AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene46020

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene46020.t1 MTR_7g066110 93.491 169 11 0 11 179 1 169 8.19e-118 330
MS.gene46020.t1 MTR_4g018860 71.598 169 48 0 1 169 1 169 2.99e-88 257
MS.gene46020.t1 MTR_4g018880 68.539 178 56 0 1 178 1 178 1.14e-84 247
MS.gene46020.t1 MTR_4g018850 68.508 181 55 1 1 179 1 181 3.22e-80 237
MS.gene46020.t1 MTR_4g018880 70.455 132 39 0 1 132 1 132 6.53e-63 191
MS.gene46020.t1 MTR_6g452730 48.256 172 85 2 6 176 3 171 3.28e-55 173
MS.gene46020.t1 MTR_1g101120 52.564 156 73 1 12 166 15 170 3.90e-55 173
MS.gene46020.t1 MTR_7g066090 82.895 76 13 0 1 76 1 76 3.14e-39 129
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene46020.t1 AT3G54040 57.222 180 71 4 1 178 1 176 8.06e-68 205
MS.gene46020.t1 AT3G54040 59.763 169 62 4 1 167 57 221 2.66e-67 205
MS.gene46020.t1 AT5G52390 45.810 179 96 1 1 178 1 179 1.52e-53 169

Find 44 sgRNAs with CRISPR-Local

Find 69 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGTTGACCTTTACTTCAATT+TGG 0.208985 7.2:-43558526 MS.gene46020:CDS
GAGCATAATCAAAGGTAATT+TGG 0.227054 7.2:+43558982 None:intergenic
CGAAGGATGCATGGATAAAA+AGG 0.255435 7.2:+43558951 None:intergenic
GTGAGCTCTGGAGCTGCACC+TGG 0.378232 7.2:-43557939 MS.gene46020:CDS
AAGTAAAGGTCAACAATGTT+GGG 0.382511 7.2:+43558534 None:intergenic
TCTTGTGACAGAGCAGAAAC+AGG 0.399775 7.2:+43557915 None:intergenic
CTTTACTTCAATTTGGCTGC+TGG 0.407213 7.2:-43558519 MS.gene46020:CDS
ATCGGGAAAACGGTGTTTGT+TGG 0.414593 7.2:-43558763 MS.gene46020:CDS
GAAGTAAAGGTCAACAATGT+TGG 0.428702 7.2:+43558533 None:intergenic
ATGATCGAGCTTGTGAGCTC+TGG 0.439225 7.2:-43557951 MS.gene46020:CDS
TTCCTTCTCAATAGCTTCAT+CGG 0.440884 7.2:-43558781 MS.gene46020:CDS
AGAAGTGGTGGTTGAGAGAA+TGG 0.457204 7.2:-43558691 MS.gene46020:CDS
TCCTTCTCAATAGCTTCATC+GGG 0.458800 7.2:-43558780 MS.gene46020:CDS
TTCAATTTGGCTGCTGGAGA+AGG 0.478209 7.2:-43558513 MS.gene46020:intron
TAATTTGTTTACAGGGGAGA+AGG 0.479581 7.2:+43557873 None:intergenic
CTTAGGATAATTTGTTTACA+GGG 0.481665 7.2:+43557866 None:intergenic
CAATAGCTTCATCGGGAAAA+CGG 0.487446 7.2:-43558773 MS.gene46020:CDS
CAGCAGCCAAATTGAAGTAA+AGG 0.504408 7.2:+43558520 None:intergenic
AATTTGTTTACAGGGGAGAA+GGG 0.524668 7.2:+43557874 None:intergenic
