AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene031411

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene031411.t1 MTR_4g021290 95.722 187 8 0 1 187 1 187 3.34e-126 353
MS.gene031411.t1 MTR_3g005450 95.722 187 8 0 1 187 1 187 3.34e-126 353
MS.gene031411.t1 MTR_3g005430 95.722 187 8 0 1 187 1 187 3.34e-126 353
MS.gene031411.t1 MTR_7g067490 94.652 187 10 0 1 187 1 187 1.70e-124 349
MS.gene031411.t1 MTR_1g068965 93.855 179 11 0 1 179 28 206 3.85e-123 347
MS.gene031411.t1 MTR_4g108310 91.304 115 10 0 1 115 1 115 6.32e-74 218
MS.gene031411.t1 MTR_4g108305 100.000 38 0 0 138 175 21 58 3.07e-22 85.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene031411.t1 AT5G39850 87.701 187 23 0 1 187 1 187 2.19e-120 339
MS.gene031411.t1 AT5G15200 83.333 198 32 1 1 197 1 198 2.35e-115 326
MS.gene031411.t1 AT5G15200 87.591 137 17 0 1 137 1 137 4.49e-84 246

Find 64 sgRNAs with CRISPR-Local

Find 93 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCCTTTGGTGGTGGTCTTCC+TGG 0.209962 2.1:-20535130 MS.gene031411:CDS
ATCACCACCAGAAGCCTTCT+TGG 0.255696 2.1:+20535075 None:intergenic
TTCCCATAGTTTCGGTAAAC+TGG 0.287392 2.1:+20536019 None:intergenic
CAGACTCTTGTCTTCAAATC+TGG 0.288805 2.1:-20535698 MS.gene031411:CDS
ATTCCAGTTTACCGAAACTA+TGG 0.305962 2.1:-20536022 MS.gene031411:CDS
TTGAAGCTGGTCGGAGAGTA+TGG 0.314070 2.1:-20535944 MS.gene031411:CDS
CCTTCTTGGCTGCAGCCTTA+AGG 0.354248 2.1:+20535089 None:intergenic
ACCATGCTAGGGTTCTTATC+AGG 0.369101 2.1:-20535658 MS.gene031411:CDS
GCTGCAGCCAAGAAGGCTTC+TGG 0.408125 2.1:-20535082 MS.gene031411:CDS
TGGACGACGTGGCTTCTTGA+AGG 0.409761 2.1:+20535994 None:intergenic
TCTTCTCATCCAATGTCAAA+AGG 0.432229 2.1:+20535852 None:intergenic
TCCATACGAGAAGGAGCGTT+TGG 0.432310 2.1:-20535975 MS.gene031411:CDS
TTATCAGGCAGAGACACATT+AGG 0.445935 2.1:-20535643 MS.gene031411:intron
CCTAGCATGGTGAATGGACT+TGG 0.448468 2.1:+20535670 None:intergenic
CATTGTTACGGATACGGCTC+AGG 0.451453 2.1:+20535882 None:intergenic
TTCTTTCGCTTCACGCGACC+AGG 0.452567 2.1:+20535112 None:intergenic
TTCTAGCATTGTTACGGATA+CGG 0.467109 2.1:+20535876 None:intergenic
ACCAGGAAGACCACCACCAA+AGG 0.473047 2.1:+20535129 None:intergenic
AAAGGGTTCTAGCATTGTTA+CGG 0.475438 2.1:+20535870 None:intergenic
AGTGAACATCCCATCCTTCA+TGG 0.476720 2.1:-20535197 MS.gene031411:CDS
TCCCTCACTAGTCCCTTTGG+TGG 0.477112 2.1:-20535142 MS.gene031411:CDS
