AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0119960


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0119960 MtrunA17_Chr1g0191731 91.358 81 7 0 1 81 189 269 1.44e-48 154
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0119960 AT3G05250.1 52.500 80 33 1 4 78 199 278 3.81e-19 79.0
Msa0119960 AT3G05250.3 52.500 80 33 1 4 78 130 209 6.11e-19 77.0
Msa0119960 AT3G05250.2 52.500 80 33 1 4 78 130 209 6.11e-19 77.0

Find 38 sgRNAs with CRISPR-Local

Find 42 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTGTTGTAATTCTTGAATAA+TGG 0.212856 1_3:+44525608 Msa0119960:three_prime_UTR
TGAAGTTTCTCAAAATAAAT+TGG 0.229625 1_3:+44525492 Msa0119960:CDS
TGAAGCAGCTAGACCTTTCC+TGG 0.256852 1_3:+44525348 Msa0119960:CDS
TGTTGTAATTCTTGAATAAT+GGG 0.275542 1_3:+44525609 Msa0119960:three_prime_UTR
ATTCAACTATTTCTTGCTTC+AGG 0.278541 1_3:+44525400 Msa0119960:CDS
AGAGAGCGATATTGTCGATT+TGG 0.340468 1_3:+44525673 Msa0119960:three_prime_UTR
GCGGTTTATATTCACCGATT+AGG 0.348195 1_3:+44525445 Msa0119960:CDS
ATCATTGTGCACCATATCTT+TGG 0.356487 1_3:+44525135 Msa0119960:five_prime_UTR
ATTTACTACCGCACCGTTTG+AGG 0.403311 1_3:-44525638 None:intergenic
CGATTAGGTTGGAGCTCACT+TGG 0.405324 1_3:+44525460 Msa0119960:CDS
AAAAGAACCTGAAAAGAAAC+AGG 0.429978 1_3:+44525303 Msa0119960:five_prime_UTR
TTGGTGTGGTCAAATCATTA+TGG 0.432135 1_3:+44525154 Msa0119960:five_prime_UTR
ACATCCTCCTCCTAAAGATT+AGG 0.441544 1_3:-44525108 None:intergenic
ATTTGACCACACCAAAGATA+TGG 0.452587 1_3:-44525146 None:intergenic
TTTATATTCACCGATTAGGT+TGG 0.460599 1_3:+44525449 Msa0119960:CDS
CAAGTGAGCTCCAACCTAAT+CGG 0.472117 1_3:-44525459 None:intergenic
TTTACCTAATCTTTAGGAGG+AGG 0.500145 1_3:+44525104 Msa0119960:five_prime_UTR
TCATCAAATATGTACAGGTA+TGG 0.500375 1_3:-44525535 None:intergenic
GATTAGGTTGGAGCTCACTT+GGG 0.510302 1_3:+44525461 Msa0119960:CDS
TCGGTTCTTGCACCCAGGAA+AGG 0.515775 1_3:-44525361 None:intergenic
TGCAAGAACCGACAGATTTG+TGG 0.518407 1_3:+44525372 Msa0119960:CDS
ACGTTATAGTTCTCCATCCA+AGG 0.524089 1_3:+44525709 Msa0119960:three_prime_UTR
TAATGGGATTGCTCCTCAAA+CGG 0.527991 1_3:+44525625 Msa0119960:three_prime_UTR
AGTCATCATCAAATATGTAC+AGG 0.530474 1_3:-44525540 None:intergenic
CCTAAAGATTAGGTAAAATG+AGG 0.546111 1_3:-44525098 None:intergenic
GAACTATAACGTGGCTAGAG+AGG 0.549132 1_3:-44525698 None:intergenic
CGTTATAGTTCTCCATCCAA+GGG 0.594178 1_3:+44525710 Msa0119960:three_prime_UTR
ATTAGGTTGGAGCTCACTTG+GGG 0.596113 1_3:+44525462 Msa0119960:CDS
ATCTGTCGGTTCTTGCACCC+AGG 0.597789 1_3:-44525366 None:intergenic
GAAGCAGCTAGACCTTTCCT+GGG 0.597899 1_3:+44525349 Msa0119960:CDS
