ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GCGCGACATCGGCTCCGGCAACTTCGGCGTTGCCCGCCTCATGCGCGACCGCCGCACCACCGAACTCGTCGCCGTCAAGTACATCGAGCGTGGCGAGAAGgtatcgcgctggtcccgttctccctcccctatggtttcatttcggcgttggctgtagttaattaataacccatcgattccaccgcaccggggcggcgcgg...

Basic information

species	Zea mays
transcript	GRMZM2G171435_T01
intron #	1
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G171435_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os03g55600.1 (Oryza sativa), 5'ss of exon 1

GCGCGACATCGGCTCCGGCAACTTCGGCGTTGCCCGCCTCATGCGCGACCGCCGCACCACCGAACTCGTCGCCGTCAAGTACATCGAGCGTGGCGAGAAGgtatcgc-gctggtcccg----ttctccctcccctatggtttcatttcggcgttggctgtagttaattaataacccatcgattccaccgcaccggggcggcgcgg
|||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||  || |||||||||||||||||||||||||| ||||||||||||  || ||||   ||     ||||||  ||  | | | |||  ||||||| |||||| ||| |   | |   ||  || |    ||  ||  || ||      
GCGCGACATCGGCTCCGGCAACTTCGGCGTCGCCCGCCTCATGCGCGACCGCCGCACCATGGAGCTCGTCGCCGTCAAGTACATCGAGCGCGGCGAGAAGgtacggccgctgactccccgccttctcctccctttctagcttcgattcggcgctggctg-agtgatcgattcgacc--cggtgtgcccaaacgtggccgattt--

upper sequence: GRMZM2G171435_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA05G09460.1 (Glycine max), 5'ss of exon 1

GCGCGACATCGGCTCCGGCAACTTCGGCGTTGCCCGCCTCATGCGCGACCGCCGCACCACCGAACTCGTCGCCGTCAAGTACATCGAGCGTGGCGAGAAGgtatcgcgctggtcccgttctccctcccctatggtttcatttcggcgttggctgta-gttaattaataacccatcgattccaccgcaccggggcggcgcgg---
 ||||||||||| ||||| || |||||||| ||  | || ||||  ||    |  ||||  ||||||||||||||||||||||||||  | || || |||||     | || |   ||         || |||     |        ||   | |  |||  ||  |   |  |   ||     |    | |  |  ||     
CCGCGACATCGGGTCCGGAAATTTCGGCGTGGCGAGGCTGATGCAGGATAAACAAACCAAGGAACTCGTCGCCGTCAAGTACATCGAAAGGGGTGATAAGgt----tgttgtttttgtctgaatgaaccaatgacccaaacaaacttttctttttctgttttttttttttcgttttgttttcttggttggtgctgttgcccctt

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments

ATGC    EST sequence
ATGC    genomic sequence (exon)
ATGC    genomic sequence (truncated intron)

EST: gi|211022079|gb|FL377464.1|FL377464

EST:     GCCGCACCACCGAACTCGTCGCCGTCAAGTACATCGAGCGTGGCGAGAAG                         ATAGATGAGAATGTCCAGCGCGAAATAATTAACCATAGATCATTGAAACAC
genomic: GCCGCACCACCGAACTCGTCGCCGTCAAGTACATCGAGCGTGGCGAGAAGgtatcgcgct ... tcatttgcagATAGATGAGAATGTCCAGCGCGAAATAATTAACCATAGATCATTGAAACAC

EST: gi|211499753|gb|FL295241.1|FL295241

EST:     G-CGCACCACCGAACTCGTCGCCGTCAAGTACATCGAGCGTGGCGAGAAG                         ATAGATGAGAATGTCCAGCGCGAAATAATTAACCATAGATCATTGAAACAC
genomic: GCCGCACCACCGAACTCGTCGCCGTCAAGTACATCGAGCGTGGCGAGAAGgtatcgcgct ... tcatttgcagATAGATGAGAATGTCCAGCGCGAAATAATTAACCATAGATCATTGAAACAC

EST: gi|211499759|gb|FL295247.1|FL295247

EST:     G-CGCACCACCGAACTCGTCGCCGTCAAGTACATCGAGCGTGGCGAGAAG                         ATAGATGAGAATGTCCAGCGCGAAATAATTAACCATAGATCATTGAAACAC
genomic: GCCGCACCACCGAACTCGTCGCCGTCAAGTACATCGAGCGTGGCGAGAAGgtatcgcgct ... tcatttgcagATAGATGAGAATGTCCAGCGCGAAATAATTAACCATAGATCATTGAAACAC

