AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0366230

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0366230 MtrunA17_Chr3g0107031 92.857 84 5 1 1 84 1 83 2.41e-44 138
Msa0366230 MtrunA17_Chr5g0448171 72.414 87 14 2 1 87 1 77 1.03e-37 121
Msa0366230 MtrunA17_Chr3g0078131 80.460 87 15 2 1 87 1 85 3.34e-37 120
Msa0366230 MtrunA17_Chr5g0432481 59.783 92 33 3 1 89 1 91 9.40e-32 106
Msa0366230 MtrunA17_Chr5g0448111 44.578 83 39 1 1 83 1 76 3.48e-20 77.0
Msa0366230 MtrunA17_Chr7g0253291 44.828 87 38 3 1 86 1 78 7.87e-16 66.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0366230 AT5G58375.1 48.936 94 36 3 1 91 1 85 2.26e-22 83.2
Msa0366230 AT5G18150.1 42.353 85 30 2 1 83 1 68 3.42e-18 72.0
Msa0366230 AT5G14602.1 39.759 83 39 1 1 83 1 72 1.28e-16 68.2

Find 26 sgRNAs with CRISPR-Local

Find 103 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCTTCATCATCATCGATCTT+AGG 0.252325 3_1:+60803011 None:intergenic
GTGTGCTACTGTTTCTGTTA+TGG 0.268984 3_1:-60802506 Msa0366230:three_prime_UTR
ATATGATTGAATCTGGGTTT+TGG 0.273834 3_1:-60802825 Msa0366230:CDS
GTTCGGAATATGATTGAATC+TGG 0.288666 3_1:-60802832 Msa0366230:CDS
TGGCTAGTGGACGTTATCTT+TGG 0.311955 3_1:-60802789 Msa0366230:CDS
TGAATTAAATGAAAATTCTA+AGG 0.317478 3_1:-60802940 Msa0366230:intron
TAGGTTGATTTCTGAAATTT+CGG 0.333725 3_1:+60803030 None:intergenic
ACGTTATCTTTGGAGGAATA+TGG 0.339509 3_1:-60802779 Msa0366230:CDS
AAAATTGACTAAAATTTGAT+TGG 0.363171 3_1:-60803345 Msa0366230:five_prime_UTR
ATAGTTGGCAAGTTGGCATT+AGG 0.366775 3_1:+60803401 None:intergenic
ATTTCGGAGAACGAAGATTC+CGG 0.399084 3_1:+60803046 None:intergenic
AAATCAAAATGTGCCCTTTG+AGG 0.417218 3_1:-60803100 Msa0366230:exon
AAATACACATGTGGGGTTGT+TGG 0.445220 3_1:+60803315 None:intergenic
GTCAAACTTTGATATTCTGT+TGG 0.467478 3_1:-60802421 Msa0366230:three_prime_UTR
AGAACATTATTATTAAGCTT+AGG 0.475364 3_1:-60803180 Msa0366230:five_prime_UTR
CTAGTGGACGTTATCTTTGG+AGG 0.484216 3_1:-60802786 Msa0366230:CDS
ATTATGTTAATGATAATAGT+TGG 0.488931 3_1:+60803386 None:intergenic
AATATGAGAATTAGCCTCAA+AGG 0.502029 3_1:+60803086 None:intergenic
AATGATAATAGTTGGCAAGT+TGG 0.510967 3_1:+60803394 None:intergenic
ATATGAGAATTAGCCTCAAA+GGG 0.515144 3_1:+60803087 None:intergenic
TTCGGAATATGATTGAATCT+GGG 0.519834 3_1:-60802831 Msa0366230:CDS
TCTAGCTGATGATGTGTACT+TGG 0.520132 3_1:-60802736 Msa0366230:exon
TTCTTGTCCGCAACACTCGC+CGG 0.522394 3_1:-60803065 Msa0366230:CDS
