AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0602240


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0602240 MtrunA17_Chr4g0029791 96.809 94 3 0 1 94 1 94 5.69e-64 188
Msa0602240 MtrunA17_Chr2g0326261 45.361 97 27 4 1 94 1 74 2.46e-11 54.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0602240 AT5G60400.3 40.449 89 51 1 6 94 5 91 1.51e-11 55.8

Find 24 sgRNAs with CRISPR-Local

Find 84 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGAGTTCCTCTCTGTCTTTC+TGG 0.075036 4_2:-45706715 Msa0602240:CDS
AAAATCAAATATGCATATTT+TGG 0.124229 4_2:-45706118 Msa0602240:three_prime_UTR
GTTTAACATGGACTGCATTT+TGG 0.222924 4_2:+45706753 None:intergenic
ACTTACTAGAATGTTAATTT+AGG 0.250075 4_2:+45706222 None:intergenic
AAAAGCTGCTTAGTTAGATT+TGG 0.304540 4_2:-45706355 Msa0602240:exon
CGAAGTTTCACCCTATTCAT+TGG 0.395651 4_2:+45706175 None:intergenic
TGATGATGATCTTGAAGATC+TGG 0.442771 4_2:-45706427 Msa0602240:CDS
TTCGTACGGACATATTTGTA+TGG 0.453259 4_2:-45706156 Msa0602240:three_prime_UTR
AGTGCATGCAAATCAAGAAA+AGG 0.472454 4_2:-45706493 Msa0602240:CDS
ACTGATGTGACCAATGAATA+GGG 0.474910 4_2:-45706185 Msa0602240:three_prime_UTR
AACTGATGTGACCAATGAAT+AGG 0.478716 4_2:-45706186 Msa0602240:three_prime_UTR
CTGTCTCTTACTTATCTCCC+AGG 0.495221 4_2:-45706387 Msa0602240:CDS
TTAAACCTTCGTGCTACTCA+TGG 0.498021 4_2:-45706736 Msa0602240:CDS
ACCGAAGAAGAAAAGATATG+AGG 0.524381 4_2:-45706527 Msa0602240:CDS
GTGCATGCAAATCAAGAAAA+GGG 0.524986 4_2:-45706492 Msa0602240:CDS
TACTCTTTGGAAAGAGCAAG+AGG 0.575505 4_2:+45706682 None:intergenic
AACATTCTAGTAAGTTCAGA+CGG 0.600784 4_2:-45706214 Msa0602240:three_prime_UTR
TTTGGAAAGAGCAAGAGGGT+TGG 0.601098 4_2:+45706687 None:intergenic
AAAAGGATGGGAAATAAAGG+AGG 0.624688 4_2:+45706804 None:intergenic
GAATAGGGTGAAACTTCGTA+CGG 0.636390 4_2:-45706170 Msa0602240:three_prime_UTR
ACTCTTTGGAAAGAGCAAGA+GGG 0.667434 4_2:+45706683 None:intergenic
AGTAGCACGAAGGTTTAACA+TGG 0.672060 4_2:+45706741 None:intergenic
GTGATTCCAGAAAGACAGAG+AGG 0.712435 4_2:+45706709 None:intergenic
GAACTCCATGAGTAGCACGA+AGG 0.732005 4_2:+45706731 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAATAAATTAATTTACTCTT+TGG + chr4_2:45706328-45706347 None:intergenic 10.0%
!! AAATAAATTAATTTACTCTT+TGG + chr4_2:45706328-45706347 None:intergenic 10.0%
!!! AAAATCAAATATGCATATTT+TGG - chr4_2:45706876-45706895 Msa0602240:five_prime_UTR 15.0%
!!! AAAATCAAATATGCATATTT+TGG - chr4_2:45706876-45706895 Msa0602240:five_prime_UTR 15.0%
!! TGATATATGTTTGAATTTGA+TGG - chr4_2:45706425-45706444 Msa0602240:CDS 20.0%
