AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene25539


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene25539.t1 MTR_5g091450 67.500 120 23 1 33 136 365 484 4.88e-43 150
MS.gene25539.t1 MTR_5g091450 74.286 35 9 0 6 40 272 306 3.69e-11 59.7
MS.gene25539.t1 MTR_5g091530 46.821 173 46 1 6 132 200 372 3.15e-38 133
MS.gene25539.t1 MTR_5g091180 63.208 106 27 1 44 137 380 485 6.53e-36 130
MS.gene25539.t1 MTR_5g091410 61.290 93 36 0 33 125 207 299 5.72e-31 115
MS.gene25539.t1 MTR_5g091430 51.613 124 41 2 33 137 176 299 5.87e-30 113
MS.gene25539.t1 MTR_5g086700 56.180 89 39 0 39 127 749 837 8.40e-28 107
MS.gene25539.t1 MTR_5g086700 56.180 89 39 0 39 127 749 837 8.40e-28 107
MS.gene25539.t1 MTR_3g079840 60.241 83 32 1 39 120 744 826 1.12e-25 101
MS.gene25539.t1 MTR_3g079840 60.241 83 32 1 39 120 745 827 1.13e-25 101
MS.gene25539.t1 MTR_5g091550 49.265 136 37 4 26 137 354 481 4.00e-22 90.9
MS.gene25539.t1 MTR_5g091550 49.265 136 37 4 26 137 349 476 4.62e-22 90.9
MS.gene25539.t1 MTR_1g041240 43.119 109 50 4 13 115 722 824 3.34e-16 74.3
MS.gene25539.t1 MTR_1g041240 45.055 91 39 3 13 98 721 805 3.47e-16 74.3
MS.gene25539.t1 MTR_1g041240 43.119 109 50 4 13 115 720 822 3.51e-16 74.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene25539.t1 AT3G11910 48.837 86 36 3 14 98 722 800 5.45e-17 76.6
MS.gene25539.t1 AT3G11910 48.837 86 36 3 14 98 722 800 5.45e-17 76.6
MS.gene25539.t1 AT3G11910 48.837 86 36 3 14 98 723 801 5.51e-17 76.6
MS.gene25539.t1 AT3G11910 48.837 86 36 3 14 98 723 801 5.51e-17 76.6
MS.gene25539.t1 AT5G06600 45.977 87 46 1 33 119 738 823 1.04e-14 70.1
MS.gene25539.t1 AT5G06600 45.977 87 46 1 33 119 738 823 1.23e-14 69.7
MS.gene25539.t1 AT5G06600 45.977 87 46 1 33 119 737 822 1.24e-14 69.7

Find 24 sgRNAs with CRISPR-Local

Find 94 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TATCTGTAGTAGAGGCTTTC+TGG 0.139170 8.2:-43118910 None:intergenic
TTCCAATGATTCTTCATCTT+TGG 0.181692 8.2:-43119148 None:intergenic
CCATGAATGCAGTTAGAAAA+TGG 0.255703 8.2:+43118872 MS.gene25539:intron
TTCCTCAACATGTGTGTTAA+TGG 0.277671 8.2:-43117642 None:intergenic
GACAATTGAGAGTGGTAAAC+AGG 0.332028 8.2:+43118146 MS.gene25539:CDS
TCATTAGCAGAGGAAGAAAA+AGG 0.334938 8.2:-43119123 None:intergenic
AATGTTAATTTCTTGTCAAC+AGG 0.355151 8.2:-43118768 None:intergenic
