AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1242660


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1242660 MtrunA17_Chr8g0356381 86.765 68 7 2 1 68 1 66 2.06e-30 110
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 16 sgRNAs with CRISPR-Local

Find 95 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CATTATTAACACTTAATAAA+AGG 0.219593 8_2:-27180315 None:intergenic
TTCAATATTCAACATCATTA+TGG 0.232391 8_2:+27179530 Msa1242660:CDS
TAGTTTGTTTGAATCTATTT+TGG 0.239427 8_2:+27179379 Msa1242660:five_prime_UTR
TCAAGAGTTGTAAAATTATC+AGG 0.281943 8_2:-27179593 None:intergenic
AAAGCGTGAAGCTGAATATT+CGG 0.355029 8_2:+27179436 Msa1242660:CDS
TTTGGAGAAGATAGATTTGA+TGG 0.374532 8_2:+27179397 Msa1242660:exon
ATTGGTTTCGCCATCCAAAA+AGG 0.418000 8_2:+27180264 Msa1242660:CDS
AAGCGTGAAGCTGAATATTC+GGG 0.448185 8_2:+27179437 Msa1242660:CDS
TCAAACAAACTAAACAGTTA+TGG 0.455254 8_2:-27179368 None:intergenic
AGATTTGATGGGAAACTCGC+AGG 0.543321 8_2:+27179409 Msa1242660:exon
TTGGAGAAGATAGATTTGAT+GGG 0.560237 8_2:+27179398 Msa1242660:exon
ACACTTAATAAAAGGCAAGC+GGG 0.578855 8_2:-27180307 None:intergenic
AACACTTAATAAAAGGCAAG+CGG 0.606159 8_2:-27180308 None:intergenic
TCTTCTTGTTGTTGAGATCG+CGG 0.610587 8_2:-27179497 None:intergenic
TAAGAAGAAGCTCTCTACGA+AGG 0.666216 8_2:+27179553 Msa1242660:CDS
AGATCGCGGTGAGAGAACTG+TGG 0.696133 8_2:-27179483 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTCGTACAAATATTTTTTAT+CGG + chr8_2:27179831-27179850 Msa1242660:intron 15.0%
!!! TTTTGAATAATCAATATGTT+TGG + chr8_2:27179925-27179944 Msa1242660:intron 15.0%
!!! TTCGTACAAATATTTTTTAT+CGG + chr8_2:27179831-27179850 Msa1242660:intron 15.0%
!!! TTTTGAATAATCAATATGTT+TGG + chr8_2:27179925-27179944 Msa1242660:intron 15.0%
!!! TAGTTTGTTTGAATCTATTT+TGG + chr8_2:27179379-27179398 Msa1242660:five_prime_UTR 20.0%
!! TTCAATATTCAACATCATTA+TGG + chr8_2:27179530-27179549 Msa1242660:CDS 20.0%
!!! AACTTTTTTTGGTTGTTTAA+TGG + chr8_2:27179701-27179720 Msa1242660:intron 20.0%
!!! ATTAACTATTTTTACTCATG+TGG - chr8_2:27180001-27180020 None:intergenic 20.0%
!! ACATGAGTAAAAATAGTTAA+TGG + chr8_2:27180000-27180019 Msa1242660:intron 20.0%
!! TATTAGTTAAATGATGCAAT+TGG - chr8_2:27180161-27180180 None:intergenic 20.0%
!!! TAGTTTGTTTGAATCTATTT+TGG + chr8_2:27179379-27179398 Msa1242660:five_prime_UTR 20.0%
!! TTCAATATTCAACATCATTA+TGG + chr8_2:27179530-27179549 Msa1242660:CDS 20.0%
!!! AACTTTTTTTGGTTGTTTAA+TGG + chr8_2:27179701-27179720 Msa1242660:intron 20.0%
