AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene44104

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene44104.t1 MTR_1g082950 97.309 223 6 0 1 223 40 262 9.91e-161 444
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene44104.t1 AT1G55000 63.303 218 77 2 7 221 2 219 1.84e-96 280
MS.gene44104.t1 AT1G55000 63.303 218 77 2 7 221 2 219 1.84e-96 280
MS.gene44104.t1 AT1G55000 63.303 218 77 2 7 221 2 219 1.84e-96 280

Find 52 sgRNAs with CRISPR-Local

Find 98 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACCCGATTTCTAGAAGCTTC+TGG 0.301921 1.3:+58522257 MS.gene44104:CDS
CTCCAGAAGCTTCTAGAAAT+CGG 0.322000 1.3:-58522259 None:intergenic
AACTTGCATGCTTCTCTTCA+AGG 0.333288 1.3:-58523356 None:intergenic
CGAGTTGCGTCTGCCGAGTC+TGG 0.340636 1.3:+58522158 MS.gene44104:CDS
GAAGGTTCTGGAAGATGATT+TGG 0.344754 1.3:-58522114 None:intergenic
AGAATATCGGGATTACTAAT+AGG 0.352325 1.3:-58523187 None:intergenic
GATCGGGGATGGGAAGGTTC+TGG 0.355186 1.3:-58522126 None:intergenic
CTCAGAAGAAACCAACAAAA+AGG 0.366398 1.3:+58523324 MS.gene44104:CDS
CGCCGTTAAGTACTCCGTTC+AGG 0.393861 1.3:+58522348 MS.gene44104:CDS
AAGAACTTGCTTTATTGAGC+TGG 0.414503 1.3:+58523216 MS.gene44104:CDS
CTTAGCACCGTGGAAATTGA+AGG 0.424552 1.3:+58522222 MS.gene44104:CDS
CAACTCGCACGTGCGAGATC+GGG 0.428494 1.3:-58522142 None:intergenic
TCCAGAAGCTTCTAGAAATC+GGG 0.438818 1.3:-58522258 None:intergenic
CCGCGGACCTTCAGTGGGGC+AGG 0.445516 1.3:+58523449 MS.gene44104:CDS
GCAACTCGCACGTGCGAGAT+CGG 0.461154 1.3:-58522143 None:intergenic
AGAAGTTGCAGTGTTGTATC+CGG 0.473663 1.3:+58523255 MS.gene44104:CDS
GACCTGAACGGAGTACTTAA+CGG 0.475918 1.3:-58522350 None:intergenic
GATTTGGAGGGTGTCGGTGG+AGG 0.478995 1.3:-58522098 None:intergenic
AACAACATGATGAGCGATCA+TGG 0.498173 1.3:+58523136 MS.gene44104:CDS
CCACGGTGCTAAGAAAGCTC+TGG 0.499969 1.3:-58522212 None:intergenic
CGCACGTGCGAGATCGGGGA+TGG 0.503094 1.3:-58522137 None:intergenic
CTACTTGCCTGCCCCACTGA+AGG 0.503713 1.3:-58523456 None:intergenic
TACTACTGGTCTGTTTCAAA+CGG 0.508801 1.3:+58523397 MS.gene44104:CDS
TGGAAATTGAAGGACGTAGT+TGG 0.509813 1.3:+58522232 MS.gene44104:CDS
TTTATGTCAGGTACATCATC+CGG 0.516672 1.3:-58523274 None:intergenic
CTTCAGTGGGGCAGGCAAGT+AGG 0.518848 1.3:+58523457 MS.gene44104:CDS
GATGATTTGGAGGGTGTCGG+TGG 0.523454 1.3:-58522101 None:intergenic