TGTACTTGGTGAATGCATGT+TGG 0.535879 3_1:-60802722 Msa0366230:three_prime_UTR
GTACTTGGTGAATGCATGTT+GGG 0.550068 3_1:-60802721 Msa0366230:three_prime_UTR
GAAGATTCCGGCGAGTGTTG+CGG 0.583534 3_1:+60803058 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTATTAAAATTAAAGCAAAA+GGG + chr3_1:60802912-60802931 None:intergenic 10.0%
!! TTTATTAAAATTAAAGCAAA+AGG + chr3_1:60802913-60802932 None:intergenic 10.0%
!! TTATTAAAATTAAAGCAAAA+GGG + chr3_1:60802912-60802931 None:intergenic 10.0%
!! TTTATTAAAATTAAAGCAAA+AGG + chr3_1:60802913-60802932 None:intergenic 10.0%
!! ATTATGTTAATGATAATAGT+TGG + chr3_1:60802430-60802449 None:intergenic 15.0%
!!! AAATTTTAGTCAATTTTTTG+GGG + chr3_1:60802465-60802484 None:intergenic 15.0%
!!! CAAATTTTAGTCAATTTTTT+GGG + chr3_1:60802466-60802485 None:intergenic 15.0%
!!! TCAAATTTTAGTCAATTTTT+TGG + chr3_1:60802467-60802486 None:intergenic 15.0%
!! AAAATTGACTAAAATTTGAT+TGG - chr3_1:60802468-60802487 Msa0366230:three_prime_UTR 15.0%
!! TGAATTAAATGAAAATTCTA+AGG - chr3_1:60802873-60802892 Msa0366230:intron 15.0%
!! ATTATGTTAATGATAATAGT+TGG + chr3_1:60802430-60802449 None:intergenic 15.0%
!!! AAATTTTAGTCAATTTTTTG+GGG + chr3_1:60802465-60802484 None:intergenic 15.0%
!!! CAAATTTTAGTCAATTTTTT+GGG + chr3_1:60802466-60802485 None:intergenic 15.0%
!!! TCAAATTTTAGTCAATTTTT+TGG + chr3_1:60802467-60802486 None:intergenic 15.0%
!! AAAATTGACTAAAATTTGAT+TGG - chr3_1:60802468-60802487 Msa0366230:three_prime_UTR 15.0%
!! TGAATTAAATGAAAATTCTA+AGG - chr3_1:60802873-60802892 Msa0366230:intron 15.0%
!! AGAACATTATTATTAAGCTT+AGG - chr3_1:60802633-60802652 Msa0366230:three_prime_UTR 20.0%
!! ATCAACAAATCACAAATTTA+GGG + chr3_1:60802956-60802975 None:intergenic 20.0%
!! AATCAACAAATCACAAATTT+AGG + chr3_1:60802957-60802976 None:intergenic 20.0%
!! AGAACATTATTATTAAGCTT+AGG - chr3_1:60802633-60802652 Msa0366230:three_prime_UTR 20.0%
!! ATCAACAAATCACAAATTTA+GGG + chr3_1:60802956-60802975 None:intergenic 20.0%
!! AATCAACAAATCACAAATTT+AGG + chr3_1:60802957-60802976 None:intergenic 20.0%
!!! TAGGTTGATTTCTGAAATTT+CGG + chr3_1:60802786-60802805 None:intergenic 25.0%
!!! TTGAAGAATCTGAGATTTTA+GGG + chr3_1:60802849-60802868 None:intergenic 25.0%
!!! TTTGAAGAATCTGAGATTTT+AGG + chr3_1:60802850-60802869 None:intergenic 25.0%
!!! ATTTGTGATTTGTTGATTCT+AGG - chr3_1:60802959-60802978 Msa0366230:CDS 25.0%
!! CCTATGATATTGTGATTTTT+CGG - chr3_1:60803135-60803154 Msa0366230:five_prime_UTR 25.0%
