AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1134750

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1134750 MtrunA17_Chr7g0215311 99.519 208 1 0 1 208 1 208 1.23e-152 421
Msa1134750 MtrunA17_Chr4g0024444 53.448 58 27 0 21 78 29 86 1.22e-13 67.0
Msa1134750 MtrunA17_Chr4g0017184 53.448 58 27 0 21 78 36 93 2.43e-13 67.0
Msa1134750 MtrunA17_CPg0492514 53.448 58 27 0 21 78 29 86 3.84e-13 66.2
Msa1134750 MtrunA17_Chr3g0090924 53.448 58 27 0 21 78 29 86 3.84e-13 66.2
Msa1134750 MtrunA17_Chr4g0015984 53.448 58 27 0 21 78 29 86 3.84e-13 66.2
Msa1134750 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
Msa1134750 ATMG00560.1 40.964 249 104 11 1 207 1 248 4.16e-37 132
Msa1134750 AT2G07715.1 40.964 249 104 11 1 207 1 248 1.99e-36 131
Msa1134750 ATCG01310.1 53.448 58 27 0 21 78 40 97 6.00e-13 66.2
Msa1134750 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:-1386692 None:intergenic
TTTGGATGAATAGGAATAAA+AGG 0.280173 7_4:+1387156 Msa1134750:CDS
GAATCTGTTTCGTCGGCGTT+AGG 0.295361 7_4:+1387032 Msa1134750:CDS
ATCCACGCTGGAAGTAGTTC+AGG 0.328737 7_4:+1386966 Msa1134750:CDS
GGAGAAATTCGTGGTGTGTT+TGG 0.372829 7_4:+1386921 Msa1134750:CDS
ATGGTGAGAAATTGGAGATT+AGG 0.384469 7_4:+1387111 Msa1134750:CDS
GAAAGGGGATGGTGAGAAAT+TGG 0.384954 7_4:+1387103 Msa1134750:CDS
ATAGTGATGTTTGGATGAAT+AGG 0.385359 7_4:+1387147 Msa1134750:CDS
AGAAATTGGAGATTAGGAAT+TGG 0.386894 7_4:+1387117 Msa1134750:CDS
AATCTGTTTCGTCGGCGTTA+GGG 0.408292 7_4:+1387033 Msa1134750:CDS
CTCGTATCGCTCTCGTTCGT+TGG 0.411886 7_4:+1386787 Msa1134750:CDS
CTACTTCCAGCGTGGATTTG+TGG 0.416480 7_4:-1386960 None:intergenic
GGAAGAAGAATAGTGATGTT+TGG 0.421549 7_4:+1387138 Msa1134750:CDS
CGAATTTCTCCGTTTGATGC+AGG 0.426190 7_4:-1386909 None:intergenic
ACCTCCTTCCACCGCGGCGG+CGG 0.434065 7_4:+1386669 Msa1134750:CDS
TGCGGTGGCGGCGTCGAGAC+CGG 0.442065 7_4:+1387067 Msa1134750:CDS
AAAGGAAAACGGCGATTTCG+TGG 0.457827 7_4:+1387174 Msa1134750:CDS
GTGGTGGTGCGTTGTGGAGG+TGG 0.469889 7_4:-1386825 None:intergenic
AGGATCGTGTTTGAGGAATC+TGG 0.477109 7_4:-1386889 None:intergenic
TTGATGCAGGATCGTGTTTG+AGG 0.482287 7_4:-1386896 None:intergenic
GTTACCGAGGATTGCGGTGG+CGG 0.487560 7_4:+1387055 Msa1134750:CDS
ATGGCCGCCGCCGCGGTGGA+AGG 0.490719 7_4:-1386673 None:intergenic
