AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1433010

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1433010 MtrunA17_Chr1g0193481 96.491 114 2 2 1 112 1 114 6.43e-75 217
Msa1433010 MtrunA17_Chr7g0271161 55.856 111 36 3 3 112 16 114 7.33e-31 105
Msa1433010 MtrunA17_Chr7g0271171 63.333 90 27 3 2 88 13 99 1.61e-30 105
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1433010 AT5G26731.1 49.275 69 32 2 9 76 6 72 6.63e-12 57.4

Find 34 sgRNAs with CRISPR-Local

Find 96 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTGATTCTTCCTCGTGTTTA+TGG 0.149688 tig0027216:-59972 Msa1433010:CDS
CTTCTTCTTTCTTAAGTATT+GGG 0.157307 tig0027216:+60583 None:intergenic
TTCTTTATACTATTGTTTAA+TGG 0.218332 tig0027216:-59819 Msa1433010:three_prime_UTR
TACAGAACTGGTAGCTTCTA+AGG 0.267532 tig0027216:+60184 None:intergenic
AAAGTTCAACGAACCTGATT+TGG 0.272646 tig0027216:+60478 None:intergenic
TCTTCTTCTTTCTTAAGTAT+TGG 0.282026 tig0027216:+60582 None:intergenic
AGTCTGACAGAAAGAATTAA+AGG 0.303186 tig0027216:-60153 Msa1433010:CDS
TTGTTTAGGACTGAATCTTT+TGG 0.327957 tig0027216:-60261 Msa1433010:CDS
TGACTATGAATCCATTGTTT+AGG 0.347576 tig0027216:-60275 Msa1433010:CDS
ATTATTCTTGACACAAATAT+TGG 0.365022 tig0027216:-59847 Msa1433010:three_prime_UTR
CTTCCTCGTGTTTATGGTAG+TGG 0.375838 tig0027216:-59966 Msa1433010:exon
GACTCTTCTTTCTACAGAAC+TGG 0.387643 tig0027216:+60172 None:intergenic
AAACAAAGCAATTCCAAATC+AGG 0.407917 tig0027216:-60491 Msa1433010:intron
AAGTTGTATGGTTAAAGTTA+AGG 0.414266 tig0027216:-60110 Msa1433010:CDS
ACGAGGAAGAATCAACTTTA+CGG 0.429447 tig0027216:+59980 None:intergenic
TAGTCACACTTCCCATGTCT+TGG 0.452486 tig0027216:+60292 None:intergenic
ATCATGGTGTAGTTCTGATC+AGG 0.472496 tig0027216:+60225 None:intergenic
GCCACTGTGTGGTGGCGTCC+TGG 0.478075 tig0027216:-60528 Msa1433010:five_prime_UTR
TAACTGTCTCTTCTCTATCA+TGG 0.494793 tig0027216:+60209 None:intergenic
TTCGTGCTAAGAAAGTTGTA+TGG 0.497025 tig0027216:-60122 Msa1433010:CDS
TTCTTCTTTCTTAAGTATTG+GGG 0.503371 tig0027216:+60584 None:intergenic
AAGACAAATGAATTACAGAC+AGG 0.551965 tig0027216:+59927 None:intergenic
GCTGTGAAAACCTTCTTCTA+CGG 0.552047 tig0027216:+60028 None:intergenic
TGCTCGTGGACTAAGAAAGT+TGG 0.556478 tig0027216:-60085 Msa1433010:CDS
AAGAATCAACTTTACGGTGG+TGG 0.557630 tig0027216:+59986 None:intergenic
TCAAAGTTCAAACCAAGACA+TGG 0.558259 tig0027216:-60304 Msa1433010:exon
GACTTTAAGCCACTGTGTGG+TGG 0.582273 tig0027216:-60536 Msa1433010:five_prime_UTR
AAAGATTCAGTCCTAAACAA+TGG 0.590266 tig0027216:+60264 None:intergenic
CAAAGTTCAAACCAAGACAT+GGG 0.635268 tig0027216:-60303 Msa1433010:exon
TAAGACTTTAAGCCACTGTG+TGG 0.667683 tig0027216:-60539 Msa1433010:five_prime_UTR
TTAAAGTTAAGGTATGCTCG+TGG 0.673922 tig0027216:-60099 Msa1433010:CDS
AGGAAGAATCAACTTTACGG+TGG 0.745414 tig0027216:+59983 None:intergenic
ACCAGGACGCCACCACACAG+TGG 0.751115 tig0027216:+60527 None:intergenic
