AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0343080

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0343080 MtrunA17_Chr5g0402121 95.385 130 4 1 1 130 1 128 2.07e-88 252
Msa0343080 MtrunA17_Chr4g0047131 52.703 74 30 4 57 130 41 109 5.38e-16 68.6
Msa0343080 MtrunA17_Chr4g0067331 38.211 123 57 5 19 130 12 126 2.53e-12 59.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0343080 AT5G67070.1 59.804 102 37 1 33 130 28 129 2.93e-41 134
Msa0343080 AT4G15800.1 50.000 72 27 4 60 130 53 116 5.11e-12 58.9
Msa0343080 AT2G33775.1 44.681 94 42 5 41 130 20 107 8.22e-12 58.2
Msa0343080 AT3G05490.1 54.545 66 21 4 66 130 62 119 1.80e-11 57.4
Msa0343080 AT1G28270.1 36.885 122 58 6 13 130 1 107 4.22e-11 56.2
Msa0343080 AT1G02900.1 34.375 128 66 7 8 129 4 119 5.35e-11 56.2

Find 29 sgRNAs with CRISPR-Local

Find 29 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCAGTAGAAGATCTTTGTTC+TGG 0.343429 3_1:-1094910 Msa0343080:CDS
GTGAAATACTACATCTCTTA+TGG 0.349611 3_1:-1094881 Msa0343080:CDS
CTTCTTCATTGTCTTCATCT+AGG 0.376491 3_1:+1094948 None:intergenic
ATCCCATGTCCACCTCGTTC+TGG 0.403176 3_1:-1094839 Msa0343080:CDS
TGAGAGTGAGAGTGAGGTTG+AGG 0.407961 3_1:+1095098 None:intergenic
CCTCTATAGTAAGGATGAAC+AGG 0.422834 3_1:+1094776 None:intergenic
GAGTGTTGAGGAGGGTAAAG+AGG 0.453446 3_1:+1095059 None:intergenic
TAAAGTGCTGACATTGTTGT+TGG 0.463963 3_1:+1094977 None:intergenic
CCTGTTCATCCTTACTATAG+AGG 0.473303 3_1:-1094776 Msa0343080:CDS
GGAGGGTAAAGAGGAGACAA+AGG 0.483029 3_1:+1095068 None:intergenic
AGTGTCTGAGATGAGGTTCA+AGG 0.500378 3_1:+1095009 None:intergenic
GCAGAACAACCTCTATAGTA+AGG 0.503378 3_1:+1094767 None:intergenic
GAAGGGTGAGAGTGAGAGTG+AGG 0.505600 3_1:+1095092 None:intergenic
CTACCAGAACGAGGTGGACA+TGG 0.522636 3_1:+1094836 None:intergenic
TAAAGAGGAGACAAAGGAGA+AGG 0.532366 3_1:+1095074 None:intergenic
AAAGAGGAGACAAAGGAGAA+GGG 0.538073 3_1:+1095075 None:intergenic
GTTCTGCTATCACACGCTGC+AGG 0.553220 3_1:-1094751 Msa0343080:CDS
AGTGAGGTTGAGGAGAGTAG+AGG 0.570642 3_1:+1095108 None:intergenic
TCATCTCAGACACTCTAGAA+TGG 0.573586 3_1:-1095000 Msa0343080:CDS
CTGCTATCACACGCTGCAGG+AGG 0.602724 3_1:-1094748 Msa0343080:CDS
TACCAGAACGAGGTGGACAT+GGG 0.611782 3_1:+1094837 None:intergenic
TCTGAGATGAGGTTCAAGGT+TGG 0.623288 3_1:+1095013 None:intergenic
ATTCTAGAGTGTCTGAGATG+AGG 0.623976 3_1:+1095002 None:intergenic
CATAAGTGTTATGAAGCTAG+AGG 0.636363 3_1:-1094800 Msa0343080:CDS
GTGCATCAACGTGAGTGTTG+AGG 0.665205 3_1:+1095047 None:intergenic
CATCAACGTGAGTGTTGAGG+AGG 0.668250 3_1:+1095050 None:intergenic
ATCAACGTGAGTGTTGAGGA+GGG 0.679056 3_1:+1095051 None:intergenic
TAAGATCTACCAGAACGAGG+TGG 0.735611 3_1:+1094830 None:intergenic
TAGTAAGATCTACCAGAACG+AGG 0.758003 3_1:+1094827 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
GTGAAATACTACATCTCTTA+TGG - chr3_1:1094979-1094998 Msa0343080:CDS 30.0%
!! TAAAGTGCTGACATTGTTGT+TGG + chr3_1:1094886-1094905 None:intergenic 35.0%
CTTCTTCATTGTCTTCATCT+AGG + chr3_1:1094915-1094934 None:intergenic 35.0%