CTCACTAGTCCCTTTGGTGG+TGG 0.477263 2.1:-20535139 MS.gene031411:CDS
GAGCCCTCGTCGGATCTTTG+AGG 0.482488 2.1:-20535831 MS.gene031411:CDS
AAGAAGGCTTCTGGTGGTGA+TGG 0.495137 2.1:-20535073 MS.gene031411:CDS
CCTTAAGGCTGCAGCCAAGA+AGG 0.517095 2.1:-20535089 MS.gene031411:CDS
TCCAAACGCTCCTTCTCGTA+TGG 0.519540 2.1:+20535974 None:intergenic
CTTCTCATCCAATGTCAAAA+GGG 0.523313 2.1:+20535853 None:intergenic
AGCCCTCGTCGGATCTTTGA+GGG 0.524524 2.1:-20535830 MS.gene031411:CDS
CCAAGTCCATTCACCATGCT+AGG 0.525789 2.1:-20535670 MS.gene031411:CDS
GTTTCGGTAAACTGGAATGT+GGG 0.529716 2.1:+20536027 None:intergenic
TCAACCCTCACCATGAAGGA+TGG 0.531047 2.1:+20535187 None:intergenic
AAGAACCCTAGCATGGTGAA+TGG 0.539163 2.1:+20535664 None:intergenic
CGTGAAGCGAAAGAACCTTA+AGG 0.541128 2.1:-20535104 MS.gene031411:CDS
TGGTCGGAGAGTATGGTCTT+CGG 0.541482 2.1:-20535937 MS.gene031411:CDS
TTCCAGTTTACCGAAACTAT+GGG 0.556730 2.1:-20536021 MS.gene031411:CDS
TTGAGGAGAATGTTTAAGCA+TGG 0.560766 2.1:-20535797 MS.gene031411:CDS
CAACCCTCACCATGAAGGAT+GGG 0.569875 2.1:+20535188 None:intergenic
TGAATCAACCCTCACCATGA+AGG 0.571223 2.1:+20535183 None:intergenic
GAACAAGCTCGATTATGTGT+TGG 0.578338 2.1:-20535756 MS.gene031411:CDS
TTTGGATGCTGAGTTGAAGC+TGG 0.579570 2.1:-20535957 MS.gene031411:CDS
CCAGGAAGACCACCACCAAA+GGG 0.581024 2.1:+20535130 None:intergenic
GGTGTAAGAGAGAGCTGTGG+AGG 0.589621 2.1:-20535916 MS.gene031411:CDS
TTCTGGTGGTGATGGAGATG+AGG 0.590267 2.1:-20535065 MS.gene031411:CDS
AGTTTCGGTAAACTGGAATG+TGG 0.592077 2.1:+20536026 None:intergenic
CATCCCATCCTTCATGGTGA+GGG 0.593258 2.1:-20535191 MS.gene031411:CDS
TCTTGTCTTCAAATCTGGCA+TGG 0.593384 2.1:-20535693 MS.gene031411:CDS
ATTGTTACGGATACGGCTCA+GGG 0.599593 2.1:+20535883 None:intergenic
CAAGTCCATTCACCATGCTA+GGG 0.599707 2.1:-20535669 MS.gene031411:CDS
GCAGCCAAGAAGGCTTCTGG+TGG 0.599775 2.1:-20535079 MS.gene031411:CDS
ACCACCAAAGGGACTAGTGA+GGG 0.615882 2.1:+20535141 None:intergenic
ACATCCCATCCTTCATGGTG+AGG 0.616704 2.1:-20535192 MS.gene031411:CDS
GCCACGTCGTCCATACGAGA+AGG 0.630150 2.1:-20535984 MS.gene031411:CDS
TGAAGACAAGAGTCTGAAGA+CGG 0.630423 2.1:+20535705 None:intergenic
GATGCTGAGTTGAAGCTGGT+CGG 0.640820 2.1:-20535953 MS.gene031411:CDS
TTTCGGTAAACTGGAATGTG+GGG 0.641183 2.1:+20536028 None:intergenic
GCCTGATAAGAACCCTAGCA+TGG 0.650504 2.1:+20535657 None:intergenic
TGGTGGTGATGGAGATGAGG+AGG 0.657794 2.1:-20535062 MS.gene031411:CDS
