AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1438250


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1438250 MtrunA17_Chr1g0168941 98.413 63 1 0 1 63 92 154 4.87e-37 124
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1438250 AT3G23930.1 76.923 39 9 0 21 59 88 126 7.14e-11 56.2

Find 28 sgRNAs with CRISPR-Local

Find 80 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAATTGAGCTTGAGAACTTT+TGG 0.234489 tig0028518:-46554 Msa1438250:CDS
TGAGAAAGAGTGGGAATTAA+TGG 0.247721 tig0028518:-47345 Msa1438250:CDS
ACTTACCATCATATGTTCTT+TGG 0.249382 tig0028518:+47210 Msa1438250:intergenic
ATTAATGGGGACTAAGCTTT+TGG 0.315398 tig0028518:-47330 Msa1438250:CDS
GAGAAAGAGTGGGAATTAAT+GGG 0.405188 tig0028518:-47344 Msa1438250:CDS
AGAATAATGAAGAAGATAGA+TGG 0.425547 tig0028518:-46529 Msa1438250:CDS
GAGGGAAGTGGTGGAAGAGA+AGG 0.429388 tig0028518:-47416 Msa1438250:five_prime_UTR
AGAAGATAGATGGTTTGTAT+TGG 0.430708 tig0028518:-46519 Msa1438250:CDS
GGTGAAGCAGTTGAGGGAAG+TGG 0.438865 tig0028518:-47428 Msa1438250:five_prime_UTR
AAGAAGAGGTGAAGCAGTTG+AGG 0.440787 tig0028518:-47435 Msa1438250:five_prime_UTR
AGAAGAATTGTGAGAAAGAG+TGG 0.454742 tig0028518:-47355 Msa1438250:CDS
GATAAGGAGATGGAAGAGGT+TGG 0.456780 tig0028518:-47386 Msa1438250:exon
TTGCTTTCAAGGAGGCAGAT+TGG 0.464224 tig0028518:-47480 None:intergenic
AGAAGAGGTGAAGCAGTTGA+GGG 0.480459 tig0028518:-47434 Msa1438250:five_prime_UTR
AAGAGAAGGAAGAGAAGATA+AGG 0.484218 tig0028518:-47402 Msa1438250:five_prime_UTR
AGAAGATAAGGAGATGGAAG+AGG 0.496133 tig0028518:-47390 Msa1438250:exon
GGAGATGGAAGAGGTTGGAA+TGG 0.504796 tig0028518:-47381 Msa1438250:exon
TCTTGCAATTAAGAATGAGT+TGG 0.505081 tig0028518:-47243 Msa1438250:CDS
GAGATGAAGCTGTTGAGAAG+TGG 0.508742 tig0028518:-47277 Msa1438250:CDS
GAAGCAGTTGAGGGAAGTGG+TGG 0.513840 tig0028518:-47425 Msa1438250:five_prime_UTR
CTCATCCAAAGAACATATGA+TGG 0.522947 tig0028518:-47215 Msa1438250:intron
GATGAAGAGGTTGAAAGAAG+AGG 0.528949 tig0028518:-47449 Msa1438250:five_prime_UTR
AGGAAGAGAAGATAAGGAGA+TGG 0.534573 tig0028518:-47396 Msa1438250:exon
ATTGGAAACAAGAGATGAAG+AGG 0.564436 tig0028518:-47462 Msa1438250:five_prime_UTR
GAAGAATTGTGAGAAAGAGT+GGG 0.599083 tig0028518:-47354 Msa1438250:CDS
AGAAAGAGTGGGAATTAATG+GGG 0.618319 tig0028518:-47343 Msa1438250:CDS
AGATGAAGGAGGAAAGAGCA+AGG 0.618929 tig0028518:-47301 Msa1438250:CDS
