ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

CCTCCCTATGTTCAGGTTAAAAGGAAGAAAGCTAAACATGCCGGGATGTTTGATATTGCCAAGACAGCAAATAGACCCATGATACATATAGGTGGCTGAGgtatcctcttatcaacatctgtacatttttactacaatgactatgtaatagattgttcacggacatgacaagattgatatttgagatgatttatcgcatg...

Basic information

species	Zea mays
transcript	GRMZM2G135816_T02
intron #	1
splice site	5'
intron type	U12 (go to U12 genes for details)

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G135816_T02 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os02g15870.2 (Oryza sativa), 5'ss of exon 6

CCTCCCTATGTTCAGGTTAAAAGGAAGAAAGCTAAACATGCCGGGATGTTTGATATTGCCAAGACAGCAAATAGACCCATGATACATATAGGTGGCTGAGgtatcctcttatcaacatctgtacatttttactac--aatgactatgtaatagattgttcacggacatgacaagattgatatttgagatgatt-tatcgcatg
 ||  || |   ||||||||||||||||||||||||||||| ||||||||||||||||| ||||| ||||||||||| ||||| || || ||||||||||||||| ||||| ||     | |||  |||   ||   ||  |  |  | |||| || ||    ||     ||   |    | |  | ||  || ||| |    
ACTTACTTTACCCAGGTTAAAAGGAAGAAAGCTAAACATGCTGGGATGTTTGATATTGCTAAGACGGCAAATAGACCTATGATTCACATTGGTGGCTGAGgtatcttcttaacactgcttctaccctttgtttaataaagaaagaattgatagtttctttgaagattatccattttcttcactcaacattgttctattgg---

upper sequence: GRMZM2G135816_T02 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os02g15870.3 (Oryza sativa), 5'ss of exon 7

CCTCCCTATGTTCAGGTTAAAAGGAAGAAAGCTAAACATGCCGGGATGTTTGATATTGCCAAGACAGCAAATAGACCCATGATACATATAGGTGGCTGAGgtatcctcttatcaacatctgtacatttttactac--aatgactatgtaatagattgttcacggacatgacaagattgatatttgagat-gatttatcgcatg
               |||||||||||||||||||||||||| ||||||||||||||||| ||||| ||||||||||| ||||| || || ||||||||||||||| ||||| ||     | |||  |||   ||   ||  |  |  | |||| || ||    ||     ||   |    | |  | || | | ||| |    
---------------GTTAAAAGGAAGAAAGCTAAACATGCTGGGATGTTTGATATTGCTAAGACGGCAAATAGACCTATGATTCACATTGGTGGCTGAGgtatcttcttaacactgcttctaccctttgtttaataaagaaagaattgatagtttctttgaagattatccattttcttcactcaacattgttctattgg---

upper sequence: GRMZM2G135816_T02 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os12g32230.1 (Oryza sativa), 5'ss of exon 7

CCTCCCTATGTTCAGGTTAAAAGGAAGAAAGCTAAACATGCCGGGATGTTTGATATTGCCAAGACAGCAAATAGACCCATGATACATATAGGTGGCTGAGgtatcctcttatcaacatctgtacatttttactacaatgactatgtaatagattgttcac--ggacatgacaagattgat---atttgagatgatttatcgcatg
               ||||||||||||||||||||||| || ||||||||||||||||| ||||||||||||||||| ||||| || || ||||||||||||||| ||||| || |   | ||  |  ||  |  | | |  |   ||| |||  ||     | |||| ||    ||  |    |   | |   | ||| |    
---------------GTTAAAAGGAAGAAAGCTAAACACGCTGGGATGTTTGATATTGCTAAGACAGCAAATAGACCTATGATTCACATTGGTGGCTGAGgtatcttcttaacaccgcttctat-tcgttgtttaattaaggaaagaattgataatttctttgaacattacccattttcttcgctcaaaaacattctattg----

upper sequence: GRMZM2G135816_T02 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA15G42290.1 (Glycine max), 5'ss of exon 6

CCTCCCTATGTTCAGGTTAAAAGGAAGAAAGCTAAACATGCCGGGATGTTTGATATTGCCAAGACAGCAAATAGACCCATGATACATATAGGTGGCTGAGgt------atcctcttatcaacatctgtacatttttactacaatgactatgtaatagattgttcacggacatgacaag--attgatatttgagatgatttatcgcatg
               || || ||||||||||||  |||||| || |||||||| || || ||||| |||||||| |||||||||||||| ||||| | ||||      ||| |    |  ||   |  |  ||||| ||| |||   ||| | | |  ||  | | | |||  |  |    |   ||||| ||               
---------------GTGAAGAGGAAGAAAGCTTCACATGCTGGTATGTTTGACATAGCAAAGACTGCAAATAGGCCCATGATACATATTGGTGGATAAGgtctgttcatctttccttttaccaataaaggtttttcctaaaatatttattttacaatttactgaggcacacaatgatttgtctctatttcag---------------

upper sequence: GRMZM2G135816_T02 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA08G16780.1 (Glycine max), 5'ss of exon 6

CCTCCCTATGTTCAGGTTAAAAGGAAGAAAGCTAAACATGCCGGGATGTTTGATATTGCCAAGACAGCAAATAGACCCATGATACATATAGGTGGCTGAGgt------atcctcttatcaacatctgtacatttttactacaatgactatgtaatagattgttcacggacatgacaagattgatatttgagatgatttatcgcatg
               || || ||||||||||||  |||||| || ||||| || || || ||||| |||||||| || ||||||||||| ||||| | ||||      ||| |    || ||   |  |  ||||| ||| |||    || |  || | |        |||  ||    |   ||||| ||               
---------------GTGAAGAGGAAGAAAGCTTCACATGCTGGTATGTTCGACATAGCAAAGACTGCAAATAGGCCTATGATACATATTGGTGGATAAGgtctgttcatctttccttctactaataaaggtttttcctaaaatattcatct--tacaatagggggatacaatactttgtctctatttcag---------------

upper sequence: GRMZM2G135816_T02 (Zea mays), 5'ss of exon 1
lower sequence: Vv13s0156g00170.t01 (Vitis vinifera), 5'ss of exon 8

