AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1465660

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1465660 MtrunA17_Chr4g0063511 98.795 166 2 0 1 166 495 660 2.71e-116 343
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1465660 AT5G20170.1 57.407 162 62 1 1 162 492 646 8.99e-53 177

Find 48 sgRNAs with CRISPR-Local

Find 128 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GATATAGCCAATTAATAATT+TGG 0.184216 tig0045397:-299 None:intergenic
GCTATATCATGAAGCTCTTA+TGG 0.252154 tig0045397:+314 Msa1465660:CDS
GAGAAGATCTTCGAGGTCTT+TGG 0.252204 tig0045397:+706 Msa1465660:three_prime_UTR
TGGCTAGCCAAATTATTAAT+TGG 0.260267 tig0045397:+292 Msa1465660:CDS
CAAAGGCAATCAAATCTATC+AGG 0.274600 tig0045397:-572 None:intergenic
ATACAACCATCACTATCTTT+TGG 0.299237 tig0045397:-423 None:intergenic
AGCTCTTATGGTTGGGATAA+AGG 0.326959 tig0045397:+326 Msa1465660:CDS
AGAAGATCTTCGAGGTCTTT+GGG 0.362397 tig0045397:+707 Msa1465660:three_prime_UTR
CCGATGGTGCATCTGAATAT+AGG 0.363383 tig0045397:+508 Msa1465660:CDS
GCCTTTGTTAGCGGCGGTGG+CGG 0.417011 tig0045397:+588 Msa1465660:CDS
ATTGCCTTTGTTAGCGGCGG+TGG 0.424051 tig0045397:+585 Msa1465660:CDS
TCTATGCTTGTCATTTGAGC+TGG 0.431061 tig0045397:+362 Msa1465660:CDS
TTTGTTAGCGGCGGTGGCGG+TGG 0.437315 tig0045397:+591 Msa1465660:CDS
TTGAACAGACCAGACACATT+AGG 0.446871 tig0045397:-80 None:intergenic
TATATCTTGGTCGTTGGTCA+TGG 0.451343 tig0045397:+443 Msa1465660:CDS
GAAGTTGTATATACTCTCTT+CGG 0.462040 tig0045397:+619 Msa1465660:exon
GCAGGGTGAAACACTGGGCC+TGG 0.464911 tig0045397:+386 Msa1465660:CDS
ATAGTGATGGTTGTATATCT+TGG 0.465606 tig0045397:+430 Msa1465660:CDS
GAGAGTATATACAACTTCAT+TGG 0.469672 tig0045397:-614 None:intergenic
CTTGTCATTTGAGCTGGAGC+AGG 0.470292 tig0045397:+368 Msa1465660:CDS
ACTCTCTTCGGTCTCAAAGT+TGG 0.479668 tig0045397:+631 Msa1465660:three_prime_UTR
ATCATGAAGCTCTTATGGTT+GGG 0.481015 tig0045397:+319 Msa1465660:CDS
TGGTTGGGATAAAGGCAAAC+CGG 0.481732 tig0045397:+334 Msa1465660:CDS
GCTGGAGCAGGGTGAAACAC+TGG 0.496632 tig0045397:+380 Msa1465660:CDS
TATCATGAAGCTCTTATGGT+TGG 0.500863 tig0045397:+318 Msa1465660:CDS
CTGGAGCAGGGTGAAACACT+GGG 0.510222 tig0045397:+381 Msa1465660:CDS
GATTTGATTGCCTTTGTTAG+CGG 0.511207 tig0045397:+579 Msa1465660:CDS
CTCTTCGGTCTCAAAGTTGG+AGG 0.516961 tig0045397:+634 Msa1465660:three_prime_UTR
ACCTGCTGCAAAATAATCAC+AGG 0.519043 tig0045397:-161 None:intergenic