!! ACTTACTAGAATGTTAATTT+AGG + chr4_2:45706775-45706794 None:intergenic 20.0%
!!! ATGCATATTTGATTTTGATT+TGG + chr4_2:45706872-45706891 None:intergenic 20.0%
!! TGATATATGTTTGAATTTGA+TGG - chr4_2:45706425-45706444 Msa0602240:CDS 20.0%
!! ACTTACTAGAATGTTAATTT+AGG + chr4_2:45706775-45706794 None:intergenic 20.0%
!!! ATGCATATTTGATTTTGATT+TGG + chr4_2:45706872-45706891 None:intergenic 20.0%
!! TTTTCTAGGTAAAGGAAAAA+AGG + chr4_2:45706210-45706229 None:intergenic 25.0%
!!! GTTTTGTTTTTTCTAGGTAA+AGG + chr4_2:45706218-45706237 None:intergenic 25.0%
!!! TGGTTTGTTTTGTTTTTTCT+AGG + chr4_2:45706224-45706243 None:intergenic 25.0%
!! TCAAAGAAACAATGATTTTG+TGG - chr4_2:45706534-45706553 Msa0602240:CDS 25.0%
!! TCTAAATCACTTTCATTTTC+TGG - chr4_2:45706676-45706695 Msa0602240:intron 25.0%
!! TTTTCTAGGTAAAGGAAAAA+AGG + chr4_2:45706210-45706229 None:intergenic 25.0%
!!! GTTTTGTTTTTTCTAGGTAA+AGG + chr4_2:45706218-45706237 None:intergenic 25.0%
!!! TGGTTTGTTTTGTTTTTTCT+AGG + chr4_2:45706224-45706243 None:intergenic 25.0%
!! TCAAAGAAACAATGATTTTG+TGG - chr4_2:45706534-45706553 Msa0602240:CDS 25.0%
!! TCTAAATCACTTTCATTTTC+TGG - chr4_2:45706676-45706695 Msa0602240:intron 25.0%
GAAAAAAGGATGGGAAATAA+AGG + chr4_2:45706196-45706215 None:intergenic 30.0%
TAGGTAAAGGAAAAAAGGAT+GGG + chr4_2:45706205-45706224 None:intergenic 30.0%
! TCCTCATATCTTTTCTTCTT+CGG + chr4_2:45706471-45706490 None:intergenic 30.0%
! AATGATTTTGTGGAGATGAA+AGG - chr4_2:45706544-45706563 Msa0602240:CDS 30.0%
AAAAGCTGCTTAGTTAGATT+TGG - chr4_2:45706639-45706658 Msa0602240:intron 30.0%
AACATTCTAGTAAGTTCAGA+CGG - chr4_2:45706780-45706799 Msa0602240:five_prime_UTR 30.0%
GAAAAAAGGATGGGAAATAA+AGG + chr4_2:45706196-45706215 None:intergenic 30.0%
TAGGTAAAGGAAAAAAGGAT+GGG + chr4_2:45706205-45706224 None:intergenic 30.0%
! TCCTCATATCTTTTCTTCTT+CGG + chr4_2:45706471-45706490 None:intergenic 30.0%
! AATGATTTTGTGGAGATGAA+AGG - chr4_2:45706544-45706563 Msa0602240:CDS 30.0%
AAAAGCTGCTTAGTTAGATT+TGG - chr4_2:45706639-45706658 Msa0602240:intron 30.0%
AACATTCTAGTAAGTTCAGA+CGG - chr4_2:45706780-45706799 Msa0602240:five_prime_UTR 30.0%
AAAAGGATGGGAAATAAAGG+AGG + chr4_2:45706193-45706212 None:intergenic 35.0%
CTAGGTAAAGGAAAAAAGGA+TGG + chr4_2:45706206-45706225 None:intergenic 35.0%
!! GTTTAACATGGACTGCATTT+TGG + chr4_2:45706244-45706263 None:intergenic 35.0%
GTGAGATCATAGATCAAAAG+AGG + chr4_2:45706367-45706386 None:intergenic 35.0%
!! ATGTTTGAATTTGATGGTGC+AGG - chr4_2:45706431-45706450 Msa0602240:CDS 35.0%
