AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene049026

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene049026.t1 MTR_8g101910 98.450 129 2 0 1 129 1 129 4.67e-94 267
MS.gene049026.t1 MTR_8g101910 96.970 99 3 0 1 99 1 99 3.41e-68 201
MS.gene049026.t1 MTR_4g094598 52.000 125 60 0 5 129 6 130 7.77e-46 145
MS.gene049026.t1 MTR_1g105415 52.000 125 60 0 5 129 6 130 7.77e-46 145
MS.gene049026.t1 MTR_4g117470 52.000 125 60 0 5 129 6 130 1.99e-45 144
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene049026.t1 AT4G29430 81.395 129 24 0 1 129 1 129 5.77e-79 229
MS.gene049026.t1 AT2G19720 79.845 129 26 0 1 129 1 129 1.60e-77 225
MS.gene049026.t1 AT2G39590 52.000 125 60 0 5 129 6 130 3.50e-46 146
MS.gene049026.t1 AT5G59850 52.000 125 60 0 5 129 6 130 1.97e-45 144
MS.gene049026.t1 AT1G07770 52.000 125 60 0 5 129 6 130 1.97e-45 144
MS.gene049026.t1 AT1G07770 52.000 125 60 0 5 129 6 130 1.97e-45 144
MS.gene049026.t1 AT1G07770 52.000 125 60 0 5 129 6 130 1.97e-45 144
MS.gene049026.t1 AT3G46040 50.400 125 62 0 5 129 6 130 2.76e-44 141