CCTCCCTATGTTCAGGTTAAAAGGAAGAAAGCTAAACATGCCGGGATGTTTGATATTGCCAAGACAGCAAATAGACCCATGATACATATAGGTGGCTGAGgtatc-ctcttatcaacatctgtacatttttactacaatgactatgtaatagattgttcacggacatgacaagattgatatttgagatgatttatcgcatg-
               || || ||||||||||||   ||||| || |||||||| ||||| ||||| |||||||| |||||||||||||| ||||||| |||| |   |||   |  || ||  | | || | || ||   | ||  | | | || ||  |   ||||    | |  | |   |  | |  |||  |   |  
---------------GTCAAGAGGAAGAAAGCTTCTCATGCTGGAATGTTTGACATTGCAAAGACCGCAAATAGGCCCATGATACATATTGGTGGCTAAGgtttggttctctcctccaactagaaacttgtcctgcatccattaaatgagatat-gtaaaactacattcttaaagggctgcctt-gttcttttcccctttaa

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|211275415|gb|FL065994.1|FL065994

EST:     TGATATTGCCAAGACAGCAAATAGACCCATGATACATATAGGTGGCTGAG                         GTGTGCAGAATTTCCTCATGTCGAATATGAGCCAATAAAATGGATTTGCCA
genomic: TGATATTGCCAAGACAGCAAATAGACCCATGATACATATAGGTGGCTGAGgtatcctctt ... ttggaatcagGTGTGCAGAATTTCCTCATGTCGAATATGAGCCAATAAAATGGATTTGCCA

EST: gi|211121393|gb|FL463011.1|FL463011

EST:     TGATATTGCCAAGACWGCAAATAGACCCATGATACATATAGGTGGCTGAG                         GTGTGCAGAATTTCCTCATGTCGAATATGAGCCAATAAAATGGATTTGCCA
genomic: TGATATTGCCAAGACAGCAAATAGACCCATGATACATATAGGTGGCTGAGgtatcctctt ... ttggaatcagGTGTGCAGAATTTCCTCATGTCGAATATGAGCCAATAAAATGGATTTGCCA

EST: gi|161590185|gb|EY959342.1|EY959342

EST:     GATATTGCCAAGACAGCAAAATAGACCCATGATACATATAGGTGGCTGAG                         GTGTGCAGAATTTCCTCATGTCGAATA
genomic: GATATTGCCAAGACAGC-AAATAGACCCATGATACATATAGGTGGCTGAGgtatcctctt ... ttggaatcagGTGTGCAGAATTTCCTCATGTCGAATA

EST: gi|211275416|gb|FL065995.1|FL065995

EST:     TGATATTGCMAAGACAGCAAATAGACCCATGATACATATAGGTGGCTGAG                         GTGTGCAGAATTTCCTCATGTCGAATATGAGCCAATAAAATGGATTTGCCA
genomic: TGATATTGCCAAGACAGCAAATAGACCCATGATACATATAGGTGGCTGAGgtatcctctt ... ttggaatcagGTGTGCAGAATTTCCTCATGTCGAATATGAGCCAATAAAATGGATTTGCCA

EST: gi|211275417|gb|FL065996.1|FL065996

EST:     TGATATTGCCAAGACAGCAAATAGACCCATGATACATATAGGTGGCTGAG                         GTGTGCAGAATTTCCTCATGTCGAATATGAGCCAATAAAATGGATTTGCCA
genomic: TGATATTGCCAAGACAGCAAATAGACCCATGATACATATAGGTGGCTGAGgtatcctctt ... ttggaatcagGTGTGCAGAATTTCCTCATGTCGAATATGAGCCAATAAAATGGATTTGCCA

EST: gi|24764636|gb|CA399800.1|CA399800

EST:     TGATATTGCCAAGACAGCAAATAGACCCATGATACATATAGGTGGCTGAG                         GTGTGCAGAATTTCCTCATGTCGAATATGAGCCAATAAAATGGATTTGCCA
genomic: TGATATTGCCAAGACAGCAAATAGACCCATGATACATATAGGTGGCTGAGgtatcctctt ... ttggaatcagGTGTGCAGAATTTCCTCATGTCGAATATGAGCCAATAAAATGGATTTGCCA

EST: gi|71449820|gb|DR830870.1|DR830870

EST:     TGATATTGCCAAGACAGCAAATAGACCCATGATACATATAGGTGGGTGAG                         GTGTGCAGAATTTCCTCATGTCGAATATGAGCCAATAAAATGGATTTGCCA
genomic: TGATATTGCCAAGACAGCAAATAGACCCATGATACATATAGGTGGCTGAGgtatcctctt ... ttggaatcagGTGTGCAGAATTTCCTCATGTCGAATATGAGCCAATAAAATGGATTTGCCA

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: 45 (upstream exon), 41 (downstream exon)
Score: 16

CCTCCCTATGTTCAGGTTAAAAGGAAGAAAGCTAAACATGCCGGGATGTTTGATATTGCCAAGACAGCAAATAGACCCATGATACATATAGGTGGCTGAGgtatcctctt ... ttggaatcagGTGTGCAGAATTTCCTCATGTCGAATATGAGCCAATAAAATGGATTTGCCAACTGCTGGGTTGCTGCCTGGTTTTACCTGAACGACCATGAAAAAGTTCT

Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 121

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 130