!!! ATTAACTATTTTTACTCATG+TGG - chr8_2:27180001-27180020 None:intergenic 20.0%
!! ACATGAGTAAAAATAGTTAA+TGG + chr8_2:27180000-27180019 Msa1242660:intron 20.0%
!! TATTAGTTAAATGATGCAAT+TGG - chr8_2:27180161-27180180 None:intergenic 20.0%
! TCAAACAAACTAAACAGTTA+TGG - chr8_2:27179371-27179390 None:intergenic 25.0%
! TCAAGAGTTGTAAAATTATC+AGG - chr8_2:27179596-27179615 None:intergenic 25.0%
!! TAATTTTACAACTCTTGAAC+AGG + chr8_2:27179598-27179617 Msa1242660:CDS 25.0%
! AAAAAAAGTTATCCATGGAT+TGG - chr8_2:27179691-27179710 None:intergenic 25.0%
!!! AATCCATGGATAACTTTTTT+TGG + chr8_2:27179690-27179709 Msa1242660:intron 25.0%
!!! GAAAAAAATTAGCTTGTTTG+TGG + chr8_2:27180024-27180043 Msa1242660:intron 25.0%
! AATCACTTGGAAAAACAAAT+TGG - chr8_2:27180214-27180233 None:intergenic 25.0%
! TCAAACAAACTAAACAGTTA+TGG - chr8_2:27179371-27179390 None:intergenic 25.0%
! TCAAGAGTTGTAAAATTATC+AGG - chr8_2:27179596-27179615 None:intergenic 25.0%
!! TAATTTTACAACTCTTGAAC+AGG + chr8_2:27179598-27179617 Msa1242660:CDS 25.0%
! AAAAAAAGTTATCCATGGAT+TGG - chr8_2:27179691-27179710 None:intergenic 25.0%
!!! AATCCATGGATAACTTTTTT+TGG + chr8_2:27179690-27179709 Msa1242660:intron 25.0%
!!! GAAAAAAATTAGCTTGTTTG+TGG + chr8_2:27180024-27180043 Msa1242660:intron 25.0%
! AATCACTTGGAAAAACAAAT+TGG - chr8_2:27180214-27180233 None:intergenic 25.0%
TTTGGAGAAGATAGATTTGA+TGG + chr8_2:27179397-27179416 Msa1242660:exon 30.0%
TTGGAGAAGATAGATTTGAT+GGG + chr8_2:27179398-27179417 Msa1242660:exon 30.0%
!!! TTCTTGCTTTGTTTTCTTTG+TGG + chr8_2:27179655-27179674 Msa1242660:intron 30.0%
CAACCAAAAAAAGTTATCCA+TGG - chr8_2:27179696-27179715 None:intergenic 30.0%
TAGTGAGTGACAATTATTGT+GGG - chr8_2:27179810-27179829 None:intergenic 30.0%
ATAGTGAGTGACAATTATTG+TGG - chr8_2:27179811-27179830 None:intergenic 30.0%
TAGACACATAAATTTGCAAG+TGG - chr8_2:27180052-27180071 None:intergenic 30.0%
!!! AACGTCATTCATTTTTTGTG+AGG - chr8_2:27180115-27180134 None:intergenic 30.0%
AATGTTGTGTTTACAAGGAT+TGG + chr8_2:27180246-27180265 Msa1242660:intron 30.0%
TTTGGAGAAGATAGATTTGA+TGG + chr8_2:27179397-27179416 Msa1242660:exon 30.0%
TTGGAGAAGATAGATTTGAT+GGG + chr8_2:27179398-27179417 Msa1242660:exon 30.0%
!!! TTCTTGCTTTGTTTTCTTTG+TGG + chr8_2:27179655-27179674 Msa1242660:intron 30.0%
CAACCAAAAAAAGTTATCCA+TGG - chr8_2:27179696-27179715 None:intergenic 30.0%
TAGTGAGTGACAATTATTGT+GGG - chr8_2:27179810-27179829 None:intergenic 30.0%
ATAGTGAGTGACAATTATTG+TGG - chr8_2:27179811-27179830 None:intergenic 30.0%
