AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1134780

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1134780 MtrunA17_Chr7g0215311 99.519 208 1 0 1 208 1 208 1.23e-152 421
Msa1134780 MtrunA17_Chr4g0024444 53.448 58 27 0 21 78 29 86 1.22e-13 67.0
Msa1134780 MtrunA17_Chr4g0017184 53.448 58 27 0 21 78 36 93 2.43e-13 67.0
Msa1134780 MtrunA17_CPg0492514 53.448 58 27 0 21 78 29 86 3.84e-13 66.2
Msa1134780 MtrunA17_Chr3g0090924 53.448 58 27 0 21 78 29 86 3.84e-13 66.2
Msa1134780 MtrunA17_Chr4g0015984 53.448 58 27 0 21 78 29 86 3.84e-13 66.2
Msa1134780 MtrunA17_Chr3g0094604 51.724 58 28 0 21 78 29 86 2.14e-12 64.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1134780 ATMG00560.1 40.964 249 104 11 1 207 1 248 4.16e-37 132
Msa1134780 AT2G07715.1 40.964 249 104 11 1 207 1 248 1.99e-36 131
Msa1134780 ATCG01310.1 53.448 58 27 0 21 78 40 97 6.00e-13 66.2
Msa1134780 ATCG00830.1 53.448 58 27 0 21 78 40 97 6.00e-13 66.2

Find 58 sgRNAs with CRISPR-Local

Find 74 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TAATTCGATGTAAACGTTTA+TGG 0.153323 7_4:-1430557 None:intergenic
TTTGGATGAATAGGAATAAA+AGG 0.280173 7_4:+1431021 Msa1134780:CDS
GAATCTGTTTCGTCGGCGTT+AGG 0.295361 7_4:+1430897 Msa1134780:CDS
ATCCACGCTGGAAGTAGTTC+AGG 0.328737 7_4:+1430831 Msa1134780:CDS
GGAGAAATTCGTGGTGTGTT+TGG 0.372829 7_4:+1430786 Msa1134780:CDS
ATGGTGAGAAATTGGAGATT+AGG 0.384469 7_4:+1430976 Msa1134780:CDS
GAAAGGGGATGGTGAGAAAT+TGG 0.384954 7_4:+1430968 Msa1134780:CDS
ATAGTGATGTTTGGATGAAT+AGG 0.385359 7_4:+1431012 Msa1134780:CDS
AGAAATTGGAGATTAGGAAT+TGG 0.386894 7_4:+1430982 Msa1134780:CDS
AATCTGTTTCGTCGGCGTTA+GGG 0.408292 7_4:+1430898 Msa1134780:CDS
CTCGTATCGCTCTCGTTCGT+TGG 0.411886 7_4:+1430652 Msa1134780:CDS
CTACTTCCAGCGTGGATTTG+TGG 0.416480 7_4:-1430825 None:intergenic
GGAAGAAGAATAGTGATGTT+TGG 0.421549 7_4:+1431003 Msa1134780:CDS
CGAATTTCTCCGTTTGATGC+AGG 0.426190 7_4:-1430774 None:intergenic
ACCTCCTTCCACCGCGGCGG+CGG 0.434065 7_4:+1430534 Msa1134780:CDS
TGCGGTGGCGGCGTCGAGAC+CGG 0.442065 7_4:+1430932 Msa1134780:CDS
AAAGGAAAACGGCGATTTCG+TGG 0.457827 7_4:+1431039 Msa1134780:CDS
GTGGTGGTGCGTTGTGGAGG+TGG 0.469889 7_4:-1430690 None:intergenic
AGGATCGTGTTTGAGGAATC+TGG 0.477109 7_4:-1430754 None:intergenic
TTGATGCAGGATCGTGTTTG+AGG 0.482287 7_4:-1430761 None:intergenic