TCCTCATGTGCCTTTATACT+TGG 0.361945 8.2:+43118952 MS.gene25539:CDS
TGCACATATTCCAAGTATAA+AGG 0.396963 8.2:-43118962 None:intergenic
AACCAAAGATGAAGAATCAT+TGG 0.407579 8.2:+43119146 MS.gene25539:CDS
ATTAACATTTGAAGAAATTG+AGG 0.425528 8.2:+43118782 MS.gene25539:CDS
ACAGGCTCACACATGACATT+TGG 0.434821 8.2:-43118750 None:intergenic
GGAATATGTGCACAATCGCC+AGG 0.502785 8.2:+43118973 MS.gene25539:CDS
TTTCTCATTATCTGTAGTAG+AGG 0.511813 8.2:-43118918 None:intergenic
AACACACATGTTGAGGAAGC+AGG 0.514896 8.2:+43117647 MS.gene25539:CDS
GCTGGTACCTTCATCATGAG+TGG 0.530191 8.2:-43119202 None:intergenic
ATCTTTGGTTTCATTAGCAG+AGG 0.553118 8.2:-43119133 None:intergenic
GAAGAAACCACTCATGATGA+AGG 0.580419 8.2:+43119195 MS.gene25539:CDS
TTTGGAAGTGGAGCATGGGA+TGG 0.593649 8.2:+43118195 MS.gene25539:CDS
TCCAAGTATAAAGGCACATG+AGG 0.597327 8.2:-43118953 None:intergenic
GTCCATTAACACACATGTTG+AGG 0.612136 8.2:+43117640 MS.gene25539:CDS
ATAAAGGCACATGAGGATAG+CGG 0.665066 8.2:-43118946 None:intergenic
ACAATTGAGAGTGGTAAACA+GGG 0.678083 8.2:+43118147 MS.gene25539:CDS
GCAGGTTGGACAATTGAGAG+TGG 0.694663 8.2:+43118138 MS.gene25539:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTTATATTATAAAGTTGTAT+AGG + chr8.2:43118223-43118242 MS.gene25539:intron 10.0%
!!! ATTTTCTTTTTCATATTTAA+AGG + chr8.2:43118997-43119016 MS.gene25539:intron 10.0%
!! ATAAAATAAGAAGATTTAAG+AGG - chr8.2:43117729-43117748 None:intergenic 15.0%
!! TAAAATAAGAAGATTTAAGA+GGG - chr8.2:43117728-43117747 None:intergenic 15.0%
!!! AGAAGAATTAAAATTGTTTT+TGG + chr8.2:43118177-43118196 MS.gene25539:CDS 15.0%
!! AAATTTAAAGAGATAACTGA+AGG - chr8.2:43117978-43117997 None:intergenic 20.0%
!! AATATGAAAAAGAAAATACC+TGG - chr8.2:43118994-43119013 None:intergenic 20.0%
!! ATAAAATGTATTTCCTTTGA+TGG + chr8.2:43118399-43118418 MS.gene25539:intron 20.0%
!! ATTAACATTTGAAGAAATTG+AGG + chr8.2:43118782-43118801 MS.gene25539:CDS 20.0%
!! TGTTAATATAGTGATTATCA+TGG + chr8.2:43117857-43117876 MS.gene25539:intron 20.0%
!!! AATACATTTTATGTCAACTA+AGG - chr8.2:43118391-43118410 None:intergenic 20.0%
!!! ATTAAAATTGTTTTTGGAAG+TGG + chr8.2:43118183-43118202 MS.gene25539:CDS 20.0%
!!! ATTTATTCATTCCTTTTTCT+AGG + chr8.2:43119063-43119082 MS.gene25539:intron 20.0%
!!! TTTTTTCATTCTGATTCAAA+TGG + chr8.2:43118116-43118135 MS.gene25539:intron 20.0%