TTTGGTTCAAGAGATGAAGG+AGG 0.645416 tig0028518:-47312 Msa1438250:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AAACTATAAACTGTTTTTAT+AGG + tig0028518:47025-47044 Msa1438250:intergenic 15.0%
!!! AAACTATAAACTGTTTTTAT+AGG + tig0028518:47025-47044 Msa1438250:intergenic 15.0%
!! AAAACAAACACTAAATTGTT+TGG + tig0028518:47139-47158 Msa1438250:intergenic 20.0%
!! TCAAACAATACTAATTCAAA+GGG + tig0028518:47213-47232 Msa1438250:intergenic 20.0%
!! TTCAAACAATACTAATTCAA+AGG + tig0028518:47214-47233 Msa1438250:intergenic 20.0%
!!! ATTTTGAAAAGTACTATGAT+GGG + tig0028518:47266-47285 Msa1438250:intergenic 20.0%
!!! AATTTTGAAAAGTACTATGA+TGG + tig0028518:47267-47286 Msa1438250:intergenic 20.0%
!! ATTAATATGTGACAATAATG+TGG - tig0028518:47291-47310 Msa1438250:CDS 20.0%
!! AAAACAAACACTAAATTGTT+TGG + tig0028518:47139-47158 Msa1438250:intergenic 20.0%
!! TCAAACAATACTAATTCAAA+GGG + tig0028518:47213-47232 Msa1438250:intergenic 20.0%
!! TTCAAACAATACTAATTCAA+AGG + tig0028518:47214-47233 Msa1438250:intergenic 20.0%
!!! ATTTTGAAAAGTACTATGAT+GGG + tig0028518:47266-47285 Msa1438250:intergenic 20.0%
!!! AATTTTGAAAAGTACTATGA+TGG + tig0028518:47267-47286 Msa1438250:intergenic 20.0%
!! ATTAATATGTGACAATAATG+TGG - tig0028518:47291-47310 Msa1438250:CDS 20.0%
!!! TTGTTTGAAAAAAGTATCTG+TGG - tig0028518:47225-47244 Msa1438250:CDS 25.0%
! AGAATAATGAAGAAGATAGA+TGG - tig0028518:47445-47464 Msa1438250:five_prime_UTR 25.0%
!!! TTGTTTGAAAAAAGTATCTG+TGG - tig0028518:47225-47244 Msa1438250:CDS 25.0%
! AGAATAATGAAGAAGATAGA+TGG - tig0028518:47445-47464 Msa1438250:five_prime_UTR 25.0%
TCTTGCAATTAAGAATGAGT+TGG - tig0028518:46731-46750 Msa1438250:intron 30.0%
ACTTACCATCATATGTTCTT+TGG + tig0028518:46767-46786 Msa1438250:intergenic 30.0%
! AGAAGATAGATGGTTTGTAT+TGG - tig0028518:47455-47474 Msa1438250:five_prime_UTR 30.0%
TCTTGCAATTAAGAATGAGT+TGG - tig0028518:46731-46750 Msa1438250:intron 30.0%
ACTTACCATCATATGTTCTT+TGG + tig0028518:46767-46786 Msa1438250:intergenic 30.0%
! AGAAGATAGATGGTTTGTAT+TGG - tig0028518:47455-47474 Msa1438250:five_prime_UTR 30.0%
ATTGGAAACAAGAGATGAAG+AGG - tig0028518:46512-46531 Msa1438250:CDS 35.0%
AAGAGAAGGAAGAGAAGATA+AGG - tig0028518:46572-46591 Msa1438250:intron 35.0%
AGAAGAATTGTGAGAAAGAG+TGG - tig0028518:46619-46638 Msa1438250:intron 35.0%
GAAGAATTGTGAGAAAGAGT+GGG - tig0028518:46620-46639 Msa1438250:intron 35.0%
TGAGAAAGAGTGGGAATTAA+TGG - tig0028518:46629-46648 Msa1438250:intron 35.0%
GAGAAAGAGTGGGAATTAAT+GGG - tig0028518:46630-46649 Msa1438250:intron 35.0%