ACCGAAGAAGAAAAGATATG+AGG - chr4_2:45706467-45706486 Msa0602240:CDS 35.0%
AGTGCATGCAAATCAAGAAA+AGG - chr4_2:45706501-45706520 Msa0602240:CDS 35.0%
GTGCATGCAAATCAAGAAAA+GGG - chr4_2:45706502-45706521 Msa0602240:CDS 35.0%
! TGATGATGATCTTGAAGATC+TGG - chr4_2:45706567-45706586 Msa0602240:intron 35.0%
AACTGATGTGACCAATGAAT+AGG - chr4_2:45706808-45706827 Msa0602240:five_prime_UTR 35.0%
ACTGATGTGACCAATGAATA+GGG - chr4_2:45706809-45706828 Msa0602240:five_prime_UTR 35.0%
TTCGTACGGACATATTTGTA+TGG - chr4_2:45706838-45706857 Msa0602240:five_prime_UTR 35.0%
AAAAGGATGGGAAATAAAGG+AGG + chr4_2:45706193-45706212 None:intergenic 35.0%
CTAGGTAAAGGAAAAAAGGA+TGG + chr4_2:45706206-45706225 None:intergenic 35.0%
!! GTTTAACATGGACTGCATTT+TGG + chr4_2:45706244-45706263 None:intergenic 35.0%
GTGAGATCATAGATCAAAAG+AGG + chr4_2:45706367-45706386 None:intergenic 35.0%
!! ATGTTTGAATTTGATGGTGC+AGG - chr4_2:45706431-45706450 Msa0602240:CDS 35.0%
ACCGAAGAAGAAAAGATATG+AGG - chr4_2:45706467-45706486 Msa0602240:CDS 35.0%
AGTGCATGCAAATCAAGAAA+AGG - chr4_2:45706501-45706520 Msa0602240:CDS 35.0%
GTGCATGCAAATCAAGAAAA+GGG - chr4_2:45706502-45706521 Msa0602240:CDS 35.0%
! TGATGATGATCTTGAAGATC+TGG - chr4_2:45706567-45706586 Msa0602240:intron 35.0%
AACTGATGTGACCAATGAAT+AGG - chr4_2:45706808-45706827 Msa0602240:five_prime_UTR 35.0%
ACTGATGTGACCAATGAATA+GGG - chr4_2:45706809-45706828 Msa0602240:five_prime_UTR 35.0%
TTCGTACGGACATATTTGTA+TGG - chr4_2:45706838-45706857 Msa0602240:five_prime_UTR 35.0%
AGTAGCACGAAGGTTTAACA+TGG + chr4_2:45706256-45706275 None:intergenic 40.0%
! TTAAACCTTCGTGCTACTCA+TGG - chr4_2:45706258-45706277 Msa0602240:three_prime_UTR 40.0%
! ACTCTTTGGAAAGAGCAAGA+GGG + chr4_2:45706314-45706333 None:intergenic 40.0%
! TACTCTTTGGAAAGAGCAAG+AGG + chr4_2:45706315-45706334 None:intergenic 40.0%
!! TTGAATTTGATGGTGCAGGA+TGG - chr4_2:45706435-45706454 Msa0602240:CDS 40.0%
! CAGCTTTTGCTGATAAACCT+GGG + chr4_2:45706627-45706646 None:intergenic 40.0%
CGAAGTTTCACCCTATTCAT+TGG + chr4_2:45706822-45706841 None:intergenic 40.0%
GAATAGGGTGAAACTTCGTA+CGG - chr4_2:45706824-45706843 Msa0602240:five_prime_UTR 40.0%
AGTAGCACGAAGGTTTAACA+TGG + chr4_2:45706256-45706275 None:intergenic 40.0%
! TTAAACCTTCGTGCTACTCA+TGG - chr4_2:45706258-45706277 Msa0602240:three_prime_UTR 40.0%
! ACTCTTTGGAAAGAGCAAGA+GGG + chr4_2:45706314-45706333 None:intergenic 40.0%
! TACTCTTTGGAAAGAGCAAG+AGG + chr4_2:45706315-45706334 None:intergenic 40.0%
!! TTGAATTTGATGGTGCAGGA+TGG - chr4_2:45706435-45706454 Msa0602240:CDS 40.0%