! AACAATAGGCATAATGAATT+TGG - chr8.2:43118709-43118728 None:intergenic 25.0%
! AAGTATAATTGAAAAGCTTC+AGG - chr8.2:43117694-43117713 None:intergenic 25.0%
! AATATAGTGATTATCATGGT+TGG + chr8.2:43117861-43117880 MS.gene25539:intron 25.0%
! AATGTTAATTTCTTGTCAAC+AGG - chr8.2:43118771-43118790 None:intergenic 25.0%
! CTAAACAAGGTTAAATAAAC+TGG + chr8.2:43118473-43118492 MS.gene25539:intron 25.0%
! GTTATATGATCCTATAAAAG+AGG + chr8.2:43118306-43118325 MS.gene25539:intron 25.0%
! TAAAATTTCATGAAGAGACT+CGG - chr8.2:43117829-43117848 None:intergenic 25.0%
! TATAGTGTATATGCAACATT+TGG + chr8.2:43118002-43118021 MS.gene25539:intron 25.0%
! TTGAGATATATTGAGGTAAA+AGG + chr8.2:43118361-43118380 MS.gene25539:intron 25.0%
!!! GGTTTTCATATTGATTGTTT+TGG + chr8.2:43118029-43118048 MS.gene25539:intron 25.0%
!!! TGCATTAGATTTCACTTTTT+GGG + chr8.2:43117885-43117904 MS.gene25539:intron 25.0%
!!! TGTGATTTTGAGATATATTG+AGG + chr8.2:43118354-43118373 MS.gene25539:intron 25.0%
!!! TTGCATTAGATTTCACTTTT+TGG + chr8.2:43117884-43117903 MS.gene25539:intron 25.0%
AACCAAAGATGAAGAATCAT+TGG + chr8.2:43119146-43119165 MS.gene25539:CDS 30.0%
ACAAGGTTAAATAAACTGGA+TGG + chr8.2:43118477-43118496 MS.gene25539:intron 30.0%
ACACTAGGTTACAGTATAAT+TGG + chr8.2:43118828-43118847 MS.gene25539:intron 30.0%
AGATATATTGAGGTAAAAGG+TGG + chr8.2:43118364-43118383 MS.gene25539:intron 30.0%
ATAACTGAAGGTAGTCAAAA+TGG - chr8.2:43117966-43117985 None:intergenic 30.0%
CATTTGAAGAAATTGAGGTA+TGG + chr8.2:43118787-43118806 MS.gene25539:intron 30.0%
TGCACATATTCCAAGTATAA+AGG - chr8.2:43118965-43118984 None:intergenic 30.0%
TTCCAATGATTCTTCATCTT+TGG - chr8.2:43119151-43119170 None:intergenic 30.0%
TTGCATATGACTTACCATAA+GGG + chr8.2:43118635-43118654 MS.gene25539:intron 30.0%
TTTCTCATTATCTGTAGTAG+AGG - chr8.2:43118921-43118940 None:intergenic 30.0%
! AACCTTGTTTAGATTTCTGA+CGG - chr8.2:43118465-43118484 None:intergenic 30.0%
! TTAAAGGCAATTAGTTTCGT+CGG + chr8.2:43119013-43119032 MS.gene25539:intron 30.0%
! TTCAAGTTTAGCCTAGAAAA+AGG - chr8.2:43119077-43119096 None:intergenic 30.0%
ACAATTGAGAGTGGTAAACA+GGG + chr8.2:43118147-43118166 MS.gene25539:CDS 35.0%
ATAATCTCCTGCACAACAAT+AGG - chr8.2:43118723-43118742 None:intergenic 35.0%
ATCCTATAAAAGAGGAGCTA+AGG + chr8.2:43118314-43118333 MS.gene25539:intron 35.0%