TCTGAATATAGGAAATTCCT+AGG 0.519495 tig0045397:+519 Msa1465660:CDS
ACCGCCACCGCCGCTAACAA+AGG 0.522482 tig0045397:-589 None:intergenic
TTGGATCCACATTTGCAACC+AGG 0.530541 tig0045397:-404 None:intergenic
ACTGGGCCTGGTTGCAAATG+TGG 0.536822 tig0045397:+398 Msa1465660:CDS
CCTATATTCAGATGCACCAT+CGG 0.551573 tig0045397:-508 None:intergenic
AGATGCACCATCGGTGATGT+TGG 0.571603 tig0045397:-499 None:intergenic
GCTCAAGAGACAAGGGACCT+AGG 0.597248 tig0045397:-536 None:intergenic
TTGATTGCCTTTGTTAGCGG+CGG 0.599362 tig0045397:+582 Msa1465660:CDS
GGTTGGGATAAAGGCAAACC+GGG 0.602980 tig0045397:+335 Msa1465660:CDS
GGTTGAAGAGAAGATCTTCG+AGG 0.603431 tig0045397:+699 Msa1465660:three_prime_UTR
AAAGGCAATCAAATCTATCA+GGG 0.604068 tig0045397:-571 None:intergenic
ATGACAAGCATAGAAAGTCC+CGG 0.606677 tig0045397:-353 None:intergenic
ATATAACAGCTCAAGAGACA+AGG 0.616568 tig0045397:-544 None:intergenic
TGGTTGTATATCTTGGTCGT+TGG 0.617310 tig0045397:+437 Msa1465660:CDS
ATCTTGGTCGTTGGTCATGG+AGG 0.624297 tig0045397:+446 Msa1465660:CDS
TTGTCATTTGAGCTGGAGCA+GGG 0.655430 tig0045397:+369 Msa1465660:CDS
CTTCATACCAACATCACCGA+TGG 0.660269 tig0045397:+492 Msa1465660:CDS
GTGGATCCAAAAGATAGTGA+TGG 0.673007 tig0045397:+417 Msa1465660:CDS
TATAACAGCTCAAGAGACAA+GGG 0.677992 tig0045397:-543 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TAAATAAAAAAGTACATATA+TGG - tig0045397:749-768 None:intergenic 10.0%
!!! TAAATAAAAAAGTACATATA+TGG - tig0045397:749-768 None:intergenic 10.0%
!! GATATAGCCAATTAATAATT+TGG - tig0045397:302-321 None:intergenic 20.0%
!! GATATAGCCAATTAATAATT+TGG - tig0045397:302-321 None:intergenic 20.0%
! TACCTTAATTGAAATCTTAC+AGG + tig0045397:269-288 Msa1465660:intron 25.0%
! TACCTTAATTGAAATCTTAC+AGG + tig0045397:269-288 Msa1465660:intron 25.0%
TAAAAGTGATTCGTAAGAGA+AGG + tig0045397:183-202 Msa1465660:intron 30.0%
CACCTGTAAGATTTCAATTA+AGG - tig0045397:274-293 None:intergenic 30.0%
CTTAATTGAAATCTTACAGG+TGG + tig0045397:272-291 Msa1465660:intron 30.0%
! TGGCTAGCCAAATTATTAAT+TGG + tig0045397:292-311 Msa1465660:CDS 30.0%
! ATACAACCATCACTATCTTT+TGG - tig0045397:426-445 None:intergenic 30.0%
ATAGTGATGGTTGTATATCT+TGG + tig0045397:430-449 Msa1465660:CDS 30.0%
TCTGAATATAGGAAATTCCT+AGG + tig0045397:519-538 Msa1465660:CDS 30.0%
AAAGGCAATCAAATCTATCA+GGG - tig0045397:574-593 None:intergenic 30.0%