GTTACCGAGGATTGCGGTGG+CGG 0.487560 7_4:+1430920 Msa1134780:CDS
ATGGCCGCCGCCGCGGTGGA+AGG 0.490719 7_4:-1430538 None:intergenic
AGCGGCGGCGGTTGCAGTAG+TGG 0.495161 7_4:-1430709 None:intergenic
GCTCTCGTTCGTTGGCTCAA+CGG 0.496850 7_4:+1430660 Msa1134780:CDS
TGCGGTGGATACAGCGGCGG+CGG 0.512467 7_4:-1430721 None:intergenic
ACCGCCGGCCGTAACTGTTA+CGG 0.517236 7_4:+1430504 Msa1134780:CDS
GCGATACGAGATGAACGGTT+AGG 0.522070 7_4:-1430639 None:intergenic
GAATAGGAATAAAAGGAAAA+CGG 0.523563 7_4:+1431028 Msa1134780:CDS
GACGCCGCCACCGCAATCCT+CGG 0.525158 7_4:-1430924 None:intergenic
TGATGCGACCGTAACAGTTA+CGG 0.537037 7_4:-1430512 None:intergenic
CGCTGGAAGTAGTTCAGGGA+AGG 0.538444 7_4:+1430836 Msa1134780:CDS
AAACACGATCCTGCATCAAA+CGG 0.538930 7_4:+1430765 Msa1134780:CDS
TCACTGAGACAATTCACATT+CGG 0.549414 7_4:+1430471 Msa1134780:CDS
GCCGCCGCCGCGGTGGAAGG+AGG 0.550965 7_4:-1430535 None:intergenic
CGCAACACTTCTTCTTCCGT+CGG 0.562201 7_4:+1430591 Msa1134780:CDS
TCCACGCTGGAAGTAGTTCA+GGG 0.565983 7_4:+1430832 Msa1134780:CDS
AACGTTTATGGCCGCCGCCG+CGG 0.570918 7_4:-1430545 None:intergenic
GCATCAAACGGAGAAATTCG+TGG 0.583721 7_4:+1430777 Msa1134780:CDS
AGACAATTCACATTCGGCGC+CGG 0.586858 7_4:+1430477 Msa1134780:CDS
GTTTATGGCCGCCGCCGCGG+TGG 0.594084 7_4:-1430542 None:intergenic
GGCGGCGGTTGCAGTAGTGG+TGG 0.604893 7_4:-1430706 None:intergenic
GTAGTGGTGGTGCGTTGTGG+AGG 0.609682 7_4:-1430693 None:intergenic
ACCGTAACAGTTACGGCCGG+CGG 0.611263 7_4:-1430505 None:intergenic
TGAAAGTGAATCTGTTTCGT+CGG 0.615360 7_4:+1430890 Msa1134780:CDS
GTTAGGGTTACCGAGGATTG+CGG 0.620929 7_4:+1430914 Msa1134780:CDS
AGGGTTACCGAGGATTGCGG+TGG 0.626019 7_4:+1430917 Msa1134780:CDS
TTGCTTCCACAAATCCACGC+TGG 0.637501 7_4:+1430819 Msa1134780:CDS
ATCACCTCCTTCCACCGCGG+CGG 0.644837 7_4:+1430531 Msa1134780:CDS
GCAGTAGTGGTGGTGCGTTG+TGG 0.654789 7_4:-1430696 None:intergenic
TCTGGAGGATGATGATGCGG+TGG 0.668026 7_4:-1430736 None:intergenic
TGATGATGCGGTGGATACAG+CGG 0.673078 7_4:-1430727 None:intergenic
CGAGAGCGATACGAGATGAA+CGG 0.676738 7_4:-1430644 None:intergenic
TCCCTGAACTACTTCCAGCG+TGG 0.686694 7_4:-1430833 None:intergenic
GATGCGTTCGACGATACCGA+CGG 0.688002 7_4:-1430607 None:intergenic
GAATCTGGAGGATGATGATG+CGG 0.700446 7_4:-1430739 None:intergenic
CGCATCACCTCCTTCCACCG+CGG 0.705661 7_4:+1430528 Msa1134780:CDS