Find 33 sgRNAs with CRISPR-Local

Find 75 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTGTGATCCTCCCCACTCTA+TGG 0.263185 4.1:-3456560 None:intergenic
GAAGAGATAACATTGGAAAT+AGG 0.265767 4.1:-3455901 None:intergenic
TACAACTCCTGATGGTGTTT+TGG 0.307095 4.1:+3456881 MS.gene049026:CDS
AATGTAGGTGGTCAGGTTCT+TGG 0.331557 4.1:+3456927 MS.gene049026:CDS
AGGATATATCAAGGACTTTC+AGG 0.389863 4.1:+3456527 MS.gene049026:intron
CCTTTGCCTTGAGGTCTTGT+CGG 0.398017 4.1:-3456626 None:intergenic
ATCATGAAGAGGCCGCAAAA+AGG 0.404793 4.1:+3456904 MS.gene049026:CDS
TGAGGTCTTGTCGGTACGTA+AGG 0.430606 4.1:-3456617 None:intergenic
TGTGATCCTCCCCACTCTAT+GGG 0.457890 4.1:-3456559 None:intergenic
GAACGATGCGTTGAGGAGTA+TGG 0.475978 4.1:+3455837 MS.gene049026:CDS
GAACACTCTTCCAACACATC+AGG 0.488180 4.1:+3456668 MS.gene049026:CDS
TCATGATCCAAAACACCATC+AGG 0.488311 4.1:-3456888 None:intergenic
AAGAAAAGAAGAGATAACAT+TGG 0.493444 4.1:-3455908 None:intergenic
GAGAAAGAGAAATGGGGAGA+AGG 0.505773 4.1:+3455809 None:intergenic
CATTAACCAACCTGATGTGT+TGG 0.507241 4.1:-3456678 None:intergenic
ATTCAATATCCTTTGCCTTG+AGG 0.544391 4.1:-3456635 None:intergenic
GAAGAGAGGCAAAGCTATGG+TGG 0.562394 4.1:+3455870 MS.gene049026:CDS
GTGTATGATCCCCATAGAGT+GGG 0.576109 4.1:+3456549 MS.gene049026:CDS
CATGTTGGCAGGATATATCA+AGG 0.581279 4.1:+3456518 MS.gene049026:intron
GAGGTCTTGTCGGTACGTAA+GGG 0.585892 4.1:-3456616 None:intergenic
TGAGAAGAGAGGCAAAGCTA+TGG 0.613395 4.1:+3455867 MS.gene049026:CDS
GGTGTATGATCCCCATAGAG+TGG 0.614660 4.1:+3456548 MS.gene049026:CDS
AGGTAGAATTAACGATTGCA+AGG 0.617470 4.1:+3456593 MS.gene049026:CDS
TACGTACCGACAAGACCTCA+AGG 0.647236 4.1:+3456620 MS.gene049026:CDS
CCGACAAGACCTCAAGGCAA+AGG 0.651183 4.1:+3456626 MS.gene049026:CDS
GGATACTGAACGATGCGTTG+AGG 0.657571 4.1:+3455830 MS.gene049026:CDS
AGGATCACAGTTGAACTACA+AGG 0.660202 4.1:+3456573 MS.gene049026:CDS
ATGGTGAATGCTGAGAAGAG+AGG 0.672519 4.1:+3455856 MS.gene049026:CDS
GTTGTGATTACAACTCCTGA+TGG 0.673437 4.1:+3456873 MS.gene049026:CDS
GTGATCCTCCCCACTCTATG+GGG 0.676832 4.1:-3456558 None:intergenic
TGTATGATCCCCATAGAGTG+GGG 0.683001 4.1:+3456550 MS.gene049026:CDS
ATGATCCCCATAGAGTGGGG+AGG 0.698167 4.1:+3456553 MS.gene049026:CDS
CTTCAAATCATGAAACACCG+CGG 0.732704 4.1:+3455928 MS.gene049026:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTTTTAAAGATATTTTTAG+TGG + chr4.1:3456163-3456182 MS.gene049026:intron 10.0%
!! AACACTAAATAAAAACAAAA+CGG - chr4.1:3456708-3456727 None:intergenic 15.0%
!!! AGAATTTAAAATATAAAAGC+TGG - chr4.1:3456780-3456799 None:intergenic 15.0%
!!! TTTTTAATAGATATGAGTAA+AGG + chr4.1:3456803-3456822 MS.gene049026:intron 15.0%
!! ATGTCTTAATTAATGGAATT+TGG - chr4.1:3456099-3456118 None:intergenic 20.0%
!! CATTAATTAAGACATACATT+AGG + chr4.1:3456104-3456123 MS.gene049026:intron 20.0%
!! CTAATGTATGTCTTAATTAA+TGG - chr4.1:3456106-3456125 None:intergenic 20.0%
!! TGTCTTAATTAATGGAATTT+GGG - chr4.1:3456098-3456117 None:intergenic 20.0%
! AAGAAAAGAAGAGATAACAT+TGG - chr4.1:3455911-3455930 None:intergenic 25.0%
! ATAGATATGAGTAAAGGAAA+AGG + chr4.1:3456809-3456828 MS.gene049026:intron 25.0%
! ATTTCAAACAAATATTACCG+CGG - chr4.1:3455948-3455967 None:intergenic 25.0%
! ATTTCATACTCATAAGATGA+AGG - chr4.1:3455999-3456018 None:intergenic 25.0%
! TAATTGTTGGAAAATAACCA+TGG - chr4.1:3456378-3456397 None:intergenic 25.0%
! TCATATCTCATGAAAAGAAA+TGG + chr4.1:3456349-3456368 MS.gene049026:intron 25.0%
! TTACTTCCATTATCTCAAAT+TGG + chr4.1:3456280-3456299 MS.gene049026:intron 25.0%
! TTTATTTATCTTGATGCAGT+GGG + chr4.1:3456845-3456864 MS.gene049026:intron 25.0%
! TTTCATACTCATAAGATGAA+GGG - chr4.1:3455998-3456017 None:intergenic 25.0%
!!! TGTGTTTTGGATAATTCATT+AGG + chr4.1:3456048-3456067 MS.gene049026:intron 25.0%
!!! TTTTATTTATCTTGATGCAG+TGG + chr4.1:3456844-3456863 MS.gene049026:intron 25.0%
ACAAATATAATCACGTGTGT+AGG - chr4.1:3456260-3456279 None:intergenic 30.0%
AGCATGTATATGTACATGAA+AGG + chr4.1:3456434-3456453 MS.gene049026:intron 30.0%
AGCATTCTCCATATACAAAT+AGG - chr4.1:3456743-3456762 None:intergenic 30.0%
CAGTTTCTCCTATTTGTATA+TGG + chr4.1:3456732-3456751 MS.gene049026:intron 30.0%
GAAGAGATAACATTGGAAAT+AGG - chr4.1:3455904-3455923 None:intergenic 30.0%
TTATTTATCTTGATGCAGTG+GGG + chr4.1:3456846-3456865 MS.gene049026:intron 30.0%
! ATTTTCCAACAATTATCAGC+TGG + chr4.1:3456383-3456402 MS.gene049026:intron 30.0%
! GTCATACCAATTTGAGATAA+TGG - chr4.1:3456289-3456308 None:intergenic 30.0%