AGCGGCGGCGGTTGCAGTAG+TGG 0.495161 7_4:-1386844 None:intergenic
GCTCTCGTTCGTTGGCTCAA+CGG 0.496850 7_4:+1386795 Msa1134750:CDS
TGCGGTGGATACAGCGGCGG+CGG 0.512467 7_4:-1386856 None:intergenic
ACCGCCGGCCGTAACTGTTA+CGG 0.517236 7_4:+1386639 Msa1134750:CDS
GCGATACGAGATGAACGGTT+AGG 0.522070 7_4:-1386774 None:intergenic
GAATAGGAATAAAAGGAAAA+CGG 0.523563 7_4:+1387163 Msa1134750:CDS
GACGCCGCCACCGCAATCCT+CGG 0.525158 7_4:-1387059 None:intergenic
TGATGCGACCGTAACAGTTA+CGG 0.537037 7_4:-1386647 None:intergenic
CGCTGGAAGTAGTTCAGGGA+AGG 0.538444 7_4:+1386971 Msa1134750:CDS
AAACACGATCCTGCATCAAA+CGG 0.538930 7_4:+1386900 Msa1134750:CDS
TCACTGAGACAATTCACATT+CGG 0.549414 7_4:+1386606 Msa1134750:CDS
GCCGCCGCCGCGGTGGAAGG+AGG 0.550965 7_4:-1386670 None:intergenic
CGCAACACTTCTTCTTCCGT+CGG 0.562201 7_4:+1386726 Msa1134750:CDS
TCCACGCTGGAAGTAGTTCA+GGG 0.565983 7_4:+1386967 Msa1134750:CDS
AACGTTTATGGCCGCCGCCG+CGG 0.570918 7_4:-1386680 None:intergenic
GCATCAAACGGAGAAATTCG+TGG 0.583721 7_4:+1386912 Msa1134750:CDS
AGACAATTCACATTCGGCGC+CGG 0.586858 7_4:+1386612 Msa1134750:CDS
GTTTATGGCCGCCGCCGCGG+TGG 0.594084 7_4:-1386677 None:intergenic
GGCGGCGGTTGCAGTAGTGG+TGG 0.604893 7_4:-1386841 None:intergenic
GTAGTGGTGGTGCGTTGTGG+AGG 0.609682 7_4:-1386828 None:intergenic
ACCGTAACAGTTACGGCCGG+CGG 0.611263 7_4:-1386640 None:intergenic
TGAAAGTGAATCTGTTTCGT+CGG 0.615360 7_4:+1387025 Msa1134750:CDS
GTTAGGGTTACCGAGGATTG+CGG 0.620929 7_4:+1387049 Msa1134750:CDS
AGGGTTACCGAGGATTGCGG+TGG 0.626019 7_4:+1387052 Msa1134750:CDS
TTGCTTCCACAAATCCACGC+TGG 0.637501 7_4:+1386954 Msa1134750:CDS
ATCACCTCCTTCCACCGCGG+CGG 0.644837 7_4:+1386666 Msa1134750:CDS
GCAGTAGTGGTGGTGCGTTG+TGG 0.654789 7_4:-1386831 None:intergenic
TCTGGAGGATGATGATGCGG+TGG 0.668026 7_4:-1386871 None:intergenic
TGATGATGCGGTGGATACAG+CGG 0.673078 7_4:-1386862 None:intergenic
CGAGAGCGATACGAGATGAA+CGG 0.676738 7_4:-1386779 None:intergenic
TCCCTGAACTACTTCCAGCG+TGG 0.686694 7_4:-1386968 None:intergenic
GATGCGTTCGACGATACCGA+CGG 0.688002 7_4:-1386742 None:intergenic
GAATCTGGAGGATGATGATG+CGG 0.700446 7_4:-1386874 None:intergenic
CGCATCACCTCCTTCCACCG+CGG 0.705661 7_4:+1386663 Msa1134750:CDS
TGATGCGGTGGATACAGCGG+CGG 0.707944 7_4:-1386859 None:intergenic
