AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1419410


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1419410 MtrunA17_Chr3g0085681 66.540 263 14 2 1 189 176 438 1.45e-113 330
Msa1419410 MtrunA17_Chr3g0085361 65.779 263 15 3 1 189 91 352 2.32e-111 321
Msa1419410 MtrunA17_Chr5g0396491 36.727 275 89 4 1 190 207 481 1.12e-47 162
Msa1419410 MtrunA17_Chr4g0038851 35.185 270 91 3 5 190 203 472 3.37e-46 157
Msa1419410 MtrunA17_Chr3g0087711 86.207 58 8 0 1 58 1 58 1.64e-29 103
Msa1419410 MtrunA17_Chr7g0224271 28.708 209 117 6 5 187 471 673 3.79e-16 75.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1419410 AT1G50420.1 34.799 273 95 5 1 190 210 482 6.38e-44 152
Msa1419410 AT1G66350.1 25.221 226 102 6 9 190 307 509 2.84e-15 73.6
Msa1419410 AT5G48150.1 25.909 220 100 4 12 187 290 490 4.89e-11 61.2
Msa1419410 AT5G48150.4 25.909 220 100 4 12 187 290 490 4.89e-11 61.2
Msa1419410 AT5G48150.2 25.909 220 100 4 12 187 290 490 4.89e-11 61.2
Msa1419410 AT5G48150.3 25.909 220 100 4 12 187 290 490 4.89e-11 61.2

Find 31 sgRNAs with CRISPR-Local

Find 98 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCTTCAAGTTTGCTAATTAT+TGG 0.118308 tig0024717:-3478 None:intergenic
CTGTATCGGCCTGGAAATTT+AGG 0.200404 tig0024717:+4185 Msa1419410:CDS
GACAGCTGAAGCAGGGATTT+TGG 0.213283 tig0024717:+3435 Msa1419410:CDS
TCTGAATGGATGTAATTTAA+TGG 0.250687 tig0024717:+3823 Msa1419410:CDS
ATGATTGTTTGCTTGTCTGC+TGG 0.372800 tig0024717:+4143 Msa1419410:CDS
TAATCATCTCCTAAATTTCC+AGG 0.378891 tig0024717:-4194 None:intergenic
TTTAGGTGCTTCACCTAAGA+TGG 0.394849 tig0024717:+3733 Msa1419410:intron
GACATGAGAAGCTCGAGAAA+TGG 0.402484 tig0024717:+4005 Msa1419410:CDS
CCTTGCCACTGATGACGAAA+TGG 0.436802 tig0024717:+3576 Msa1419410:CDS
ATTCGAAGGCTTGAAATGAA+TGG 0.452467 tig0024717:+4028 Msa1419410:CDS
GACGAAATGGTCTCCTCAGC+AGG 0.469157 tig0024717:+3589 Msa1419410:CDS
TTTCATTTGACAGCTGAAGC+AGG 0.472492 tig0024717:+3427 Msa1419410:CDS
GAAAACTTGCCTGTCAAGAC+AGG 0.495316 tig0024717:+3511 Msa1419410:CDS
GAACAGGAATCAAATCTGAA+TGG 0.501626 tig0024717:+3809 Msa1419410:CDS
AGCTCGAGAAATGGATTCGA+AGG 0.510467 tig0024717:+4014 Msa1419410:CDS
ACAGCATCTCCTGTCTTGAC+AGG 0.515953 tig0024717:-3520 None:intergenic
ATTATTGGATTGAACTGCAA+AGG 0.517946 tig0024717:-3463 None:intergenic
TTCATTTGACAGCTGAAGCA+GGG 0.544408 tig0024717:+3428 Msa1419410:CDS