GACAGAGCAGAAACAGGGCC+AGG 0.529854 7.2:+43557921 None:intergenic
TCCCGATGAAGCTATTGAGA+AGG 0.547199 7.2:+43558779 None:intergenic
GTGGTGGTTGAGAGAATGGC+GGG 0.547487 7.2:-43558687 MS.gene46020:CDS
GCTCGATCATAGCGCGATGA+GGG 0.572009 7.2:+43557964 None:intergenic
GAGACAGAGAAGGCCGCAGA+TGG 0.573015 7.2:-43558741 MS.gene46020:CDS
ACAGAGAAGGCCGCAGATGG+TGG 0.578762 7.2:-43558738 MS.gene46020:CDS
GTGTTTGTTGGAGACAGAGA+AGG 0.584309 7.2:-43558751 MS.gene46020:CDS
GATCAATGTGTGAAAGCTTG+TGG 0.593710 7.2:-43558651 MS.gene46020:CDS
ATTTGTTTACAGGGGAGAAG+GGG 0.601670 7.2:+43557875 None:intergenic
GATCATAGCGCGATGAGGGT+CGG 0.606329 7.2:+43557968 None:intergenic
TGTGTGTACCGAAGGATGCA+TGG 0.608900 7.2:+43558942 None:intergenic
AGCTCGATCATAGCGCGATG+AGG 0.614616 7.2:+43557963 None:intergenic
TGTGTGTGAGGAGTTGCAAA+AGG 0.620931 7.2:-43558811 MS.gene46020:CDS
CCACTTCTGATGTCCTACAT+TGG 0.621979 7.2:+43558706 None:intergenic
TTAGGATAATTTGTTTACAG+GGG 0.622904 7.2:+43557867 None:intergenic
TGAAAGCTTGTGGAGTTGAA+AGG 0.628133 7.2:-43558641 MS.gene46020:CDS
GAACACAAGAGCATAATCAA+AGG 0.628881 7.2:+43558974 None:intergenic
CTTGTGACAGAGCAGAAACA+GGG 0.634654 7.2:+43557916 None:intergenic
GTGGCGTCGAGTACCAATGT+AGG 0.640711 7.2:-43558719 MS.gene46020:CDS
ATGTAGGACATCAGAAGTGG+TGG 0.644390 7.2:-43558703 MS.gene46020:CDS
AGTAAAGGTCAACAATGTTG+GGG 0.655444 7.2:+43558535 None:intergenic
CCAATGTAGGACATCAGAAG+TGG 0.655889 7.2:-43558706 MS.gene46020:CDS
GACAGCTGAAGTTGTGTGTG+AGG 0.677896 7.2:-43558823 MS.gene46020:intron
GTACTCGACGCCACCATCTG+CGG 0.692101 7.2:+43558728 None:intergenic
AGTGGTGGTTGAGAGAATGG+CGG 0.692695 7.2:-43558688 MS.gene46020:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTAAAATAAATAAATTGCAT+AGG + chr7.2:43558005-43558024 None:intergenic 10.0%
!! AACAAAAAATAAAACAAAGA+AGG - chr7.2:43558749-43558768 MS.gene46020:CDS 15.0%
!! TAACTTCAAATTTAATCAAA+GGG - chr7.2:43558704-43558723 MS.gene46020:CDS 15.0%
!! TTAACTTCAAATTTAATCAA+AGG - chr7.2:43558703-43558722 MS.gene46020:CDS 15.0%
!!! TTTTCTAGAAAAAAAACATA+AGG - chr7.2:43558573-43558592 MS.gene46020:CDS 15.0%
!! CTCTCTTGATATTATAATAA+AGG - chr7.2:43558824-43558843 MS.gene46020:intron 20.0%
!! TAATTGGAAAATATATAGCA+GGG + chr7.2:43557971-43557990 None:intergenic 20.0%
! AAGAAATTAAGACAAAAGGA+AGG + chr7.2:43558546-43558565 None:intergenic 25.0%