TAGACACATAAATTTGCAAG+TGG - chr8_2:27180052-27180071 None:intergenic 30.0%
!!! AACGTCATTCATTTTTTGTG+AGG - chr8_2:27180115-27180134 None:intergenic 30.0%
AATGTTGTGTTTACAAGGAT+TGG + chr8_2:27180246-27180265 Msa1242660:intron 30.0%
CCAACAAAATGCGTGAAAAA+CGG - chr8_2:27179327-27179346 None:intergenic 35.0%
AAAGCGTGAAGCTGAATATT+CGG + chr8_2:27179436-27179455 Msa1242660:CDS 35.0%
TTCCACAAGCTACTCTTATT+CGG - chr8_2:27179751-27179770 None:intergenic 35.0%
! TGTTTTTCCAAGTGATTCCT+AGG + chr8_2:27180217-27180236 Msa1242660:intron 35.0%
CCTTGTAAACACAACATTCA+TGG - chr8_2:27180244-27180263 None:intergenic 35.0%
CCATGAATGTTGTGTTTACA+AGG + chr8_2:27180241-27180260 Msa1242660:intron 35.0%
CCAACAAAATGCGTGAAAAA+CGG - chr8_2:27179327-27179346 None:intergenic 35.0%
AAAGCGTGAAGCTGAATATT+CGG + chr8_2:27179436-27179455 Msa1242660:CDS 35.0%
TTCCACAAGCTACTCTTATT+CGG - chr8_2:27179751-27179770 None:intergenic 35.0%
! TGTTTTTCCAAGTGATTCCT+AGG + chr8_2:27180217-27180236 Msa1242660:intron 35.0%
CCTTGTAAACACAACATTCA+TGG - chr8_2:27180244-27180263 None:intergenic 35.0%
CCATGAATGTTGTGTTTACA+AGG + chr8_2:27180241-27180260 Msa1242660:intron 35.0%
!! CCGTTTTTCACGCATTTTGT+TGG + chr8_2:27179324-27179343 Msa1242660:five_prime_UTR 40.0%
AAGCGTGAAGCTGAATATTC+GGG + chr8_2:27179437-27179456 Msa1242660:CDS 40.0%
!! TCTTCTTGTTGTTGAGATCG+CGG - chr8_2:27179500-27179519 None:intergenic 40.0%
TAAGAAGAAGCTCTCTACGA+AGG + chr8_2:27179553-27179572 Msa1242660:CDS 40.0%
GGATTTCGTTTACCAATCCA+TGG + chr8_2:27179676-27179695 Msa1242660:intron 40.0%
AGCTACTCTTATTCGGTCAA+CGG - chr8_2:27179744-27179763 None:intergenic 40.0%
AGTGACAATTATTGTGGGAC+AGG - chr8_2:27179805-27179824 None:intergenic 40.0%
AACACAACATTCATGGACCT+AGG - chr8_2:27180237-27180256 None:intergenic 40.0%
! ATTGGTTTCGCCATCCAAAA+AGG + chr8_2:27180264-27180283 Msa1242660:CDS 40.0%
!! CCGTTTTTCACGCATTTTGT+TGG + chr8_2:27179324-27179343 Msa1242660:five_prime_UTR 40.0%
AAGCGTGAAGCTGAATATTC+GGG + chr8_2:27179437-27179456 Msa1242660:CDS 40.0%
!! TCTTCTTGTTGTTGAGATCG+CGG - chr8_2:27179500-27179519 None:intergenic 40.0%
TAAGAAGAAGCTCTCTACGA+AGG + chr8_2:27179553-27179572 Msa1242660:CDS 40.0%
GGATTTCGTTTACCAATCCA+TGG + chr8_2:27179676-27179695 Msa1242660:intron 40.0%
AGCTACTCTTATTCGGTCAA+CGG - chr8_2:27179744-27179763 None:intergenic 40.0%
AGTGACAATTATTGTGGGAC+AGG - chr8_2:27179805-27179824 None:intergenic 40.0%
AACACAACATTCATGGACCT+AGG - chr8_2:27180237-27180256 None:intergenic 40.0%
! ATTGGTTTCGCCATCCAAAA+AGG + chr8_2:27180264-27180283 Msa1242660:CDS 40.0%