GAAGGTACCTTTGAGTTACA+AGG 0.545129 tig0024717:+4057 Msa1419410:CDS
TACCTTTGAGTTACAAGGGG+AGG 0.564683 tig0024717:+4062 Msa1419410:CDS
TATGCAGAGAGCAGCGCACA+TGG 0.577233 tig0024717:+3627 Msa1419410:CDS
ATCCTCCCCTTGTAACTCAA+AGG 0.581446 tig0024717:-4064 None:intergenic
GAAAGATGCCTCACCTGCTG+AGG 0.590092 tig0024717:-3602 None:intergenic
AATGGTCTCCTCAGCAGGTG+AGG 0.601907 tig0024717:+3594 Msa1419410:CDS
CCATTTCGTCATCAGTGGCA+AGG 0.614165 tig0024717:-3576 None:intergenic
AAGGTACCTTTGAGTTACAA+GGG 0.614903 tig0024717:+4058 Msa1419410:CDS
TGAAATGAATGGATTTGTGA+AGG 0.615702 tig0024717:+4039 Msa1419410:CDS
GGAGACCATTTCGTCATCAG+TGG 0.638809 tig0024717:-3581 None:intergenic
ATGCAGAGAGCAGCGCACAT+GGG 0.647261 tig0024717:+3628 Msa1419410:CDS
AGGTACCTTTGAGTTACAAG+GGG 0.670763 tig0024717:+4059 Msa1419410:CDS
CAGGCCGATACAGAAAACTG+TGG 0.752207 tig0024717:-4175 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TCTTCAAGTTTGCTAATTAT+TGG - tig0024717:3481-3500 None:intergenic 25.0%
!!! GAATTATCACCTCTTTTTTT+AGG + tig0024717:3716-3735 Msa1419410:intron 25.0%
! TCAGTAATCACAAAAAGTTT+CGG - tig0024717:3791-3810 None:intergenic 25.0%
! TCTGAATGGATGTAATTTAA+TGG + tig0024717:3823-3842 Msa1419410:CDS 25.0%
!!! TCTTCAAGTTTGCTAATTAT+TGG - tig0024717:3481-3500 None:intergenic 25.0%
!!! GAATTATCACCTCTTTTTTT+AGG + tig0024717:3716-3735 Msa1419410:intron 25.0%
! TCAGTAATCACAAAAAGTTT+CGG - tig0024717:3791-3810 None:intergenic 25.0%
! TCTGAATGGATGTAATTTAA+TGG + tig0024717:3823-3842 Msa1419410:CDS 25.0%
ATTATTGGATTGAACTGCAA+AGG - tig0024717:3466-3485 None:intergenic 30.0%
AAGAGGTGATAATTCTGAAT+CGG - tig0024717:3711-3730 None:intergenic 30.0%
TTCAGAAAAATCTCCATCTT+AGG - tig0024717:3749-3768 None:intergenic 30.0%
! ACTTTTTGTGATTACTGAAC+AGG + tig0024717:3793-3812 Msa1419410:CDS 30.0%
AAAGAACATTATTACCTGTG+TGG + tig0024717:3964-3983 Msa1419410:intron 30.0%
AAGAACATTATTACCTGTGT+GGG + tig0024717:3965-3984 Msa1419410:intron 30.0%
! TGAAATGAATGGATTTGTGA+AGG + tig0024717:4039-4058 Msa1419410:CDS 30.0%
ATTATTGGATTGAACTGCAA+AGG - tig0024717:3466-3485 None:intergenic 30.0%
AAGAGGTGATAATTCTGAAT+CGG - tig0024717:3711-3730 None:intergenic 30.0%
TTCAGAAAAATCTCCATCTT+AGG - tig0024717:3749-3768 None:intergenic 30.0%
! ACTTTTTGTGATTACTGAAC+AGG + tig0024717:3793-3812 Msa1419410:CDS 30.0%
AAAGAACATTATTACCTGTG+TGG + tig0024717:3964-3983 Msa1419410:intron 30.0%
AAGAACATTATTACCTGTGT+GGG + tig0024717:3965-3984 Msa1419410:intron 30.0%