!!! TAGGTTGATTTCTGAAATTT+CGG + chr3_1:60802786-60802805 None:intergenic 25.0%
!!! TTGAAGAATCTGAGATTTTA+GGG + chr3_1:60802849-60802868 None:intergenic 25.0%
!!! TTTGAAGAATCTGAGATTTT+AGG + chr3_1:60802850-60802869 None:intergenic 25.0%
!!! ATTTGTGATTTGTTGATTCT+AGG - chr3_1:60802959-60802978 Msa0366230:CDS 25.0%
!! CCTATGATATTGTGATTTTT+CGG - chr3_1:60803135-60803154 Msa0366230:five_prime_UTR 25.0%
AATGATAATAGTTGGCAAGT+TGG + chr3_1:60802422-60802441 None:intergenic 30.0%
AAGAGAAAAATACACATGTG+GGG + chr3_1:60802508-60802527 None:intergenic 30.0%
CAAGAGAAAAATACACATGT+GGG + chr3_1:60802509-60802528 None:intergenic 30.0%
! ATATGAGAATTAGCCTCAAA+GGG + chr3_1:60802729-60802748 None:intergenic 30.0%
! AATATGAGAATTAGCCTCAA+AGG + chr3_1:60802730-60802749 None:intergenic 30.0%
TTAAAGCAAAAGGGTCAAAT+GGG + chr3_1:60802903-60802922 None:intergenic 30.0%
ATTAAAGCAAAAGGGTCAAA+TGG + chr3_1:60802904-60802923 None:intergenic 30.0%
!! TGATTTGTTGATTCTAGGTT+CGG - chr3_1:60802964-60802983 Msa0366230:CDS 30.0%
TTCGGAATATGATTGAATCT+GGG - chr3_1:60802982-60803001 Msa0366230:CDS 30.0%
! ATATGATTGAATCTGGGTTT+TGG - chr3_1:60802988-60803007 Msa0366230:CDS 30.0%
CCGAAAAATCACAATATCAT+AGG + chr3_1:60803138-60803157 None:intergenic 30.0%
GTCAAACTTTGATATTCTGT+TGG - chr3_1:60803392-60803411 Msa0366230:five_prime_UTR 30.0%
AATGATAATAGTTGGCAAGT+TGG + chr3_1:60802422-60802441 None:intergenic 30.0%
AAGAGAAAAATACACATGTG+GGG + chr3_1:60802508-60802527 None:intergenic 30.0%
CAAGAGAAAAATACACATGT+GGG + chr3_1:60802509-60802528 None:intergenic 30.0%
! ATATGAGAATTAGCCTCAAA+GGG + chr3_1:60802729-60802748 None:intergenic 30.0%
! AATATGAGAATTAGCCTCAA+AGG + chr3_1:60802730-60802749 None:intergenic 30.0%
TTAAAGCAAAAGGGTCAAAT+GGG + chr3_1:60802903-60802922 None:intergenic 30.0%
ATTAAAGCAAAAGGGTCAAA+TGG + chr3_1:60802904-60802923 None:intergenic 30.0%
!! TGATTTGTTGATTCTAGGTT+CGG - chr3_1:60802964-60802983 Msa0366230:CDS 30.0%
TTCGGAATATGATTGAATCT+GGG - chr3_1:60802982-60803001 Msa0366230:CDS 30.0%
! ATATGATTGAATCTGGGTTT+TGG - chr3_1:60802988-60803007 Msa0366230:CDS 30.0%
CCGAAAAATCACAATATCAT+AGG + chr3_1:60803138-60803157 None:intergenic 30.0%
GTCAAACTTTGATATTCTGT+TGG - chr3_1:60803392-60803411 Msa0366230:five_prime_UTR 30.0%
CCAAGAGAAAAATACACATG+TGG + chr3_1:60802510-60802529 None:intergenic 35.0%
! CCACATGTGTATTTTTCTCT+TGG - chr3_1:60802507-60802526 Msa0366230:three_prime_UTR 35.0%