AGAAAGAGTGGGAATTAATG+GGG - tig0028518:46631-46650 Msa1438250:intron 35.0%
! ATTAATGGGGACTAAGCTTT+TGG - tig0028518:46644-46663 Msa1438250:intron 35.0%
CTCATCCAAAGAACATATGA+TGG - tig0028518:46759-46778 Msa1438250:intron 35.0%
!! AAAAAAGTATCTGTGGCAGA+TGG - tig0028518:47232-47251 Msa1438250:CDS 35.0%
!! AAAAAGTATCTGTGGCAGAT+GGG - tig0028518:47233-47252 Msa1438250:CDS 35.0%
! CAATTGAGCTTGAGAACTTT+TGG - tig0028518:47420-47439 Msa1438250:five_prime_UTR 35.0%
ATTGGAAACAAGAGATGAAG+AGG - tig0028518:46512-46531 Msa1438250:CDS 35.0%
AAGAGAAGGAAGAGAAGATA+AGG - tig0028518:46572-46591 Msa1438250:intron 35.0%
AGAAGAATTGTGAGAAAGAG+TGG - tig0028518:46619-46638 Msa1438250:intron 35.0%
GAAGAATTGTGAGAAAGAGT+GGG - tig0028518:46620-46639 Msa1438250:intron 35.0%
TGAGAAAGAGTGGGAATTAA+TGG - tig0028518:46629-46648 Msa1438250:intron 35.0%
GAGAAAGAGTGGGAATTAAT+GGG - tig0028518:46630-46649 Msa1438250:intron 35.0%
AGAAAGAGTGGGAATTAATG+GGG - tig0028518:46631-46650 Msa1438250:intron 35.0%
! ATTAATGGGGACTAAGCTTT+TGG - tig0028518:46644-46663 Msa1438250:intron 35.0%
CTCATCCAAAGAACATATGA+TGG - tig0028518:46759-46778 Msa1438250:intron 35.0%
!! AAAAAAGTATCTGTGGCAGA+TGG - tig0028518:47232-47251 Msa1438250:CDS 35.0%
!! AAAAAGTATCTGTGGCAGAT+GGG - tig0028518:47233-47252 Msa1438250:CDS 35.0%
! CAATTGAGCTTGAGAACTTT+TGG - tig0028518:47420-47439 Msa1438250:five_prime_UTR 35.0%
GATGAAGAGGTTGAAAGAAG+AGG - tig0028518:46525-46544 Msa1438250:CDS 40.0%
AGGAAGAGAAGATAAGGAGA+TGG - tig0028518:46578-46597 Msa1438250:intron 40.0%
AGAAGATAAGGAGATGGAAG+AGG - tig0028518:46584-46603 Msa1438250:intron 40.0%
!!! GCTTTTGGTTCAAGAGATGA+AGG - tig0028518:46659-46678 Msa1438250:intron 40.0%
! TTTGGTTCAAGAGATGAAGG+AGG - tig0028518:46662-46681 Msa1438250:intron 40.0%
!! AAAAGTATCTGTGGCAGATG+GGG - tig0028518:47234-47253 Msa1438250:CDS 40.0%
GATGAAGAGGTTGAAAGAAG+AGG - tig0028518:46525-46544 Msa1438250:CDS 40.0%
AGGAAGAGAAGATAAGGAGA+TGG - tig0028518:46578-46597 Msa1438250:intron 40.0%
AGAAGATAAGGAGATGGAAG+AGG - tig0028518:46584-46603 Msa1438250:intron 40.0%
!!! GCTTTTGGTTCAAGAGATGA+AGG - tig0028518:46659-46678 Msa1438250:intron 40.0%
! TTTGGTTCAAGAGATGAAGG+AGG - tig0028518:46662-46681 Msa1438250:intron 40.0%
!! AAAAGTATCTGTGGCAGATG+GGG - tig0028518:47234-47253 Msa1438250:CDS 40.0%
AAGAAGAGGTGAAGCAGTTG+AGG - tig0028518:46539-46558 Msa1438250:CDS 45.0%
AGAAGAGGTGAAGCAGTTGA+GGG - tig0028518:46540-46559 Msa1438250:CDS 45.0%