CCATGAATGCAGTTAGAAAA+TGG + chr8.2:43118872-43118891 MS.gene25539:intron 35.0%
CCTATTGCAGCACTTAATAA+AGG + chr8.2:43118254-43118273 MS.gene25539:intron 35.0%
CTTGCATATGACTTACCATA+AGG + chr8.2:43118634-43118653 MS.gene25539:intron 35.0%
GATAGAATTAACTGTTGACC+TGG - chr8.2:43117911-43117930 None:intergenic 35.0%
GTATATGCAACATTTGGAAG+TGG + chr8.2:43118008-43118027 MS.gene25539:intron 35.0%
TAAAGTTCAATTCCTTCGTC+AGG - chr8.2:43118510-43118529 None:intergenic 35.0%
TATGACTTACCATAAGGGAA+AGG + chr8.2:43118640-43118659 MS.gene25539:intron 35.0%
TCAAAAGTTCCTTTCCCTTA+TGG - chr8.2:43118652-43118671 None:intergenic 35.0%
TCATTAGCAGAGGAAGAAAA+AGG - chr8.2:43119126-43119145 None:intergenic 35.0%
TCCAACATAACTTCCATCAA+AGG - chr8.2:43118415-43118434 None:intergenic 35.0%
TCCTTTGATGGAAGTTATGT+TGG + chr8.2:43118411-43118430 MS.gene25539:intron 35.0%
TGCAGCACTTAATAAAGGAA+AGG + chr8.2:43118259-43118278 MS.gene25539:intron 35.0%
TTACGTGAAGAAACAGCTAT+GGG - chr8.2:43118057-43118076 None:intergenic 35.0%
TTCATTCTGATTCAAATGGC+AGG + chr8.2:43118120-43118139 MS.gene25539:intron 35.0%
TTCCTCAACATGTGTGTTAA+TGG - chr8.2:43117645-43117664 None:intergenic 35.0%
TTGATGGAAGTTATGTTGGA+AGG + chr8.2:43118415-43118434 MS.gene25539:intron 35.0%
! AACTTTTGAATGGCATCTTC+AGG + chr8.2:43118663-43118682 MS.gene25539:intron 35.0%
! AAGGGAAAGGAACTTTTGAA+TGG + chr8.2:43118653-43118672 MS.gene25539:intron 35.0%
! ATCTTTGGTTTCATTAGCAG+AGG - chr8.2:43119136-43119155 None:intergenic 35.0%
! CCATTTTCTAACTGCATTCA+TGG - chr8.2:43118875-43118894 None:intergenic 35.0%
! CCTTTATTAAGTGCTGCAAT+AGG - chr8.2:43118257-43118276 None:intergenic 35.0%
! TACCTTAGCTCCTCTTTTAT+AGG - chr8.2:43118319-43118338 None:intergenic 35.0%
!!! GAACGTTTTTTCGTTGTTCA+GGG + chr8.2:43119099-43119118 MS.gene25539:intron 35.0%
!!! TGAACGTTTTTTCGTTGTTC+AGG + chr8.2:43119098-43119117 MS.gene25539:intron 35.0%
AGCCGTCAGAAATCTAAACA+AGG + chr8.2:43118460-43118479 MS.gene25539:intron 40.0%
AGGCATTCTCATGAACTTAC+AGG - chr8.2:43117674-43117693 None:intergenic 40.0%
CATTATGCCTATTGTTGTGC+AGG + chr8.2:43118713-43118732 MS.gene25539:intron 40.0%
CGAAGGAATTGAACTTTACG+AGG + chr8.2:43118512-43118531 MS.gene25539:intron 40.0%
GAAGAAACCACTCATGATGA+AGG + chr8.2:43119195-43119214 MS.gene25539:CDS 40.0%