! TACATTTTGTGCATGACTAG+TGG + chr3_1:60802547-60802566 None:intergenic 35.0%
AAATCAAAATGTGCCCTTTG+AGG - chr3_1:60802713-60802732 Msa0366230:three_prime_UTR 35.0%
TCTTCATCATCATCGATCTT+AGG + chr3_1:60802805-60802824 None:intergenic 35.0%
!!! TCTGAGATTTTAGGGTTTGT+AGG + chr3_1:60802841-60802860 None:intergenic 35.0%
GTTCGGAATATGATTGAATC+TGG - chr3_1:60802981-60803000 Msa0366230:CDS 35.0%
!! GTTTTGGACTTTTGTGGATA+TGG - chr3_1:60803004-60803023 Msa0366230:CDS 35.0%
! ACGTTATCTTTGGAGGAATA+TGG - chr3_1:60803034-60803053 Msa0366230:CDS 35.0%
!! CTGTTGGCTTAATTAAATGC+TGG - chr3_1:60803408-60803427 Msa0366230:five_prime_UTR 35.0%
CCAAGAGAAAAATACACATG+TGG + chr3_1:60802510-60802529 None:intergenic 35.0%
! CCACATGTGTATTTTTCTCT+TGG - chr3_1:60802507-60802526 Msa0366230:three_prime_UTR 35.0%
! TACATTTTGTGCATGACTAG+TGG + chr3_1:60802547-60802566 None:intergenic 35.0%
AAATCAAAATGTGCCCTTTG+AGG - chr3_1:60802713-60802732 Msa0366230:three_prime_UTR 35.0%
TCTTCATCATCATCGATCTT+AGG + chr3_1:60802805-60802824 None:intergenic 35.0%
!!! TCTGAGATTTTAGGGTTTGT+AGG + chr3_1:60802841-60802860 None:intergenic 35.0%
GTTCGGAATATGATTGAATC+TGG - chr3_1:60802981-60803000 Msa0366230:CDS 35.0%
!! GTTTTGGACTTTTGTGGATA+TGG - chr3_1:60803004-60803023 Msa0366230:CDS 35.0%
! ACGTTATCTTTGGAGGAATA+TGG - chr3_1:60803034-60803053 Msa0366230:CDS 35.0%
! ATAGTTGGCAAGTTGGCATT+AGG + chr3_1:60802415-60802434 None:intergenic 40.0%
!!! ATTTTTTGGGGCAGTGTTTG+TGG + chr3_1:60802453-60802472 None:intergenic 40.0%
AAATACACATGTGGGGTTGT+TGG + chr3_1:60802501-60802520 None:intergenic 40.0%
ATTTCGGAGAACGAAGATTC+CGG + chr3_1:60802770-60802789 None:intergenic 40.0%
!!! ATCTGGGTTTTGGACTTTTG+TGG - chr3_1:60802998-60803017 Msa0366230:CDS 40.0%
! ACTTTTGTGGATATGGCTAG+TGG - chr3_1:60803011-60803030 Msa0366230:CDS 40.0%
! TCTAGCTGATGATGTGTACT+TGG - chr3_1:60803077-60803096 Msa0366230:CDS 40.0%
! TGTACTTGGTGAATGCATGT+TGG - chr3_1:60803091-60803110 Msa0366230:CDS 40.0%
! GTACTTGGTGAATGCATGTT+GGG - chr3_1:60803092-60803111 Msa0366230:CDS 40.0%
!! GTGTGCTACTGTTTCTGTTA+TGG - chr3_1:60803307-60803326 Msa0366230:five_prime_UTR 40.0%
! ATAGTTGGCAAGTTGGCATT+AGG + chr3_1:60802415-60802434 None:intergenic 40.0%
!!! ATTTTTTGGGGCAGTGTTTG+TGG + chr3_1:60802453-60802472 None:intergenic 40.0%
AAATACACATGTGGGGTTGT+TGG + chr3_1:60802501-60802520 None:intergenic 40.0%
