AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1390790

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1390790 MtrunA17_Chr8g0383161 87.162 148 11 2 1 148 1 140 1.20e-87 251
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1390790 AT5G64820.1 36.029 136 73 4 15 141 13 143 6.48e-17 72.8
Msa1390790 AT1G16850.1 35.659 129 72 2 12 135 13 135 2.63e-15 68.9

Find 33 sgRNAs with CRISPR-Local

Find 125 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGTATGAAACAATTTATTTA+TGG 0.128479 tig0021384:-88605 Msa1390790:three_prime_UTR
CTACAAACTTACTCCAAATT+TGG 0.167313 tig0021384:+89350 None:intergenic
CAAAATTGTGATGCTGTTAT+TGG 0.228818 tig0021384:-88650 Msa1390790:three_prime_UTR
TTCCAAGTATTGGCCTAAAT+TGG 0.235754 tig0021384:+88546 None:intergenic
AACGGTGTCAGTTAGTAATT+TGG 0.243488 tig0021384:+89454 None:intergenic
GAGAATCTTTGGCCACATTT+TGG 0.261276 tig0021384:+89495 None:intergenic
GAAACGTATGCTAAGGTATA+TGG 0.379291 tig0021384:+89666 None:intergenic
CAGGGGTTACATGCTGGAAT+TGG 0.395685 tig0021384:+89534 None:intergenic
AAATCAGCAGCTGAATTTGT+TGG 0.419411 tig0021384:-88787 Msa1390790:CDS
TACCAATTTAGGCCAATACT+TGG 0.442164 tig0021384:-88548 Msa1390790:three_prime_UTR
TGGCCACCTTCATCAGCAGC+AGG 0.453286 tig0021384:+89515 None:intergenic
ATTAAAATGACCCCAAAAGA+AGG 0.454890 tig0021384:+88673 None:intergenic
CAGCAGCAGGGGTTACATGC+TGG 0.456273 tig0021384:+89528 None:intergenic
AAAATCCCATGAAAGCTCTT+GGG 0.505602 tig0021384:-89420 Msa1390790:CDS
AAAAGCAAAGAATCAGTTGA+AGG 0.507499 tig0021384:-88817 Msa1390790:CDS
GTAACCCCTGCTGCTGATGA+AGG 0.514461 tig0021384:-89521 Msa1390790:CDS
CAAACTTACTCCAAATTTGG+TGG 0.516547 tig0021384:+89353 None:intergenic
GGCCACCTTCATCAGCAGCA+GGG 0.529923 tig0021384:+89516 None:intergenic
AAAACTGCATCTGAAGATCA+TGG 0.536891 tig0021384:+89378 None:intergenic
AGACACTACAGATTCTGATA+AGG 0.542472 tig0021384:-88731 Msa1390790:CDS
GCCACCTTCATCAGCAGCAG+GGG 0.559916 tig0021384:+89517 None:intergenic
TTTCTCCCAAGAGCTTTCAT+GGG 0.569638 tig0021384:+89415 None:intergenic
GATATGAGAAACGTATGCTA+AGG 0.583457 tig0021384:+89659 None:intergenic
AATTGTGATGCTGTTATTGG+AGG 0.583515 tig0021384:-88647 Msa1390790:three_prime_UTR
CGTATGCTAAGGTATATGGC+TGG 0.593588 tig0021384:+89670 None:intergenic
AACTAGAAGCGTCATTCACA+TGG 0.599531 tig0021384:+88451 None:intergenic
GATGCTGTTATTGGAGGAGA+TGG 0.605362 tig0021384:-88641 Msa1390790:three_prime_UTR
TGTCAGTTAGTAATTTGGAA+AGG 0.607458 tig0021384:+89459 None:intergenic
AATCCATAAGACAAAAGAGA+AGG 0.608547 tig0021384:-88758 Msa1390790:CDS
GTTAGTAATTTGGAAAGGCG+TGG 0.619952 tig0021384:+89464 None:intergenic
AGGGGAAAAGGAGAACATGA+AGG 0.650023 tig0021384:-88871 Msa1390790:CDS
ACCCCTGCTGCTGATGAAGG+TGG 0.657057 tig0021384:-89518 Msa1390790:CDS