ATCGTGTTTGAGGAATCTGG+AGG 0.723414 7_4:-1386886 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! TAATTCGATGTAAACGTTTA+TGG - chr7_4:1386695-1386714 None:intergenic 25.0%
! TTTGGATGAATAGGAATAAA+AGG + chr7_4:1387156-1387175 Msa1134750:CDS 25.0%
! GAATAGGAATAAAAGGAAAA+CGG + chr7_4:1387163-1387182 Msa1134750:CDS 25.0%
AGAAATTGGAGATTAGGAAT+TGG + chr7_4:1387117-1387136 Msa1134750:CDS 30.0%
ATAGTGATGTTTGGATGAAT+AGG + chr7_4:1387147-1387166 Msa1134750:CDS 30.0%
TCACTGAGACAATTCACATT+CGG + chr7_4:1386606-1386625 Msa1134750:CDS 35.0%
TGAAAGTGAATCTGTTTCGT+CGG + chr7_4:1387025-1387044 Msa1134750:CDS 35.0%
ATGGTGAGAAATTGGAGATT+AGG + chr7_4:1387111-1387130 Msa1134750:CDS 35.0%
GGAAGAAGAATAGTGATGTT+TGG + chr7_4:1387138-1387157 Msa1134750:CDS 35.0%
AAACACGATCCTGCATCAAA+CGG + chr7_4:1386900-1386919 Msa1134750:CDS 40.0%
! TTCAGGGAAGGTTTTTCTGT+CGG + chr7_4:1386983-1387002 Msa1134750:CDS 40.0%
CCTTTCACACCAAAAAACTC+CGG - chr7_4:1387089-1387108 None:intergenic 40.0%
!!! CGGAGTTTTTTGGTGTGAAA+GGG + chr7_4:1387087-1387106 Msa1134750:CDS 40.0%
!!! GGAGTTTTTTGGTGTGAAAG+GGG + chr7_4:1387088-1387107 Msa1134750:CDS 40.0%
!!! TTTTTTGGTGTGAAAGGGGA+TGG + chr7_4:1387092-1387111 Msa1134750:CDS 40.0%
TGATGCGACCGTAACAGTTA+CGG - chr7_4:1386650-1386669 None:intergenic 45.0%
! GAATCTGGAGGATGATGATG+CGG - chr7_4:1386877-1386896 None:intergenic 45.0%
ATCGTGTTTGAGGAATCTGG+AGG - chr7_4:1386889-1386908 None:intergenic 45.0%
AGGATCGTGTTTGAGGAATC+TGG - chr7_4:1386892-1386911 None:intergenic 45.0%
TTGATGCAGGATCGTGTTTG+AGG - chr7_4:1386899-1386918 None:intergenic 45.0%
CGAATTTCTCCGTTTGATGC+AGG - chr7_4:1386912-1386931 None:intergenic 45.0%
GCATCAAACGGAGAAATTCG+TGG + chr7_4:1386912-1386931 Msa1134750:CDS 45.0%
GGAGAAATTCGTGGTGTGTT+TGG + chr7_4:1386921-1386940 Msa1134750:CDS 45.0%
! GGTTTTTCTGTCGGCGTTTT+CGG + chr7_4:1386992-1387011 Msa1134750:CDS 45.0%
! GTTTTTCTGTCGGCGTTTTC+GGG + chr7_4:1386993-1387012 Msa1134750:CDS 45.0%
! TTTTTCTGTCGGCGTTTTCG+GGG + chr7_4:1386994-1387013 Msa1134750:CDS 45.0%
AATCTGTTTCGTCGGCGTTA+GGG + chr7_4:1387033-1387052 Msa1134750:CDS 45.0%
!!! CCGGAGTTTTTTGGTGTGAA+AGG + chr7_4:1387086-1387105 Msa1134750:CDS 45.0%
GAAAGGGGATGGTGAGAAAT+TGG + chr7_4:1387103-1387122 Msa1134750:CDS 45.0%
AAAGGAAAACGGCGATTTCG+TGG + chr7_4:1387174-1387193 Msa1134750:CDS 45.0%