EST: gi|148932906|gb|EE285698.2|EE285698

EST:     GCCGCACCACCGAACTCGTCGCCGTCAAGTACATCGAGCGTGGCGAGAAG                         ATAGATGAGAATGTCCAGCGCGAAATAATTAACCATAGATCATTGAAACAC
genomic: GCCGCACCACCGAACTCGTCGCCGTCAAGTACATCGAGCGTGGCGAGAAGgtatcgcgct ... tcatttgcagATAGATGAGAATGTCCAGCGCGAAATAATTAACCATAGATCATTGAAACAC

EST: gi|211204702|gb|FL178018.1|FL178018

EST:     GCCGCACCACCGAACTCGTCGCCGTCAAGTACATCGAGCGTGGCGAGAAG                         ATAGATGAGAATGTCCAGCGCGAAATAATTAACCATAGATCATTGAAACAC
genomic: GCCGCACCACCGAACTCGTCGCCGTCAAGTACATCGAGCGTGGCGAGAAGgtatcgcgct ... tcatttgcagATAGATGAGAATGTCCAGCGCGAAATAATTAACCATAGATCATTGAAACAC

EST: gi|211214981|gb|FL178065.1|FL178065

EST:     GCCGCACCACCGAACTCGTCGCCGTCAAGTACATCGAGCGTGGCGAGAAG                         ATAGATGAGAATGTCCAGCGCGAAATAATTAACCATAGATCATTGA
genomic: GCCGCACCACCGAACTCGTCGCCGTCAAGTACATCGAGCGTGGCGAGAAGgtatcgcgct ... tcatttgcagATAGATGAGAATGTCCAGCGCGAAATAATTAACCATAGATCATTGA

EST: gi|78107855|gb|DV526273.1|DV526273

EST:     GCCGCACCACCGAACTCGTCGCCGTCAAGTACATCGAGCGTGGCGAGAAG                         ATAGATGAGAATGTCCAGCGCGAAATAATTAACCATAGATCATTGAAACAC
genomic: GCCGCACCACCGAACTCGTCGCCGTCAAGTACATCGAGCGTGGCGAGAAGgtatcgcgct ... tcatttgcagATAGATGAGAATGTCCAGCGCGAAATAATTAACCATAGATCATTGAAACAC

EST: gi|211108565|gb|FL429107.1|FL429107

EST:     GCGGCACCACCGAACTCGTCGCCGTCAAGTACATCGAGCGTGGCGAGAAG                         ATAGATGAGAATGTCCAGCGCGAAATAATTAACCATAGATCATTGAAACAC
genomic: GCCGCACCACCGAACTCGTCGCCGTCAAGTACATCGAGCGTGGCGAGAAGgtatcgcgct ... tcatttgcagATAGATGAGAATGTCCAGCGCGAAATAATTAACCATAGATCATTGAAACAC

EST: gi|211166134|gb|FL157545.1|FL157545

EST:     GCCGCACCACCGAACTCGTCGCCGTCAAGTACATCGAGCGTGGCGAGAAG                         ATAGATGAGAATGTCCAGCGCGAAATAATTAACCATAGATCATTGAAACAC
genomic: GCCGCACCACCGAACTCGTCGCCGTCAAGTACATCGAGCGTGGCGAGAAGgtatcgcgct ... tcatttgcagATAGATGAGAATGTCCAGCGCGAAATAATTAACCATAGATCATTGAAACAC

RNA-Seq data

ATGC Supported by RNA-Seq exonic block that spans over the splice site

atgs Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.

Found data for 4 RNA-Seq libraries.

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 131

GCGCGACATCGGCTCCGGCAACTTCGGCGTTGCCCGCCTCATGCGCGACCGCCGCACCACCGAACTCGTCGCCGTCAAGTACATCGAGCGTGGCGAGAAGgtatcgcgct ... tcatttgcagATAGATGAGAATGTCCAGCGCGAAATAATTAACCATAGATCATTGAAACACCCTAACATTATTAGGTTTAAAGAG

Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 96

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 149