! TGAAATGAATGGATTTGTGA+AGG + tig0024717:4039-4058 Msa1419410:CDS 30.0%
AGAGGTGATAATTCTGAATC+GGG - tig0024717:3710-3729 None:intergenic 35.0%
GAACAGGAATCAAATCTGAA+TGG + tig0024717:3809-3828 Msa1419410:CDS 35.0%
!! GATCGAGCATTGTACTTTTA+CGG + tig0024717:3854-3873 Msa1419410:intron 35.0%
ATTCGAAGGCTTGAAATGAA+TGG + tig0024717:4028-4047 Msa1419410:CDS 35.0%
! AAGGTACCTTTGAGTTACAA+GGG + tig0024717:4058-4077 Msa1419410:CDS 35.0%
AGAGGTGATAATTCTGAATC+GGG - tig0024717:3710-3729 None:intergenic 35.0%
GAACAGGAATCAAATCTGAA+TGG + tig0024717:3809-3828 Msa1419410:CDS 35.0%
!! GATCGAGCATTGTACTTTTA+CGG + tig0024717:3854-3873 Msa1419410:intron 35.0%
ATTCGAAGGCTTGAAATGAA+TGG + tig0024717:4028-4047 Msa1419410:CDS 35.0%
! AAGGTACCTTTGAGTTACAA+GGG + tig0024717:4058-4077 Msa1419410:CDS 35.0%
TTTCATTTGACAGCTGAAGC+AGG + tig0024717:3427-3446 Msa1419410:CDS 40.0%
TTCATTTGACAGCTGAAGCA+GGG + tig0024717:3428-3447 Msa1419410:CDS 40.0%
ATAATTCTGAATCGGGACTC+AGG - tig0024717:3703-3722 None:intergenic 40.0%
! GGTGAAGCACCTAAAAAAAG+AGG - tig0024717:3728-3747 None:intergenic 40.0%
TTTAGGTGCTTCACCTAAGA+TGG + tig0024717:3733-3752 Msa1419410:intron 40.0%
! AAACTTGAGAGCATGCTTCT+TGG + tig0024717:3932-3951 Msa1419410:intron 40.0%
!! GAAGGTACCTTTGAGTTACA+AGG + tig0024717:4057-4076 Msa1419410:CDS 40.0%
! AGGTACCTTTGAGTTACAAG+GGG + tig0024717:4059-4078 Msa1419410:CDS 40.0%
ATGATTGTTTGCTTGTCTGC+TGG + tig0024717:4143-4162 Msa1419410:CDS 40.0%
! CAGACCACAGTTTTCTGTAT+CGG + tig0024717:4171-4190 Msa1419410:CDS 40.0%
TTTCATTTGACAGCTGAAGC+AGG + tig0024717:3427-3446 Msa1419410:CDS 40.0%
TTCATTTGACAGCTGAAGCA+GGG + tig0024717:3428-3447 Msa1419410:CDS 40.0%
ATAATTCTGAATCGGGACTC+AGG - tig0024717:3703-3722 None:intergenic 40.0%
! GGTGAAGCACCTAAAAAAAG+AGG - tig0024717:3728-3747 None:intergenic 40.0%
TTTAGGTGCTTCACCTAAGA+TGG + tig0024717:3733-3752 Msa1419410:intron 40.0%
! AAACTTGAGAGCATGCTTCT+TGG + tig0024717:3932-3951 Msa1419410:intron 40.0%
!! GAAGGTACCTTTGAGTTACA+AGG + tig0024717:4057-4076 Msa1419410:CDS 40.0%
! AGGTACCTTTGAGTTACAAG+GGG + tig0024717:4059-4078 Msa1419410:CDS 40.0%
ATGATTGTTTGCTTGTCTGC+TGG + tig0024717:4143-4162 Msa1419410:CDS 40.0%
! CAGACCACAGTTTTCTGTAT+CGG + tig0024717:4171-4190 Msa1419410:CDS 40.0%
GAAAACTTGCCTGTCAAGAC+AGG + tig0024717:3511-3530 Msa1419410:CDS 45.0%
!!! CGGTTCACTTTTTGACTGCT+TGG + tig0024717:3874-3893 Msa1419410:intron 45.0%
