AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1336670


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1336670 MtrunA17_Chr5g0407081 69.591 171 21 1 20 159 580 750 1.20e-69 226
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1336670 AT2G17550.2 41.379 174 68 4 20 159 431 604 3.97e-27 107
Msa1336670 AT2G17550.1 40.782 179 72 4 15 159 500 678 4.65e-27 107

Find 17 sgRNAs with CRISPR-Local

Find 70 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GACAAATCGGGAGTTGAAAT+TGG 0.229970 tig0001314:-7805 Msa1336660:intron
GACATCAGCTCTGGTTTAAA+TGG 0.302718 tig0001314:+7865 Msa1336670:CDS
CACTTTCAGTTGTGGAATAT+AGG 0.336396 tig0001314:+8392 Msa1336670:CDS
GAATGATGAAAATTCTATTA+AGG 0.338748 tig0001314:+8315 Msa1336670:CDS
ATCGTCTCTTGATGACAAAT+CGG 0.417961 tig0001314:-7818 Msa1336660:intron
AAAACCTTCCGAGTCTGAAT+TGG 0.428325 tig0001314:+8124 Msa1336670:CDS
AAATGAATCACTTTCAGTTG+TGG 0.503850 tig0001314:+8384 Msa1336670:CDS
AAACTGCTGCACACATATGC+AGG 0.536095 tig0001314:-7745 Msa1336660:intron
TCGTCTCTTGATGACAAATC+GGG 0.538251 tig0001314:-7817 Msa1336660:intron
CTGCACACATATGCAGGACT+AGG 0.542789 tig0001314:-7739 Msa1336660:intron
ACTTGATTCTGATTATGTTG+AGG 0.549512 tig0001314:+8085 Msa1336670:CDS
TACACCAATTCAGACTCGGA+AGG 0.608526 tig0001314:-8128 Msa1336660:intron
CTGATGTCTCTGAAAACTTG+TGG 0.622401 tig0001314:-7850 Msa1336660:intron
TTGTTGATTTGACAGTGCTA+AGG 0.626661 tig0001314:+8048 Msa1336670:intron
TTGAGTGACACTCATCCACA+TGG 0.628662 tig0001314:+8418 Msa1336670:CDS
TAGTTACACCAATTCAGACT+CGG 0.633593 tig0001314:-8132 Msa1336660:intron
CACACATATGCAGGACTAGG+AGG 0.645754 tig0001314:-7736 Msa1336660:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TATAGTTTTGATTCAAGAAA+AGG + tig0001314:7915-7934 Msa1336670:intron 20.0%
!!! AAATATTCAGCATTGAAAAA+AGG - tig0001314:7998-8017 Msa1336660:intron 20.0%
!!! ATATTTTTTCAAACTCTTTC+TGG + tig0001314:8012-8031 Msa1336670:intron 20.0%
!! TCAAAAACAGAATTTCTAAT+AGG - tig0001314:8259-8278 Msa1336660:intron 20.0%
!! GAATGATGAAAATTCTATTA+AGG + tig0001314:8315-8334 Msa1336670:CDS 20.0%
!!! TATAGTTTTGATTCAAGAAA+AGG + tig0001314:7915-7934 Msa1336670:intron 20.0%
!!! AAATATTCAGCATTGAAAAA+AGG - tig0001314:7998-8017 Msa1336660:intron 20.0%
!!! ATATTTTTTCAAACTCTTTC+TGG + tig0001314:8012-8031 Msa1336670:intron 20.0%
!! TCAAAAACAGAATTTCTAAT+AGG - tig0001314:8259-8278 Msa1336660:intron 20.0%
!! GAATGATGAAAATTCTATTA+AGG + tig0001314:8315-8334 Msa1336670:CDS 20.0%
! TGGAATAAATCTTTGTTAAG+AGG + tig0001314:8218-8237 Msa1336670:intron 25.0%
! GGAATAAATCTTTGTTAAGA+GGG + tig0001314:8219-8238 Msa1336670:intron 25.0%
!!! AAATTCTGTTTTTGAAGAAG+TGG + tig0001314:8264-8283 Msa1336670:CDS 25.0%
! TGGAATAAATCTTTGTTAAG+AGG + tig0001314:8218-8237 Msa1336670:intron 25.0%
! GGAATAAATCTTTGTTAAGA+GGG + tig0001314:8219-8238 Msa1336670:intron 25.0%
!!! AAATTCTGTTTTTGAAGAAG+TGG + tig0001314:8264-8283 Msa1336670:CDS 25.0%
! TTTTCTGCTATATGCTCTTT+TGG + tig0001314:7696-7715 Msa1336670:CDS 30.0%
!!! AGTTTTGATTCAAGAAAAGG+CGG + tig0001314:7918-7937 Msa1336670:intron 30.0%
ACTTGATTCTGATTATGTTG+AGG + tig0001314:8085-8104 Msa1336670:CDS 30.0%
AAATGAATCACTTTCAGTTG+TGG + tig0001314:8384-8403 Msa1336670:CDS 30.0%
! TTTTCTGCTATATGCTCTTT+TGG + tig0001314:7696-7715 Msa1336670:CDS 30.0%
!!! AGTTTTGATTCAAGAAAAGG+CGG + tig0001314:7918-7937 Msa1336670:intron 30.0%
ACTTGATTCTGATTATGTTG+AGG + tig0001314:8085-8104 Msa1336670:CDS 30.0%
AAATGAATCACTTTCAGTTG+TGG + tig0001314:8384-8403 Msa1336670:CDS 30.0%
! GCAGTTTTCATGAAGACTTT+TGG + tig0001314:7761-7780 Msa1336670:CDS 35.0%
! GTTTTCATGAAGACTTTTGG+AGG + tig0001314:7764-7783 Msa1336670:CDS 35.0%
! ATCGTCTCTTGATGACAAAT+CGG - tig0001314:7821-7840 Msa1336660:intron 35.0%
!! TTGTTGATTTGACAGTGCTA+AGG + tig0001314:8048-8067 Msa1336670:intron 35.0%