TGATGCGGTGGATACAGCGG+CGG 0.707944 7_4:-1430724 None:intergenic
ATCGTGTTTGAGGAATCTGG+AGG 0.723414 7_4:-1430751 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! TAATTCGATGTAAACGTTTA+TGG - chr7_4:1430560-1430579 None:intergenic 25.0%
! TTTGGATGAATAGGAATAAA+AGG + chr7_4:1431021-1431040 Msa1134780:CDS 25.0%
! GAATAGGAATAAAAGGAAAA+CGG + chr7_4:1431028-1431047 Msa1134780:CDS 25.0%
AGAAATTGGAGATTAGGAAT+TGG + chr7_4:1430982-1431001 Msa1134780:CDS 30.0%
ATAGTGATGTTTGGATGAAT+AGG + chr7_4:1431012-1431031 Msa1134780:CDS 30.0%
TCACTGAGACAATTCACATT+CGG + chr7_4:1430471-1430490 Msa1134780:CDS 35.0%
TGAAAGTGAATCTGTTTCGT+CGG + chr7_4:1430890-1430909 Msa1134780:CDS 35.0%
ATGGTGAGAAATTGGAGATT+AGG + chr7_4:1430976-1430995 Msa1134780:CDS 35.0%
GGAAGAAGAATAGTGATGTT+TGG + chr7_4:1431003-1431022 Msa1134780:CDS 35.0%
AAACACGATCCTGCATCAAA+CGG + chr7_4:1430765-1430784 Msa1134780:CDS 40.0%
! TTCAGGGAAGGTTTTTCTGT+CGG + chr7_4:1430848-1430867 Msa1134780:CDS 40.0%
CCTTTCACACCAAAAAACTC+CGG - chr7_4:1430954-1430973 None:intergenic 40.0%
!!! CGGAGTTTTTTGGTGTGAAA+GGG + chr7_4:1430952-1430971 Msa1134780:CDS 40.0%
!!! GGAGTTTTTTGGTGTGAAAG+GGG + chr7_4:1430953-1430972 Msa1134780:CDS 40.0%
!!! TTTTTTGGTGTGAAAGGGGA+TGG + chr7_4:1430957-1430976 Msa1134780:CDS 40.0%
TGATGCGACCGTAACAGTTA+CGG - chr7_4:1430515-1430534 None:intergenic 45.0%
! GAATCTGGAGGATGATGATG+CGG - chr7_4:1430742-1430761 None:intergenic 45.0%
ATCGTGTTTGAGGAATCTGG+AGG - chr7_4:1430754-1430773 None:intergenic 45.0%
AGGATCGTGTTTGAGGAATC+TGG - chr7_4:1430757-1430776 None:intergenic 45.0%
TTGATGCAGGATCGTGTTTG+AGG - chr7_4:1430764-1430783 None:intergenic 45.0%
CGAATTTCTCCGTTTGATGC+AGG - chr7_4:1430777-1430796 None:intergenic 45.0%
GCATCAAACGGAGAAATTCG+TGG + chr7_4:1430777-1430796 Msa1134780:CDS 45.0%
GGAGAAATTCGTGGTGTGTT+TGG + chr7_4:1430786-1430805 Msa1134780:CDS 45.0%
! GGTTTTTCTGTCGGCGTTTT+CGG + chr7_4:1430857-1430876 Msa1134780:CDS 45.0%
! GTTTTTCTGTCGGCGTTTTC+GGG + chr7_4:1430858-1430877 Msa1134780:CDS 45.0%
! TTTTTCTGTCGGCGTTTTCG+GGG + chr7_4:1430859-1430878 Msa1134780:CDS 45.0%
AATCTGTTTCGTCGGCGTTA+GGG + chr7_4:1430898-1430917 Msa1134780:CDS 45.0%
!!! CCGGAGTTTTTTGGTGTGAA+AGG + chr7_4:1430951-1430970 Msa1134780:CDS 45.0%
GAAAGGGGATGGTGAGAAAT+TGG + chr7_4:1430968-1430987 Msa1134780:CDS 45.0%