AGATTTGATGGGAAACTCGC+AGG + chr8_2:27179409-27179428 Msa1242660:exon 45.0%
GACCGAATAAGAGTAGCTTG+TGG + chr8_2:27179746-27179765 Msa1242660:intron 45.0%
TCATGGACCTAGGAATCACT+TGG - chr8_2:27180227-27180246 None:intergenic 45.0%
TTTCGCCATCCAAAAAGGTC+TGG + chr8_2:27180269-27180288 Msa1242660:CDS 45.0%
! GCCCGCTTGCCTTTTATTAA+AGG + chr8_2:27180306-27180325 Msa1242660:CDS 45.0%
AGATTTGATGGGAAACTCGC+AGG + chr8_2:27179409-27179428 Msa1242660:exon 45.0%
GACCGAATAAGAGTAGCTTG+TGG + chr8_2:27179746-27179765 Msa1242660:intron 45.0%
TCATGGACCTAGGAATCACT+TGG - chr8_2:27180227-27180246 None:intergenic 45.0%
TTTCGCCATCCAAAAAGGTC+TGG + chr8_2:27180269-27180288 Msa1242660:CDS 45.0%
AGATCGCGGTGAGAGAACTG+TGG - chr8_2:27179486-27179505 None:intergenic 55.0%
CGCCATCCAAAAAGGTCTGG+CGG + chr8_2:27180272-27180291 Msa1242660:CDS 55.0%
AGATCGCGGTGAGAGAACTG+TGG - chr8_2:27179486-27179505 None:intergenic 55.0%
CGCCATCCAAAAAGGTCTGG+CGG + chr8_2:27180272-27180291 Msa1242660:CDS 55.0%
! CGCCGCCAGACCTTTTTGGA+TGG - chr8_2:27180277-27180296 None:intergenic 60.0%
! ACTGCGCCGCCAGACCTTTT+TGG - chr8_2:27180281-27180300 None:intergenic 60.0%
! CGCCGCCAGACCTTTTTGGA+TGG - chr8_2:27180277-27180296 None:intergenic 60.0%
! ACTGCGCCGCCAGACCTTTT+TGG - chr8_2:27180281-27180300 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr8_2 gene 27179316 27180325 27179316 ID=Msa1242660;Name=Msa1242660
chr8_2 mRNA 27179316 27180325 27179316 ID=Msa1242660-mRNA-1;Parent=Msa1242660;Name=Msa1242660-mRNA-1;_AED=0.57;_eAED=0.57;_QI=100|0|0.5|0.5|1|1|2|0|88
chr8_2 exon 27179316 27179619 27179316 ID=Msa1242660-mRNA-1:exon:9574;Parent=Msa1242660-mRNA-1
chr8_2 exon 27180263 27180325 27180263 ID=Msa1242660-mRNA-1:exon:9575;Parent=Msa1242660-mRNA-1
chr8_2 five_prime_UTR 27179316 27179415 27179316 ID=Msa1242660-mRNA-1:five_prime_utr;Parent=Msa1242660-mRNA-1
chr8_2 CDS 27179416 27179619 27179416 ID=Msa1242660-mRNA-1:cds;Parent=Msa1242660-mRNA-1
chr8_2 CDS 27180263 27180325 27180263 ID=Msa1242660-mRNA-1:cds;Parent=Msa1242660-mRNA-1
Gene Sequence

>Msa1242660

ATGGGAAACTCGCAGGCGAAAAAGCGTGAAGCTGAATATTCGGGAAATGTTGAAGCGAGAAACAAGTCCACAGTTCTCTCACCGCGATCTCAACAACAAGAAGAAGAAGTGTCTTTCAATATTCAACATCATTATGGTAAGAAGAAGCTCTCTACGAAGGAGAAATATGCTTTAATTCCTGATAATTTTACAACTCTTGAACAGGATTGGTTTCGCCATCCAAAAAGGTCTGGCGGCGCAGTTTGTTGCCCGCTTGCCTTTTATTAA

Protein sequence

>Msa1242660

MGNSQAKKREAEYSGNVEARNKSTVLSPRSQQQEEEVSFNIQHHYGKKKLSTKEKYALIPDNFTTLEQDWFRHPKRSGGAVCCPLAFY*