GTGCGAGATCGGGGATGGGA+AGG 0.529104 1.3:-58522132 None:intergenic
GCGGAGAAATGAGAATTCAT+TGG 0.531909 1.3:-58522070 None:intergenic
GTGAAACTGCTCAATACTAC+TGG 0.532559 1.3:+58523383 MS.gene44104:CDS
TTGATGTTTCGACAGGTGAT+GGG 0.534406 1.3:+58523100 MS.gene44104:intron
GGTTCTGGAAGATGATTTGG+AGG 0.546672 1.3:-58522111 None:intergenic
ACATAGCTACTCTTTATGTC+AGG 0.547238 1.3:-58523286 None:intergenic
GCACGTGCGAGATCGGGGAT+GGG 0.550351 1.3:-58522136 None:intergenic
GCGATCATGGTATATACTCA+AGG 0.575308 1.3:+58523149 MS.gene44104:CDS
AACTCGCACGTGCGAGATCG+GGG 0.575733 1.3:-58522141 None:intergenic
GAAGATGATTTGGAGGGTGT+CGG 0.579288 1.3:-58522104 None:intergenic
ATGGTATATACTCAAGGGAA+AGG 0.586472 1.3:+58523155 MS.gene44104:CDS
ACTACGTCCTTCAATTTCCA+CGG 0.587526 1.3:-58522229 None:intergenic
GGTGTCGGTGGAGGAAAGTG+CGG 0.588317 1.3:-58522089 None:intergenic
GAACTCGGTAGCGTCACAAA+GGG 0.590787 1.3:+58522180 MS.gene44104:CDS
CGTCTGCCGAGTCTGGAACT+CGG 0.602052 1.3:+58522165 MS.gene44104:CDS
CGATCATGGTATATACTCAA+GGG 0.604160 1.3:+58523150 MS.gene44104:CDS
GGAACTCGGTAGCGTCACAA+AGG 0.607432 1.3:+58522179 MS.gene44104:CDS
GGTAGCGTCACAAAGGGAGA+TGG 0.617996 1.3:+58522186 MS.gene44104:CDS
ATCTCGCATCGTATTGTGCG+TGG 0.618881 1.3:+58522307 MS.gene44104:CDS
CCTGCCCCACTGAAGGTCCG+CGG 0.625706 1.3:-58523449 None:intergenic
TAAACCCAAACGGACCTGAA+CGG 0.641440 1.3:-58522362 None:intergenic
ACGCTACCGAGTTCCAGACT+CGG 0.693008 1.3:-58522171 None:intergenic
GTTCTGGAAGATGATTTGGA+GGG 0.706445 1.3:-58522110 None:intergenic
AATTCAGCAAGAGCAGCACG+AGG 0.707212 1.3:-58523424 None:intergenic
CCAGAGCTTTCTTAGCACCG+TGG 0.711370 1.3:+58522212 MS.gene44104:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTAAAATGTTTTTAATTTCA+TGG + chr1.3:58522843-58522862 MS.gene44104:intron 10.0%
!! CTAGTTTATAAATTCTTAAT+AGG - chr1.3:58522972-58522991 None:intergenic 15.0%
!! AAATCACATAATATATGTGT+TGG + chr1.3:58522549-58522568 MS.gene44104:intron 20.0%
!! AAATGATGACAATGAAATTA+TGG + chr1.3:58522459-58522478 MS.gene44104:intron 20.0%
!!! AGTTCTTTTAACAAGAATAT+CGG - chr1.3:58523203-58523222 None:intergenic 20.0%
! AACAAAGTAATAAACCCAAA+CGG - chr1.3:58522375-58522394 None:intergenic 25.0%
! AGTATTAAACAGAAAAAACC+AGG - chr1.3:58523054-58523073 None:intergenic 25.0%
! TACTGTGATCAAATATGTTA+GGG + chr1.3:58522812-58522831 MS.gene44104:intron 25.0%