GTGTAAGAGAGAGCTGTGGA+GGG 0.669438 2.1:-20535915 MS.gene031411:CDS
CACCACCAAAGGGACTAGTG+AGG 0.678453 2.1:+20535140 None:intergenic
CACCCTCAAAGATCCGACGA+GGG 0.691605 2.1:+20535828 None:intergenic
TTCGGTGTAAGAGAGAGCTG+TGG 0.694839 2.1:-20535919 MS.gene031411:CDS
TCCTTCTCGTATGGACGACG+TGG 0.696550 2.1:+20535983 None:intergenic
TGGATGAGAAGAGCCCTCGT+CGG 0.701475 2.1:-20535841 MS.gene031411:CDS
TCACCCTCAAAGATCCGACG+AGG 0.706908 2.1:+20535827 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TAATTATTTAATTGTAAGTT+TGG - chr2.1:20535513-20535532 MS.gene031411:intron 10.0%
!!! ATATCATTTTTTGTTTTCAT+AGG - chr2.1:20535848-20535867 MS.gene031411:CDS 15.0%
!!! TATCATTTTTTGTTTTCATA+GGG - chr2.1:20535849-20535868 MS.gene031411:CDS 15.0%
! AGAAAACCCAATCAAATAAA+AGG + chr2.1:20535785-20535804 None:intergenic 25.0%
! ATAAAAGGCAGAAATAAACT+AGG + chr2.1:20535770-20535789 None:intergenic 25.0%
!! ATGTCAATAGAACTTACTTT+TGG - chr2.1:20535603-20535622 MS.gene031411:intron 25.0%
!! GTAAAGGTTTAAGCAAATTT+TGG + chr2.1:20535726-20535745 None:intergenic 25.0%
!!! ATTTCTGCCTTTTATTTGAT+TGG - chr2.1:20535775-20535794 MS.gene031411:CDS 25.0%
!!! ATTTTTTGTTTTCATAGGGT+TGG - chr2.1:20535853-20535872 MS.gene031411:CDS 25.0%
!!! TGTCAATAGAACTTACTTTT+GGG - chr2.1:20535604-20535623 MS.gene031411:intron 25.0%
!!! TTTCTGCCTTTTATTTGATT+GGG - chr2.1:20535776-20535795 MS.gene031411:CDS 25.0%
!!! TTTTTTGTTTTCATAGGGTT+GGG - chr2.1:20535854-20535873 MS.gene031411:CDS 25.0%
AAAAGTTACGTGTCTATACT+TGG - chr2.1:20535666-20535685 MS.gene031411:CDS 30.0%
TTGTCAAAATTGTGCAAACA+GGG + chr2.1:20535647-20535666 None:intergenic 30.0%
TTTGTCAAAATTGTGCAAAC+AGG + chr2.1:20535648-20535667 None:intergenic 30.0%
! ATCTGAGAGTTCGAATTTTT+GGG - chr2.1:20535561-20535580 MS.gene031411:intron 30.0%
! TATCTGAGAGTTCGAATTTT+TGG - chr2.1:20535560-20535579 MS.gene031411:intron 30.0%
ATTCCAGTTTACCGAAACTA+TGG - chr2.1:20535060-20535079 MS.gene031411:CDS 35.0%
CTTCTCATCCAATGTCAAAA+GGG + chr2.1:20535232-20535251 None:intergenic 35.0%
GATCAGATAATCAACGGTAA+AGG + chr2.1:20535742-20535761 None:intergenic 35.0%
TCATCGTTGTGAAACATGTT+TGG - chr2.1:20535813-20535832 MS.gene031411:CDS 35.0%
TCTTCTCATCCAATGTCAAA+AGG + chr2.1:20535233-20535252 None:intergenic 35.0%
TTCCAGTTTACCGAAACTAT+GGG - chr2.1:20535061-20535080 MS.gene031411:CDS 35.0%
TTCTAGCATTGTTACGGATA+CGG + chr2.1:20535209-20535228 None:intergenic 35.0%