TGATGAAGGTGGCCAAAATG+TGG 0.672717 tig0021384:-89507 Msa1390790:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTCATATATATACATTAAAT+TGG + tig0021384:89173-89192 None:intergenic 10.0%
!! ATATATATGAATATTAATGT+AGG - tig0021384:89182-89201 Msa1390790:intron 10.0%
!! TTCATATATATACATTAAAT+TGG + tig0021384:89173-89192 None:intergenic 10.0%
!! ATATATATGAATATTAATGT+AGG - tig0021384:89182-89201 Msa1390790:intron 10.0%
!! AATTAAAAACTAATTGTTCA+AGG + tig0021384:88480-88499 None:intergenic 15.0%
!! AAAATAGTTTAATGTTGATA+TGG - tig0021384:88897-88916 Msa1390790:intron 15.0%
!! TGTAAATTCATAAAAATGAT+TGG + tig0021384:88972-88991 None:intergenic 15.0%
!!! ATATATATATGATTTGTTGA+CGG - tig0021384:89087-89106 Msa1390790:intron 15.0%
!!! AAATATTTTTTTCCTTCTTT+TGG - tig0021384:89423-89442 Msa1390790:CDS 15.0%
!!! AATATTTTTTTCCTTCTTTT+GGG - tig0021384:89424-89443 Msa1390790:CDS 15.0%
!! TGTATGAAACAATTTATTTA+TGG - tig0021384:89503-89522 Msa1390790:CDS 15.0%
!! AATTAAAAACTAATTGTTCA+AGG + tig0021384:88480-88499 None:intergenic 15.0%
!! AAAATAGTTTAATGTTGATA+TGG - tig0021384:88897-88916 Msa1390790:intron 15.0%
!! TGTAAATTCATAAAAATGAT+TGG + tig0021384:88972-88991 None:intergenic 15.0%
!!! ATATATATATGATTTGTTGA+CGG - tig0021384:89087-89106 Msa1390790:intron 15.0%
!!! AAATATTTTTTTCCTTCTTT+TGG - tig0021384:89423-89442 Msa1390790:CDS 15.0%
!!! AATATTTTTTTCCTTCTTTT+GGG - tig0021384:89424-89443 Msa1390790:CDS 15.0%
!! TGTATGAAACAATTTATTTA+TGG - tig0021384:89503-89522 Msa1390790:CDS 15.0%
!! AAAAAGAAGAAAAAGTAGTA+TGG + tig0021384:88537-88556 None:intergenic 20.0%
!!! CAAAAGTCTATTTCATTTTT+AGG - tig0021384:88786-88805 Msa1390790:CDS 20.0%
!! CAATACAATCTTGAAATTAT+AGG - tig0021384:88819-88838 Msa1390790:CDS 20.0%
!!! TTATGACTGAATATTTTTCA+AGG + tig0021384:89021-89040 None:intergenic 20.0%
!! ATATGAATATTAATGTAGGT+AGG - tig0021384:89186-89205 Msa1390790:intron 20.0%
!!! ATATTTTTTTCCTTCTTTTG+GGG - tig0021384:89425-89444 Msa1390790:CDS 20.0%
!!! TTCATACATTTTACCAATTT+AGG - tig0021384:89549-89568 Msa1390790:CDS 20.0%
!!! GAATTGCTATTATGTATTTT+TGG + tig0021384:89631-89650 None:intergenic 20.0%
!! AAAAAGAAGAAAAAGTAGTA+TGG + tig0021384:88537-88556 None:intergenic 20.0%
!!! CAAAAGTCTATTTCATTTTT+AGG - tig0021384:88786-88805 Msa1390790:CDS 20.0%
!! CAATACAATCTTGAAATTAT+AGG - tig0021384:88819-88838 Msa1390790:CDS 20.0%
!!! TTATGACTGAATATTTTTCA+AGG + tig0021384:89021-89040 None:intergenic 20.0%
!! ATATGAATATTAATGTAGGT+AGG - tig0021384:89186-89205 Msa1390790:intron 20.0%
!!! ATATTTTTTTCCTTCTTTTG+GGG - tig0021384:89425-89444 Msa1390790:CDS 20.0%
!!! TTCATACATTTTACCAATTT+AGG - tig0021384:89549-89568 Msa1390790:CDS 20.0%
!!! GAATTGCTATTATGTATTTT+TGG + tig0021384:89631-89650 None:intergenic 20.0%
!!! GTTTTTAATTAGCATTAGCA+TGG - tig0021384:88490-88509 Msa1390790:three_prime_UTR 25.0%