GACAATTGAGAGTGGTAAAC+AGG + chr8.2:43118146-43118165 MS.gene25539:CDS 40.0%
GGAATTGAACTTTACGAGGT+TGG + chr8.2:43118516-43118535 MS.gene25539:intron 40.0%
GTCCATTAACACACATGTTG+AGG + chr8.2:43117640-43117659 MS.gene25539:CDS 40.0%
GTTACGTGAAGAAACAGCTA+TGG - chr8.2:43118058-43118077 None:intergenic 40.0%
TATCTGTAGTAGAGGCTTTC+TGG - chr8.2:43118913-43118932 None:intergenic 40.0%
TCCTCATGTGCCTTTATACT+TGG + chr8.2:43118952-43118971 MS.gene25539:CDS 40.0%
TTCTGATTCAAATGGCAGGT+TGG + chr8.2:43118124-43118143 MS.gene25539:intron 40.0%
! ATAAAGGCACATGAGGATAG+CGG - chr8.2:43118949-43118968 None:intergenic 40.0%
! TCCAAGTATAAAGGCACATG+AGG - chr8.2:43118956-43118975 None:intergenic 40.0%
!!! GTTAGCTTTTACGCAAATGC+TGG + chr8.2:43117768-43117787 MS.gene25539:intron 40.0%
!!! TAGATTTCACTTTTTGGGCC+AGG + chr8.2:43117890-43117909 MS.gene25539:intron 40.0%
!!! TGTTTTTGGAAGTGGAGCAT+GGG + chr8.2:43118191-43118210 MS.gene25539:CDS 40.0%
!!! TTGTTTTTGGAAGTGGAGCA+TGG + chr8.2:43118190-43118209 MS.gene25539:CDS 40.0%
AACACACATGTTGAGGAAGC+AGG + chr8.2:43117647-43117666 MS.gene25539:CDS 45.0%
ACAGGCTCACACATGACATT+TGG - chr8.2:43118753-43118772 None:intergenic 45.0%
ATAACCGCTTGATGCACACT+AGG + chr8.2:43118813-43118832 MS.gene25539:intron 45.0%
GTAACCTAGTGTGCATCAAG+CGG - chr8.2:43118820-43118839 None:intergenic 45.0%
GATGGTTACGATCCTGACGA+AGG + chr8.2:43118495-43118514 MS.gene25539:intron 50.0%
GCTGGTACCTTCATCATGAG+TGG - chr8.2:43119205-43119224 None:intergenic 50.0%
GGAATATGTGCACAATCGCC+AGG + chr8.2:43118973-43118992 MS.gene25539:CDS 50.0%
TTTGGAAGTGGAGCATGGGA+TGG + chr8.2:43118195-43118214 MS.gene25539:CDS 50.0%
! GCAGGTTGGACAATTGAGAG+TGG + chr8.2:43118138-43118157 MS.gene25539:intron 50.0%


Chromosome Type Strat End Strand Name
chr8.2 gene 43117635 43119239 43117635 ID=MS.gene25539
chr8.2 mRNA 43117635 43119239 43117635 ID=MS.gene25539.t1;Parent=MS.gene25539
chr8.2 exon 43117635 43117673 43117635 ID=MS.gene25539.t1.exon1;Parent=MS.gene25539.t1
chr8.2 CDS 43117635 43117673 43117635 ID=cds.MS.gene25539.t1;Parent=MS.gene25539.t1
chr8.2 exon 43118142 43118216 43118142 ID=MS.gene25539.t1.exon2;Parent=MS.gene25539.t1
chr8.2 CDS 43118142 43118216 43118142 ID=cds.MS.gene25539.t1;Parent=MS.gene25539.t1
chr8.2 exon 43118735 43118803 43118735 ID=MS.gene25539.t1.exon3;Parent=MS.gene25539.t1