! ATACTCATGCATAAAAGTTA+TGG + chr7.2:43558410-43558429 None:intergenic 25.0%
! ATAGGTAACTAGATAGTAAT+TGG + chr7.2:43557987-43558006 None:intergenic 25.0%
! GTAATTGGAAAATATATAGC+AGG + chr7.2:43557972-43557991 None:intergenic 25.0%
! GTTAAAATGTTAGATCATGA+CGG + chr7.2:43558688-43558707 None:intergenic 25.0%
! TTGTTCAAACTAAGATGAAA+AGG + chr7.2:43558513-43558532 None:intergenic 25.0%
!! TTCCTTTTGTCTTAATTTCT+TGG - chr7.2:43558545-43558564 MS.gene46020:CDS 25.0%
!!! CACTTTTATTTGAGTTGTAT+GGG + chr7.2:43558466-43558485 None:intergenic 25.0%
!!! TCACTTTTATTTGAGTTGTA+TGG + chr7.2:43558467-43558486 None:intergenic 25.0%
AAGTAAAGGTCAACAATGTT+GGG + chr7.2:43558345-43558364 None:intergenic 30.0%
CACCAAGAAATTAAGACAAA+AGG + chr7.2:43558550-43558569 None:intergenic 30.0%
GAGCATAATCAAAGGTAATT+TGG + chr7.2:43557897-43557916 None:intergenic 30.0%
TGTTGACCTTTACTTCAATT+TGG - chr7.2:43558350-43558369 MS.gene46020:intron 30.0%
! ACTTTTATGCATGAGTATCA+TGG - chr7.2:43558412-43558431 MS.gene46020:intron 30.0%
! CTTTTGTCTTAATTTCTTGG+TGG - chr7.2:43558548-43558567 MS.gene46020:CDS 30.0%
! GGAGTTGAAAGGAATTTTAT+CGG - chr7.2:43558246-43558265 MS.gene46020:intron 30.0%
AGTAAAGGTCAACAATGTTG+GGG + chr7.2:43558344-43558363 None:intergenic 35.0%
CTTTGATACTATGCAAATGC+AGG - chr7.2:43558850-43558869 MS.gene46020:intron 35.0%
GAAGGATGCATGGATAAAAA+GGG + chr7.2:43557927-43557946 None:intergenic 35.0%
GAAGTAAAGGTCAACAATGT+TGG + chr7.2:43558346-43558365 None:intergenic 35.0%
TTCCTTCTCAATAGCTTCAT+CGG - chr7.2:43558095-43558114 MS.gene46020:intron 35.0%
! CTTTTTATCCATGCATCCTT+CGG - chr7.2:43557926-43557945 MS.gene46020:CDS 35.0%
! GAACACAAGAGCATAATCAA+AGG + chr7.2:43557905-43557924 None:intergenic 35.0%
! GAAGGTTCTTTTCTTGTAGA+AGG - chr7.2:43558767-43558786 MS.gene46020:CDS 35.0%
!! CAAAGTTTTGCTGTGAATTG+CGG + chr7.2:43558297-43558316 None:intergenic 35.0%
CAATAGCTTCATCGGGAAAA+CGG - chr7.2:43558103-43558122 MS.gene46020:intron 40.0%
CAGCAGCCAAATTGAAGTAA+AGG + chr7.2:43558359-43558378 None:intergenic 40.0%
CGAAGGATGCATGGATAAAA+AGG + chr7.2:43557928-43557947 None:intergenic 40.0%
CTTTACTTCAATTTGGCTGC+TGG - chr7.2:43558357-43558376 MS.gene46020:intron 40.0%
GATCAATGTGTGAAAGCTTG+TGG - chr7.2:43558225-43558244 MS.gene46020:intron 40.0%