!!! TGTATCTATTTTTCAGTTTC+AGG - tig0021384:89217-89236 Msa1390790:intron 25.0%
!!! GTATCTATTTTTCAGTTTCA+GGG - tig0021384:89218-89237 Msa1390790:intron 25.0%
!!! TATCTATTTTTCAGTTTCAG+GGG - tig0021384:89219-89238 Msa1390790:intron 25.0%
!! TTTTCAAATCTTCCAAGTAT+TGG + tig0021384:89575-89594 None:intergenic 25.0%
!!! GTTTTTAATTAGCATTAGCA+TGG - tig0021384:88490-88509 Msa1390790:three_prime_UTR 25.0%
!!! TGTATCTATTTTTCAGTTTC+AGG - tig0021384:89217-89236 Msa1390790:intron 25.0%
!!! GTATCTATTTTTCAGTTTCA+GGG - tig0021384:89218-89237 Msa1390790:intron 25.0%
!!! TATCTATTTTTCAGTTTCAG+GGG - tig0021384:89219-89238 Msa1390790:intron 25.0%
!! TTTTCAAATCTTCCAAGTAT+TGG + tig0021384:89575-89594 None:intergenic 25.0%
TGTCAGTTAGTAATTTGGAA+AGG + tig0021384:88652-88671 None:intergenic 30.0%
!!! GGATTTTTTAAGCAGAGAAA+CGG + tig0021384:88675-88694 None:intergenic 30.0%
CTACAAACTTACTCCAAATT+TGG + tig0021384:88761-88780 None:intergenic 30.0%
TATATGTCTGACTTTAGACA+TGG + tig0021384:89072-89091 None:intergenic 30.0%
AAAAGCAAAGAATCAGTTGA+AGG - tig0021384:89291-89310 Msa1390790:intron 30.0%
AATCCATAAGACAAAAGAGA+AGG - tig0021384:89350-89369 Msa1390790:intron 30.0%
ATTAAAATGACCCCAAAAGA+AGG + tig0021384:89438-89457 None:intergenic 30.0%
CAAAATTGTGATGCTGTTAT+TGG - tig0021384:89458-89477 Msa1390790:CDS 30.0%
TGTCAGTTAGTAATTTGGAA+AGG + tig0021384:88652-88671 None:intergenic 30.0%
!!! GGATTTTTTAAGCAGAGAAA+CGG + tig0021384:88675-88694 None:intergenic 30.0%
CTACAAACTTACTCCAAATT+TGG + tig0021384:88761-88780 None:intergenic 30.0%
TATATGTCTGACTTTAGACA+TGG + tig0021384:89072-89091 None:intergenic 30.0%
AAAAGCAAAGAATCAGTTGA+AGG - tig0021384:89291-89310 Msa1390790:intron 30.0%
AATCCATAAGACAAAAGAGA+AGG - tig0021384:89350-89369 Msa1390790:intron 30.0%
ATTAAAATGACCCCAAAAGA+AGG + tig0021384:89438-89457 None:intergenic 30.0%
CAAAATTGTGATGCTGTTAT+TGG - tig0021384:89458-89477 Msa1390790:CDS 30.0%
GAAACGTATGCTAAGGTATA+TGG + tig0021384:88445-88464 None:intergenic 35.0%
GATATGAGAAACGTATGCTA+AGG + tig0021384:88452-88471 None:intergenic 35.0%
!! TGGTTTTTCTGGAGAATCTT+TGG + tig0021384:88627-88646 None:intergenic 35.0%
! AACGGTGTCAGTTAGTAATT+TGG + tig0021384:88657-88676 None:intergenic 35.0%
AAAAATCCCATGAAAGCTCT+TGG - tig0021384:88687-88706 Msa1390790:three_prime_UTR 35.0%
AAAATCCCATGAAAGCTCTT+GGG - tig0021384:88688-88707 Msa1390790:three_prime_UTR 35.0%
AAAACTGCATCTGAAGATCA+TGG + tig0021384:88733-88752 None:intergenic 35.0%
CAAACTTACTCCAAATTTGG+TGG + tig0021384:88758-88777 None:intergenic 35.0%
!! TTTTTCAGTTTCAGGGGAAA+AGG - tig0021384:89225-89244 Msa1390790:intron 35.0%
AAATCAGCAGCTGAATTTGT+TGG - tig0021384:89321-89340 Msa1390790:intron 35.0%
! TCACCTTCTCTTTTGTCTTA+TGG + tig0021384:89356-89375 None:intergenic 35.0%