chr8.2 CDS 43118735 43118803 43118735 ID=cds.MS.gene25539.t1;Parent=MS.gene25539.t1
chr8.2 exon 43118884 43118994 43118884 ID=MS.gene25539.t1.exon4;Parent=MS.gene25539.t1
chr8.2 CDS 43118884 43118994 43118884 ID=cds.MS.gene25539.t1;Parent=MS.gene25539.t1
chr8.2 exon 43119120 43119239 43119120 ID=MS.gene25539.t1.exon5;Parent=MS.gene25539.t1
chr8.2 CDS 43119120 43119239 43119120 ID=cds.MS.gene25539.t1;Parent=MS.gene25539.t1
Gene Sequence

>MS.gene25539

ATGTCGTCCATTAACACACATGTTGAGGAAGCAGGACCTGTAAGTTCATGAGAATGCCTGAAGCTTTTCAATTATACTTTTCTCACATATCCCTCTTAAATCTTCTTATTTTATGACTTTATCATATCTGCTTGTTAGCTTTTACGCAAATGCTGGTTTTGTTTTAAAAAATACTTAATTTATGTTTTATGCCGAGTCTCTTCATGAAATTTTATATCAAACTGTTAATATAGTGATTATCATGGTTGGTTGCATTAGATTTCACTTTTTGGGCCAGGTCAACAGTTAATTCTATCTGTGTTAGCTTTTTCTTTTACTTTAATTTTTTCCATTTTGACTACCTTCAGTTATCTCTTTAAATTTATTTTATAGTGTATATGCAACATTTGGAAGTGGTTTTCATATTGATTGTTTTGGATCCCATAGCTGTTTCTTCACGTAACACATCAATTTCTCTTTGATTTGAAGTTTTTTTTTTTTTTTTTTTCATTCTGATTCAAATGGCAGGTTGGACAATTGAGAGTGGTAAACAGGGTTCACAAAGAAGAATTAAAATTGTTTTTGGAAGTGGAGCATGGGATGGTAACGTTTATATTATAAAGTTGTATAGGATTTATGTCCTATTGCAGCACTTAATAAAGGAAAGGATGATATATTACTTATTTTTTCAAGTTATATGATCCTATAAAAGAGGAGCTAAGGTACTGAGTAATTTCTTGTGTGATTTTGAGATATATTGAGGTAAAAGGTGGACCTTAGTTGACATAAAATGTATTTCCTTTGATGGAAGTTATGTTGGAAGGCTCTTTGCGAACTGTACTGATAAGCCGTCAGAAATCTAAACAAGGTTAAATAAACTGGATGGTTACGATCCTGACGAAGGAATTGAACTTTACGAGGTTGGTTTGAGTTGTCTGTTTATTATTTATCTGTTGTATGTATAACTTCATAAACATTTATATTTATGAAGTGCATTGTGTACTATGAAAATTTATCATTCTTGCATATGACTTACCATAAGGGAAAGGAACTTTTGAATGGCATCTTCAGGATCTGAATCATTTAGCGTTACCAAATTCATTATGCCTATTGTTGTGCAGGAGATTATGTTTGAACCAAATGTCATGTGTGAGCCTGTTGACAAGAAATTAACATTTGAAGAAATTGAGGTATGGTACATAACCGCTTGATGCACACTAGGTTACAGTATAATTGGCTTTTTTATTGATTTGTTTTTCCATGAATGCAGTTAGAAAATGGTGATATTATATGCTTCCAGAAAGCCTCTACTACAGATAATGAGAAACATTTCCGCTATCCTCATGTGCCTTTATACTTGGAATATGTGCACAATCGCCAGGTATTTTCTTTTTCATATTTAAAGGCAATTAGTTTCGTCGGAACGTGATGCAAAAATGAAAGCTACACATTTATTCATTCCTTTTTCTAGGCTAAACTTGAAATGAACGTTTTTTCGTTGTTCAGGGACCTTTTTCTTCCTCTGCTAATGAAACCAAAGATGAAGAATCATTGGAAGAGCAAAACAAATATATTATAGCTGAAGAAACCACTCATGATGAAGGTACCAGCAAAGCCAACACTTGA

Protein sequence

>MS.gene25539.t1

MSSINTHVEEAGPVGQLRVVNRVHKEELKLFLEVEHGMEIMFEPNVMCEPVDKKLTFEEIELENGDIICFQKASTTDNEKHFRYPHVPLYLEYVHNRQGPFSSSANETKDEESLEEQNKYIIAEETTHDEGTSKANT