! GAGAGTATATACAACTTCAT+TGG - tig0045397:617-636 None:intergenic 30.0%
GAAGTTGTATATACTCTCTT+CGG + tig0045397:619-638 Msa1465660:exon 30.0%
!!! TGTTTTTTTCTTGCATTGTC+AGG + tig0045397:678-697 Msa1465660:three_prime_UTR 30.0%
TAAAAGTGATTCGTAAGAGA+AGG + tig0045397:183-202 Msa1465660:intron 30.0%
CACCTGTAAGATTTCAATTA+AGG - tig0045397:274-293 None:intergenic 30.0%
CTTAATTGAAATCTTACAGG+TGG + tig0045397:272-291 Msa1465660:intron 30.0%
! TGGCTAGCCAAATTATTAAT+TGG + tig0045397:292-311 Msa1465660:CDS 30.0%
! ATACAACCATCACTATCTTT+TGG - tig0045397:426-445 None:intergenic 30.0%
ATAGTGATGGTTGTATATCT+TGG + tig0045397:430-449 Msa1465660:CDS 30.0%
TCTGAATATAGGAAATTCCT+AGG + tig0045397:519-538 Msa1465660:CDS 30.0%
AAAGGCAATCAAATCTATCA+GGG - tig0045397:574-593 None:intergenic 30.0%
! GAGAGTATATACAACTTCAT+TGG - tig0045397:617-636 None:intergenic 30.0%
GAAGTTGTATATACTCTCTT+CGG + tig0045397:619-638 Msa1465660:exon 30.0%
!!! TGTTTTTTTCTTGCATTGTC+AGG + tig0045397:678-697 Msa1465660:three_prime_UTR 30.0%
GCTATATCATGAAGCTCTTA+TGG + tig0045397:314-333 Msa1465660:CDS 35.0%
TATCATGAAGCTCTTATGGT+TGG + tig0045397:318-337 Msa1465660:CDS 35.0%
ATCATGAAGCTCTTATGGTT+GGG + tig0045397:319-338 Msa1465660:CDS 35.0%
TATAACAGCTCAAGAGACAA+GGG - tig0045397:546-565 None:intergenic 35.0%
ATATAACAGCTCAAGAGACA+AGG - tig0045397:547-566 None:intergenic 35.0%
CAAAGGCAATCAAATCTATC+AGG - tig0045397:575-594 None:intergenic 35.0%
GATTTGATTGCCTTTGTTAG+CGG + tig0045397:579-598 Msa1465660:CDS 35.0%
GCTATATCATGAAGCTCTTA+TGG + tig0045397:314-333 Msa1465660:CDS 35.0%
TATCATGAAGCTCTTATGGT+TGG + tig0045397:318-337 Msa1465660:CDS 35.0%
ATCATGAAGCTCTTATGGTT+GGG + tig0045397:319-338 Msa1465660:CDS 35.0%
TATAACAGCTCAAGAGACAA+GGG - tig0045397:546-565 None:intergenic 35.0%
ATATAACAGCTCAAGAGACA+AGG - tig0045397:547-566 None:intergenic 35.0%
CAAAGGCAATCAAATCTATC+AGG - tig0045397:575-594 None:intergenic 35.0%
GATTTGATTGCCTTTGTTAG+CGG + tig0045397:579-598 Msa1465660:CDS 35.0%
TGCATCAGTGTTAAAGCAGA+AGG + tig0045397:53-72 Msa1465660:CDS 40.0%
TTGAACAGACCAGACACATT+AGG - tig0045397:83-102 None:intergenic 40.0%
TAATGTGTCTGGTCTGTTCA+AGG + tig0045397:82-101 Msa1465660:CDS 40.0%
AATGTGTCTGGTCTGTTCAA+GGG + tig0045397:83-102 Msa1465660:CDS 40.0%
!! TCCTGTGATTATTTTGCAGC+AGG + tig0045397:160-179 Msa1465660:CDS 40.0%
ACCTGCTGCAAAATAATCAC+AGG - tig0045397:164-183 None:intergenic 40.0%