AGACACTACAGATTCTGATA+AGG - tig0021384:89377-89396 Msa1390790:CDS 35.0%
AATTGTGATGCTGTTATTGG+AGG - tig0021384:89461-89480 Msa1390790:CDS 35.0%
TACCAATTTAGGCCAATACT+TGG - tig0021384:89560-89579 Msa1390790:CDS 35.0%
!! TTCCAAGTATTGGCCTAAAT+TGG + tig0021384:89565-89584 None:intergenic 35.0%
GAAACGTATGCTAAGGTATA+TGG + tig0021384:88445-88464 None:intergenic 35.0%
GATATGAGAAACGTATGCTA+AGG + tig0021384:88452-88471 None:intergenic 35.0%
!! TGGTTTTTCTGGAGAATCTT+TGG + tig0021384:88627-88646 None:intergenic 35.0%
! AACGGTGTCAGTTAGTAATT+TGG + tig0021384:88657-88676 None:intergenic 35.0%
AAAAATCCCATGAAAGCTCT+TGG - tig0021384:88687-88706 Msa1390790:three_prime_UTR 35.0%
AAAATCCCATGAAAGCTCTT+GGG - tig0021384:88688-88707 Msa1390790:three_prime_UTR 35.0%
AAAACTGCATCTGAAGATCA+TGG + tig0021384:88733-88752 None:intergenic 35.0%
CAAACTTACTCCAAATTTGG+TGG + tig0021384:88758-88777 None:intergenic 35.0%
!! TTTTTCAGTTTCAGGGGAAA+AGG - tig0021384:89225-89244 Msa1390790:intron 35.0%
AAATCAGCAGCTGAATTTGT+TGG - tig0021384:89321-89340 Msa1390790:intron 35.0%
! TCACCTTCTCTTTTGTCTTA+TGG + tig0021384:89356-89375 None:intergenic 35.0%
AGACACTACAGATTCTGATA+AGG - tig0021384:89377-89396 Msa1390790:CDS 35.0%
AATTGTGATGCTGTTATTGG+AGG - tig0021384:89461-89480 Msa1390790:CDS 35.0%
TACCAATTTAGGCCAATACT+TGG - tig0021384:89560-89579 Msa1390790:CDS 35.0%
!! TTCCAAGTATTGGCCTAAAT+TGG + tig0021384:89565-89584 None:intergenic 35.0%
! GAGAATCTTTGGCCACATTT+TGG + tig0021384:88616-88635 None:intergenic 40.0%
GTTAGTAATTTGGAAAGGCG+TGG + tig0021384:88647-88666 None:intergenic 40.0%
TTTCTCCCAAGAGCTTTCAT+GGG + tig0021384:88696-88715 None:intergenic 40.0%
! TTTTCTCCCAAGAGCTTTCA+TGG + tig0021384:88697-88716 None:intergenic 40.0%
! GCAGTTTTCACCACCAAATT+TGG - tig0021384:88745-88764 Msa1390790:CDS 40.0%
!! AACTAGAAGCGTCATTCACA+TGG + tig0021384:89660-89679 None:intergenic 40.0%
! GAGAATCTTTGGCCACATTT+TGG + tig0021384:88616-88635 None:intergenic 40.0%
GTTAGTAATTTGGAAAGGCG+TGG + tig0021384:88647-88666 None:intergenic 40.0%
TTTCTCCCAAGAGCTTTCAT+GGG + tig0021384:88696-88715 None:intergenic 40.0%
! TTTTCTCCCAAGAGCTTTCA+TGG + tig0021384:88697-88716 None:intergenic 40.0%
! GCAGTTTTCACCACCAAATT+TGG - tig0021384:88745-88764 Msa1390790:CDS 40.0%
!! AACTAGAAGCGTCATTCACA+TGG + tig0021384:89660-89679 None:intergenic 40.0%
TGATGAAGGTGGCCAAAATG+TGG - tig0021384:88601-88620 Msa1390790:three_prime_UTR 45.0%
!! TTGGAAAGGCGTGGTTTTTC+TGG + tig0021384:88638-88657 None:intergenic 45.0%
AGGGGAAAAGGAGAACATGA+AGG - tig0021384:89237-89256 Msa1390790:intron 45.0%
GATGCTGTTATTGGAGGAGA+TGG - tig0021384:89467-89486 Msa1390790:CDS 45.0%
CGTATGCTAAGGTATATGGC+TGG + tig0021384:88441-88460 None:intergenic 45.0%
TGATGAAGGTGGCCAAAATG+TGG - tig0021384:88601-88620 Msa1390790:three_prime_UTR 45.0%