TTACCACTACCATAAACACG+AGG 0.787473 tig0027216:+59963 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTCTTTATACTATTGTTTAA+TGG - tig0027216:60550-60569 Msa1433010:five_prime_UTR 15.0%
!! TTCTTTATACTATTGTTTAA+TGG - tig0027216:60550-60569 Msa1433010:five_prime_UTR 15.0%
!! GAATATGAATATGAAGTATA+AGG + tig0027216:59921-59940 None:intergenic 20.0%
!! AAGAAAAAGAAGAATAAAAG+GGG + tig0027216:59948-59967 None:intergenic 20.0%
!! GAAGAAAAAGAAGAATAAAA+GGG + tig0027216:59949-59968 None:intergenic 20.0%
!! TGAAGAAAAAGAAGAATAAA+AGG + tig0027216:59950-59969 None:intergenic 20.0%
!!! TAAGTTTTAAGATTAGAGTT+TGG - tig0027216:60479-60498 Msa1433010:intron 20.0%
!! ATTATTCTTGACACAAATAT+TGG - tig0027216:60522-60541 Msa1433010:five_prime_UTR 20.0%
!! GAATATGAATATGAAGTATA+AGG + tig0027216:59921-59940 None:intergenic 20.0%
!! AAGAAAAAGAAGAATAAAAG+GGG + tig0027216:59948-59967 None:intergenic 20.0%
!! GAAGAAAAAGAAGAATAAAA+GGG + tig0027216:59949-59968 None:intergenic 20.0%
!! TGAAGAAAAAGAAGAATAAA+AGG + tig0027216:59950-59969 None:intergenic 20.0%
!!! TAAGTTTTAAGATTAGAGTT+TGG - tig0027216:60479-60498 Msa1433010:intron 20.0%
!! ATTATTCTTGACACAAATAT+TGG - tig0027216:60522-60541 Msa1433010:five_prime_UTR 20.0%
! TCTTCTTCTTTCTTAAGTAT+TGG + tig0027216:59790-59809 None:intergenic 25.0%
! AGAAAAAGAAGAATAAAAGG+GGG + tig0027216:59947-59966 None:intergenic 25.0%
!!! ACTTTGTAGTTTTTCAAAGA+TGG + tig0027216:59991-60010 None:intergenic 25.0%
! AAGTTGTATGGTTAAAGTTA+AGG - tig0027216:60259-60278 Msa1433010:CDS 25.0%
!!! TTTTTTCCAAGGTTTAAATG+CGG - tig0027216:60309-60328 Msa1433010:five_prime_UTR 25.0%
! TCTTCTTCTTTCTTAAGTAT+TGG + tig0027216:59790-59809 None:intergenic 25.0%
! AGAAAAAGAAGAATAAAAGG+GGG + tig0027216:59947-59966 None:intergenic 25.0%
!!! ACTTTGTAGTTTTTCAAAGA+TGG + tig0027216:59991-60010 None:intergenic 25.0%
! AAGTTGTATGGTTAAAGTTA+AGG - tig0027216:60259-60278 Msa1433010:CDS 25.0%
!!! TTTTTTCCAAGGTTTAAATG+CGG - tig0027216:60309-60328 Msa1433010:five_prime_UTR 25.0%
AAACAAAGCAATTCCAAATC+AGG - tig0027216:59878-59897 Msa1433010:three_prime_UTR 30.0%
TGACTATGAATCCATTGTTT+AGG - tig0027216:60094-60113 Msa1433010:CDS 30.0%
AAAGATTCAGTCCTAAACAA+TGG + tig0027216:60108-60127 None:intergenic 30.0%
!! TTGTTTAGGACTGAATCTTT+TGG - tig0027216:60108-60127 Msa1433010:CDS 30.0%
AGTCTGACAGAAAGAATTAA+AGG - tig0027216:60216-60235 Msa1433010:CDS 30.0%
TAAAAACCGCATTTAAACCT+TGG + tig0027216:60318-60337 None:intergenic 30.0%
! GTTTTTATTACCGTAGAAGA+AGG - tig0027216:60331-60350 Msa1433010:intron 30.0%
AAGACAAATGAATTACAGAC+AGG + tig0027216:60445-60464 None:intergenic 30.0%
!! CTATTGTTTAATGGTTTTGC+TGG - tig0027216:60559-60578 Msa1433010:five_prime_UTR 30.0%
AAACAAAGCAATTCCAAATC+AGG - tig0027216:59878-59897 Msa1433010:three_prime_UTR 30.0%
TGACTATGAATCCATTGTTT+AGG - tig0027216:60094-60113 Msa1433010:CDS 30.0%
AAAGATTCAGTCCTAAACAA+TGG + tig0027216:60108-60127 None:intergenic 30.0%
!! TTGTTTAGGACTGAATCTTT+TGG - tig0027216:60108-60127 Msa1433010:CDS 30.0%