GATAAGGAGATGGAAGAGGT+TGG - tig0028518:46588-46607 Msa1438250:intron 45.0%
AGATGAAGGAGGAAAGAGCA+AGG - tig0028518:46673-46692 Msa1438250:intron 45.0%
GAGATGAAGCTGTTGAGAAG+TGG - tig0028518:46697-46716 Msa1438250:intron 45.0%
AAGAAGAGGTGAAGCAGTTG+AGG - tig0028518:46539-46558 Msa1438250:CDS 45.0%
AGAAGAGGTGAAGCAGTTGA+GGG - tig0028518:46540-46559 Msa1438250:CDS 45.0%
GATAAGGAGATGGAAGAGGT+TGG - tig0028518:46588-46607 Msa1438250:intron 45.0%
AGATGAAGGAGGAAAGAGCA+AGG - tig0028518:46673-46692 Msa1438250:intron 45.0%
GAGATGAAGCTGTTGAGAAG+TGG - tig0028518:46697-46716 Msa1438250:intron 45.0%
!! AAAAATTAAATAAAATTCTT+TGG + tig0028518:47051-47070 Msa1438250:intergenic 5.0%
!! AAAAATTAAATAAAATTCTT+TGG + tig0028518:47051-47070 Msa1438250:intergenic 5.0%
GGAGATGGAAGAGGTTGGAA+TGG - tig0028518:46593-46612 Msa1438250:intron 50.0%
GGAGATGGAAGAGGTTGGAA+TGG - tig0028518:46593-46612 Msa1438250:intron 50.0%
GGTGAAGCAGTTGAGGGAAG+TGG - tig0028518:46546-46565 Msa1438250:CDS 55.0%
GAAGCAGTTGAGGGAAGTGG+TGG - tig0028518:46549-46568 Msa1438250:CDS 55.0%
! GAGGGAAGTGGTGGAAGAGA+AGG - tig0028518:46558-46577 Msa1438250:CDS 55.0%
GGTGAAGCAGTTGAGGGAAG+TGG - tig0028518:46546-46565 Msa1438250:CDS 55.0%
GAAGCAGTTGAGGGAAGTGG+TGG - tig0028518:46549-46568 Msa1438250:CDS 55.0%
! GAGGGAAGTGGTGGAAGAGA+AGG - tig0028518:46558-46577 Msa1438250:CDS 55.0%
Chromosome Type Strat End Strand Name
tig0028518 gene 46505 47491 46505 ID=Msa1438250;Name=Msa1438250
tig0028518 mRNA 46505 47491 46505 ID=Msa1438250-mRNA-1;Parent=Msa1438250;Name=Msa1438250-mRNA-1;_AED=0.31;_eAED=0.54;_QI=92|0|0|0.5|1|1|2|0|88
tig0028518 exon 47216 47491 47216 ID=Msa1438250-mRNA-1:exon:11137;Parent=Msa1438250-mRNA-1
tig0028518 exon 46505 46584 46505 ID=Msa1438250-mRNA-1:exon:11136;Parent=Msa1438250-mRNA-1
tig0028518 five_prime_UTR 47400 47491 47400 ID=Msa1438250-mRNA-1:five_prime_utr;Parent=Msa1438250-mRNA-1
tig0028518 CDS 47216 47399 47216 ID=Msa1438250-mRNA-1:cds;Parent=Msa1438250-mRNA-1
tig0028518 CDS 46505 46584 46505 ID=Msa1438250-mRNA-1:cds;Parent=Msa1438250-mRNA-1
Gene Sequence

>Msa1438250

ATGGAAGAGGTTGGAATGGTTGAGAAGAATTGTGAGAAAGAGTGGGAATTAATGGGGACTAAGCTTTTGGTTCAAGAGATGAAGGAGGAAAGAGCAAGGAGAGATGAAGCTGTTGAGAAGTGGAAACAACTTTATCTTGCAATTAAGAATGAGTTGGATGATCTCATCCAAAGAACATATGATGTAGACTATCAATTGAGCTTGAGAACTTTTGGAGAGAATAATGAAGAAGATAGATGGTTTGTATTGGAAGATATGAGTGAT

Protein sequence

>Msa1438250

MEEVGMVEKNCEKEWELMGTKLLVQEMKEERARRDEAVEKWKQLYLAIKNELDDLIQRTYDVDYQLSLRTFGENNEEDRWFVLEDMSD