TTGAGGAGAATGTTTAAGCA+TGG - chr2.1:20535285-20535304 MS.gene031411:intron 35.0%
! AAAGGGTTCTAGCATTGTTA+CGG + chr2.1:20535215-20535234 None:intergenic 35.0%
! GTCTAGGATCAGATAATCAA+CGG + chr2.1:20535748-20535767 None:intergenic 35.0%
! TGAAGGTTTTCCCATAGTTT+CGG + chr2.1:20535074-20535093 None:intergenic 35.0%
!! GTTTAAGCAAATTTTGGCAG+TGG + chr2.1:20535720-20535739 None:intergenic 35.0%
AGTTTCGGTAAACTGGAATG+TGG + chr2.1:20535059-20535078 None:intergenic 40.0%
CAGACTCTTGTCTTCAAATC+TGG - chr2.1:20535384-20535403 MS.gene031411:intron 40.0%
CAGTGGCAACAAAACATGTA+AGG + chr2.1:20535703-20535722 None:intergenic 40.0%
GAACAAGCTCGATTATGTGT+TGG - chr2.1:20535326-20535345 MS.gene031411:intron 40.0%
GGCAGAAATAAACTAGGTCT+AGG + chr2.1:20535764-20535783 None:intergenic 40.0%
GTTTCGGTAAACTGGAATGT+GGG + chr2.1:20535058-20535077 None:intergenic 40.0%
TCTTGTCTTCAAATCTGGCA+TGG - chr2.1:20535389-20535408 MS.gene031411:intron 40.0%
TGAAGACAAGAGTCTGAAGA+CGG + chr2.1:20535380-20535399 None:intergenic 40.0%
TTATCAGGCAGAGACACATT+AGG - chr2.1:20535439-20535458 MS.gene031411:intron 40.0%
TTCCCATAGTTTCGGTAAAC+TGG + chr2.1:20535066-20535085 None:intergenic 40.0%
TTTCGGTAAACTGGAATGTG+GGG + chr2.1:20535057-20535076 None:intergenic 40.0%
! TGCTAGAACCCTTTTGACAT+TGG - chr2.1:20535221-20535240 MS.gene031411:intron 40.0%
!! TTTGTTTTCATAGGGTTGGG+AGG - chr2.1:20535857-20535876 MS.gene031411:CDS 40.0%
AAGAACCCTAGCATGGTGAA+TGG + chr2.1:20535421-20535440 None:intergenic 45.0%
ACCATGCTAGGGTTCTTATC+AGG - chr2.1:20535424-20535443 MS.gene031411:intron 45.0%
AGTGAACATCCCATCCTTCA+TGG - chr2.1:20535885-20535904 MS.gene031411:CDS 45.0%
ATTGTTACGGATACGGCTCA+GGG + chr2.1:20535202-20535221 None:intergenic 45.0%
CAAGTCCATTCACCATGCTA+GGG - chr2.1:20535413-20535432 MS.gene031411:intron 45.0%
CGTGAAGCGAAAGAACCTTA+AGG - chr2.1:20535978-20535997 MS.gene031411:CDS 45.0%
TGAATCAACCCTCACCATGA+AGG + chr2.1:20535902-20535921 None:intergenic 45.0%
! TTTGGATGCTGAGTTGAAGC+TGG - chr2.1:20535125-20535144 MS.gene031411:CDS 45.0%
! TTTTCCCTCACTAGTCCCTT+TGG - chr2.1:20535937-20535956 MS.gene031411:CDS 45.0%
ACATCCCATCCTTCATGGTG+AGG - chr2.1:20535890-20535909 MS.gene031411:CDS 50.0%
ATCACCACCAGAAGCCTTCT+TGG + chr2.1:20536010-20536029 None:intergenic 50.0%
CAACCCTCACCATGAAGGAT+GGG + chr2.1:20535897-20535916 None:intergenic 50.0%
CATCCCATCCTTCATGGTGA+GGG - chr2.1:20535891-20535910 MS.gene031411:CDS 50.0%