GTATATAGTGTGTGTACCGA+AGG + chr7.2:43557945-43557964 None:intergenic 40.0%
TCCTTCTCAATAGCTTCATC+GGG - chr7.2:43558096-43558115 MS.gene46020:intron 40.0%
TGAAAGCTTGTGGAGTTGAA+AGG - chr7.2:43558235-43558254 MS.gene46020:intron 40.0%
! TGTATGGGTAGAAGTGCAAT+TGG + chr7.2:43558451-43558470 None:intergenic 40.0%
! TTTTGCATCTCACAAAGGTC+AGG + chr7.2:43558886-43558905 None:intergenic 40.0%
AGAAGTGGTGGTTGAGAGAA+TGG - chr7.2:43558185-43558204 MS.gene46020:intron 45.0%
ATCGGGAAAACGGTGTTTGT+TGG - chr7.2:43558113-43558132 MS.gene46020:intron 45.0%
ATGTAGGACATCAGAAGTGG+TGG - chr7.2:43558173-43558192 MS.gene46020:intron 45.0%
CCAATGTAGGACATCAGAAG+TGG - chr7.2:43558170-43558189 MS.gene46020:intron 45.0%
CCACTTCTGATGTCCTACAT+TGG + chr7.2:43558173-43558192 None:intergenic 45.0%
CTTGTGACAGAGCAGAAACA+GGG + chr7.2:43558963-43558982 None:intergenic 45.0%
TCCCGATGAAGCTATTGAGA+AGG + chr7.2:43558100-43558119 None:intergenic 45.0%
TCTTGTGACAGAGCAGAAAC+AGG + chr7.2:43558964-43558983 None:intergenic 45.0%
TGTGTGTGAGGAGTTGCAAA+AGG - chr7.2:43558065-43558084 MS.gene46020:intron 45.0%
TTCAATTTGGCTGCTGGAGA+AGG - chr7.2:43558363-43558382 MS.gene46020:intron 45.0%
! CGGTCTTTTGCATCTCACAA+AGG + chr7.2:43558891-43558910 None:intergenic 45.0%
! GTGTTTGTTGGAGACAGAGA+AGG - chr7.2:43558125-43558144 MS.gene46020:intron 45.0%
AGTGGTGGTTGAGAGAATGG+CGG - chr7.2:43558188-43558207 MS.gene46020:intron 50.0%
ATGATCGAGCTTGTGAGCTC+TGG - chr7.2:43558925-43558944 MS.gene46020:intron 50.0%
ATTTGGCTGCTGGAGAAGGT+AGG - chr7.2:43558367-43558386 MS.gene46020:intron 50.0%
GACAGCTGAAGTTGTGTGTG+AGG - chr7.2:43558053-43558072 MS.gene46020:intron 50.0%
TGTGTGTACCGAAGGATGCA+TGG + chr7.2:43557937-43557956 None:intergenic 50.0%
AGCTCGATCATAGCGCGATG+AGG + chr7.2:43558916-43558935 None:intergenic 55.0%
GATCATAGCGCGATGAGGGT+CGG + chr7.2:43558911-43558930 None:intergenic 55.0%
GCTCGATCATAGCGCGATGA+GGG + chr7.2:43558915-43558934 None:intergenic 55.0%
GTGGTGGTTGAGAGAATGGC+GGG - chr7.2:43558189-43558208 MS.gene46020:intron 55.0%
! GTGGCGTCGAGTACCAATGT+AGG - chr7.2:43558157-43558176 MS.gene46020:intron 55.0%
ACAGAGAAGGCCGCAGATGG+TGG - chr7.2:43558138-43558157 MS.gene46020:intron 60.0%
GACAGAGCAGAAACAGGGCC+AGG + chr7.2:43558958-43558977 None:intergenic 60.0%
GAGACAGAGAAGGCCGCAGA+TGG - chr7.2:43558135-43558154 MS.gene46020:intron 60.0%