!!! TATGTATTCGTTTTTTGAGC+TGG + chr4.1:3456020-3456039 MS.gene049026:intron 30.0%
AATTATCAGCTGGATAAGCA+TGG + chr4.1:3456393-3456412 MS.gene049026:intron 35.0%
AGGATATATCAAGGACTTTC+AGG + chr4.1:3456527-3456546 MS.gene049026:intron 35.0%
AGGTAGAATTAACGATTGCA+AGG + chr4.1:3456593-3456612 MS.gene049026:CDS 35.0%
ATGAAAAGAAATGGTCTCCA+TGG + chr4.1:3456358-3456377 MS.gene049026:intron 35.0%
ATTCAATATCCTTTGCCTTG+AGG - chr4.1:3456638-3456657 None:intergenic 35.0%
CTTATCCAGCTGATAATTGT+TGG - chr4.1:3456391-3456410 None:intergenic 35.0%
GCTACATAGTTCTTGAGAAA+TGG - chr4.1:3456197-3456216 None:intergenic 35.0%
! TGAGCTGGATTTATGTGTTT+TGG + chr4.1:3456035-3456054 MS.gene049026:intron 35.0%
!! TAATTTGCTGTCGTTCATGT+TGG + chr4.1:3456503-3456522 MS.gene049026:intron 35.0%
AAAAAGGAATGTAGGTGGTC+AGG + chr4.1:3456920-3456939 MS.gene049026:CDS 40.0%
AGGATCACAGTTGAACTACA+AGG + chr4.1:3456573-3456592 MS.gene049026:CDS 40.0%
CATGTTGGCAGGATATATCA+AGG + chr4.1:3456518-3456537 MS.gene049026:intron 40.0%
CATTAACCAACCTGATGTGT+TGG - chr4.1:3456681-3456700 None:intergenic 40.0%
CTCAAATTGGTATGACGTTG+AGG + chr4.1:3456293-3456312 MS.gene049026:intron 40.0%
CTTCAAATCATGAAACACCG+CGG + chr4.1:3455928-3455947 MS.gene049026:CDS 40.0%
GTTGTGATTACAACTCCTGA+TGG + chr4.1:3456873-3456892 MS.gene049026:CDS 40.0%
TCATGATCCAAAACACCATC+AGG - chr4.1:3456891-3456910 None:intergenic 40.0%
! ACCACCTACATTCCTTTTTG+CGG - chr4.1:3456919-3456938 None:intergenic 40.0%
!! TACAACTCCTGATGGTGTTT+TGG + chr4.1:3456881-3456900 MS.gene049026:CDS 40.0%
!! TGGTGTTTTGGATCATGAAG+AGG + chr4.1:3456893-3456912 MS.gene049026:CDS 40.0%
AATGTAGGTGGTCAGGTTCT+TGG + chr4.1:3456927-3456946 MS.gene049026:CDS 45.0%
ACTCTTCCAACACATCAGGT+TGG + chr4.1:3456672-3456691 MS.gene049026:intron 45.0%
ATCATGAAGAGGCCGCAAAA+AGG + chr4.1:3456904-3456923 MS.gene049026:CDS 45.0%
ATGGTGAATGCTGAGAAGAG+AGG + chr4.1:3455856-3455875 MS.gene049026:CDS 45.0%
ATTGGTATGACGTTGAGGTG+TGG + chr4.1:3456298-3456317 MS.gene049026:intron 45.0%
GAACACTCTTCCAACACATC+AGG + chr4.1:3456668-3456687 MS.gene049026:CDS 45.0%
GTGTATGATCCCCATAGAGT+GGG + chr4.1:3456549-3456568 MS.gene049026:CDS 45.0%
TGAGAAGAGAGGCAAAGCTA+TGG + chr4.1:3455867-3455886 MS.gene049026:CDS 45.0%
TGTATGATCCCCATAGAGTG+GGG + chr4.1:3456550-3456569 MS.gene049026:CDS 45.0%
TTGGTATGACGTTGAGGTGT+GGG + chr4.1:3456299-3456318 MS.gene049026:intron 45.0%
!!! TATTATTAATTTTAGATTTT+TGG + chr4.1:3456128-3456147 MS.gene049026:intron 5.0%
GAACGATGCGTTGAGGAGTA+TGG + chr4.1:3455837-3455856 MS.gene049026:CDS 50.0%
GAAGAGAGGCAAAGCTATGG+TGG + chr4.1:3455870-3455889 MS.gene049026:CDS 50.0%
GAGGCCGCAAAAAGGAATGT+AGG + chr4.1:3456912-3456931 MS.gene049026:CDS 50.0%
GCCGCAAAAAGGAATGTAGG+TGG + chr4.1:3456915-3456934 MS.gene049026:CDS 50.0%
GGATACTGAACGATGCGTTG+AGG + chr4.1:3455830-3455849 MS.gene049026:CDS 50.0%
GGTGTATGATCCCCATAGAG+TGG + chr4.1:3456548-3456567 MS.gene049026:CDS 50.0%
TGTGATCCTCCCCACTCTAT+GGG - chr4.1:3456562-3456581 None:intergenic 50.0%
TTGCTGTCGTTCATGTTGGC+AGG + chr4.1:3456507-3456526 MS.gene049026:intron 50.0%
! CCTTTGCCTTGAGGTCTTGT+CGG - chr4.1:3456629-3456648 None:intergenic 50.0%
! GAGGTCTTGTCGGTACGTAA+GGG - chr4.1:3456619-3456638 None:intergenic 50.0%
! TACGTACCGACAAGACCTCA+AGG + chr4.1:3456620-3456639 MS.gene049026:CDS 50.0%
! TGAGGTCTTGTCGGTACGTA+AGG - chr4.1:3456620-3456639 None:intergenic 50.0%
ATGATCCCCATAGAGTGGGG+AGG + chr4.1:3456553-3456572 MS.gene049026:CDS 55.0%
CCGACAAGACCTCAAGGCAA+AGG + chr4.1:3456626-3456645 MS.gene049026:CDS 55.0%
CTGTGATCCTCCCCACTCTA+TGG - chr4.1:3456563-3456582 None:intergenic 55.0%
GTGATCCTCCCCACTCTATG+GGG - chr4.1:3456561-3456580 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr4.1 gene 3455820 3456962 3455820 ID=MS.gene049026
chr4.1 mRNA 3455820 3456962 3455820 ID=MS.gene049026.t1;Parent=MS.gene049026
chr4.1 exon 3455820 3455949 3455820 ID=MS.gene049026.t1.exon1;Parent=MS.gene049026.t1
chr4.1 CDS 3455820 3455949 3455820 ID=cds.MS.gene049026.t1;Parent=MS.gene049026.t1
chr4.1 exon 3456529 3456689 3456529 ID=MS.gene049026.t1.exon2;Parent=MS.gene049026.t1
chr4.1 CDS 3456529 3456689 3456529 ID=cds.MS.gene049026.t1;Parent=MS.gene049026.t1
chr4.1 exon 3456864 3456962 3456864 ID=MS.gene049026.t1.exon3;Parent=MS.gene049026.t1
chr4.1 CDS 3456864 3456962 3456864 ID=cds.MS.gene049026.t1;Parent=MS.gene049026.t1
Gene Sequence