! TGAATATAGTTCATATGAGA+TGG + chr1.3:58522514-58522533 MS.gene44104:intron 25.0%
!! GTTCTTTTAACAAGAATATC+GGG - chr1.3:58523202-58523221 None:intergenic 25.0%
!!! AAATTTTTTGATGTTTCGAC+AGG + chr1.3:58523093-58523112 MS.gene44104:intron 25.0%
AGAATATCGGGATTACTAAT+AGG - chr1.3:58523190-58523209 None:intergenic 30.0%
GTACTGTGATCAAATATGTT+AGG + chr1.3:58522811-58522830 MS.gene44104:intron 30.0%
AATGTTATCTCCATTACGGA+TGG - chr1.3:58522647-58522666 None:intergenic 35.0%
ACATAGCTACTCTTTATGTC+AGG - chr1.3:58523289-58523308 None:intergenic 35.0%
ATGGTATATACTCAAGGGAA+AGG + chr1.3:58523155-58523174 MS.gene44104:CDS 35.0%
CACCAATGTTATCTCCATTA+CGG - chr1.3:58522651-58522670 None:intergenic 35.0%
CGATCATGGTATATACTCAA+GGG + chr1.3:58523150-58523169 MS.gene44104:CDS 35.0%
CTCAGAAGAAACCAACAAAA+AGG + chr1.3:58523324-58523343 MS.gene44104:CDS 35.0%
GATAACATTGGTGGGAATAT+AGG + chr1.3:58522658-58522677 MS.gene44104:intron 35.0%
GTAAAGCACAGAAATCTCTA+AGG - chr1.3:58522755-58522774 None:intergenic 35.0%
TTTATGTCAGGTACATCATC+CGG - chr1.3:58523277-58523296 None:intergenic 35.0%
! AAGAACTTGCTTTATTGAGC+TGG + chr1.3:58523216-58523235 MS.gene44104:CDS 35.0%
! ATCCGTAATGGAGATAACAT+TGG + chr1.3:58522646-58522665 MS.gene44104:intron 35.0%
! GTAATGGAGATAACATTGGT+GGG + chr1.3:58522650-58522669 MS.gene44104:intron 35.0%
! TACTACTGGTCTGTTTCAAA+CGG + chr1.3:58523397-58523416 MS.gene44104:CDS 35.0%
! TATTTTCATTGTTCTGTGCC+TGG + chr1.3:58523033-58523052 MS.gene44104:intron 35.0%
! TCACTGCAATATCAGGTTTT+AGG + chr1.3:58522880-58522899 MS.gene44104:intron 35.0%
!!! CTTTTTGTTGGTTTCTTCTG+AGG - chr1.3:58523326-58523345 None:intergenic 35.0%
AAACCTGATATTGCAGTGAC+AGG - chr1.3:58522879-58522898 None:intergenic 40.0%
AACAACATGATGAGCGATCA+TGG + chr1.3:58523136-58523155 MS.gene44104:CDS 40.0%
AACCTGATATTGCAGTGACA+GGG - chr1.3:58522878-58522897 None:intergenic 40.0%
AACTTGCATGCTTCTCTTCA+AGG - chr1.3:58523359-58523378 None:intergenic 40.0%
ACAGATTTGTCCATCCGTAA+TGG + chr1.3:58522634-58522653 MS.gene44104:intron 40.0%
ACTACGTCCTTCAATTTCCA+CGG - chr1.3:58522232-58522251 None:intergenic 40.0%
AGAAGTTGCAGTGTTGTATC+CGG + chr1.3:58523255-58523274 MS.gene44104:CDS 40.0%
AGTGACCATGCTTCATAGAT+TGG + chr1.3:58522704-58522723 MS.gene44104:intron 40.0%