GTACTCGACGCCACCATCTG+CGG + chr7.2:43558151-43558170 None:intergenic 60.0%
!! GTGAGCTCTGGAGCTGCACC+TGG - chr7.2:43558937-43558956 MS.gene46020:intron 65.0%


Chromosome Type Strat End Strand Name
chr7.2 gene 43557881 43559017 43557881 ID=MS.gene46020
chr7.2 mRNA 43557881 43559017 43557881 ID=MS.gene46020.t1;Parent=MS.gene46020
chr7.2 exon 43558951 43559017 43558951 ID=MS.gene46020.t1.exon1;Parent=MS.gene46020.t1
chr7.2 CDS 43558951 43559017 43558951 ID=cds.MS.gene46020.t1;Parent=MS.gene46020.t1
chr7.2 exon 43558514 43558840 43558514 ID=MS.gene46020.t1.exon2;Parent=MS.gene46020.t1
chr7.2 CDS 43558514 43558840 43558514 ID=cds.MS.gene46020.t1;Parent=MS.gene46020.t1
chr7.2 exon 43557881 43558026 43557881 ID=MS.gene46020.t1.exon3;Parent=MS.gene46020.t1
chr7.2 CDS 43557881 43558026 43557881 ID=cds.MS.gene46020.t1;Parent=MS.gene46020.t1
Gene Sequence

>MS.gene46020

ATGTCTTTCTCATCCAAATTACCTTTGATTATGCTCTTGTGTTCCCTTTTTATCCATGCATCCTTCGGTACACACACTATATACACACCCTGCTATATATTTTCCAATTACTATCTAGTTACCTATGCAATTTATTTATTTTAAATATTAACATGTGTTTAATTCTTCAATTGACAGCTGAAGTTGTGTGTGAGGAGTTGCAAAAGGATCTATGTTCCTTCTCAATAGCTTCATCGGGAAAACGGTGTTTGTTGGAGACAGAGAAGGCCGCAGATGGTGGCGTCGAGTACCAATGTAGGACATCAGAAGTGGTGGTTGAGAGAATGGCGGGATACATAGAGACAGATCAATGTGTGAAAGCTTGTGGAGTTGAAAGGAATTTTATCGGAATTTCTTCTGATGCATTGCTTGAGCCGCAATTCACAGCAAAACTTTGTTCTTCGTCTTGTTATCAAAATTGCCCCAACATTGTTGACCTTTACTTCAATTTGGCTGCTGGAGAAGGTAGGATATTTTTCATTTAGTGCCATAACTTTTATGCATGAGTATCATGGTTAACTTGTAAGACCAATTGCACTTCTACCCATACAACTCAAATAAAAGTGAGATGCATTTGATGATGTGTTATTCCTTTTCATCTTAGTTTGAACAATTCAAATAAACCTTCCTTTTGTCTTAATTTCTTGGTGGCATTTTCTAGAAAAAAAACATAAGGTCATTTCACAAATTTTTTATTTTTTGCTTAATAACAAAGCAATGCTTATTCATGCTCACTTTTCACTGTGATAGTATCAATATAGCTTACCGTCATGATCTAACATTTTAACTTCAAATTTAATCAAAGGGACACATATAGTCACTCTTCAAAAACAAAAAATAAAACAAAGAAGGTTCTTTTCTTGTAGAAGGAAAACATTTTTGTTATTTTCTTGTACTATTTTCTCTCTCTTGATATTATAATAAAGGTTACTTTGATACTATGCAAATGCAGGTGTATTTTTGCCTGACCTTTGTGAGATGCAAAAGACCGACCCTCATCGCGCTATGATCGAGCTTGTGAGCTCTGGAGCTGCACCTGGCCCTGTTTCTGCTCTGTCACAAGACAAGCATGCAGCATTTGCCCCTTCTCCCCTGTAA
Protein sequence

>MS.gene46020.t1

MSFSSKLPLIMLLCSLFIHASFAEVVCEELQKDLCSFSIASSGKRCLLETEKAADGGVEYQCRTSEVVVERMAGYIETDQCVKACGVERNFIGISSDALLEPQFTAKLCSSSCYQNCPNIVDLYFNLAAGEGVFLPDLCEMQKTDPHRAMIELVSSGAAPGPVSALSQDKHAAFAPSPL