AGTCTGACAGAAAGAATTAA+AGG - tig0027216:60216-60235 Msa1433010:CDS 30.0%
TAAAAACCGCATTTAAACCT+TGG + tig0027216:60318-60337 None:intergenic 30.0%
! GTTTTTATTACCGTAGAAGA+AGG - tig0027216:60331-60350 Msa1433010:intron 30.0%
AAGACAAATGAATTACAGAC+AGG + tig0027216:60445-60464 None:intergenic 30.0%
!! CTATTGTTTAATGGTTTTGC+TGG - tig0027216:60559-60578 Msa1433010:five_prime_UTR 30.0%
AAAGTTCAACGAACCTGATT+TGG + tig0027216:59894-59913 None:intergenic 35.0%
! GAACTTTGAAGAACTCTGTT+TGG + tig0027216:60054-60073 None:intergenic 35.0%
TCAAAGTTCAAACCAAGACA+TGG - tig0027216:60065-60084 Msa1433010:CDS 35.0%
CAAAGTTCAAACCAAGACAT+GGG - tig0027216:60066-60085 Msa1433010:CDS 35.0%
TAACTGTCTCTTCTCTATCA+TGG + tig0027216:60163-60182 None:intergenic 35.0%
TTCGTGCTAAGAAAGTTGTA+TGG - tig0027216:60247-60266 Msa1433010:CDS 35.0%
TTAAAGTTAAGGTATGCTCG+TGG - tig0027216:60270-60289 Msa1433010:CDS 35.0%
!!! GAAAGTTGGTGTTTTTTCCA+AGG - tig0027216:60298-60317 Msa1433010:exon 35.0%
ACGAGGAAGAATCAACTTTA+CGG + tig0027216:60392-60411 None:intergenic 35.0%
TTGATTCTTCCTCGTGTTTA+TGG - tig0027216:60397-60416 Msa1433010:intron 35.0%
!! TGTTTAATGGTTTTGCTGGT+AGG - tig0027216:60563-60582 Msa1433010:five_prime_UTR 35.0%
AAAGTTCAACGAACCTGATT+TGG + tig0027216:59894-59913 None:intergenic 35.0%
! GAACTTTGAAGAACTCTGTT+TGG + tig0027216:60054-60073 None:intergenic 35.0%
TCAAAGTTCAAACCAAGACA+TGG - tig0027216:60065-60084 Msa1433010:CDS 35.0%
CAAAGTTCAAACCAAGACAT+GGG - tig0027216:60066-60085 Msa1433010:CDS 35.0%
TAACTGTCTCTTCTCTATCA+TGG + tig0027216:60163-60182 None:intergenic 35.0%
TTCGTGCTAAGAAAGTTGTA+TGG - tig0027216:60247-60266 Msa1433010:CDS 35.0%
TTAAAGTTAAGGTATGCTCG+TGG - tig0027216:60270-60289 Msa1433010:CDS 35.0%
!!! GAAAGTTGGTGTTTTTTCCA+AGG - tig0027216:60298-60317 Msa1433010:exon 35.0%
ACGAGGAAGAATCAACTTTA+CGG + tig0027216:60392-60411 None:intergenic 35.0%
TTGATTCTTCCTCGTGTTTA+TGG - tig0027216:60397-60416 Msa1433010:intron 35.0%
!! TGTTTAATGGTTTTGCTGGT+AGG - tig0027216:60563-60582 Msa1433010:five_prime_UTR 35.0%
TAAGACTTTAAGCCACTGTG+TGG - tig0027216:59830-59849 Msa1433010:three_prime_UTR 40.0%
CAAAGATGGAGACAAATACG+TGG + tig0027216:59977-59996 None:intergenic 40.0%
!! ATCATGGTGTAGTTCTGATC+AGG + tig0027216:60147-60166 None:intergenic 40.0%
TACAGAACTGGTAGCTTCTA+AGG + tig0027216:60188-60207 None:intergenic 40.0%
GACTCTTCTTTCTACAGAAC+TGG + tig0027216:60200-60219 None:intergenic 40.0%
GCTGTGAAAACCTTCTTCTA+CGG + tig0027216:60344-60363 None:intergenic 40.0%
AAGAATCAACTTTACGGTGG+TGG + tig0027216:60386-60405 None:intergenic 40.0%
AGGAAGAATCAACTTTACGG+TGG + tig0027216:60389-60408 None:intergenic 40.0%
TTACCACTACCATAAACACG+AGG + tig0027216:60409-60428 None:intergenic 40.0%
TAAGACTTTAAGCCACTGTG+TGG - tig0027216:59830-59849 Msa1433010:three_prime_UTR 40.0%
CAAAGATGGAGACAAATACG+TGG + tig0027216:59977-59996 None:intergenic 40.0%
!! ATCATGGTGTAGTTCTGATC+AGG + tig0027216:60147-60166 None:intergenic 40.0%
