ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

ATCAGCCTTGTCGACAATATAATCCTTGTGGTTGTCAATCTACATGCGGAAAGCAGTGTCCATGTCTTTCAAATGGGACATGTTGTGAGAAATACTGTGGgtgagttacatgttttctttgcatcagcctattagcatgcataaatttggttgtcaatctgcatgtggaaaccagtgtccatgtcttacaaatgggacac...

Basic information

species	Zea mays
transcript	GRMZM2G157820_T02
intron #	11
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G157820_T02 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os06g16390.1 (Oryza sativa), 5'ss of exon 11

ATCAGCCTTGTCGACAATATAATCCTTGTGGTTGTCAATCTACATGCGGAAAGCAGTGTCCATGTCTTTCAAATGGGACATGTTGTGAGAAATACTGTGGgtgagttacatgttttctttgcat--cagcctattag--catgcataaatttggttgtcaat----ctgcatgtggaaaccagtgtccat-gtcttacaaatgggacac
||||||||||||||||||| | |||||||||||| || ||| |||| || ||||| |||||||||||  ||||||| || || |||||||||||||||||||||| ||| |   || ||   ||  ||| ||   ||  |||   |   | | | | | |||     ||| | || |||| |   |   | |   || |          
ATCAGCCTTGTCGACAATACACTCCTTGTGGTTGCCAGTCTGCATGTGGGAAGCAATGTCCATGTCTCACAAATGGTACCTGCTGTGAGAAATACTGTGGgtgagctacttcaattattcatattgcagactccgagaacattttttcttctagatattaataatgttgcttatgaaaacaaaactgtgtagatgtatac---------

upper sequence: GRMZM2G157820_T02 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA11G05760.1 (Glycine max), 5'ss of exon 13

ATCAGCCTTGTCGACAATATAATCCTTGTGGTTGTCAATCTACATGCGGAAAGCAGTGTCCATGTCTTTCAAATGGGACATGTTGTGAGAAATACTGTGGgtgag-ttacatgttttctttgcatcagcctattagcatgcataaatttggttgtcaatctgcatgtggaaaccagtgtccatgtcttacaaatgggacac---
|||| || || ||||| |||||||| |||||||| ||| |  | || |||||||||||||| ||||||  |||||| || || |||||||| |||||||||| || ||    | || ||    |  | | |  |   |   |   |||| |   |  |   |  | |||  |    | | |||  |   |   |   |||    
ATCAACCCTGCCGACAGTATAATCCATGTGGTTGCCAAACGGCTTGTGGAAAGCAGTGTCCTTGTCTTCAAAATGGAACCTGCTGTGAGAAGTACTGTGGgtaagcttttgaggttgctaaatagaaccttgatgaaagagaggcatttagaattgta---gtgtttggggattt-tctacattccacgctggtttcacaaatt

upper sequence: GRMZM2G157820_T02 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA01G39490.1 (Glycine max), 5'ss of exon 13

ATCAGCCTTGTCGACAATATAATCCTTGTGGTTGTCAATCTACATGCGGAAAGCAGTGTCCATGTCTTTCAAATGGGACATGTTGTGAGAAATACTGTGGgtgag-ttacatgttttctttgcatcagcctatta--------gcatgcataaatttggttgtcaatctgcatgtggaaaccagtgtccatgtcttacaaatgggacac
|||||||||| || || |||||||| |||||||| |||||  | || |||||||||||||| ||||||  |||||| || || |||||||| |||||||||| || ||    | || ||    |  | | |  |         ||||| | || | | ||  |         |   | |  |  ||     || | ||||||       
ATCAGCCTTGCCGGCAGTATAATCCATGTGGTTGCCAATCGGCTTGTGGAAAGCAGTGTCCTTGTCTTCAAAATGGAACCTGCTGTGAGAAGTACTGTGGgtaagcttttgaggttgctaaatagaaccttgatgaaagagaggcatgtagaattgtagtgttttgctgattttctgcattccatgct--ggtttcacaaat-------

upper sequence: GRMZM2G157820_T02 (Zea mays), 5'ss of exon 11
lower sequence: Vv07s0031g00320.t01 (Vitis vinifera), 5'ss of exon 9

ATCAGCCTTGTCGACAATATAATCCTTGTGGTTGTCAATCTACATGCGGAAAGCAGTGTCCATGTCTTTCAAATGGGACATGTTGTGAGAAATACTGTGGgtgagt-tacatgttttctttgcatcagcctattagcatgcataaatttggttgtca-atctgcatgtggaaaccagtgtccatgtcttacaaatgggacac
||||||||||||| || || || || |||||||| |||||| |||| |||||||||||| | ||||||  |||||||||||| ||||| ||||||||||||||||  |   | | |  ||   |  |||  |  |  |   ||||| |   ||     || | ||| |   ||      ||||    |  | ||      | 
ATCAGCCTTGTCGGCAGTACAACCCATGTGGTTGCCAATCTGCATGTGGAAAGCAGTGTGCTTGTCTTCTAAATGGGACATGCTGTGAAAAATACTGTGGgtgagcctttgtttctcattctgaatagcacagaattaaatataaactcatttcctggattttcatttcccaatt--cttccaaaaatggccaagtactgat

upper sequence: GRMZM2G157820_T02 (Zea mays), 5'ss of exon 11
lower sequence: Vv07s0031g00320.t01 (Vitis vinifera), 5'ss of exon 9

ATCAGCCTTGTCGACAATATAATCCTTGTGGTTGTCAATCTACATGCGGAAAGCAGTGTCCATGTCTTTCAAATGGGACATGTTGTGAGAAATACTGTGGgtgagt-tacatgttttctttgcatcagcctattagcatgcataaatttggttgtca-atctgcatgtggaaaccagtgtccatgtcttacaaatgggacac
||||||||||||| || || || || |||||||| |||||| |||| |||||||||||| | ||||||  |||||||||||| ||||| ||||||||||||||||  |   | | |  ||   |  |||  |  |  |   ||||| |   ||     || | ||| |   ||      ||||    |  | ||      | 
ATCAGCCTTGTCGGCAGTACAACCCATGTGGTTGCCAATCTGCATGTGGAAAGCAGTGTGCTTGTCTTCTAAATGGGACATGCTGTGAAAAATACTGTGGgtgagcctttgtttctcattctgaatagcacagaattaaatataaactcatttcctggattttcatttcccaatt--cttccaaaaatggccaagtactgat

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|18385061|gb|BM418260.1|BM418260

EST:     GCAGTGTCCATGTCTTTCAAATGGGACATGTTGTGTAGAAATACTGTGG                         GTGTCCAAAAATTTGCAAGAATCGTTTTCGAGGATGTCACTGTGCAAAGAG
genomic: GCAGTGTCCATGTCTTTCAAATGGGACATGTTGTG-AGAAATACTGTGGgtgagttaca ... gtgcattcagGTGTCCAAAAATTTGCAAGAATCGTTTTCGAGGATGTCACTGTGCAAAGAG

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: 156

ATCAGCCTTGTCGACAATATAATCCTTGTGGTTGTCAATCTACATGCGGAAAGCAGTGTCCATGTCTTTCAAATGGGACATGTTGTGAGAAATACTGTGGgtgagttaca ... gtgcattcagGTGTCCAAAAATTTGCAAGAATCGTTTTCGAGGATGTCACTGTGCAAAGAGCCAGTGTCGCAGCCGCCAATGTCCATGTTTTGCAGCTGACAGGGAATGC

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 39

Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 17