!! TTGGAAAGGCGTGGTTTTTC+TGG + tig0021384:88638-88657 None:intergenic 45.0%
AGGGGAAAAGGAGAACATGA+AGG - tig0021384:89237-89256 Msa1390790:intron 45.0%
GATGCTGTTATTGGAGGAGA+TGG - tig0021384:89467-89486 Msa1390790:CDS 45.0%
CAGGGGTTACATGCTGGAAT+TGG + tig0021384:88577-88596 None:intergenic 50.0%
CAGGGGTTACATGCTGGAAT+TGG + tig0021384:88577-88596 None:intergenic 50.0%
GTAACCCCTGCTGCTGATGA+AGG - tig0021384:88587-88606 Msa1390790:three_prime_UTR 55.0%
GTAACCCCTGCTGCTGATGA+AGG - tig0021384:88587-88606 Msa1390790:three_prime_UTR 55.0%
CAGCAGCAGGGGTTACATGC+TGG + tig0021384:88583-88602 None:intergenic 60.0%
ACCCCTGCTGCTGATGAAGG+TGG - tig0021384:88590-88609 Msa1390790:three_prime_UTR 60.0%
GCCACCTTCATCAGCAGCAG+GGG + tig0021384:88594-88613 None:intergenic 60.0%
GGCCACCTTCATCAGCAGCA+GGG + tig0021384:88595-88614 None:intergenic 60.0%
TGGCCACCTTCATCAGCAGC+AGG + tig0021384:88596-88615 None:intergenic 60.0%
CAGCAGCAGGGGTTACATGC+TGG + tig0021384:88583-88602 None:intergenic 60.0%
ACCCCTGCTGCTGATGAAGG+TGG - tig0021384:88590-88609 Msa1390790:three_prime_UTR 60.0%
GCCACCTTCATCAGCAGCAG+GGG + tig0021384:88594-88613 None:intergenic 60.0%
GGCCACCTTCATCAGCAGCA+GGG + tig0021384:88595-88614 None:intergenic 60.0%
TGGCCACCTTCATCAGCAGC+AGG + tig0021384:88596-88615 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
tig0021384 gene 88439 89691 88439 ID=Msa1390790;Name=Msa1390790
tig0021384 mRNA 88439 89691 88439 ID=Msa1390790-mRNA-1;Parent=Msa1390790;Name=Msa1390790-mRNA-1;_AED=0.00;_eAED=0.00;_QI=70|1|1|1|1|1|2|272|148
tig0021384 exon 88439 88897 88439 ID=Msa1390790-mRNA-1:exon:12393;Parent=Msa1390790-mRNA-1
tig0021384 exon 89362 89691 89362 ID=Msa1390790-mRNA-1:exon:12392;Parent=Msa1390790-mRNA-1
tig0021384 five_prime_UTR 89622 89691 89622 ID=Msa1390790-mRNA-1:five_prime_utr;Parent=Msa1390790-mRNA-1
tig0021384 CDS 89362 89621 89362 ID=Msa1390790-mRNA-1:cds;Parent=Msa1390790-mRNA-1
tig0021384 CDS 88711 88897 88711 ID=Msa1390790-mRNA-1:cds;Parent=Msa1390790-mRNA-1
tig0021384 three_prime_UTR 88439 88710 88439 ID=Msa1390790-mRNA-1:three_prime_utr;Parent=Msa1390790-mRNA-1
Gene Sequence

>Msa1390790

ATGGAAAATAAATTGATTAGCAGAACCATACTACTTTTTCTTCTTTTTAGCATCTTGATCATTCTCCAATTCCAGCATGTAACCCCTGCTGCTGATGAAGGTGGCCAAAATGTGGCCAAAGATTCTCCAGAAAAACCACGCCTTTCCAAATTACTAACTGACACCGTTTCTCTGCTTAAAAAATCCCATGAAAGCTCTTGGGAGAAAATCAAAACTGTCATCCATGATCTTCAGATGCAGTTTTCACCACCAAATTTGGATTTCAGGGGAAAAGGAGAACATGAAGGAGTGAAAGAAGCAGTTGAGAAGAGTTTTGACAAAAGCAAAGAATCAGTTGAAGGAACTGCTAAATCAGCAGCTGAATTTGTTGGAGAAACAATCCATAAGACAAAAGAGAAGGTGAAAGACACTACAGATTCTGATAAGGATTCTAAAGCAGAACTTTGA
Protein sequence

>Msa1390790

MENKLISRTILLFLLFSILIILQFQHVTPAADEGGQNVAKDSPEKPRLSKLLTDTVSLLKKSHESSWEKIKTVIHDLQMQFSPPNLDFRGKGEHEGVKEAVEKSFDKSKESVEGTAKSAAEFVGETIHKTKEKVKDTTDSDKDSKAEL*