TACAGAACTGGTAGCTTCTA+AGG + tig0027216:60188-60207 None:intergenic 40.0%
GACTCTTCTTTCTACAGAAC+TGG + tig0027216:60200-60219 None:intergenic 40.0%
GCTGTGAAAACCTTCTTCTA+CGG + tig0027216:60344-60363 None:intergenic 40.0%
AAGAATCAACTTTACGGTGG+TGG + tig0027216:60386-60405 None:intergenic 40.0%
AGGAAGAATCAACTTTACGG+TGG + tig0027216:60389-60408 None:intergenic 40.0%
TTACCACTACCATAAACACG+AGG + tig0027216:60409-60428 None:intergenic 40.0%
TAGTCACACTTCCCATGTCT+TGG + tig0027216:60080-60099 None:intergenic 45.0%
! TGCTCGTGGACTAAGAAAGT+TGG - tig0027216:60284-60303 Msa1433010:CDS 45.0%
CTTCCTCGTGTTTATGGTAG+TGG - tig0027216:60403-60422 Msa1433010:intron 45.0%
TAGTCACACTTCCCATGTCT+TGG + tig0027216:60080-60099 None:intergenic 45.0%
! TGCTCGTGGACTAAGAAAGT+TGG - tig0027216:60284-60303 Msa1433010:CDS 45.0%
CTTCCTCGTGTTTATGGTAG+TGG - tig0027216:60403-60422 Msa1433010:intron 45.0%
GACTTTAAGCCACTGTGTGG+TGG - tig0027216:59833-59852 Msa1433010:three_prime_UTR 50.0%
! GTTTTCGCTGCGTTATGACC+AGG + tig0027216:59862-59881 None:intergenic 50.0%
GACTTTAAGCCACTGTGTGG+TGG - tig0027216:59833-59852 Msa1433010:three_prime_UTR 50.0%
! GTTTTCGCTGCGTTATGACC+AGG + tig0027216:59862-59881 None:intergenic 50.0%
ACCAGGACGCCACCACACAG+TGG + tig0027216:59845-59864 None:intergenic 65.0%
ACCAGGACGCCACCACACAG+TGG + tig0027216:59845-59864 None:intergenic 65.0%
! GCCACTGTGTGGTGGCGTCC+TGG - tig0027216:59841-59860 Msa1433010:three_prime_UTR 70.0%
! GCCACTGTGTGGTGGCGTCC+TGG - tig0027216:59841-59860 Msa1433010:three_prime_UTR 70.0%
Chromosome Type Strat End Strand Name
tig0027216 gene 59787 60604 59787 ID=Msa1433010;Name=Msa1433010
tig0027216 mRNA 59787 60604 59787 ID=Msa1433010-mRNA-1;Parent=Msa1433010;Name=Msa1433010-mRNA-1;_AED=0.00;_eAED=0.00;_QI=138|1|1|1|0|0.5|2|182|112
tig0027216 exon 59787 60332 59787 ID=Msa1433010-mRNA-1:exon:8399;Parent=Msa1433010-mRNA-1
tig0027216 exon 60492 60604 60492 ID=Msa1433010-mRNA-1:exon:8398;Parent=Msa1433010-mRNA-1
tig0027216 five_prime_UTR 60492 60604 60492 ID=Msa1433010-mRNA-1:five_prime_utr;Parent=Msa1433010-mRNA-1
tig0027216 five_prime_UTR 60308 60332 60308 ID=Msa1433010-mRNA-1:five_prime_utr;Parent=Msa1433010-mRNA-1
tig0027216 CDS 59969 60307 59969 ID=Msa1433010-mRNA-1:cds;Parent=Msa1433010-mRNA-1
tig0027216 three_prime_UTR 59787 59968 59787 ID=Msa1433010-mRNA-1:three_prime_utr;Parent=Msa1433010-mRNA-1
Gene Sequence

>Msa1433010

ATGGGAAGTGTGACTATGAATCCATTGTTTAGGACTGAATCTTTTGGATATTACAACTTTCCTGATCAGAACTACACCATGATAGAGAAGAGACAGTTATTCCTTAGAAGCTACCAGTTCTGTAGAAAGAAGAGTCTGACAGAAAGAATTAAAGGATCTTTTGTTCGTGCTAAGAAAGTTGTATGGTTAAAGTTAAGGTATGCTCGTGGACTAAGAAAGTTGGTGTTTTTTCCAAGGTTTAAATGCGGTTTTTATTACCGTAGAAGAAGGTTTTCACAGCTTTTAAACAGTAGCAGCAGCCACCACCGTAAAGTTGATTCTTCCTCGTGTTTATGGTAG
Protein sequence

>Msa1433010

MGSVTMNPLFRTESFGYYNFPDQNYTMIEKRQLFLRSYQFCRKKSLTERIKGSFVRAKKVVWLKLRYARGLRKLVFFPRFKCGFYYRRRRFSQLLNSSSSHHRKVDSSSCLW*