AAAGGAAAACGGCGATTTCG+TGG + chr7_4:1431039-1431058 Msa1134780:CDS 45.0%
AGACAATTCACATTCGGCGC+CGG + chr7_4:1430477-1430496 Msa1134780:CDS 50.0%
CGCAACACTTCTTCTTCCGT+CGG + chr7_4:1430591-1430610 Msa1134780:CDS 50.0%
GCGATACGAGATGAACGGTT+AGG - chr7_4:1430642-1430661 None:intergenic 50.0%
CGAGAGCGATACGAGATGAA+CGG - chr7_4:1430647-1430666 None:intergenic 50.0%
! TGATGATGCGGTGGATACAG+CGG - chr7_4:1430730-1430749 None:intergenic 50.0%
TTGCTTCCACAAATCCACGC+TGG + chr7_4:1430819-1430838 Msa1134780:CDS 50.0%
CTACTTCCAGCGTGGATTTG+TGG - chr7_4:1430828-1430847 None:intergenic 50.0%
ATCCACGCTGGAAGTAGTTC+AGG + chr7_4:1430831-1430850 Msa1134780:CDS 50.0%
TCCACGCTGGAAGTAGTTCA+GGG + chr7_4:1430832-1430851 Msa1134780:CDS 50.0%
GAATCTGTTTCGTCGGCGTT+AGG + chr7_4:1430897-1430916 Msa1134780:CDS 50.0%
GTTAGGGTTACCGAGGATTG+CGG + chr7_4:1430914-1430933 Msa1134780:CDS 50.0%
GATGCGTTCGACGATACCGA+CGG - chr7_4:1430610-1430629 None:intergenic 55.0%
CTCGTATCGCTCTCGTTCGT+TGG + chr7_4:1430652-1430671 Msa1134780:CDS 55.0%
!! GCTCTCGTTCGTTGGCTCAA+CGG + chr7_4:1430660-1430679 Msa1134780:CDS 55.0%
! TCTGGAGGATGATGATGCGG+TGG - chr7_4:1430739-1430758 None:intergenic 55.0%
TCCCTGAACTACTTCCAGCG+TGG - chr7_4:1430836-1430855 None:intergenic 55.0%
CGCTGGAAGTAGTTCAGGGA+AGG + chr7_4:1430836-1430855 Msa1134780:CDS 55.0%
!!! GCGTCGAGACCGGAGTTTTT+TGG + chr7_4:1430942-1430961 Msa1134780:CDS 55.0%
! GTTACGGCCGGCGGTTTTTC+CGG - chr7_4:1430499-1430518 None:intergenic 60.0%
ACCGCCGGCCGTAACTGTTA+CGG + chr7_4:1430504-1430523 Msa1134780:CDS 60.0%
ACCGTAACAGTTACGGCCGG+CGG - chr7_4:1430508-1430527 None:intergenic 60.0%
GCGACCGTAACAGTTACGGC+CGG - chr7_4:1430511-1430530 None:intergenic 60.0%
! GTAGTGGTGGTGCGTTGTGG+AGG - chr7_4:1430696-1430715 None:intergenic 60.0%
! GCAGTAGTGGTGGTGCGTTG+TGG - chr7_4:1430699-1430718 None:intergenic 60.0%
TGATGCGGTGGATACAGCGG+CGG - chr7_4:1430727-1430746 None:intergenic 60.0%
!! TCTGTCGGCGTTTTCGGGGA+AGG + chr7_4:1430863-1430882 Msa1134780:CDS 60.0%
!! CTGTCGGCGTTTTCGGGGAA+GGG + chr7_4:1430864-1430883 Msa1134780:CDS 60.0%
AGGGTTACCGAGGATTGCGG+TGG + chr7_4:1430917-1430936 Msa1134780:CDS 60.0%
GTTACCGAGGATTGCGGTGG+CGG + chr7_4:1430920-1430939 Msa1134780:CDS 60.0%
! TTCGGCGCCGGAAAAACCGC+CGG + chr7_4:1430489-1430508 Msa1134780:CDS 65.0%
CGCATCACCTCCTTCCACCG+CGG + chr7_4:1430528-1430547 Msa1134780:CDS 65.0%