TCAGTAGAAGATCTTTGTTC+TGG - chr3_1:1094950-1094969 Msa0343080:CDS 35.0%
CATAAGTGTTATGAAGCTAG+AGG - chr3_1:1095060-1095079 Msa0343080:CDS 35.0%
AAAGAGGAGACAAAGGAGAA+GGG + chr3_1:1094788-1094807 None:intergenic 40.0%
TAAAGAGGAGACAAAGGAGA+AGG + chr3_1:1094789-1094808 None:intergenic 40.0%
!! ATTCTAGAGTGTCTGAGATG+AGG + chr3_1:1094861-1094880 None:intergenic 40.0%
! TCATCTCAGACACTCTAGAA+TGG - chr3_1:1094860-1094879 Msa0343080:CDS 40.0%
TAGTAAGATCTACCAGAACG+AGG + chr3_1:1095036-1095055 None:intergenic 40.0%
CCTCTATAGTAAGGATGAAC+AGG + chr3_1:1095087-1095106 None:intergenic 40.0%
CCTGTTCATCCTTACTATAG+AGG - chr3_1:1095084-1095103 Msa0343080:CDS 40.0%
GCAGAACAACCTCTATAGTA+AGG + chr3_1:1095096-1095115 None:intergenic 40.0%
!! ATCAACGTGAGTGTTGAGGA+GGG + chr3_1:1094812-1094831 None:intergenic 45.0%
! TCTGAGATGAGGTTCAAGGT+TGG + chr3_1:1094850-1094869 None:intergenic 45.0%
! AGTGTCTGAGATGAGGTTCA+AGG + chr3_1:1094854-1094873 None:intergenic 45.0%
TAAGATCTACCAGAACGAGG+TGG + chr3_1:1095033-1095052 None:intergenic 45.0%
AGTGAGGTTGAGGAGAGTAG+AGG + chr3_1:1094755-1094774 None:intergenic 50.0%
TGAGAGTGAGAGTGAGGTTG+AGG + chr3_1:1094765-1094784 None:intergenic 50.0%
GGAGGGTAAAGAGGAGACAA+AGG + chr3_1:1094795-1094814 None:intergenic 50.0%
!! GAGTGTTGAGGAGGGTAAAG+AGG + chr3_1:1094804-1094823 None:intergenic 50.0%
!! CATCAACGTGAGTGTTGAGG+AGG + chr3_1:1094813-1094832 None:intergenic 50.0%
! GTGCATCAACGTGAGTGTTG+AGG + chr3_1:1094816-1094835 None:intergenic 50.0%
TACCAGAACGAGGTGGACAT+GGG + chr3_1:1095026-1095045 None:intergenic 50.0%
GAAGGGTGAGAGTGAGAGTG+AGG + chr3_1:1094771-1094790 None:intergenic 55.0%
ATCCCATGTCCACCTCGTTC+TGG - chr3_1:1095021-1095040 Msa0343080:CDS 55.0%
CTACCAGAACGAGGTGGACA+TGG + chr3_1:1095027-1095046 None:intergenic 55.0%
GTTCTGCTATCACACGCTGC+AGG - chr3_1:1095109-1095128 Msa0343080:CDS 55.0%
CTGCTATCACACGCTGCAGG+AGG - chr3_1:1095112-1095131 Msa0343080:CDS 60.0%
Chromosome Type Strat End Strand Name
chr3_1 gene 1094745 1095137 1094745 ID=Msa0343080;Name=Msa0343080
chr3_1 mRNA 1094745 1095137 1094745 ID=Msa0343080-mRNA-1;Parent=Msa0343080;Name=Msa0343080-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|130
chr3_1 exon 1094745 1095137 1094745 ID=Msa0343080-mRNA-1:exon:379;Parent=Msa0343080-mRNA-1
chr3_1 CDS 1094745 1095137 1094745 ID=Msa0343080-mRNA-1:cds;Parent=Msa0343080-mRNA-1
Gene Sequence

>Msa0343080

ATGGCTTCCTCTACTCTCCTCAACCTCACTCTCACTCTCACCCTTCTCCTTTGTCTCCTCTTTACCCTCCTCAACACTCACGTTGATGCACAGATCGAAGAACCAACCTTGAACCTCATCTCAGACACTCTAGAATGGCCAACAACAATGTCAGCACTTTACAATGACCTAGATGAAGACAATGAAGAAGACACAGACAGTGATTTCAGTAGAAGATCTTTGTTCTGGAGTAGAGTGAAATACTACATCTCTTATGGTGCTCTTTCTGCTAACAGAATCCCATGTCCACCTCGTTCTGGTAGATCTTACTACACTCATAAGTGTTATGAAGCTAGAGGTCCTGTTCATCCTTACTATAGAGGTTGTTCTGCTATCACACGCTGCAGGAGGTGA
Protein sequence

>Msa0343080

MASSTLLNLTLTLTLLLCLLFTLLNTHVDAQIEEPTLNLISDTLEWPTTMSALYNDLDEDNEEDTDSDFSRRSLFWSRVKYYISYGALSANRIPCPPRSGRSYYTHKCYEARGPVHPYYRGCSAITRCRR*