:2110136-2110155 None:intergenic 30.0%
!!! ATGAACAACGTTGTTGTTTT+TGG + chr3_3:2110203-2110222 None:intergenic 30.0%
TCGACGATTTATTTGATTCA+TGG + chr3_3:2110276-2110295 None:intergenic 30.0%
!! TGAACTTTTTGTTGCTTCTT+AGG + chr3_3:2110373-2110392 None:intergenic 30.0%
AAAGTTCAAGATGAAAGAAG+AGG - chr3_3:2110385-2110404 Msa0438070:CDS 30.0%
AAGATATCAAACAGTAGTAC+AGG - chr3_3:2110562-2110581 Msa0438070:CDS 30.0%
! GATGATACAAAGTTCTAGTA+TGG - chr3_3:2110009-2110028 Msa0438070:CDS 30.0%
TATAATTCAGAAAGCCTAGA+TGG + chr3_3:2110136-2110155 None:intergenic 30.0%
!!! ATGAACAACGTTGTTGTTTT+TGG + chr3_3:2110203-2110222 None:intergenic 30.0%
TCGACGATTTATTTGATTCA+TGG + chr3_3:2110276-2110295 None:intergenic 30.0%
!! TGAACTTTTTGTTGCTTCTT+AGG + chr3_3:2110373-2110392 None:intergenic 30.0%
AAAGTTCAAGATGAAAGAAG+AGG - chr3_3:2110385-2110404 Msa0438070:CDS 30.0%
AAGATATCAAACAGTAGTAC+AGG - chr3_3:2110562-2110581 Msa0438070:CDS 30.0%
! GATGATGATGATGATAAGCA+AGG - chr3_3:2110229-2110248 Msa0438070:CDS 35.0%
!! TTGTTTAGAAGTGCTTCAGA+AGG - chr3_3:2110637-2110656 Msa0438070:CDS 35.0%
!! TCTGATTCGTTTTCACATCA+TGG - chr3_3:2110754-2110773 Msa0438070:CDS 35.0%
!! CTGATTCGTTTTCACATCAT+GGG - chr3_3:2110755-2110774 Msa0438070:CDS 35.0%
ACTTTCTTGCCTTATAGACA+AGG - chr3_3:2110859-2110878 Msa0438070:CDS 35.0%
CTTTCTTGCCTTATAGACAA+GGG - chr3_3:2110860-2110879 Msa0438070:CDS 35.0%
! CCTTATAGACAAGGGATTTT+GGG - chr3_3:2110868-2110887 Msa0438070:CDS 35.0%
! GATGATGATGATGATAAGCA+AGG - chr3_3:2110229-2110248 Msa0438070:CDS 35.0%
!! TTGTTTAGAAGTGCTTCAGA+AGG - chr3_3:2110637-2110656 Msa0438070:CDS 35.0%
!! TCTGATTCGTTTTCACATCA+TGG - chr3_3:2110754-2110773 Msa0438070:CDS 35.0%
!! CTGATTCGTTTTCACATCAT+GGG - chr3_3:2110755-2110774 Msa0438070:CDS 35.0%
ACTTTCTTGCCTTATAGACA+AGG - chr3_3:2110859-2110878 Msa0438070:CDS 35.0%
CTTTCTTGCCTTATAGACAA+GGG - chr3_3:2110860-2110879 Msa0438070:CDS 35.0%
! CCTTATAGACAAGGGATTTT+GGG - chr3_3:2110868-2110887 Msa0438070:CDS 35.0%
GAAGATGGAGGACTTAGATA+CGG + chr3_3:2110070-2110089 None:intergenic 40.0%
!!! AAACGTTTTGGAGAAGATGG+AGG + chr3_3:2110082-2110101 None:intergenic 40.0%
!!! CCAAAACGTTTTGGAGAAGA+TGG + chr3_3:2110085-2110104 None:intergenic 40.0%
! CCATCTTCTCCAAAACGTTT+TGG - chr3_3:2110082-2110101 Msa0438070:CDS 40.0%
! AAAGCCTAGATGGACTTGAA+GGG + chr3_3:2110126-2110145 None:intergenic 40.0%
! GATGATGATGATAAGCAAGG+TGG - chr3_3:2110232-2110251 Msa0438070:CDS 40.0%
TCAGCTGAAGAACTCTTTCA+TGG - chr3_3:2110301-2110320 Msa0438070:CDS 40.0%
ACAACCTAGTAGCAACAAAG+AGG - chr3_3:2110534-2110553 Msa0438070:CDS 40.0%
GATTCCTCTTTGTTGCTACT+AGG + chr3_3:2110541-2110560 None:intergenic 40.0%
ACATCATGGGTCGAGAAAAA+AGG - chr3_3:2110768-2110787 Msa0438070:CDS 40.0%
! GCCTTATAGACAAGGGATTT+TGG - chr3_3:2110867-2110886 Msa0438070:CDS 40.0%
CCCAAAATCCCTTGTCTATA+AGG + chr3_3:2110871-2110890 None:intergenic 40.0%
!! ATAGACAAGGGATTTTGGGA+AGG - chr3_3:2110872-2110891 Msa0438070:CDS 40.0%
GAAGATGGAGGACTTAGATA+CGG + chr3_3:2110070-2110089 None:intergenic 40.0%
!!! AAACGTTTTGGAGAAGATGG+AGG + chr3_3:2110082-2110101 None:intergenic 40.0%
!!! CCAAAACGTTTTGGAGAAGA+TGG + chr3_3:2110085-2110104 None:intergenic 40.0%
! CCATCTTCTCCAAAACGTTT+TGG - chr3_3:2110082-2110101 Msa0438070:CDS 40.0%
! AAAGCCTAGATGGACTTGAA+GGG + chr3_3:2110126-2110145 None:intergenic 40.0%
! GATGATGATGATAAGCAAGG+TGG - chr3_3:2110232-2110251 Msa0438070:CDS 40.0%
TCAGCTGAAGAACTCTTTCA+TGG - chr3_3:2110301-2110320 Msa0438070:CDS 40.0%
ACAACCTAGTAGCAACAAAG+AGG - chr3_3:2110534-2110553 Msa0438070:CDS 40.0%
GATTCCTCTTTGTTGCTACT+AGG + chr3_3:2110541-2110560 None:intergenic 40.0%
ACATCATGGGTCGAGAAAAA+AGG - chr3_3:2110768-2110787 Msa0438070:CDS 40.0%
! GCCTTATAGACAAGGGATTT+TGG - chr3_3:2110867-2110886 Msa0438070:CDS 40.0%
CCCAAAATCCCTTGTCTATA+AGG + chr3_3:2110871-2110890 None:intergenic 40.0%
!! ATAGACAAGGGATTTTGGGA+AGG - chr3_3:2110872-2110891 Msa0438070:CDS 40.0%
! AAGCCTAGATGGACTTGAAG+GGG + chr3_3:2110125-2110144 None:intergenic 45.0%
! GAAAGCCTAGATGGACTTGA+AGG + chr3_3:2110127-2110146 None:intergenic 45.0%
GCTGAAGAACTCTTTCATGG+TGG - chr3_3:2110304-2110323 Msa0438070:CDS 45.0%
TCAAACAGTAGTACAGGTCC+TGG - chr3_3:2110568-2110587 Msa0438070:CDS 45.0%
!! AGAAGTGCTTCAGAAGGAAG+AGG - chr3_3:2110643-2110662 Msa0438070:CDS 45.0%
AGAAGGAAGAGGTTCAAGCA+AGG - chr3_3:2110654-2110673 Msa0438070:CDS 45.0%
TTGGGAAGGTTGTCTGGATT+TGG - chr3_3:2110886-2110905 Msa0438070:CDS 45.0%
! AAGCCTAGATGGACTTGAAG+GGG + chr3_3:2110125-2110144 None:intergenic 45.0%
! GAAAGCCTAGATGGACTTGA+AGG + chr3_3:2110127-2110146 None:intergenic 45.0%
GCTGAAGAACTCTTTCATGG+TGG - chr3_3:2110304-2110323 Msa0438070:CDS 45.0%
TCAAACAGTAGTACAGGTCC+TGG - chr3_3:2110568-2110587 Msa0438070:CDS 45.0%
!! AGAAGTGCTTCAGAAGGAAG+AGG - chr3_3:2110643-2110662 Msa0438070:CDS 45.0%
AGAAGGAAGAGGTTCAAGCA+AGG - chr3_3:2110654-2110673 Msa0438070:CDS 45.0%
TTGGGAAGGTTGTCTGGATT+TGG - chr3_3:2110886-2110905 Msa0438070:CDS 45.0%
! AGGTCCTGGTTCGATTTCGA+AGG - chr3_3:2110582-2110601 Msa0438070:CDS 50.0%
! GGTCCTGGTTCGATTTCGAA+GGG - chr3_3:2110583-2110602 Msa0438070:CDS 50.0%
GAACCCTTCGAAATCGAACC+AGG + chr3_3:2110589-2110608 None:intergenic 50.0%
GTTCGATTTCGAAGGGTTCG+AGG - chr3_3:2110590-2110609 Msa0438070:CDS 50.0%
TTTCGAAGGGTTCGAGGAGA+TGG - chr3_3:2110596-2110615 Msa0438070:CDS 50.0%
!! GGGATTTTGGGAAGGTTGTC+TGG - chr3_3:2110880-2110899 Msa0438070:CDS 50.0%
! AGGTCCTGGTTCGATTTCGA+AGG - chr3_3:2110582-2110601 Msa0438070:CDS 50.0%
! GGTCCTGGTTCGATTTCGAA+GGG - chr3_3:2110583-2110602 Msa0438070:CDS 50.0%
GAACCCTTCGAAATCGAACC+AGG + chr3_3:2110589-2110608 None:intergenic 50.0%
GTTCGATTTCGAAGGGTTCG+AGG - chr3_3:2110590-2110609 Msa0438070:CDS 50.0%
TTTCGAAGGGTTCGAGGAGA+TGG - chr3_3:2110596-2110615 Msa0438070:CDS 50.0%
!! GGGATTTTGGGAAGGTTGTC+TGG - chr3_3:2110880-2110899 Msa0438070:CDS 50.0%
GTGCCCCTTCAAGTCCATCT+AGG - chr3_3:2110119-2110138 Msa0438070:CDS 55.0%
GTGCCCCTTCAAGTCCATCT+AGG - chr3_3:2110119-2110138 Msa0438070:CDS 55.0%
Chromosome Type Strat End Strand Name
chr3_3 gene 2110001 2110915 2110001 ID=Msa0438070;Name=Msa0438070
chr3_3 mRNA 2110001 2110915 2110001 ID=Msa0438070-mRNA-1;Parent=Msa0438070;Name=Msa0438070-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|304
chr3_3 exon 2110001 2110915 2110001 ID=Msa0438070-mRNA-1:exon:474;Parent=Msa0438070-mRNA-1
chr3_3 CDS 2110001 2110915 2110001 ID=Msa0438070-mRNA-1:cds;Parent=Msa0438070-mRNA-1
Gene Sequence

