ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

AGAGGTGAAGCTAAACTTCTCTCAGAAGATTGGGAAGGAGCAGTTCAGGATTTAAAAGAGGCCGCCCAGAAATCTCCACAGgtattatatttggcctgaaagcacaaaatttgggtggtatagctcttgcattttgttcttttcctgacattgtcacccccaaaacaacaccaacagacac...

Basic information

species	Zea mays
transcript	GRMZM2G341404_T01
intron #	8
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G341404_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os02g10180.1 (Oryza sativa), 5'ss of exon 8

AGAGGTGAAGCTAAACTTCTCTCAGAAGATTGGGAAGGAGCAGTTCAGGATTTAAAAGAGGCCGCCCAGAAATCTCCACAGgtattatatttggcctgaaagcacaaaatttgggtggtatagctcttgcattttgttctt--ttcctgacattgt-cacccccaaaacaacaccaacagacac
|||||||||||||| |||||  ||||||| ||||||||||| ||||||||| |||||||||| |||||||||||||| |||| |     |||    || |   |     |||      ||     || |     ||||     |   ||   |  |  | |  || | |  |       | |  
AGAGGTGAAGCTAAGCTTCTTACAGAAGACTGGGAAGGAGCGGTTCAGGATCTAAAAGAGGCTGCCCAGAAATCTCCCCAGgcaa---gttttatgtggacctatctcctttttcccctaccctcctaggcaaatgttagggataagtgtgctcatatatcagcatatcttctttttttgtcct

upper sequence: GRMZM2G341404_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os01g74580.1 (Oryza sativa), 5'ss of exon 7

AGAGGTGAAGCTAAACTTCTCTCAGAAGATTGGGAAGGAGCAGTTCAGGATTTAAAAGAGGCCGCCCAGAAATCTCCACAGgta--ttatatttggcctgaaagc-------acaaaatttgggtggtatagctcttgcat---tttgttcttttcctgacattgtcacccccaaaacaacaccaacagacac
|||||||||||||| |||||  ||||||| ||||||||||| ||||||||| ||||||| ||  ||||||||||||| |||| |  || ||| ||| |  |   |        |  |   |    || | |  |   | ||   | || || | |     |||     |        |               
AGAGGTGAAGCTAAGCTTCTTACAGAAGACTGGGAAGGAGCGGTTCAGGATCTAAAAGAAGCTTCCCAGAAATCTCCCCAGgcaagttttatgtggacctatctcttttttcccctaccctcctaggcaaatgttagggataagtgtgctcatatatcagcatatcttcttttttgtcgtt------------

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|60394505|gb|DN227375.1|DN227375

EST:     GGGAAGGAGCAGTTCAGGATTTAAAAGAGGCCGCCCAGAAATCTCCACAG                         GACATGGGTATCCGTGAAGCACTTATGAGAGCTGAAAAGCAGCTTAAGTTG
genomic: GGGAAGGAGCAGTTCAGGATTTAAAAGAGGCCGCCCAGAAATCTCCACAGgtattatatt ... taacaaccagGACATGGGTATCCGTGAAGCACTTATGAGAGCTGAAAAGCAGCTTAAGTTG

EST: gi|26456221|gb|CA827804.1|CA827804

EST:     GGGAAGGAGCAGTTCAGGATTTAAAAGAGGCCGCCCAGAAATCTCCACAG                         GACATGGGTATCCGTGAAGCACTTATGAGAGCTGAAAAGCAGCTTAAGTTG
genomic: GGGAAGGAGCAGTTCAGGATTTAAAAGAGGCCGCCCAGAAATCTCCACAGgtattatatt ... taacaaccagGACATGGGTATCCGTGAAGCACTTATGAGAGCTGAAAAGCAGCTTAAGTTG

EST: gi|86468537|gb|DY234907.1|DY234907

EST:     GAGCAGTTCAGGATTTAAAAGAGGCCGCCCAGAAATCTCCACAG                         GACATGGGTATCCGTGAAGCACTTATGAGAGCTGAAAAGCAGCTTAAGTTG
genomic: GAGCAGTTCAGGATTTAAAAGAGGCCGCCCAGAAATCTCCACAGgtattatatt ... taacaaccagGACATGGGTATCCGTGAAGCACTTATGAGAGCTGAAAAGCAGCTTAAGTTG

EST: gi|71323580|gb|DR798458.1|DR798458

EST:     GGGAAGGAGCAGTTCAGGATTTAAAAGAGGCCGCCCAGAAATCTCCACAG                         GACATGGGTATCCGTGAAGCACTTATGAGAGCTGAAAAGCAGCTTAAGTTG
genomic: GGGAAGGAGCAGTTCAGGATTTAAAAGAGGCCGCCCAGAAATCTCCACAGgtattatatt ... taacaaccagGACATGGGTATCCGTGAAGCACTTATGAGAGCTGAAAAGCAGCTTAAGTTG

EST: gi|78104564|gb|DV522982.1|DV522982

EST:     GGGAAGGAGCAGTTCAGGATTTAAAAGAGGCCGCCCAGAAATCTCCACAG                         GACATGGGTATCCGTGAAGCACTTATGAGAGCTGAAAAGCAGCTTAAGTTG
genomic: GGGAAGGAGCAGTTCAGGATTTAAAAGAGGCCGCCCAGAAATCTCCACAGgtattatatt ... taacaaccagGACATGGGTATCCGTGAAGCACTTATGAGAGCTGAAAAGCAGCTTAAGTTG