ATTGCAGTGACAGGGAAATT+TGG - chr1.3:58522870-58522889 None:intergenic 40.0%
GATTTCTGTGCTTTACAGTC+AGG + chr1.3:58522759-58522778 MS.gene44104:intron 40.0%
GCGATCATGGTATATACTCA+AGG + chr1.3:58523149-58523168 MS.gene44104:CDS 40.0%
GTGAAACTGCTCAATACTAC+TGG + chr1.3:58523383-58523402 MS.gene44104:CDS 40.0%
TACGGATGGACAAATCTGTT+TGG - chr1.3:58522633-58522652 None:intergenic 40.0%
TCACAGTACAGTAGTCAACA+AGG - chr1.3:58522800-58522819 None:intergenic 40.0%
TGGAAATTGAAGGACGTAGT+TGG + chr1.3:58522232-58522251 MS.gene44104:CDS 40.0%
TTGATGTTTCGACAGGTGAT+GGG + chr1.3:58523100-58523119 MS.gene44104:intron 40.0%
TTTGATGTTTCGACAGGTGA+TGG + chr1.3:58523099-58523118 MS.gene44104:intron 40.0%
! CGTAATGGAGATAACATTGG+TGG + chr1.3:58522649-58522668 MS.gene44104:intron 40.0%
! CTCCAGAAGCTTCTAGAAAT+CGG - chr1.3:58522262-58522281 None:intergenic 40.0%
! GAAACAGAGCTCTTTTATCG+CGG - chr1.3:58522611-58522630 None:intergenic 40.0%
! GGAATCAAGCACCTTTTTGT+TGG - chr1.3:58523338-58523357 None:intergenic 40.0%
! TCCAGAAGCTTCTAGAAATC+GGG - chr1.3:58522261-58522280 None:intergenic 40.0%
!! GAAGGTTCTGGAAGATGATT+TGG - chr1.3:58522117-58522136 None:intergenic 40.0%
!! GTTCTGGAAGATGATTTGGA+GGG - chr1.3:58522113-58522132 None:intergenic 40.0%
CCATGCTTCATAGATTGGTG+CGG + chr1.3:58522709-58522728 MS.gene44104:intron 45.0%
CTTAGCACCGTGGAAATTGA+AGG + chr1.3:58522222-58522241 MS.gene44104:CDS 45.0%
TAAACCCAAACGGACCTGAA+CGG - chr1.3:58522365-58522384 None:intergenic 45.0%
TTCCCTGTCACTGCAATATC+AGG + chr1.3:58522873-58522892 MS.gene44104:intron 45.0%
! ACCCGATTTCTAGAAGCTTC+TGG + chr1.3:58522257-58522276 MS.gene44104:CDS 45.0%
! GAAGATGATTTGGAGGGTGT+CGG - chr1.3:58522107-58522126 None:intergenic 45.0%
! GACCTGAACGGAGTACTTAA+CGG - chr1.3:58522353-58522372 None:intergenic 45.0%
! TGCTCTTGCTGAATTTTCCG+CGG + chr1.3:58523432-58523451 MS.gene44104:CDS 45.0%
!! GGTTCTGGAAGATGATTTGG+AGG - chr1.3:58522114-58522133 None:intergenic 45.0%
AATTCAGCAAGAGCAGCACG+AGG - chr1.3:58523427-58523446 None:intergenic 50.0%
ATCTCGCATCGTATTGTGCG+TGG + chr1.3:58522307-58522326 MS.gene44104:CDS 50.0%
CCGCACCAATCTATGAAGCA+TGG - chr1.3:58522712-58522731 None:intergenic 50.0%
GAACTCGGTAGCGTCACAAA+GGG + chr1.3:58522180-58522199 MS.gene44104:CDS 50.0%
TACTCCGTTCAGGTCCGTTT+GGG + chr1.3:58522358-58522377 MS.gene44104:intron 50.0%