AGACAATTCACATTCGGCGC+CGG + chr7_4:1386612-1386631 Msa1134750:CDS 50.0%
CGCAACACTTCTTCTTCCGT+CGG + chr7_4:1386726-1386745 Msa1134750:CDS 50.0%
GCGATACGAGATGAACGGTT+AGG - chr7_4:1386777-1386796 None:intergenic 50.0%
CGAGAGCGATACGAGATGAA+CGG - chr7_4:1386782-1386801 None:intergenic 50.0%
! TGATGATGCGGTGGATACAG+CGG - chr7_4:1386865-1386884 None:intergenic 50.0%
TTGCTTCCACAAATCCACGC+TGG + chr7_4:1386954-1386973 Msa1134750:CDS 50.0%
CTACTTCCAGCGTGGATTTG+TGG - chr7_4:1386963-1386982 None:intergenic 50.0%
ATCCACGCTGGAAGTAGTTC+AGG + chr7_4:1386966-1386985 Msa1134750:CDS 50.0%
TCCACGCTGGAAGTAGTTCA+GGG + chr7_4:1386967-1386986 Msa1134750:CDS 50.0%
GAATCTGTTTCGTCGGCGTT+AGG + chr7_4:1387032-1387051 Msa1134750:CDS 50.0%
GTTAGGGTTACCGAGGATTG+CGG + chr7_4:1387049-1387068 Msa1134750:CDS 50.0%
GATGCGTTCGACGATACCGA+CGG - chr7_4:1386745-1386764 None:intergenic 55.0%
CTCGTATCGCTCTCGTTCGT+TGG + chr7_4:1386787-1386806 Msa1134750:CDS 55.0%
!! GCTCTCGTTCGTTGGCTCAA+CGG + chr7_4:1386795-1386814 Msa1134750:CDS 55.0%
! TCTGGAGGATGATGATGCGG+TGG - chr7_4:1386874-1386893 None:intergenic 55.0%
TCCCTGAACTACTTCCAGCG+TGG - chr7_4:1386971-1386990 None:intergenic 55.0%
CGCTGGAAGTAGTTCAGGGA+AGG + chr7_4:1386971-1386990 Msa1134750:CDS 55.0%
!!! GCGTCGAGACCGGAGTTTTT+TGG + chr7_4:1387077-1387096 Msa1134750:CDS 55.0%
! GTTACGGCCGGCGGTTTTTC+CGG - chr7_4:1386634-1386653 None:intergenic 60.0%
ACCGCCGGCCGTAACTGTTA+CGG + chr7_4:1386639-1386658 Msa1134750:CDS 60.0%
ACCGTAACAGTTACGGCCGG+CGG - chr7_4:1386643-1386662 None:intergenic 60.0%
GCGACCGTAACAGTTACGGC+CGG - chr7_4:1386646-1386665 None:intergenic 60.0%
! GTAGTGGTGGTGCGTTGTGG+AGG - chr7_4:1386831-1386850 None:intergenic 60.0%
! GCAGTAGTGGTGGTGCGTTG+TGG - chr7_4:1386834-1386853 None:intergenic 60.0%
TGATGCGGTGGATACAGCGG+CGG - chr7_4:1386862-1386881 None:intergenic 60.0%
!! TCTGTCGGCGTTTTCGGGGA+AGG + chr7_4:1386998-1387017 Msa1134750:CDS 60.0%
!! CTGTCGGCGTTTTCGGGGAA+GGG + chr7_4:1386999-1387018 Msa1134750:CDS 60.0%
AGGGTTACCGAGGATTGCGG+TGG + chr7_4:1387052-1387071 Msa1134750:CDS 60.0%
GTTACCGAGGATTGCGGTGG+CGG + chr7_4:1387055-1387074 Msa1134750:CDS 60.0%
! TTCGGCGCCGGAAAAACCGC+CGG + chr7_4:1386624-1386643 Msa1134750:CDS 65.0%
CGCATCACCTCCTTCCACCG+CGG + chr7_4:1386663-1386682 Msa1134750:CDS 65.0%