AGCTCTTATGGTTGGGATAA+AGG + tig0045397:326-345 Msa1465660:CDS 40.0%
ATGACAAGCATAGAAAGTCC+CGG - tig0045397:356-375 None:intergenic 40.0%
! TCTATGCTTGTCATTTGAGC+TGG + tig0045397:362-381 Msa1465660:CDS 40.0%
GTGGATCCAAAAGATAGTGA+TGG + tig0045397:417-436 Msa1465660:CDS 40.0%
TGGTTGTATATCTTGGTCGT+TGG + tig0045397:437-456 Msa1465660:CDS 40.0%
TATATCTTGGTCGTTGGTCA+TGG + tig0045397:443-462 Msa1465660:CDS 40.0%
CCTATATTCAGATGCACCAT+CGG - tig0045397:511-530 None:intergenic 40.0%
AGAAGATCTTCGAGGTCTTT+GGG + tig0045397:707-726 Msa1465660:three_prime_UTR 40.0%
TGCATCAGTGTTAAAGCAGA+AGG + tig0045397:53-72 Msa1465660:CDS 40.0%
TTGAACAGACCAGACACATT+AGG - tig0045397:83-102 None:intergenic 40.0%
TAATGTGTCTGGTCTGTTCA+AGG + tig0045397:82-101 Msa1465660:CDS 40.0%
AATGTGTCTGGTCTGTTCAA+GGG + tig0045397:83-102 Msa1465660:CDS 40.0%
!! TCCTGTGATTATTTTGCAGC+AGG + tig0045397:160-179 Msa1465660:CDS 40.0%
ACCTGCTGCAAAATAATCAC+AGG - tig0045397:164-183 None:intergenic 40.0%
AGCTCTTATGGTTGGGATAA+AGG + tig0045397:326-345 Msa1465660:CDS 40.0%
ATGACAAGCATAGAAAGTCC+CGG - tig0045397:356-375 None:intergenic 40.0%
! TCTATGCTTGTCATTTGAGC+TGG + tig0045397:362-381 Msa1465660:CDS 40.0%
GTGGATCCAAAAGATAGTGA+TGG + tig0045397:417-436 Msa1465660:CDS 40.0%
TGGTTGTATATCTTGGTCGT+TGG + tig0045397:437-456 Msa1465660:CDS 40.0%
TATATCTTGGTCGTTGGTCA+TGG + tig0045397:443-462 Msa1465660:CDS 40.0%
CCTATATTCAGATGCACCAT+CGG - tig0045397:511-530 None:intergenic 40.0%
AGAAGATCTTCGAGGTCTTT+GGG + tig0045397:707-726 Msa1465660:three_prime_UTR 40.0%
!!! CAAGCGTCAGTTTTGGACTA+AGG + tig0045397:13-32 Msa1465660:CDS 45.0%
!!! TCAGTTTTGGACTAAGGTCG+TGG + tig0045397:19-38 Msa1465660:CDS 45.0%
GAAGGTTCTCCTAATGTGTC+TGG + tig0045397:71-90 Msa1465660:CDS 45.0%
TCTGTTCAAGGGAAAGTCTG+AGG + tig0045397:94-113 Msa1465660:CDS 45.0%
TGGTTGGGATAAAGGCAAAC+CGG + tig0045397:334-353 Msa1465660:CDS 45.0%
! TTGTCATTTGAGCTGGAGCA+GGG + tig0045397:369-388 Msa1465660:CDS 45.0%
TTGGATCCACATTTGCAACC+AGG - tig0045397:407-426 None:intergenic 45.0%
!! GGTCATGGAGGATAGTTTTG+CGG + tig0045397:458-477 Msa1465660:CDS 45.0%
CTTCATACCAACATCACCGA+TGG + tig0045397:492-511 Msa1465660:CDS 45.0%
CCGATGGTGCATCTGAATAT+AGG + tig0045397:508-527 Msa1465660:CDS 45.0%
TTGATTGCCTTTGTTAGCGG+CGG + tig0045397:582-601 Msa1465660:CDS 45.0%
ACTCTCTTCGGTCTCAAAGT+TGG + tig0045397:631-650 Msa1465660:three_prime_UTR 45.0%