ATATTTGATGATGACTCTGA+TGG 0.611424 1_3:+44525547 Msa0119960:CDS
TGGTCAAATCATTATGGACA+AGG 0.622389 1_3:+44525160 Msa0119960:five_prime_UTR
TGTGCACCATATCTTTGGTG+TGG 0.633296 1_3:+44525140 Msa0119960:five_prime_UTR
GATTATCGAAGCTTATGATG+CGG 0.639557 1_3:+44525426 Msa0119960:CDS
AATCTCGTCCACAAATCTGT+CGG 0.648073 1_3:-44525380 None:intergenic
AGAACCTGAAAAGAAACAGG+AGG 0.686534 1_3:+44525306 Msa0119960:five_prime_UTR
GGATTGCTCCTCAAACGGTG+CGG 0.725777 1_3:+44525630 Msa0119960:three_prime_UTR
TTGGATGGAGAACTATAACG+TGG 0.742663 1_3:-44525707 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TGAAGTTTCTCAAAATAAAT+TGG + chr1_3:44525492-44525511 Msa0119960:CDS 20.0%
!! TTGTTGTAATTCTTGAATAA+TGG + chr1_3:44525608-44525627 Msa0119960:three_prime_UTR 20.0%
!! TGTTGTAATTCTTGAATAAT+GGG + chr1_3:44525609-44525628 Msa0119960:three_prime_UTR 20.0%
! CATTTTACCTAATCTTTAGG+AGG + chr1_3:44525101-44525120 Msa0119960:five_prime_UTR 30.0%
AAAAGAACCTGAAAAGAAAC+AGG + chr1_3:44525303-44525322 Msa0119960:five_prime_UTR 30.0%
! ATTCAACTATTTCTTGCTTC+AGG + chr1_3:44525400-44525419 Msa0119960:CDS 30.0%
! TTTATATTCACCGATTAGGT+TGG + chr1_3:44525449-44525468 Msa0119960:CDS 30.0%
TCATCAAATATGTACAGGTA+TGG - chr1_3:44525538-44525557 None:intergenic 30.0%
AGTCATCATCAAATATGTAC+AGG - chr1_3:44525543-44525562 None:intergenic 30.0%
!! ATATTTGATGATGACTCTGA+TGG + chr1_3:44525547-44525566 Msa0119960:CDS 30.0%
! TTTACCTAATCTTTAGGAGG+AGG + chr1_3:44525104-44525123 Msa0119960:five_prime_UTR 35.0%
ATCATTGTGCACCATATCTT+TGG + chr1_3:44525135-44525154 Msa0119960:five_prime_UTR 35.0%
ATTTGACCACACCAAAGATA+TGG - chr1_3:44525149-44525168 None:intergenic 35.0%
TTGGTGTGGTCAAATCATTA+TGG + chr1_3:44525154-44525173 Msa0119960:five_prime_UTR 35.0%
TGGTCAAATCATTATGGACA+AGG + chr1_3:44525160-44525179 Msa0119960:five_prime_UTR 35.0%
GATTATCGAAGCTTATGATG+CGG + chr1_3:44525426-44525445 Msa0119960:CDS 35.0%
GTTTAAAAACTTCAAGCCCT+TGG - chr1_3:44525729-44525748 None:intergenic 35.0%
ACATCCTCCTCCTAAAGATT+AGG - chr1_3:44525111-44525130 None:intergenic 40.0%
AGAACCTGAAAAGAAACAGG+AGG + chr1_3:44525306-44525325 Msa0119960:five_prime_UTR 40.0%
!! AACTCCTCCTGTTTCTTTTC+AGG - chr1_3:44525313-44525332 None:intergenic 40.0%
AATCTCGTCCACAAATCTGT+CGG - chr1_3:44525383-44525402 None:intergenic 40.0%
! GCGGTTTATATTCACCGATT+AGG + chr1_3:44525445-44525464 Msa0119960:CDS 40.0%
TAATGGGATTGCTCCTCAAA+CGG + chr1_3:44525625-44525644 Msa0119960:three_prime_UTR 40.0%
! AGAGAGCGATATTGTCGATT+TGG + chr1_3:44525673-44525692 Msa0119960:three_prime_UTR 40.0%
TTGGATGGAGAACTATAACG+TGG - chr1_3:44525710-44525729 None:intergenic 40.0%