TAGTTACACCAATTCAGACT+CGG - tig0001314:8135-8154 Msa1336660:intron 35.0%
TCTCTTATGTAAGATTCTGC+TGG - tig0001314:8164-8183 Msa1336660:intron 35.0%
! AGAGATTTACTTGTTGCTTC+TGG + tig0001314:8179-8198 Msa1336670:intron 35.0%
!! GTTGCTTCTGGTTTATACTT+TGG + tig0001314:8191-8210 Msa1336670:intron 35.0%
!! CTGGTTTATACTTTGGTTCT+TGG + tig0001314:8198-8217 Msa1336670:intron 35.0%
CACTTTCAGTTGTGGAATAT+AGG + tig0001314:8392-8411 Msa1336670:CDS 35.0%
! GCAGTTTTCATGAAGACTTT+TGG + tig0001314:7761-7780 Msa1336670:CDS 35.0%
! GTTTTCATGAAGACTTTTGG+AGG + tig0001314:7764-7783 Msa1336670:CDS 35.0%
! ATCGTCTCTTGATGACAAAT+CGG - tig0001314:7821-7840 Msa1336660:intron 35.0%
!! TTGTTGATTTGACAGTGCTA+AGG + tig0001314:8048-8067 Msa1336670:intron 35.0%
TAGTTACACCAATTCAGACT+CGG - tig0001314:8135-8154 Msa1336660:intron 35.0%
TCTCTTATGTAAGATTCTGC+TGG - tig0001314:8164-8183 Msa1336660:intron 35.0%
! AGAGATTTACTTGTTGCTTC+TGG + tig0001314:8179-8198 Msa1336670:intron 35.0%
!! GTTGCTTCTGGTTTATACTT+TGG + tig0001314:8191-8210 Msa1336670:intron 35.0%
!! CTGGTTTATACTTTGGTTCT+TGG + tig0001314:8198-8217 Msa1336670:intron 35.0%
CACTTTCAGTTGTGGAATAT+AGG + tig0001314:8392-8411 Msa1336670:CDS 35.0%
!! TCTTTTGGAGAACTACACTG+AGG + tig0001314:7711-7730 Msa1336670:CDS 40.0%
GACAAATCGGGAGTTGAAAT+TGG - tig0001314:7808-7827 Msa1336660:intron 40.0%
! TCGTCTCTTGATGACAAATC+GGG - tig0001314:7820-7839 Msa1336660:intron 40.0%
! CTGATGTCTCTGAAAACTTG+TGG - tig0001314:7853-7872 Msa1336660:intron 40.0%
! GACATCAGCTCTGGTTTAAA+TGG + tig0001314:7865-7884 Msa1336670:CDS 40.0%
AAAACCTTCCGAGTCTGAAT+TGG + tig0001314:8124-8143 Msa1336670:CDS 40.0%
!! TCTTTTGGAGAACTACACTG+AGG + tig0001314:7711-7730 Msa1336670:CDS 40.0%
GACAAATCGGGAGTTGAAAT+TGG - tig0001314:7808-7827 Msa1336660:intron 40.0%
! TCGTCTCTTGATGACAAATC+GGG - tig0001314:7820-7839 Msa1336660:intron 40.0%
! CTGATGTCTCTGAAAACTTG+TGG - tig0001314:7853-7872 Msa1336660:intron 40.0%
! GACATCAGCTCTGGTTTAAA+TGG + tig0001314:7865-7884 Msa1336670:CDS 40.0%
AAAACCTTCCGAGTCTGAAT+TGG + tig0001314:8124-8143 Msa1336670:CDS 40.0%
AAACTGCTGCACACATATGC+AGG - tig0001314:7748-7767 Msa1336660:intron 45.0%
! GTTTTCAGAGACATCAGCTC+TGG + tig0001314:7856-7875 Msa1336670:CDS 45.0%
TACACCAATTCAGACTCGGA+AGG - tig0001314:8131-8150 Msa1336660:intron 45.0%
TTGAGTGACACTCATCCACA+TGG + tig0001314:8418-8437 Msa1336670:CDS 45.0%
!! CACTTTTGAGTGAGACCATG+TGG - tig0001314:8436-8455 Msa1336660:intron 45.0%
AAACTGCTGCACACATATGC+AGG - tig0001314:7748-7767 Msa1336660:intron 45.0%
! GTTTTCAGAGACATCAGCTC+TGG + tig0001314:7856-7875 Msa1336670:CDS 45.0%
TACACCAATTCAGACTCGGA+AGG - tig0001314:8131-8150 Msa1336660:intron 45.0%
TTGAGTGACACTCATCCACA+TGG + tig0001314:8418-8437 Msa1336670:CDS 45.0%
!! CACTTTTGAGTGAGACCATG+TGG - tig0001314:8436-8455 Msa1336660:intron 45.0%
CACACATATGCAGGACTAGG+AGG - tig0001314:7739-7758 Msa1336660:intron 50.0%
CTGCACACATATGCAGGACT+AGG - tig0001314:7742-7761 Msa1336660:intron 50.0%
CACACATATGCAGGACTAGG+AGG - tig0001314:7739-7758 Msa1336660:intron 50.0%
CTGCACACATATGCAGGACT+AGG - tig0001314:7742-7761 Msa1336660:intron 50.0%
Chromosome Type Strat End Strand Name
tig0001314 gene 7661 8456 7661 ID=Msa1336670;Name=Msa1336670
tig0001314 mRNA 7661 8456 7661 ID=Msa1336670-mRNA-1;Parent=Msa1336670;Name=Msa1336670-mRNA-1;_AED=0.33;_eAED=0.34;_QI=0|0|0|1|1|1|3|0|175
tig0001314 exon 7661 7886 7661 ID=Msa1336670-mRNA-1:exon:809;Parent=Msa1336670-mRNA-1
tig0001314 exon 8063 8145 8063 ID=Msa1336670-mRNA-1:exon:810;Parent=Msa1336670-mRNA-1
tig0001314 exon 8238 8456 8238 ID=Msa1336670-mRNA-1:exon:811;Parent=Msa1336670-mRNA-1
tig0001314 CDS 7661 7886 7661 ID=Msa1336670-mRNA-1:cds;Parent=Msa1336670-mRNA-1
tig0001314 CDS 8063 8145 8063 ID=Msa1336670-mRNA-1:cds;Parent=Msa1336670-mRNA-1
tig0001314 CDS 8238 8456 8238 ID=Msa1336670-mRNA-1:cds;Parent=Msa1336670-mRNA-1
Gene Sequence