ATCACCTCCTTCCACCGCGG+CGG + chr7_4:1386666-1386685 Msa1134750:CDS 65.0%
AACGTTTATGGCCGCCGCCG+CGG - chr7_4:1386683-1386702 None:intergenic 65.0%
! GTGGTGGTGCGTTGTGGAGG+TGG - chr7_4:1386828-1386847 None:intergenic 65.0%
CGTCGGCGTTAGGGTTACCG+AGG + chr7_4:1387042-1387061 Msa1134750:CDS 65.0%
GGCGGCGGTTGCAGTAGTGG+TGG - chr7_4:1386844-1386863 None:intergenic 70.0%
AGCGGCGGCGGTTGCAGTAG+TGG - chr7_4:1386847-1386866 None:intergenic 70.0%
TGCGGTGGATACAGCGGCGG+CGG - chr7_4:1386859-1386878 None:intergenic 70.0%
GACGCCGCCACCGCAATCCT+CGG - chr7_4:1387062-1387081 None:intergenic 70.0%
ACCTCCTTCCACCGCGGCGG+CGG + chr7_4:1386669-1386688 Msa1134750:CDS 75.0%
GTTTATGGCCGCCGCCGCGG+TGG - chr7_4:1386680-1386699 None:intergenic 75.0%
! TGCGGTGGCGGCGTCGAGAC+CGG + chr7_4:1387067-1387086 Msa1134750:CDS 75.0%
! ATGGCCGCCGCCGCGGTGGA+AGG - chr7_4:1386676-1386695 None:intergenic 80.0%
! GCCGCCGCCGCGGTGGAAGG+AGG - chr7_4:1386673-1386692 None:intergenic 85.0%
Chromosome Type Strat End Strand Name
chr7_4 gene 1386585 1387211 1386585 ID=Msa1134750;Name=Msa1134750
chr7_4 mRNA 1386585 1387211 1386585 ID=Msa1134750-mRNA-1;Parent=Msa1134750;Name=Msa1134750-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|208
chr7_4 exon 1386585 1387211 1386585 ID=Msa1134750-mRNA-1:exon:487;Parent=Msa1134750-mRNA-1
chr7_4 CDS 1386585 1387211 1386585 ID=Msa1134750-mRNA-1:cds;Parent=Msa1134750-mRNA-1
Gene Sequence

>Msa1134750

ATGTCAGGAGGAGTGAAGAGATCACTGAGACAATTCACATTCGGCGCCGGAAAAACCGCCGGCCGTAACTGTTACGGTCGCATCACCTCCTTCCACCGCGGCGGCGGCCATAAACGTTTACATCGAATTATCGATCTCAAACGCAACACTTCTTCTTCCGTCGGTATCGTCGAACGCATCGAATACGATCCTAACCGTTCATCTCGTATCGCTCTCGTTCGTTGGCTCAACGGTATTAATCCACCTCCACAACGCACCACCACTACTGCAACCGCCGCCGCTGTATCCACCGCATCATCATCCTCCAGATTCCTCAAACACGATCCTGCATCAAACGGAGAAATTCGTGGTGTGTTTGGTTTGAATTCGTTGCTTCCACAAATCCACGCTGGAAGTAGTTCAGGGAAGGTTTTTCTGTCGGCGTTTTCGGGGAAGGGAGATGAAAGTGAATCTGTTTCGTCGGCGTTAGGGTTACCGAGGATTGCGGTGGCGGCGTCGAGACCGGAGTTTTTTGGTGTGAAAGGGGATGGTGAGAAATTGGAGATTAGGAATTGGAAGAAGAATAGTGATGTTTGGATGAATAGGAATAAAAGGAAAACGGCGATTTCGTGGCAGAATATTGCTTGA
Protein sequence

>Msa1134750

MSGGVKRSLRQFTFGAGKTAGRNCYGRITSFHRGGGHKRLHRIIDLKRNTSSSVGIVERIEYDPNRSSRIALVRWLNGINPPPQRTTTTATAAAVSTASSSSRFLKHDPASNGEIRGVFGLNSLLPQIHAGSSSGKVFLSAFSGKGDESESVSSALGLPRIAVAASRPEFFGVKGDGEKLEIRNWKKNSDVWMNRNKRKTAISWQNIA*