GGTTGAAGAGAAGATCTTCG+AGG + tig0045397:699-718 Msa1465660:three_prime_UTR 45.0%
GAGAAGATCTTCGAGGTCTT+TGG + tig0045397:706-725 Msa1465660:three_prime_UTR 45.0%
!!! CAAGCGTCAGTTTTGGACTA+AGG + tig0045397:13-32 Msa1465660:CDS 45.0%
!!! TCAGTTTTGGACTAAGGTCG+TGG + tig0045397:19-38 Msa1465660:CDS 45.0%
GAAGGTTCTCCTAATGTGTC+TGG + tig0045397:71-90 Msa1465660:CDS 45.0%
TCTGTTCAAGGGAAAGTCTG+AGG + tig0045397:94-113 Msa1465660:CDS 45.0%
TGGTTGGGATAAAGGCAAAC+CGG + tig0045397:334-353 Msa1465660:CDS 45.0%
! TTGTCATTTGAGCTGGAGCA+GGG + tig0045397:369-388 Msa1465660:CDS 45.0%
TTGGATCCACATTTGCAACC+AGG - tig0045397:407-426 None:intergenic 45.0%
!! GGTCATGGAGGATAGTTTTG+CGG + tig0045397:458-477 Msa1465660:CDS 45.0%
CTTCATACCAACATCACCGA+TGG + tig0045397:492-511 Msa1465660:CDS 45.0%
CCGATGGTGCATCTGAATAT+AGG + tig0045397:508-527 Msa1465660:CDS 45.0%
TTGATTGCCTTTGTTAGCGG+CGG + tig0045397:582-601 Msa1465660:CDS 45.0%
ACTCTCTTCGGTCTCAAAGT+TGG + tig0045397:631-650 Msa1465660:three_prime_UTR 45.0%
GGTTGAAGAGAAGATCTTCG+AGG + tig0045397:699-718 Msa1465660:three_prime_UTR 45.0%
GAGAAGATCTTCGAGGTCTT+TGG + tig0045397:706-725 Msa1465660:three_prime_UTR 45.0%
GGTTGGGATAAAGGCAAACC+GGG + tig0045397:335-354 Msa1465660:CDS 50.0%
! CTTGTCATTTGAGCTGGAGC+AGG + tig0045397:368-387 Msa1465660:CDS 50.0%
ATCTTGGTCGTTGGTCATGG+AGG + tig0045397:446-465 Msa1465660:CDS 50.0%
!! CATGGAGGATAGTTTTGCGG+AGG + tig0045397:461-480 Msa1465660:CDS 50.0%
AGATGCACCATCGGTGATGT+TGG - tig0045397:502-521 None:intergenic 50.0%
CTCTTCGGTCTCAAAGTTGG+AGG + tig0045397:634-653 Msa1465660:three_prime_UTR 50.0%
GGTTGGGATAAAGGCAAACC+GGG + tig0045397:335-354 Msa1465660:CDS 50.0%
! CTTGTCATTTGAGCTGGAGC+AGG + tig0045397:368-387 Msa1465660:CDS 50.0%
ATCTTGGTCGTTGGTCATGG+AGG + tig0045397:446-465 Msa1465660:CDS 50.0%
!! CATGGAGGATAGTTTTGCGG+AGG + tig0045397:461-480 Msa1465660:CDS 50.0%
AGATGCACCATCGGTGATGT+TGG - tig0045397:502-521 None:intergenic 50.0%
CTCTTCGGTCTCAAAGTTGG+AGG + tig0045397:634-653 Msa1465660:three_prime_UTR 50.0%
CTGGAGCAGGGTGAAACACT+GGG + tig0045397:381-400 Msa1465660:CDS 55.0%
ACTGGGCCTGGTTGCAAATG+TGG + tig0045397:398-417 Msa1465660:CDS 55.0%
GCTCAAGAGACAAGGGACCT+AGG - tig0045397:539-558 None:intergenic 55.0%
ATTGCCTTTGTTAGCGGCGG+TGG + tig0045397:585-604 Msa1465660:CDS 55.0%
CTGGAGCAGGGTGAAACACT+GGG + tig0045397:381-400 Msa1465660:CDS 55.0%