EST: gi|78543655|gb|DV621153.1|DV621153

EST:     GGGAAGGAGCAGTTCAGGATTTAAAAGAGGCCGCCCAGAAATCTCCACAG                         GACATGGGTATCCGTGAAGCACTTATGAGAGCTGAAAAGCAGCTTAAGTTG
genomic: GGGAAGGAGCAGTTCAGGATTTAAAAGAGGCCGCCCAGAAATCTCCACAGgtattatatt ... taacaaccagGACATGGGTATCCGTGAAGCACTTATGAGAGCTGAAAAGCAGCTTAAGTTG

EST: gi|78080723|gb|DV509135.1|DV509135

EST:     GGGAAGGAGCAGTTCAGGATTTAAAAGAGGCCGCCCAGAAATCTCCACAG                         GACATGGGTATCCGTGAAGCACTTATGAGAGCTGAAAAGCAGCTTAAGTTG
genomic: GGGAAGGAGCAGTTCAGGATTTAAAAGAGGCCGCCCAGAAATCTCCACAGgtattatatt ... taacaaccagGACATGGGTATCCGTGAAGCACTTATGAGAGCTGAAAAGCAGCTTAAGTTG

EST: gi|91875153|gb|EB405110.1|EB405110

EST:     GGGAAGGAGCAGTTCAGGATTTAAAAGAGGCCGCCCAGAAATCTCCACAG                         GACATGGGTATCCGTGAAGCACTTATGAGAGCTGAAAAGCAGCTTAAGTTG
genomic: GGGAAGGAGCAGTTCAGGATTTAAAAGAGGCCGCCCAGAAATCTCCACAGgtattatatt ... taacaaccagGACATGGGTATCCGTGAAGCACTTATGAGAGCTGAAAAGCAGCTTAAGTTG

EST: gi|26456078|gb|CA827661.1|CA827661

EST:     GGGAAGGAGCAGTTCAGGATTTAAAAGAGGCCGCCCAGAAATCTCCACAG                         GACATGGGTATCCGTGAAGCACTTATGAGAGCTGAAAAGCAGCTTAAGTTG
genomic: GGGAAGGAGCAGTTCAGGATTTAAAAGAGGCCGCCCAGAAATCTCCACAGgtattatatt ... taacaaccagGACATGGGTATCCGTGAAGCACTTATGAGAGCTGAAAAGCAGCTTAAGTTG

EST: gi|60350920|gb|DN217893.1|DN217893

EST:     GGGAAGGAGCAGTTCAGGATTTAAAAGAGGCCGCCCAGAAATCTCCACAG                         GACATGGGTATCCGTGAAGCACTTATGAGAGCTGAAAAGCAGCTTAAGTTG
genomic: GGGAAGGAGCAGTTCAGGATTTAAAAGAGGCCGCCCAGAAATCTCCACAGgtattatatt ... taacaaccagGACATGGGTATCCGTGAAGCACTTATGAGAGCTGAAAAGCAGCTTAAGTTG

EST: gi|67016841|gb|CO445590.1|CO445590

EST:     GNGAANGAGCAGTTCAGGATTTAAAAGAGGCCGCCCAGAAATCTC-ACAG                         GACATGGGTATCCGTGAA-CACTTATGAGAGCTGAAAA-CAGCTTAAGT-G
genomic: GGGAAGGAGCAGTTCAGGATTTAAAAGAGGCCGCCCAGAAATCTCCACAGgtattatatt ... taacaaccagGACATGGGTATCCGTGAAGCACTTATGAGAGCTGAAAAGCAGCTTAAGTTG

EST: gi|149010181|gb|EE041996.2|EE041996

EST:     ATTTAAAAGAGGCCGCCCAGAAATCTCCACAG                         GACATGGGTATCCGTGAAGCACTTATGAGAGCTGAAAAGCAGCTTAAGTTG
genomic: ATTTAAAAGAGGCCGCCCAGAAATCTCCACAGgtattatatt ... taacaaccagGACATGGGTATCCGTGAAGCACTTATGAGAGCTGAAAAGCAGCTTAAGTTG

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: 39 (upstream exon), 49 (downstream exon)
Score: 111

AGAGGTGAAGCTAAACTTCTCTCAGAAGATTGGGAAGGAGCAGTTCAGGATTTAAAAGAGGCCGCCCAGAAATCTCCACAGgtattatatt ... taacaaccagGACATGGGTATCCGTGAAGCACTTATGAGAGCTGAAAAGCAGCTTAAGTTGAGCAAAAGAAAAGACTGGTATAAAATCCTTGGTGTTTCAAAGACAGCAT

Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 54

Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 28

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 209

Putative cis-regulatory sequences

atgc	intron	ATGC	exonic elements by Pertea et al.
ATGC	exon	atgc	putative intronic elements
		ATGC	putative exonic elements identified for retained introns

        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAGGTGAAGCTAAACTTCTCTCAGAAGATTGGGAAGGAGCAGTTCAGGATTTAAAAGAGGCCGCCCAGAAATCTCCACAGgtattatatttggcctgaaagcacaaaatttgggtggtatagctcttgcattttgttcttttcctgacattgtcacccccaaaacaacaccaacagacac

- - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcacaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caccccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaacaac