AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0051480


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0051480 MtrunA17_Chr1g0153961 95.082 305 11 2 1 304 1 302 0.0 575
Msa0051480 MtrunA17_Chr3g0133621 49.701 334 98 14 1 303 1 295 4.37e-78 239
Msa0051480 MtrunA17_Chr4g0045231 39.130 322 152 8 1 299 1 301 1.29e-53 177
Msa0051480 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
Msa0051480 AT2G15760.1 39.274 303 153 12 13 302 13 297 1.16e-29 115
Msa0051480 AT2G26530.2 34.219 301 156 10 25 300 6 289 1.89e-25 103
Msa0051480 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_2:-5573714 Msa0051480:CDS
CCCAAAATCCCTTGTCTATA+AGG 0.209177 1_2:+5573713 None:intergenic
TGATGATGTTTGATCAATTA+TGG 0.230244 1_2:+5574405 None:intergenic
TTAGCTTCTTCATTAGTAAA+TGG 0.259977 1_2:+5574244 None:intergenic
TTGGGAAGGTTGTCTGGATT+TGG 0.260298 1_2:-5573695 Msa0051480:CDS
CCATCTTCTCCAAAACGTTT+TGG 0.280265 1_2:-5574499 Msa0051480:CDS
TAAAATTCACCAAAACGTTT+TGG 0.288002 1_2:+5574490 None:intergenic
TCGACGATTTATTTGATTCA+TGG 0.314817 1_2:+5574308 None:intergenic
GATGATACAAAGTTCTAGTA+TGG 0.343620 1_2:-5574572 Msa0051480:CDS
AATACAAGTGAAGAAGTTAA+AGG 0.350409 1_2:-5573869 Msa0051480:CDS
GAATCATCATCAAATAATTC+TGG 0.360745 1_2:-5574154 Msa0051480:CDS
GATTCCTCTTTGTTGCTACT+AGG 0.362236 1_2:+5574043 None:intergenic
TTCTGAATTATATAGTGAAA+TGG 0.377274 1_2:-5574437 Msa0051480:CDS
TTTCGAAGGGTTCGAGGAGA+TGG 0.388899 1_2:-5573985 Msa0051480:CDS
CCAACAAAATATTTCTTCAA+TGG 0.389000 1_2:+5573902 None:intergenic
TATAATTCAGAAAGCCTAGA+TGG 0.397292 1_2:+5574448 None:intergenic
TCAGCTGAAGAACTCTTTCA+TGG 0.412277 1_2:-5574280 Msa0051480:CDS
GAAAGCCTAGATGGACTTGA+AGG 0.448937 1_2:+5574457 None:intergenic
GTGCCCCTTCAAGTCCATCT+AGG 0.450184 1_2:-5574462 Msa0051480:CDS
GTTCGATTTCGAAGGGTTCG+AGG 0.475655 1_2:-5573991 Msa0051480:CDS
AAGATATCAAACAGTAGTAC+AGG 0.498075 1_2:-5574019 Msa0051480:CDS
AGGTCCTGGTTCGATTTCGA+AGG 0.504546 1_2:-5573999 Msa0051480:CDS
GAACCCTTCGAAATCGAACC+AGG 0.510031 1_2:+5573995 None:intergenic
AGAAGTGCTTCAGAAGGAAG+AGG 0.521434 1_2:-5573938 Msa0051480:CDS
TCAAACAGTAGTACAGGTCC+TGG 0.538921 1_2:-5574013 Msa0051480:CDS
ATTTACTAATGAAGAAGCTA+AGG 0.540876 1_2:-5574242 Msa0051480:CDS
AAAGTTCAAGATGAAAGAAG+AGG 0.559986 1_2:-5574196 Msa0051480:CDS
GGTCCTGGTTCGATTTCGAA+GGG 0.575115 1_2:-5573998 Msa0051480:CDS
GAAGATGGAGGACTTAGATA+CGG 0.590817 1_2:+5574514 None:intergenic
AAAGCCTAGATGGACTTGAA+GGG 0.592999 1_2:+5574458 None:intergenic
CTTTCTTGCCTTATAGACAA+GGG 0.596379 1_2:-5573721 Msa0051480:CDS
ACTTTCTTGCCTTATAGACA+AGG 0.596868 1_2:-5573722 Msa0051480:CDS
TTGTTTAGAAGTGCTTCAGA+AGG 0.602019 1_2:-5573944 Msa0051480:CDS
ACAACCTAGTAGCAACAAAG+AGG 0.606605 1_2:-5574047 Msa0051480:CDS
AAGCCTAGATGGACTTGAAG+GGG 0.623098 1_2:+5574459 None:intergenic
AGAAGGAAGAGGTTCAAGCA+AGG 0.639581 1_2:-5573927 Msa0051480:CDS
GCTGAAGAACTCTTTCATGG+TGG 0.696192 1_2:-5574277 Msa0051480:CDS
GATGATGATGATAAGCAAGG+TGG 0.748240 1_2:-5574349 Msa0051480:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTCTGAATTATATAGTGAAA+TGG - chr1_2:5573831-5573850 Msa0051480:CDS 20.0%
!!! ATGTAGTTTGATTTTCTATA+AGG + chr1_2:5574165-5574184 None:intergenic 20.0%
!!! CATTGAAGAAATATTTTGTT+GGG - chr1_2:5574367-5574386 Msa0051480:CDS 20.0%
!! TTCTGAATTATATAGTGAAA+TGG - chr1_2:5573831-5573850 Msa0051480:CDS 20.0%
!!! ATGTAGTTTGATTTTCTATA+AGG + chr1_2:5574165-5574184 None:intergenic 20.0%
!!! CATTGAAGAAATATTTTGTT+GGG - chr1_2:5574367-5574386 Msa0051480:CDS 20.0%
!!! GATACATTCAATTTTAGTAG+TGG - chr1_2:5573718-5573737 Msa0051480:CDS 25.0%
!! TAAAATTCACCAAAACGTTT+TGG + chr1_2:5573781-5573800 None:intergenic 25.0%
!! TGATGATGTTTGATCAATTA+TGG + chr1_2:5573866-5573885 None:intergenic 25.0%
! TTAGCTTCTTCATTAGTAAA+TGG + chr1_2:5574027-5574046 None:intergenic 25.0%
! ATTTACTAATGAAGAAGCTA+AGG - chr1_2:5574026-5574045 Msa0051480:CDS 25.0%
! GAATCATCATCAAATAATTC+TGG - chr1_2:5574114-5574133 Msa0051480:CDS 25.0%
! CCAACAAAATATTTCTTCAA+TGG + chr1_2:5574369-5574388 None:intergenic 25.0%
!! CCATTGAAGAAATATTTTGT+TGG - chr1_2:5574366-5574385 Msa0051480:CDS 25.0%
! AATACAAGTGAAGAAGTTAA+AGG - chr1_2:5574399-5574418 Msa0051480:CDS 25.0%
!!! GATACATTCAATTTTAGTAG+TGG - chr1_2:5573718-5573737 Msa0051480:CDS 25.0%
!! TAAAATTCACCAAAACGTTT+TGG + chr1_2:5573781-5573800 None:intergenic 25.0%
!! TGATGATGTTTGATCAATTA+TGG + chr1_2:5573866-5573885 None:intergenic 25.0%
! TTAGCTTCTTCATTAGTAAA+TGG + chr1_2:5574027-5574046 None:intergenic 25.0%
! ATTTACTAATGAAGAAGCTA+AGG - chr1_2:5574026-5574045 Msa0051480:CDS 25.0%
! GAATCATCATCAAATAATTC+TGG - chr1_2:5574114-5574133 Msa0051480:CDS 25.0%
! CCAACAAAATATTTCTTCAA+TGG + chr1_2:5574369-5574388 None:intergenic 25.0%
!! CCATTGAAGAAATATTTTGT+TGG - chr1_2:5574366-5574385 Msa0051480:CDS 25.0%
! AATACAAGTGAAGAAGTTAA+AGG - chr1_2:5574399-5574418 Msa0051480:CDS 25.0%
! GATGATACAAAGTTCTAGTA+TGG - chr1_2:5573696-5573715 Msa0051480:CDS 30.0%
TATAATTCAGAAAGCCTAGA+TGG + chr1_2:5573823-5573842 None:intergenic 30.0%
!!! ATGAACAACGTTGTTGTTTT+TGG + chr1_2:5573890-5573909 None:intergenic 30.0%
TCGACGATTTATTTGATTCA+TGG + chr1_2:5573963-5573982 None:intergenic 30.0%
!! TGAACTTTTTGTTGCTTCTT+AGG + chr1_2:5574060-5574079 None:intergenic 30.0%
AAAGTTCAAGATGAAAGAAG+AGG - chr1_2:5574072-5574091 Msa0051480:CDS 30.0%
AAGATATCAAACAGTAGTAC+AGG - chr1_2:5574249-5574268 Msa0051480:CDS 30.0%
! GATGATACAAAGTTCTAGTA+TGG - chr1_2:5573696-5573715 Msa0051480:CDS 30.0%
TATAATTCAGAAAGCCTAGA+TGG + chr1_2:5573823-5573842 None:intergenic 30.0%
!!! ATGAACAACGTTGTTGTTTT+TGG + chr1_2:5573890-5573909 None:intergenic 30.0%
TCGACGATTTATTTGATTCA+TGG + chr1_2:5573963-5573982 None:intergenic 30.0%
!! TGAACTTTTTGTTGCTTCTT+AGG + chr1_2:5574060-5574079 None:intergenic 30.0%
AAAGTTCAAGATGAAAGAAG+AGG - chr1_2:5574072-5574091 Msa0051480:CDS 30.0%
AAGATATCAAACAGTAGTAC+AGG - chr1_2:5574249-5574268 Msa0051480:CDS 30.0%
! GATGATGATGATGATAAGCA+AGG - chr1_2:5573916-5573935 Msa0051480:CDS 35.0%
!! TTGTTTAGAAGTGCTTCAGA+AGG - chr1_2:5574324-5574343 Msa0051480:CDS 35.0%
!! TCTGATTCGTTTTCACATCA+TGG - chr1_2:5574441-5574460 Msa0051480:CDS 35.0%
!! CTGATTCGTTTTCACATCAT+GGG - chr1_2:5574442-5574461 Msa0051480:CDS 35.0%
ACTTTCTTGCCTTATAGACA+AGG - chr1_2:5574546-5574565 Msa0051480:CDS 35.0%
CTTTCTTGCCTTATAGACAA+GGG - chr1_2:5574547-5574566 Msa0051480:CDS 35.0%
! CCTTATAGACAAGGGATTTT+GGG - chr1_2:5574555-5574574 Msa0051480:CDS 35.0%
! GATGATGATGATGATAAGCA+AGG - chr1_2:5573916-5573935 Msa0051480:CDS 35.0%
!! TTGTTTAGAAGTGCTTCAGA+AGG - chr1_2:5574324-5574343 Msa0051480:CDS 35.0%
!! TCTGATTCGTTTTCACATCA+TGG - chr1_2:5574441-5574460 Msa0051480:CDS 35.0%
!! CTGATTCGTTTTCACATCAT+GGG - chr1_2:5574442-5574461 Msa0051480:CDS 35.0%
ACTTTCTTGCCTTATAGACA+AGG - chr1_2:5574546-5574565 Msa0051480:CDS 35.0%
CTTTCTTGCCTTATAGACAA+GGG - chr1_2:5574547-5574566 Msa0051480:CDS 35.0%
! CCTTATAGACAAGGGATTTT+GGG - chr1_2:5574555-5574574 Msa0051480:CDS 35.0%
GAAGATGGAGGACTTAGATA+CGG + chr1_2:5573757-5573776 None:intergenic 40.0%
!!! AAACGTTTTGGAGAAGATGG+AGG + chr1_2:5573769-5573788 None:intergenic 40.0%
!!! CCAAAACGTTTTGGAGAAGA+TGG + chr1_2:5573772-5573791 None:intergenic 40.0%
! CCATCTTCTCCAAAACGTTT+TGG - chr1_2:5573769-5573788 Msa0051480:CDS 40.0%
! AAAGCCTAGATGGACTTGAA+GGG + chr1_2:5573813-5573832 None:intergenic 40.0%
! GATGATGATGATAAGCAAGG+TGG - chr1_2:5573919-5573938 Msa0051480:CDS 40.0%
TCAGCTGAAGAACTCTTTCA+TGG - chr1_2:5573988-5574007 Msa0051480:CDS 40.0%
ACAACCTAGTAGCAACAAAG+AGG - chr1_2:5574221-5574240 Msa0051480:CDS 40.0%
GATTCCTCTTTGTTGCTACT+AGG + chr1_2:5574228-5574247 None:intergenic 40.0%