GACATGAGAAGCTCGAGAAA+TGG + tig0024717:4005-4024 Msa1419410:CDS 45.0%
! AGCTCGAGAAATGGATTCGA+AGG + tig0024717:4014-4033 Msa1419410:CDS 45.0%
! TACCTTTGAGTTACAAGGGG+AGG + tig0024717:4062-4081 Msa1419410:CDS 45.0%
ATCCTCCCCTTGTAACTCAA+AGG - tig0024717:4067-4086 None:intergenic 45.0%
! CTGTATCGGCCTGGAAATTT+AGG + tig0024717:4185-4204 Msa1419410:CDS 45.0%
GAAAACTTGCCTGTCAAGAC+AGG + tig0024717:3511-3530 Msa1419410:CDS 45.0%
!!! CGGTTCACTTTTTGACTGCT+TGG + tig0024717:3874-3893 Msa1419410:intron 45.0%
GACATGAGAAGCTCGAGAAA+TGG + tig0024717:4005-4024 Msa1419410:CDS 45.0%
! AGCTCGAGAAATGGATTCGA+AGG + tig0024717:4014-4033 Msa1419410:CDS 45.0%
! TACCTTTGAGTTACAAGGGG+AGG + tig0024717:4062-4081 Msa1419410:CDS 45.0%
ATCCTCCCCTTGTAACTCAA+AGG - tig0024717:4067-4086 None:intergenic 45.0%
! CTGTATCGGCCTGGAAATTT+AGG + tig0024717:4185-4204 Msa1419410:CDS 45.0%
! GACAGCTGAAGCAGGGATTT+TGG + tig0024717:3435-3454 Msa1419410:CDS 50.0%
ACAGCATCTCCTGTCTTGAC+AGG - tig0024717:3523-3542 None:intergenic 50.0%
CCATTTCGTCATCAGTGGCA+AGG - tig0024717:3579-3598 None:intergenic 50.0%
! CCTTGCCACTGATGACGAAA+TGG + tig0024717:3576-3595 Msa1419410:CDS 50.0%
GGAGACCATTTCGTCATCAG+TGG - tig0024717:3584-3603 None:intergenic 50.0%
!! CTTTCTATCGACTCCCACAC+AGG - tig0024717:3981-4000 None:intergenic 50.0%
CTGTGTGGGAGTCGATAGAA+AGG + tig0024717:3979-3998 Msa1419410:intron 50.0%
CAGGCCGATACAGAAAACTG+TGG - tig0024717:4178-4197 None:intergenic 50.0%
!! CACAGTTTTCTGTATCGGCC+TGG + tig0024717:4176-4195 Msa1419410:CDS 50.0%
! GACAGCTGAAGCAGGGATTT+TGG + tig0024717:3435-3454 Msa1419410:CDS 50.0%
ACAGCATCTCCTGTCTTGAC+AGG - tig0024717:3523-3542 None:intergenic 50.0%
CCATTTCGTCATCAGTGGCA+AGG - tig0024717:3579-3598 None:intergenic 50.0%
! CCTTGCCACTGATGACGAAA+TGG + tig0024717:3576-3595 Msa1419410:CDS 50.0%
GGAGACCATTTCGTCATCAG+TGG - tig0024717:3584-3603 None:intergenic 50.0%
!! CTTTCTATCGACTCCCACAC+AGG - tig0024717:3981-4000 None:intergenic 50.0%
CTGTGTGGGAGTCGATAGAA+AGG + tig0024717:3979-3998 Msa1419410:intron 50.0%
CAGGCCGATACAGAAAACTG+TGG - tig0024717:4178-4197 None:intergenic 50.0%
!! CACAGTTTTCTGTATCGGCC+TGG + tig0024717:4176-4195 Msa1419410:CDS 50.0%
GACGAAATGGTCTCCTCAGC+AGG + tig0024717:3589-3608 Msa1419410:CDS 55.0%
AATGGTCTCCTCAGCAGGTG+AGG + tig0024717:3594-3613 Msa1419410:CDS 55.0%
GAAAGATGCCTCACCTGCTG+AGG - tig0024717:3605-3624 None:intergenic 55.0%