CATTGTTACGGATACGGCTC+AGG + chr2.1:20535203-20535222 None:intergenic 50.0%
CCAAGTCCATTCACCATGCT+AGG - chr2.1:20535412-20535431 MS.gene031411:intron 50.0%
GCCTGATAAGAACCCTAGCA+TGG + chr2.1:20535428-20535447 None:intergenic 50.0%
GTGTAAGAGAGAGCTGTGGA+GGG - chr2.1:20535167-20535186 MS.gene031411:CDS 50.0%
TCAACCCTCACCATGAAGGA+TGG + chr2.1:20535898-20535917 None:intergenic 50.0%
TCCAAACGCTCCTTCTCGTA+TGG + chr2.1:20535111-20535130 None:intergenic 50.0%
TTGAAGCTGGTCGGAGAGTA+TGG - chr2.1:20535138-20535157 MS.gene031411:CDS 50.0%
! AAGAAGGCTTCTGGTGGTGA+TGG - chr2.1:20536009-20536028 MS.gene031411:CDS 50.0%
! ACCACCAAAGGGACTAGTGA+GGG + chr2.1:20535944-20535963 None:intergenic 50.0%
! CCTAGCATGGTGAATGGACT+TGG + chr2.1:20535415-20535434 None:intergenic 50.0%
! GATGCTGAGTTGAAGCTGGT+CGG - chr2.1:20535129-20535148 MS.gene031411:CDS 50.0%
! TGGTCGGAGAGTATGGTCTT+CGG - chr2.1:20535145-20535164 MS.gene031411:CDS 50.0%
! TTCGGTGTAAGAGAGAGCTG+TGG - chr2.1:20535163-20535182 MS.gene031411:CDS 50.0%
! TTGAGGGTGACGCACTTTTG+AGG - chr2.1:20535268-20535287 MS.gene031411:intron 50.0%
! TTTTCATAGGGTTGGGAGGC+AGG - chr2.1:20535861-20535880 MS.gene031411:CDS 50.0%
!! TCCATACGAGAAGGAGCGTT+TGG - chr2.1:20535107-20535126 MS.gene031411:CDS 50.0%
!! TTCTGGTGGTGATGGAGATG+AGG - chr2.1:20536017-20536036 MS.gene031411:CDS 50.0%
ACCAGGAAGACCACCACCAA+AGG + chr2.1:20535956-20535975 None:intergenic 55.0%
AGCCCTCGTCGGATCTTTGA+GGG - chr2.1:20535252-20535271 MS.gene031411:intron 55.0%
CACCCTCAAAGATCCGACGA+GGG + chr2.1:20535257-20535276 None:intergenic 55.0%
CCAGGAAGACCACCACCAAA+GGG + chr2.1:20535955-20535974 None:intergenic 55.0%
CCTTAAGGCTGCAGCCAAGA+AGG - chr2.1:20535993-20536012 MS.gene031411:CDS 55.0%
CCTTCTTGGCTGCAGCCTTA+AGG + chr2.1:20535996-20536015 None:intergenic 55.0%
CTCACTAGTCCCTTTGGTGG+TGG - chr2.1:20535943-20535962 MS.gene031411:CDS 55.0%
GGTGTAAGAGAGAGCTGTGG+AGG - chr2.1:20535166-20535185 MS.gene031411:CDS 55.0%
TCACCCTCAAAGATCCGACG+AGG + chr2.1:20535258-20535277 None:intergenic 55.0%
TCCCTCACTAGTCCCTTTGG+TGG - chr2.1:20535940-20535959 MS.gene031411:CDS 55.0%
TCCTTCTCGTATGGACGACG+TGG + chr2.1:20535102-20535121 None:intergenic 55.0%
TGGACGACGTGGCTTCTTGA+AGG + chr2.1:20535091-20535110 None:intergenic 55.0%
TGGATGAGAAGAGCCCTCGT+CGG - chr2.1:20535241-20535260 MS.gene031411:intron 55.0%
TTCTTTCGCTTCACGCGACC+AGG + chr2.1:20535973-20535992 None:intergenic 55.0%