ACATCATGGGTCGAGAAAAA+AGG - chr1_2:5574455-5574474 Msa0051480:CDS 40.0%
! GCCTTATAGACAAGGGATTT+TGG - chr1_2:5574554-5574573 Msa0051480:CDS 40.0%
CCCAAAATCCCTTGTCTATA+AGG + chr1_2:5574558-5574577 None:intergenic 40.0%
!! ATAGACAAGGGATTTTGGGA+AGG - chr1_2:5574559-5574578 Msa0051480:CDS 40.0%
GAAGATGGAGGACTTAGATA+CGG + chr1_2:5573757-5573776 None:intergenic 40.0%
!!! AAACGTTTTGGAGAAGATGG+AGG + chr1_2:5573769-5573788 None:intergenic 40.0%
!!! CCAAAACGTTTTGGAGAAGA+TGG + chr1_2:5573772-5573791 None:intergenic 40.0%
! CCATCTTCTCCAAAACGTTT+TGG - chr1_2:5573769-5573788 Msa0051480:CDS 40.0%
! AAAGCCTAGATGGACTTGAA+GGG + chr1_2:5573813-5573832 None:intergenic 40.0%
! GATGATGATGATAAGCAAGG+TGG - chr1_2:5573919-5573938 Msa0051480:CDS 40.0%
TCAGCTGAAGAACTCTTTCA+TGG - chr1_2:5573988-5574007 Msa0051480:CDS 40.0%
ACAACCTAGTAGCAACAAAG+AGG - chr1_2:5574221-5574240 Msa0051480:CDS 40.0%
GATTCCTCTTTGTTGCTACT+AGG + chr1_2:5574228-5574247 None:intergenic 40.0%
ACATCATGGGTCGAGAAAAA+AGG - chr1_2:5574455-5574474 Msa0051480:CDS 40.0%
! GCCTTATAGACAAGGGATTT+TGG - chr1_2:5574554-5574573 Msa0051480:CDS 40.0%
CCCAAAATCCCTTGTCTATA+AGG + chr1_2:5574558-5574577 None:intergenic 40.0%
!! ATAGACAAGGGATTTTGGGA+AGG - chr1_2:5574559-5574578 Msa0051480:CDS 40.0%
! AAGCCTAGATGGACTTGAAG+GGG + chr1_2:5573812-5573831 None:intergenic 45.0%
! GAAAGCCTAGATGGACTTGA+AGG + chr1_2:5573814-5573833 None:intergenic 45.0%
GCTGAAGAACTCTTTCATGG+TGG - chr1_2:5573991-5574010 Msa0051480:CDS 45.0%
TCAAACAGTAGTACAGGTCC+TGG - chr1_2:5574255-5574274 Msa0051480:CDS 45.0%
!! AGAAGTGCTTCAGAAGGAAG+AGG - chr1_2:5574330-5574349 Msa0051480:CDS 45.0%
AGAAGGAAGAGGTTCAAGCA+AGG - chr1_2:5574341-5574360 Msa0051480:CDS 45.0%
TTGGGAAGGTTGTCTGGATT+TGG - chr1_2:5574573-5574592 Msa0051480:CDS 45.0%
! AAGCCTAGATGGACTTGAAG+GGG + chr1_2:5573812-5573831 None:intergenic 45.0%
! GAAAGCCTAGATGGACTTGA+AGG + chr1_2:5573814-5573833 None:intergenic 45.0%
GCTGAAGAACTCTTTCATGG+TGG - chr1_2:5573991-5574010 Msa0051480:CDS 45.0%
TCAAACAGTAGTACAGGTCC+TGG - chr1_2:5574255-5574274 Msa0051480:CDS 45.0%
!! AGAAGTGCTTCAGAAGGAAG+AGG - chr1_2:5574330-5574349 Msa0051480:CDS 45.0%
AGAAGGAAGAGGTTCAAGCA+AGG - chr1_2:5574341-5574360 Msa0051480:CDS 45.0%
TTGGGAAGGTTGTCTGGATT+TGG - chr1_2:5574573-5574592 Msa0051480:CDS 45.0%
! AGGTCCTGGTTCGATTTCGA+AGG - chr1_2:5574269-5574288 Msa0051480:CDS 50.0%
! GGTCCTGGTTCGATTTCGAA+GGG - chr1_2:5574270-5574289 Msa0051480:CDS 50.0%
GAACCCTTCGAAATCGAACC+AGG + chr1_2:5574276-5574295 None:intergenic 50.0%