ACGTTATAGTTCTCCATCCA+AGG + chr1_3:44525709-44525728 Msa0119960:three_prime_UTR 40.0%
CGTTATAGTTCTCCATCCAA+GGG + chr1_3:44525710-44525729 Msa0119960:three_prime_UTR 40.0%
AAAAACTTCAAGCCCTTGGA+TGG - chr1_3:44525725-44525744 None:intergenic 40.0%
TGTGCACCATATCTTTGGTG+TGG + chr1_3:44525140-44525159 Msa0119960:five_prime_UTR 45.0%
TGCAAGAACCGACAGATTTG+TGG + chr1_3:44525372-44525391 Msa0119960:CDS 45.0%
CAAGTGAGCTCCAACCTAAT+CGG - chr1_3:44525462-44525481 None:intergenic 45.0%
!! GATTAGGTTGGAGCTCACTT+GGG + chr1_3:44525461-44525480 Msa0119960:CDS 45.0%
!! ATTAGGTTGGAGCTCACTTG+GGG + chr1_3:44525462-44525481 Msa0119960:CDS 45.0%
ATTTACTACCGCACCGTTTG+AGG - chr1_3:44525641-44525660 None:intergenic 45.0%
GAACTATAACGTGGCTAGAG+AGG - chr1_3:44525701-44525720 None:intergenic 45.0%
GCGAGACTTCTGCTCTCTAA+TGG - chr1_3:44525281-44525300 None:intergenic 50.0%
TGAAGCAGCTAGACCTTTCC+TGG + chr1_3:44525348-44525367 Msa0119960:CDS 50.0%
GAAGCAGCTAGACCTTTCCT+GGG + chr1_3:44525349-44525368 Msa0119960:CDS 50.0%
!! CGATTAGGTTGGAGCTCACT+TGG + chr1_3:44525460-44525479 Msa0119960:CDS 50.0%
TCGGTTCTTGCACCCAGGAA+AGG - chr1_3:44525364-44525383 None:intergenic 55.0%
!! ATCTGTCGGTTCTTGCACCC+AGG - chr1_3:44525369-44525388 None:intergenic 55.0%
GGATTGCTCCTCAAACGGTG+CGG + chr1_3:44525630-44525649 Msa0119960:three_prime_UTR 55.0%
Chromosome Type Strat End Strand Name
chr1_3 gene 44525101 44525750 44525101 ID=Msa0119960;Name=Msa0119960
chr1_3 mRNA 44525101 44525750 44525101 ID=Msa0119960-mRNA-1;Parent=Msa0119960;Name=Msa0119960-mRNA-1;_AED=0.24;_eAED=0.24;_QI=130|1|1|1|0|0|2|171|81
chr1_3 exon 44525101 44525181 44525101 ID=Msa0119960-mRNA-1:exon:13277;Parent=Msa0119960-mRNA-1
chr1_3 exon 44525285 44525750 44525285 ID=Msa0119960-mRNA-1:exon:13278;Parent=Msa0119960-mRNA-1
chr1_3 five_prime_UTR 44525101 44525181 44525101 ID=Msa0119960-mRNA-1:five_prime_utr;Parent=Msa0119960-mRNA-1
chr1_3 five_prime_UTR 44525285 44525333 44525285 ID=Msa0119960-mRNA-1:five_prime_utr;Parent=Msa0119960-mRNA-1
chr1_3 CDS 44525334 44525579 44525334 ID=Msa0119960-mRNA-1:cds;Parent=Msa0119960-mRNA-1
chr1_3 three_prime_UTR 44525580 44525750 44525580 ID=Msa0119960-mRNA-1:three_prime_utr;Parent=Msa0119960-mRNA-1
Gene Sequence

>Msa0119960

ATGATGTCAGTCTCTGAAGCAGCTAGACCTTTCCTGGGTGCAAGAACCGACAGATTTGTGGACGAGATTCAACTATTTCTTGCTTCAGGATTGATTATCGAAGCTTATGATGCGGTTTATATTCACCGATTAGGTTGGAGCTCACTTGGGGAAAACACTGAAGTTTCTCAAAATAAATTGGTTGATCACACTACTGTGATTCCATACCTGTACATATTTGATGATGACTCTGATGGAAATGAGTAG

Protein sequence

>Msa0119960

MMSVSEAARPFLGARTDRFVDEIQLFLASGLIIEAYDAVYIHRLGWSSLGENTEVSQNKLVDHTTVIPYLYIFDDDSDGNE*