! AATTTTCCGCGGACCTTCAG+TGG + chr1.3:58523443-58523462 MS.gene44104:CDS 50.0%
! ATTTTCCGCGGACCTTCAGT+GGG + chr1.3:58523444-58523463 MS.gene44104:CDS 50.0%
!! TGTTGGTGTCATGTCCGTGT+CGG + chr1.3:58522566-58522585 MS.gene44104:intron 50.0%
ACGCTACCGAGTTCCAGACT+CGG - chr1.3:58522174-58522193 None:intergenic 55.0%
CCAGAGCTTTCTTAGCACCG+TGG + chr1.3:58522212-58522231 MS.gene44104:CDS 55.0%
CCTCGCATTAGGCGTGTCAT+CGG - chr1.3:58522684-58522703 None:intergenic 55.0%
CGCCGTTAAGTACTCCGTTC+AGG + chr1.3:58522348-58522367 MS.gene44104:CDS 55.0%
GACATGTGTCGTGTCCGACA+CGG - chr1.3:58522583-58522602 None:intergenic 55.0%
GCATGGTCACTCCTCGCATT+AGG - chr1.3:58522695-58522714 None:intergenic 55.0%
GGAACTCGGTAGCGTCACAA+AGG + chr1.3:58522179-58522198 MS.gene44104:CDS 55.0%
GGTAGCGTCACAAAGGGAGA+TGG + chr1.3:58522186-58522205 MS.gene44104:CDS 55.0%
GTACTCCGTTCAGGTCCGTT+TGG + chr1.3:58522357-58522376 MS.gene44104:intron 55.0%
! CCACGGTGCTAAGAAAGCTC+TGG - chr1.3:58522215-58522234 None:intergenic 55.0%
! TTTTCCGCGGACCTTCAGTG+GGG + chr1.3:58523445-58523464 MS.gene44104:CDS 55.0%
!! GATGATTTGGAGGGTGTCGG+TGG - chr1.3:58522104-58522123 None:intergenic 55.0%
AACTCGCACGTGCGAGATCG+GGG - chr1.3:58522144-58522163 None:intergenic 60.0%
CAACTCGCACGTGCGAGATC+GGG - chr1.3:58522145-58522164 None:intergenic 60.0%
CCGATGACACGCCTAATGCG+AGG + chr1.3:58522681-58522700 MS.gene44104:intron 60.0%
CTACTTGCCTGCCCCACTGA+AGG - chr1.3:58523459-58523478 None:intergenic 60.0%
CTTCAGTGGGGCAGGCAAGT+AGG + chr1.3:58523457-58523476 MS.gene44104:CDS 60.0%
GATCGGGGATGGGAAGGTTC+TGG - chr1.3:58522129-58522148 None:intergenic 60.0%
GCAACTCGCACGTGCGAGAT+CGG - chr1.3:58522146-58522165 None:intergenic 60.0%
! CGTCTGCCGAGTCTGGAACT+CGG + chr1.3:58522165-58522184 MS.gene44104:CDS 60.0%
!! GATTTGGAGGGTGTCGGTGG+AGG - chr1.3:58522101-58522120 None:intergenic 60.0%
!! GGTGTCGGTGGAGGAAAGTG+CGG - chr1.3:58522092-58522111 None:intergenic 60.0%
CGAGTTGCGTCTGCCGAGTC+TGG + chr1.3:58522158-58522177 MS.gene44104:CDS 65.0%
GCACGTGCGAGATCGGGGAT+GGG - chr1.3:58522139-58522158 None:intergenic 65.0%
GTGCGAGATCGGGGATGGGA+AGG - chr1.3:58522135-58522154 None:intergenic 65.0%
CCTGCCCCACTGAAGGTCCG+CGG - chr1.3:58523452-58523471 None:intergenic 70.0%
CGCACGTGCGAGATCGGGGA+TGG - chr1.3:58522140-58522159 None:intergenic 70.0%