ATCACCTCCTTCCACCGCGG+CGG + chr7_4:1430531-1430550 Msa1134780:CDS 65.0%
AACGTTTATGGCCGCCGCCG+CGG - chr7_4:1430548-1430567 None:intergenic 65.0%
! GTGGTGGTGCGTTGTGGAGG+TGG - chr7_4:1430693-1430712 None:intergenic 65.0%
CGTCGGCGTTAGGGTTACCG+AGG + chr7_4:1430907-1430926 Msa1134780:CDS 65.0%
GGCGGCGGTTGCAGTAGTGG+TGG - chr7_4:1430709-1430728 None:intergenic 70.0%
AGCGGCGGCGGTTGCAGTAG+TGG - chr7_4:1430712-1430731 None:intergenic 70.0%
TGCGGTGGATACAGCGGCGG+CGG - chr7_4:1430724-1430743 None:intergenic 70.0%
GACGCCGCCACCGCAATCCT+CGG - chr7_4:1430927-1430946 None:intergenic 70.0%
ACCTCCTTCCACCGCGGCGG+CGG + chr7_4:1430534-1430553 Msa1134780:CDS 75.0%
GTTTATGGCCGCCGCCGCGG+TGG - chr7_4:1430545-1430564 None:intergenic 75.0%
! TGCGGTGGCGGCGTCGAGAC+CGG + chr7_4:1430932-1430951 Msa1134780:CDS 75.0%
! ATGGCCGCCGCCGCGGTGGA+AGG - chr7_4:1430541-1430560 None:intergenic 80.0%
! GCCGCCGCCGCGGTGGAAGG+AGG - chr7_4:1430538-1430557 None:intergenic 85.0%
Chromosome Type Strat End Strand Name
chr7_4 gene 1430450 1431076 1430450 ID=Msa1134780;Name=Msa1134780
chr7_4 mRNA 1430450 1431076 1430450 ID=Msa1134780-mRNA-1;Parent=Msa1134780;Name=Msa1134780-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|208
chr7_4 exon 1430450 1431076 1430450 ID=Msa1134780-mRNA-1:exon:522;Parent=Msa1134780-mRNA-1
chr7_4 CDS 1430450 1431076 1430450 ID=Msa1134780-mRNA-1:cds;Parent=Msa1134780-mRNA-1
Gene Sequence

>Msa1134780

ATGTCAGGAGGAGTGAAGAGATCACTGAGACAATTCACATTCGGCGCCGGAAAAACCGCCGGCCGTAACTGTTACGGTCGCATCACCTCCTTCCACCGCGGCGGCGGCCATAAACGTTTACATCGAATTATCGATCTCAAACGCAACACTTCTTCTTCCGTCGGTATCGTCGAACGCATCGAATACGATCCTAACCGTTCATCTCGTATCGCTCTCGTTCGTTGGCTCAACGGTATTAATCCACCTCCACAACGCACCACCACTACTGCAACCGCCGCCGCTGTATCCACCGCATCATCATCCTCCAGATTCCTCAAACACGATCCTGCATCAAACGGAGAAATTCGTGGTGTGTTTGGTTTGAATTCGTTGCTTCCACAAATCCACGCTGGAAGTAGTTCAGGGAAGGTTTTTCTGTCGGCGTTTTCGGGGAAGGGAGATGAAAGTGAATCTGTTTCGTCGGCGTTAGGGTTACCGAGGATTGCGGTGGCGGCGTCGAGACCGGAGTTTTTTGGTGTGAAAGGGGATGGTGAGAAATTGGAGATTAGGAATTGGAAGAAGAATAGTGATGTTTGGATGAATAGGAATAAAAGGAAAACGGCGATTTCGTGGCAGAATATTGCTTGA
Protein sequence

>Msa1134780

MSGGVKRSLRQFTFGAGKTAGRNCYGRITSFHRGGGHKRLHRIIDLKRNTSSSVGIVERIEYDPNRSSRIALVRWLNGINPPPQRTTTTATAAAVSTASSSSRFLKHDPASNGEIRGVFGLNSLLPQIHAGSSSGKVFLSAFSGKGDESESVSSALGLPRIAVAASRPEFFGVKGDGEKLEIRNWKKNSDVWMNRNKRKTAISWQNIA*