! CAGCTTTTGCTGATAAACCT+GGG + chr4_2:45706627-45706646 None:intergenic 40.0%
CGAAGTTTCACCCTATTCAT+TGG + chr4_2:45706822-45706841 None:intergenic 40.0%
GAATAGGGTGAAACTTCGTA+CGG - chr4_2:45706824-45706843 Msa0602240:five_prime_UTR 40.0%
GTGATTCCAGAAAGACAGAG+AGG + chr4_2:45706288-45706307 None:intergenic 45.0%
TTTGGAAAGAGCAAGAGGGT+TGG + chr4_2:45706310-45706329 None:intergenic 45.0%
CTGTCTCTTACTTATCTCCC+AGG - chr4_2:45706607-45706626 Msa0602240:intron 45.0%
! GCAGCTTTTGCTGATAAACC+TGG + chr4_2:45706628-45706647 None:intergenic 45.0%
GTGATTCCAGAAAGACAGAG+AGG + chr4_2:45706288-45706307 None:intergenic 45.0%
TTTGGAAAGAGCAAGAGGGT+TGG + chr4_2:45706310-45706329 None:intergenic 45.0%
CTGTCTCTTACTTATCTCCC+AGG - chr4_2:45706607-45706626 Msa0602240:intron 45.0%
! GCAGCTTTTGCTGATAAACC+TGG + chr4_2:45706628-45706647 None:intergenic 45.0%
GAACTCCATGAGTAGCACGA+AGG + chr4_2:45706266-45706285 None:intergenic 50.0%
GGAGTTCCTCTCTGTCTTTC+TGG - chr4_2:45706279-45706298 Msa0602240:three_prime_UTR 50.0%
GAACTCCATGAGTAGCACGA+AGG + chr4_2:45706266-45706285 None:intergenic 50.0%
GGAGTTCCTCTCTGTCTTTC+TGG - chr4_2:45706279-45706298 Msa0602240:three_prime_UTR 50.0%
Chromosome Type Strat End Strand Name
chr4_2 gene 45706116 45706900 45706116 ID=Msa0602240;Name=Msa0602240
chr4_2 mRNA 45706116 45706900 45706116 ID=Msa0602240-mRNA-1;Parent=Msa0602240;Name=Msa0602240-mRNA-1;_AED=0.00;_eAED=0.00;_QI=130|1|1|1|1|1|2|249|94
chr4_2 exon 45706116 45706563 45706116 ID=Msa0602240-mRNA-1:exon:10269;Parent=Msa0602240-mRNA-1
chr4_2 exon 45706685 45706900 45706685 ID=Msa0602240-mRNA-1:exon:10268;Parent=Msa0602240-mRNA-1
chr4_2 five_prime_UTR 45706771 45706900 45706771 ID=Msa0602240-mRNA-1:five_prime_utr;Parent=Msa0602240-mRNA-1
chr4_2 CDS 45706685 45706770 45706685 ID=Msa0602240-mRNA-1:cds;Parent=Msa0602240-mRNA-1
chr4_2 CDS 45706365 45706563 45706365 ID=Msa0602240-mRNA-1:cds;Parent=Msa0602240-mRNA-1
chr4_2 three_prime_UTR 45706116 45706364 45706116 ID=Msa0602240-mRNA-1:three_prime_utr;Parent=Msa0602240-mRNA-1
Gene Sequence

>Msa0602240

ATGCAGTCCATGTTAAACCTTCGTGCTACTCATGGAGTTCCTCTCTGTCTTTCTGGAATCACCAACCCTCTTGCTCTTTCCAAAGAGATGGCAGATCACGACCGAAGAAGAAAAGATATGAGGAAGCAAAGATCAGTGCATGCAAATCAAGAAAAGGGTGCACAAAGTCAAAGAAACAATGATTTTGTGGAGATGAAAGGTGATGATGATCTTGAAGATCTGGATGAAATCTTGCATCAACTGTCTCTTACTTATCTCCCAGGTTTATCAGCAAAAGCTGCTTAG

Protein sequence

>Msa0602240

MQSMLNLRATHGVPLCLSGITNPLALSKEMADHDRRRKDMRKQRSVHANQEKGAQSQRNNDFVEMKGDDDLEDLDEILHQLSLTYLPGLSAKAA*