ATTTCGGAGAACGAAGATTC+CGG + chr3_1:60802770-60802789 None:intergenic 40.0%
!!! ATCTGGGTTTTGGACTTTTG+TGG - chr3_1:60802998-60803017 Msa0366230:CDS 40.0%
! ACTTTTGTGGATATGGCTAG+TGG - chr3_1:60803011-60803030 Msa0366230:CDS 40.0%
! TCTAGCTGATGATGTGTACT+TGG - chr3_1:60803077-60803096 Msa0366230:CDS 40.0%
! TGTACTTGGTGAATGCATGT+TGG - chr3_1:60803091-60803110 Msa0366230:CDS 40.0%
! GTACTTGGTGAATGCATGTT+GGG - chr3_1:60803092-60803111 Msa0366230:CDS 40.0%
!! GTGTGCTACTGTTTCTGTTA+TGG - chr3_1:60803307-60803326 Msa0366230:five_prime_UTR 40.0%
! TGGCTAGTGGACGTTATCTT+TGG - chr3_1:60803024-60803043 Msa0366230:CDS 45.0%
! CTAGTGGACGTTATCTTTGG+AGG - chr3_1:60803027-60803046 Msa0366230:CDS 45.0%
! TGGCTAGTGGACGTTATCTT+TGG - chr3_1:60803024-60803043 Msa0366230:CDS 45.0%
! CTAGTGGACGTTATCTTTGG+AGG - chr3_1:60803027-60803046 Msa0366230:CDS 45.0%
TTCTTGTCCGCAACACTCGC+CGG - chr3_1:60802748-60802767 Msa0366230:exon 55.0%
! GAAGATTCCGGCGAGTGTTG+CGG + chr3_1:60802758-60802777 None:intergenic 55.0%
TTCTTGTCCGCAACACTCGC+CGG - chr3_1:60802748-60802767 Msa0366230:exon 55.0%
! GAAGATTCCGGCGAGTGTTG+CGG + chr3_1:60802758-60802777 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr3_1 gene 60802406 60803429 60802406 ID=Msa0366230;Name=Msa0366230
chr3_1 mRNA 60802406 60803429 60802406 ID=Msa0366230-mRNA-1;Parent=Msa0366230;Name=Msa0366230-mRNA-1;_AED=0.00;_eAED=0.00;_QI=315|1|1|1|1|1|2|344|92
chr3_1 exon 60802406 60802854 60802406 ID=Msa0366230-mRNA-1:exon:11746;Parent=Msa0366230-mRNA-1
chr3_1 exon 60802941 60803429 60802941 ID=Msa0366230-mRNA-1:exon:11745;Parent=Msa0366230-mRNA-1
chr3_1 five_prime_UTR 60803115 60803429 60803115 ID=Msa0366230-mRNA-1:five_prime_utr;Parent=Msa0366230-mRNA-1
chr3_1 CDS 60802941 60803114 60802941 ID=Msa0366230-mRNA-1:cds;Parent=Msa0366230-mRNA-1
chr3_1 CDS 60802750 60802854 60802750 ID=Msa0366230-mRNA-1:cds;Parent=Msa0366230-mRNA-1
chr3_1 three_prime_UTR 60802406 60802749 60802406 ID=Msa0366230-mRNA-1:three_prime_utr;Parent=Msa0366230-mRNA-1
Gene Sequence

>Msa0366230

ATGTGCCCTTTGAGGCTAATTCTCATATTCTTGTCCGCAACACTCGCCGGAATCTTCGTTCTCCGAAATTTCAGAAATCAACCTAAGATCGATGATGATGAAGATGAAGATCTTGCTCCTACAAACCCTAAAATCTCAGATTCTTCAAATGCTGAATTAAATGAAAATTCTAAGGTTCGGAATATGATTGAATCTGGGTTTTGGACTTTTGTGGATATGGCTAGTGGACGTTATCTTTGGAGGAATATGGTATCATCATCTTCAAAGAAATCTAGCTGA
Protein sequence

>Msa0366230

MCPLRLILIFLSATLAGIFVLRNFRNQPKIDDDEDEDLAPTNPKISDSSNAELNENSKVRNMIESGFWTFVDMASGRYLWRNMVSSSSKKSS*