>MS.gene049026

ATGGGGAGAAGGATACTGAACGATGCGTTGAGGAGTATGGTGAATGCTGAGAAGAGAGGCAAAGCTATGGTGGAGCTTAAACCTATTTCCAATGTTATCTCTTCTTTTCTTCAAATCATGAAACACCGCGGTAATATTTGTTTGAAATCTTTCATTATTTATTTTCTTTTATTTTCCCTTCATCTTATGAGTATGAAATTTATGTATTCGTTTTTTGAGCTGGATTTATGTGTTTTGGATAATTCATTAGGATATTGTTATTGTTTTAGTAAATACCCAAATTCCATTAATTAAGACATACATTAGGATATTATTAATTTTAGATTTTTGGCATATTAGTATAATTTTTAAAGATATTTTTAGTGGTATTTTATCCATTTCTCAAGAACTATGTAGCGTATACACTTTAGATTGAAGACATGTTTAGTGTCTAGACACCTACACACGTGATTATATTTGTTTACTTCCATTATCTCAAATTGGTATGACGTTGAGGTGTGGGTGCAGTTGTCGTGTTTTCGTCAGTGCTTCATATCTCATGAAAAGAAATGGTCTCCATGGTTATTTTCCAACAATTATCAGCTGGATAAGCATGGTCTTGCTTTCTGTATGTTAGCATGTATATGTACATGAAAGGCACTAAACGTACTAGAATAATTTGATATTTAGATAATCGCTACAGTTAATTTGCTGTCGTTCATGTTGGCAGGATATATCAAGGACTTTCAGGTGTATGATCCCCATAGAGTGGGGAGGATCACAGTTGAACTACAAGGTAGAATTAACGATTGCAAGGCCCTTACGTACCGACAAGACCTCAAGGCAAAGGATATTGAATCTTACAGATTGAACACTCTTCCAACACATCAGGTTGGTTAATGCTTACCGTTTTGTTTTTATTTAGTGTTATAGCAGTTTCTCCTATTTGTATATGGAGAATGCTGTTTGTTATAGCTGCCAGCTTTTATATTTTAAATTCTTTCTTTTTAATAGATATGAGTAAAGGAAAAGGATATTCATTTCATTTTATTTATCTTGATGCAGTGGGGTTATGTTGTGATTACAACTCCTGATGGTGTTTTGGATCATGAAGAGGCCGCAAAAAGGAATGTAGGTGGTCAGGTTCTTGGTTACTTTCACTAA
Protein sequence

>MS.gene049026.t1

MGRRILNDALRSMVNAEKRGKAMVELKPISNVISSFLQIMKHRGYIKDFQVYDPHRVGRITVELQGRINDCKALTYRQDLKAKDIESYRLNTLPTHQWGYVVITTPDGVLDHEEAAKRNVGGQVLGYFH