>Msa1336670

ATGATGATCTTTTTATTGTATAAAACATCATTTGATTTTCTGCTATATGCTCTTTTGGAGAACTACACTGAGGTACCTCCTAGTCCTGCATATGTGTGCAGCAGTTTTCATGAAGACTTTTGGAGGCGAATCGAATATTTAAATCCAATTTCAACTCCCGATTTGTCATCAAGAGACGATACTGTTGTGCCACAAGTTTTCAGAGACATCAGCTCTGGTTTAAATGTGCTAAGGAGACAACTCAATCAACTTGATTCTGATTATGTTGAGGAATTCTCTATGAAACAAAAACCTTCCGAGTCTGAATTGAGGGACACATATGCAAAGCCTATTAGAAATTCTGTTTTTGAAGAAGTGGAAGAATCTCATAAGAAATTGATCAAGCAGAATGATGAAAATTCTATTAAGGATCAAACTGAGAACATACTAGACAATAAGATTTTTCTTGATTTGTTAAATGAATCACTTTCAGTTGTGGAATATAGGCTTTTGAGTGACACTCATCCACATGGTCTCACTCAAAAGTGA

Protein sequence

>Msa1336670

MMIFLLYKTSFDFLLYALLENYTEVPPSPAYVCSSFHEDFWRRIEYLNPISTPDLSSRDDTVVPQVFRDISSGLNVLRRQLNQLDSDYVEEFSMKQKPSESELRDTYAKPIRNSVFEEVEESHKKLIKQNDENSIKDQTENILDNKIFLDLLNESLSVVEYRLLSDTHPHGLTQK*