ACTGGGCCTGGTTGCAAATG+TGG + tig0045397:398-417 Msa1465660:CDS 55.0%
GCTCAAGAGACAAGGGACCT+AGG - tig0045397:539-558 None:intergenic 55.0%
ATTGCCTTTGTTAGCGGCGG+TGG + tig0045397:585-604 Msa1465660:CDS 55.0%
GCTGGAGCAGGGTGAAACAC+TGG + tig0045397:380-399 Msa1465660:CDS 60.0%
GCTGGAGCAGGGTGAAACAC+TGG + tig0045397:380-399 Msa1465660:CDS 60.0%
GCAGGGTGAAACACTGGGCC+TGG + tig0045397:386-405 Msa1465660:CDS 65.0%
GCCTTTGTTAGCGGCGGTGG+CGG + tig0045397:588-607 Msa1465660:CDS 65.0%
ACCGCCACCGCCGCTAACAA+AGG - tig0045397:592-611 None:intergenic 65.0%
! TTTGTTAGCGGCGGTGGCGG+TGG + tig0045397:591-610 Msa1465660:CDS 65.0%
GCAGGGTGAAACACTGGGCC+TGG + tig0045397:386-405 Msa1465660:CDS 65.0%
GCCTTTGTTAGCGGCGGTGG+CGG + tig0045397:588-607 Msa1465660:CDS 65.0%
ACCGCCACCGCCGCTAACAA+AGG - tig0045397:592-611 None:intergenic 65.0%
! TTTGTTAGCGGCGGTGGCGG+TGG + tig0045397:591-610 Msa1465660:CDS 65.0%
Chromosome Type Strat End Strand Name
tig0045397 gene 11 813 11 ID=Msa1465660;Name=Msa1465660
tig0045397 mRNA 11 813 11 ID=Msa1465660-mRNA-1;Parent=Msa1465660;Name=Msa1465660-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|1|0.5|1|1|1|2|193|166
tig0045397 exon 11 181 11 ID=Msa1465660-mRNA-1:exon:24847;Parent=Msa1465660-mRNA-1
tig0045397 exon 291 813 291 ID=Msa1465660-mRNA-1:exon:24848;Parent=Msa1465660-mRNA-1
tig0045397 CDS 11 181 11 ID=Msa1465660-mRNA-1:cds;Parent=Msa1465660-mRNA-1
tig0045397 CDS 291 620 291 ID=Msa1465660-mRNA-1:cds;Parent=Msa1465660-mRNA-1
tig0045397 three_prime_UTR 621 813 621 ID=Msa1465660-mRNA-1:three_prime_utr;Parent=Msa1465660-mRNA-1
Gene Sequence

>Msa1465660

ATCAAGCGTCAGTTTTGGACTAAGGTCGTGGTAATCGATGATTGCATCAGTGTTAAAGCAGAAGGTTCTCCTAATGTGTCTGGTCTGTTCAAGGGAAAGTCTGAGGATACTCACTCAATAAACAAATATGAGTGCAACTTAGCTGATCTTCCTGTGATTATTTTGCAGCAGGTGGCTAGCCAAATTATTAATTGGCTATATCATGAAGCTCTTATGGTTGGGATAAAGGCAAACCGGGACTTTCTATGCTTGTCATTTGAGCTGGAGCAGGGTGAAACACTGGGCCTGGTTGCAAATGTGGATCCAAAAGATAGTGATGGTTGTATATCTTGGTCGTTGGTCATGGAGGATAGTTTTGCGGAGGTGCAAAAGCTTCATACCAACATCACCGATGGTGCATCTGAATATAGGAAATTCCTAGGTCCCTTGTCTCTTGAGCTGTTATATGCTACCCTGATAGATTTGATTGCCTTTGTTAGCGGCGGTGGCGGTGGCCAATGA
Protein sequence

>Msa1465660

IKRQFWTKVVVIDDCISVKAEGSPNVSGLFKGKSEDTHSINKYECNLADLPVIILQQVASQIINWLYHEALMVGIKANRDFLCLSFELEQGETLGLVANVDPKDSDGCISWSLVMEDSFAEVQKLHTNITDGASEYRKFLGPLSLELLYATLIDLIAFVSGGGGGQ*