TATGCAGAGAGCAGCGCACA+TGG + tig0024717:3627-3646 Msa1419410:CDS 55.0%
ATGCAGAGAGCAGCGCACAT+GGG + tig0024717:3628-3647 Msa1419410:CDS 55.0%
GTCAGAGGACTTTCGCAGAG+TGG + tig0024717:3650-3669 Msa1419410:intron 55.0%
GACGAAATGGTCTCCTCAGC+AGG + tig0024717:3589-3608 Msa1419410:CDS 55.0%
AATGGTCTCCTCAGCAGGTG+AGG + tig0024717:3594-3613 Msa1419410:CDS 55.0%
GAAAGATGCCTCACCTGCTG+AGG - tig0024717:3605-3624 None:intergenic 55.0%
TATGCAGAGAGCAGCGCACA+TGG + tig0024717:3627-3646 Msa1419410:CDS 55.0%
ATGCAGAGAGCAGCGCACAT+GGG + tig0024717:3628-3647 Msa1419410:CDS 55.0%
GTCAGAGGACTTTCGCAGAG+TGG + tig0024717:3650-3669 Msa1419410:intron 55.0%
GAGCAGCGCACATGGGTCAG+AGG + tig0024717:3635-3654 Msa1419410:intron 65.0%
GAGCAGCGCACATGGGTCAG+AGG + tig0024717:3635-3654 Msa1419410:intron 65.0%
Chromosome Type Strat End Strand Name
tig0024717 gene 3421 4213 3421 ID=Msa1419410;Name=Msa1419410
tig0024717 mRNA 3421 4213 3421 ID=Msa1419410-mRNA-1;Parent=Msa1419410;Name=Msa1419410-mRNA-1;_AED=0.14;_eAED=0.14;_QI=0|0|0|1|1|1|3|0|190
tig0024717 exon 3421 3649 3421 ID=Msa1419410-mRNA-1:exon:886;Parent=Msa1419410-mRNA-1
tig0024717 exon 3738 3864 3738 ID=Msa1419410-mRNA-1:exon:887;Parent=Msa1419410-mRNA-1
tig0024717 exon 3997 4213 3997 ID=Msa1419410-mRNA-1:exon:888;Parent=Msa1419410-mRNA-1
tig0024717 CDS 3421 3649 3421 ID=Msa1419410-mRNA-1:cds;Parent=Msa1419410-mRNA-1
tig0024717 CDS 3738 3864 3738 ID=Msa1419410-mRNA-1:cds;Parent=Msa1419410-mRNA-1
tig0024717 CDS 3997 4213 3997 ID=Msa1419410-mRNA-1:cds;Parent=Msa1419410-mRNA-1
Gene Sequence

>Msa1419410

ATGAGCTTTCATTTGACAGCTGAAGCAGGGATTTTGGATTTTCCTTTGCAGTTCAATCCAATAATTAGCAAACTTGAAGATGTCGATTTCGAAAACTTGCCTGTCAAGACAGGAGATGCTGTTGCAATTTCTTCTGTTCTTCAGCTGCATTCTCTCCTTGCCACTGATGACGAAATGGTCTCCTCAGCAGGTGAGGCATCTTTCAATATGCAGAGAGCAGCGCACATGGGTGCTTCACCTAAGATGGAGATTTTTCTGAACGCTATGCGAAAACTACAACCGAAACTTTTTGTGATTACTGAACAGGAATCAAATCTGAATGGATGTAATTTAATGGAGAGAATCGATCGAGCATTAAAGGAAAGACATGAGAAGCTCGAGAAATGGATTCGAAGGCTTGAAATGAATGGATTTGTGAAGGTACCTTTGAGTTACAAGGGGAGGATAGAAGCAACTAATCTATTGCAGCGATATAGTCACAAGTACAAGTTTAAAGAAGAACATGATTGTTTGCTTGTCTGCTGGAGTGACAGACCACAGTTTTCTGTATCGGCCTGGAAATTTAGGAGATGA

Protein sequence

>Msa1419410

MSFHLTAEAGILDFPLQFNPIISKLEDVDFENLPVKTGDAVAISSVLQLHSLLATDDEMVSSAGEASFNMQRAAHMGASPKMEIFLNAMRKLQPKLFVITEQESNLNGCNLMERIDRALKERHEKLEKWIRRLEMNGFVKVPLSYKGRIEATNLLQRYSHKYKFKEEHDCLLVCWSDRPQFSVSAWKFRR*