CCGCGGACCTTCAGTGGGGC+AGG + chr1.3:58523449-58523468 MS.gene44104:CDS 75.0%


Chromosome Type Strat End Strand Name
chr1.3 gene 58522073 58523489 58522073 ID=MS.gene44104
chr1.3 mRNA 58522073 58523489 58522073 ID=MS.gene44104.t1;Parent=MS.gene44104
chr1.3 exon 58522073 58522369 58522073 ID=MS.gene44104.t1.exon1;Parent=MS.gene44104.t1
chr1.3 CDS 58522073 58522369 58522073 ID=cds.MS.gene44104.t1;Parent=MS.gene44104.t1
chr1.3 exon 58523115 58523489 58523115 ID=MS.gene44104.t1.exon2;Parent=MS.gene44104.t1
chr1.3 CDS 58523115 58523489 58523115 ID=cds.MS.gene44104.t1;Parent=MS.gene44104.t1
Gene Sequence

>MS.gene44104

ATGAATTCTCATTTCTCCGCACTTTCCTCCACCGACACCCTCCAAATCATCTTCCAGAACCTTCCCATCCCCGATCTCGCACGTGCGAGTTGCGTCTGCCGAGTCTGGAACTCGGTAGCGTCACAAAGGGAGATGGTAACCAGAGCTTTCTTAGCACCGTGGAAATTGAAGGACGTAGTTGGAAACCCGATTTCTAGAAGCTTCTGGAGAGATAATTCACTTGCTAAATTCGCAATCTCGCATCGTATTGTGCGTGGTGATAGTGTTGCTAGTCTCGCCGTTAAGTACTCCGTTCAGGTCCGTTTGGGTTTATTACTTTGTTTCAGAAATTGAAATGCATAATTTTTTGTTGTTGTTGATAATACACTATGCGCTTGTGCTTTTGAAAATGATGACAATGAAATTATGGAATCATCTCTCTCTGAAATTCAAGATTATGTTTGAATATAGTTCATATGAGATGGTTTTATATGTATAAATCACATAATATATGTGTTGGTGTCATGTCCGTGTCGGACACGACACATGTCTAATTCCGCGATAAAAGAGCTCTGTTTCCAAACAGATTTGTCCATCCGTAATGGAGATAACATTGGTGGGAATATAGGCCGATGACACGCCTAATGCGAGGAGTGACCATGCTTCATAGATTGGTGCGGCAAACAGTAGAAATGCATAACCTTAGAGATTTCTGTGCTTTACAGTCAGGACTAAATTAATCGTTCCTTGTTGACTACTGTACTGTGATCAAATATGTTAGGGATATCATTTTAAAATGTTTTTAATTTCATGGACCAAATTTCCCTGTCACTGCAATATCAGGTTTTAGGATTAAAATTTTGATTAGCTCAAATCAAATTGTTAACATCTACTTGTTGTGTATAATTTAGCATTTTCCTATTAAGAATTTATAAACTAGTTGATCTTTTTCTGACTATTTTTACTGTAAGCACTAAGCTATATTTTCATTGTTCTGTGCCTGGTTTTTTCTGTTTAATACTTTTGATAAAGTTGAATGATAAATTTTTTGATGTTTCGACAGGTGATGGGCATAAAACGATTGAACAACATGATGAGCGATCATGGTATATACTCAAGGGAAAGGTTATTAATTCCTATTAGTAATCCCGATATTCTTGTTAAAAGAACTTGCTTTATTGAGCTGGATGTTAATGCGAAACGAGAAGTTGCAGTGTTGTATCCGGATGATGTACCTGACATAAAGAGTAGCTATGTATCAAACAGAATATCCTCAGAAGAAACCAACAAAAAGGTGCTTGATTCCTTGAAGAGAAGCATGCAAGTTGATAGTGAAACTGCTCAATACTACTGGTCTGTTTCAAACGGTGATCCTCGTGCTGCTCTTGCTGAATTTTCCGCGGACCTTCAGTGGGGCAGGCAAGTAGGTCACTCCTAG
Protein sequence

>MS.gene44104.t1

MNSHFSALSSTDTLQIIFQNLPIPDLARASCVCRVWNSVASQREMVTRAFLAPWKLKDVVGNPISRSFWRDNSLAKFAISHRIVRGDSVASLAVKYSVQVMGIKRLNNMMSDHGIYSRERLLIPISNPDILVKRTCFIELDVNAKREVAVLYPDDVPDIKSSYVSNRISSEETNKKVLDSLKRSMQVDSETAQYYWSVSNGDPRAALAEFSADLQWGRQVGHS