GTTCGATTTCGAAGGGTTCG+AGG - chr1_2:5574277-5574296 Msa0051480:CDS 50.0%
TTTCGAAGGGTTCGAGGAGA+TGG - chr1_2:5574283-5574302 Msa0051480:CDS 50.0%
!! GGGATTTTGGGAAGGTTGTC+TGG - chr1_2:5574567-5574586 Msa0051480:CDS 50.0%
! AGGTCCTGGTTCGATTTCGA+AGG - chr1_2:5574269-5574288 Msa0051480:CDS 50.0%
! GGTCCTGGTTCGATTTCGAA+GGG - chr1_2:5574270-5574289 Msa0051480:CDS 50.0%
GAACCCTTCGAAATCGAACC+AGG + chr1_2:5574276-5574295 None:intergenic 50.0%
GTTCGATTTCGAAGGGTTCG+AGG - chr1_2:5574277-5574296 Msa0051480:CDS 50.0%
TTTCGAAGGGTTCGAGGAGA+TGG - chr1_2:5574283-5574302 Msa0051480:CDS 50.0%
!! GGGATTTTGGGAAGGTTGTC+TGG - chr1_2:5574567-5574586 Msa0051480:CDS 50.0%
GTGCCCCTTCAAGTCCATCT+AGG - chr1_2:5573806-5573825 Msa0051480:CDS 55.0%
GTGCCCCTTCAAGTCCATCT+AGG - chr1_2:5573806-5573825 Msa0051480:CDS 55.0%
Chromosome Type Strat End Strand Name
chr1_2 gene 5573688 5574602 5573688 ID=Msa0051480;Name=Msa0051480
chr1_2 mRNA 5573688 5574602 5573688 ID=Msa0051480-mRNA-1;Parent=Msa0051480;Name=Msa0051480-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|304
chr1_2 exon 5573688 5574602 5573688 ID=Msa0051480-mRNA-1:exon:1670;Parent=Msa0051480-mRNA-1
chr1_2 CDS 5573688 5574602 5573688 ID=Msa0051480-mRNA-1:cds;Parent=Msa0051480-mRNA-1
Gene Sequence

>Msa0051480

ATGGAAGTGATGATACAAAGTTCTAGTATGGATACATTCAATTTTAGTAGTGGAACAATGAGTTCACCGTATCTAAGTCCTCCATCTTCTCCAAAACGTTTTGGTGAATTTTACTTAAGTGCCCCTTCAAGTCCATCTAGGCTTTCTGAATTATATAGTGAAATGGATTACTTGTCCATAATTGATCAAACATCATCAACCAAAAACAACAACGTTGTTCATGAAGATGATGATGATGATGATAAGCAAGGTGGTTTTGCTTTCTTTGTTAACCATGAATCAAATAAATCGTCGACACGTTCAGCTGAAGAACTCTTTCATGGTGGCAAAATCAAACCATTTACTAATGAAGAAGCTAAGGTTGTTGTACCTAAGAAGCAACAAAAAGTTCAAGATGAAAGAAGAGGAAGAGACAGAGAGAGAATAGAATCATCATCAAATAATTCTGGTAGAAGAAGTTCAAGATCACATTCTCCTTATAGAAAATCAAACTACATATCAGAATTAGAAGAACAAAACTCTCAAAAACAGAAACAACCTAGTAGCAACAAAGAGGAATCAAAGATATCAAACAGTAGTACAGGTCCTGGTTCGATTTCGAAGGGTTCGAGGAGATGGAAATTGAGTGATCTATTGTTGTTTAGAAGTGCTTCAGAAGGAAGAGGTTCAAGCAAGGATCCATTGAAGAAATATTTTGTTGGGTATAAGAAGAATACAAGTGAAGAAGTTAAAGGTTCAAGCAGCTTTAGATCTTCTGATTCGTTTTCACATCATGGGTCGAGAAAAAAGGCTCAAGTTTCAGCTCATGAAATGCATTATGCTATGAAGAAAGCTGAGTCACAAGATATGAAGAAGAGAACTTTCTTGCCTTATAGACAAGGGATTTTGGGAAGGTTGTCTGGATTTGGACTCTAG

Protein sequence

>Msa0051480

MEVMIQSSSMDTFNFSSGTMSSPYLSPPSSPKRFGEFYLSAPSSPSRLSELYSEMDYLSIIDQTSSTKNNNVVHEDDDDDDKQGGFAFFVNHESNKSSTRSAEELFHGGKIKPFTNEEAKVVVPKKQQKVQDERRGRDRERIESSSNNSGRRSSRSHSPYRKSNYISELEEQNSQKQKQPSSNKEESKISNSSTGPGSISKGSRRWKLSDLLLFRSASEGRGSSKDPLKKYFVGYKKNTSEEVKGSSSFRSSDSFSHHGSRKKAQVSAHEMHYAMKKAESQDMKKRTFLPYRQGILGRLSGFGL*