>Msa0438070

ATGGAAGTGATGATACAAAGTTCTAGTATGGATACATTCAATTTTAGTAGTGGAACAATGAGTTCACCGTATCTAAGTCCTCCATCTTCTCCAAAACGTTTTGGTGAATTTTACTTAAGTGCCCCTTCAAGTCCATCTAGGCTTTCTGAATTATATAGTGAAATGGATTACTTGTCCATAATTGATCAAACATCATCAACCAAAAACAACAACGTTGTTCATGAAGATGATGATGATGATGATAAGCAAGGTGGTTTTGCTTTCTTTGTTAACCATGAATCAAATAAATCGTCGACACGTTCAGCTGAAGAACTCTTTCATGGTGGCAAAATCAAACCATTTACTAATGAAGAAGCTAAGGTTGTTGTACCTAAGAAGCAACAAAAAGTTCAAGATGAAAGAAGAGGAAGAGACAGAGAGAGAATAGAATCATCATCAAATAATTCTGGTAGAAGAAGTTCAAGATCACATTCTCCTTATAGAAAATCAAACTACATATCAGAATTAGAAGAACAAAACTCTCAAAAACAGAAACAACCTAGTAGCAACAAAGAGGAATCAAAGATATCAAACAGTAGTACAGGTCCTGGTTCGATTTCGAAGGGTTCGAGGAGATGGAAATTGAGTGATCTATTGTTGTTTAGAAGTGCTTCAGAAGGAAGAGGTTCAAGCAAGGATCCATTGAAGAAATATTTTGTTGGGTATAAGAAGAATACAAGTGAAGAAGTTAAAGGTTCAAGCAGCTTTAGATCTTCTGATTCGTTTTCACATCATGGGTCGAGAAAAAAGGCTCAAGTTTCAGCTCATGAAATGCATTATGCTATGAAGAAAGCTGAGTCACAAGATATGAAGAAGAGAACTTTCTTGCCTTATAGACAAGGGATTTTGGGAAGGTTGTCTGGATTTGGACTCTAG

Protein sequence

>Msa0438070

MEVMIQSSSMDTFNFSSGTMSSPYLSPPSSPKRFGEFYLSAPSSPSRLSELYSEMDYLSIIDQTSSTKNNNVVHEDDDDDDKQGGFAFFVNHESNKSSTRSAEELFHGGKIKPFTNEEAKVVVPKKQQKVQDERRGRDRERIESSSNNSGRRSSRSHSPYRKSNYISELEEQNSQKQKQPSSNKEESKISNSSTGPGSISKGSRRWKLSDLLLFRSASEGRGSSKDPLKKYFVGYKKNTSEEVKGSSSFRSSDSFSHHGSRKKAQVSAHEMHYAMKKAESQDMKKRTFLPYRQGILGRLSGFGL*