! CACCACCAAAGGGACTAGTG+AGG + chr2.1:20535945-20535964 None:intergenic 55.0%
!! TGGTGGTGATGGAGATGAGG+AGG - chr2.1:20536020-20536039 MS.gene031411:CDS 55.0%
GAGCCCTCGTCGGATCTTTG+AGG - chr2.1:20535251-20535270 MS.gene031411:intron 60.0%
GCAGCCAAGAAGGCTTCTGG+TGG - chr2.1:20536003-20536022 MS.gene031411:CDS 60.0%
GCCACGTCGTCCATACGAGA+AGG - chr2.1:20535098-20535117 MS.gene031411:CDS 60.0%
GCTGCAGCCAAGAAGGCTTC+TGG - chr2.1:20536000-20536019 MS.gene031411:CDS 60.0%
!! CCCTTTGGTGGTGGTCTTCC+TGG - chr2.1:20535952-20535971 MS.gene031411:CDS 60.0%


Chromosome Type Strat End Strand Name
chr2.1 gene 20535051 20536053 20535051 ID=MS.gene031411
chr2.1 mRNA 20535051 20536053 20535051 ID=MS.gene031411.t1;Parent=MS.gene031411
chr2.1 exon 20535644 20536053 20535644 ID=MS.gene031411.t1.exon1;Parent=MS.gene031411.t1
chr2.1 CDS 20535644 20536053 20535644 ID=cds.MS.gene031411.t1;Parent=MS.gene031411.t1
chr2.1 exon 20535051 20535234 20535051 ID=MS.gene031411.t1.exon2;Parent=MS.gene031411.t1
chr2.1 CDS 20535051 20535234 20535051 ID=cds.MS.gene031411.t1;Parent=MS.gene031411.t1
Gene Sequence

>MS.gene031411

ATGCCCCACATTCCAGTTTACCGAAACTATGGGAAAACCTTCAAGAAGCCACGTCGTCCATACGAGAAGGAGCGTTTGGATGCTGAGTTGAAGCTGGTCGGAGAGTATGGTCTTCGGTGTAAGAGAGAGCTGTGGAGGGTTCAATACTCCCTGAGCCGTATCCGTAACAATGCTAGAACCCTTTTGACATTGGATGAGAAGAGCCCTCGTCGGATCTTTGAGGGTGACGCACTTTTGAGGAGAATGTTTAAGCATGGTCTTCTCGATGATACTCAGAACAAGCTCGATTATGTGTTGGCTCTCACTGTTGAGAATTTTCTCGAGCGCCGTCTTCAGACTCTTGTCTTCAAATCTGGCATGGCCAAGTCCATTCACCATGCTAGGGTTCTTATCAGGCAGAGACACATTAGGTAATCTTTTGATTTCATTTTAATTATCAATGATAAATACTTTTATTGTCGTTAATTATTTAATTGTAAGTTTGGATCAATGTCTTTAATATAATCGATTATCTGAGAGTTCGAATTTTTGGGTTTGCTTTGTGATTAATTGATGTCAATAGAACTTACTTTTGGGTTTGCTGCTTTGTGATGCCCTGTTTGCACAATTTTGACAAAAAGTTACGTGTCTATACTTGGTTTCTTCAATTCCTTACATGTTTTGTTGCCACTGCCAAAATTTGCTTAAACCTTTACCGTTGATTATCTGATCCTAGACCTAGTTTATTTCTGCCTTTTATTTGATTGGGTTTTCTTTCATAAATCATCGTTGTGAAACATGTTTGGATATGATTGATAATATCATTTTTTGTTTTCATAGGGTTGGGAGGCAGGTAGTGAACATCCCATCCTTCATGGTGAGGGTTGATTCACAGAAGCACATTGACTTTTCCCTCACTAGTCCCTTTGGTGGTGGTCTTCCTGGTCGCGTGAAGCGAAAGAACCTTAAGGCTGCAGCCAAGAAGGCTTCTGGTGGTGATGGAGATGAGGAGGATGAAGATTAA
Protein sequence

>MS.gene031411.t1

MPHIPVYRNYGKTFKKPRRPYEKERLDAELKLVGEYGLRCKRELWRVQYSLSRIRNNARTLLTLDEKSPRRIFEGDALLRRMFKHGLLDDTQNKLDYVLALTVENFLERRLQTLVFKSGMAKSIHHARVLIRQRHIRVGRQVVNIPSFMVRVDSQKHIDFSLTSPFGGGLPGRVKRKNLKAAAKKASGGDGDEEDED