ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

TGAGAGCGGAGGAATAATCAATATGATGGGCACTTATCAGATAGCTCTTGTGGCTCATACTATGGACAAACCTGTTTATGTGGCAGCTGAAAGCTACAAGgtaatgcatgttatgataatgtacttcaataatatattatccttgtttcactcatcttatttctttgcatcattacttttgtaatttaatgaatttggta...

Basic information

species	Zea mays
transcript	GRMZM2G084647_T01
intron #	4
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G084647_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os12g31380.1 (Oryza sativa), 5'ss of exon 4

TGAGAGCGGAGGAATAATCAATATGATGGGCACTTATCAGATAGCTCTTGTGGCTCATACTATGGACAAACCTGTTTATGTGGCAGCTGAAAGCTACAAGgtaatg-cat-gttatgataatgtacttcaataatatattatccttgtttcactcatcttatttctttgcatcattacttttgta-atttaatgaatttggta
||| || ||||||||||||||||||||||||||||||||||||||||| || ||||| | |||| ||||||||||||||||||| |||||||| |||||||||||  ||| | | |  | || |  || |   ||    | | |   | | |  |   ||  | ||    ||   ||   | |||     ||  ||| |  ||
TGAAAGTGGAGGAATAATCAATATGATGGGCACTTATCAGATAGCTCTCGTCGCTCACAGTATGAACAAACCTGTTTATGTGGCTGCTGAAAGTTACAAGgtaataacattgcttttctcatattgttgatcgatgagctcttccgttgttatgc---ttggtactagaaatatataaggtggtacgcagaaaaaatctccta

upper sequence: GRMZM2G084647_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA03G42430.1 (Glycine max), 5'ss of exon 4

TGAGAGCGGAGGAATAATCAATATGATGGGCACTTATCAGATAGCTCTTGTGGCTCATACTATGGACAAACCTGTTTATGTGGCAGCTGAAAGCTACAAGgtaatgcatgttatgataatgtacttcaataatatattatccttgtttcactcatcttatttctttgcatcattacttttgtaatttaatgaatttggta
 || || || || |||||||| |||||||| || ||||| |||||  | || ||||| | |||| | ||||| |||||||| || ||||| |||||||||||| |   ||  |||      | |||   | |   ||||      |||   |  |||| |||    |  | | |     || |                 
CGAAAGTGGGGGCATAATCAACATGATGGGGACCTATCAAATAGCATTGGTTGCTCACAGTATGAATAAACCAGTTTATGTCGCTGCTGAGAGCTACAAGgta-tatttgc-atgcattcatccttttttgacgaattagg--aatttatgttgtcttgttt----gtgttactgtgcctgcag----------------

upper sequence: GRMZM2G084647_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA07G05070.1 (Glycine max), 5'ss of exon 4

TGAGAGCGGAGGAATAATCAATATGATGGGCACTTATCAGATAGCTCTTGTGGCTCATACTATGGACAAACCTGTTTATGTGGCAGCTGAAAGCTACAAGgtaa---tgcatgttatgataatgtacttcaataatatattatccttgtttcactcatctt--atttctttgcatcattacttttgtaatttaatgaatttggta
||| || || || |||||||| |||||||| ||||| || ||  |  | || ||| | | ||||  ||| |||||||||||||| |||||||||||||||||||   ||||    |    |||         |  | |    |  ||| || |     |||  || | | ||||| | |  |  |     | | | |        
TGAAAGTGGTGGCATAATCAACATGATGGGGACTTACCAAATCTCATTGGTTGCTAAGAGTATGAGCAAGCCTGTTTATGTGGCTGCTGAAAGCTACAAGgtaagcttgcaacccacagaaattagtgaatgtggtgtgaagttgttgctttagaatgcttgcatctttctgcataaattgtcatactgatcagtaagaa-----

upper sequence: GRMZM2G084647_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv09s0002g00390.t01 (Vitis vinifera), 5'ss of exon 7

TGAGAGCGGAGGAATAATCAATATGATGGGCACTTATCAGATAGCTCTTGTGGCTCATACTATGGACAAACCTGTTTATGTGGCAGCTGAAAGCTACAAGgtaa--tgcatgttatgata-atgtacttcaataatatattatccttgtttcactcatcttatttctttgcatcattactt-ttgtaatttaatgaatttggta-
||| || ||||| ||||| || |||||||| || ||||| || ||  | |||||||| |  ||| ||||||| |||||||| || ||||||||||||||||||   || | |  |  | | |  | ||  |||| | |  ||      |      |  || ||||   | |  | | ||   |  | |  || |    || | | 
TGAAAGTGGAGGTATAATTAACATGATGGGGACATATCAAATCGCATTGGTGGCTCACAGCATGAACAAACCAGTTTATGTTGCTGCTGAAAGCTACAAGgtatgttgaaagaaaaaacataccttctgtaatagtctggtagaggaatcatcggctactgattttacttccacttgacaaatcatcacatactttgctttgcag

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|32928780|gb|CF033592.1|CF033592

EST:     TGGCTCATACTATGGACAAACCTGTTTATGTGGCAGCTGAAAGCTACAAG                         TTTGCTCGGCTATATCCCTTGGATCAAAAGGACATGACGCCAGCTCACCGA
genomic: TGGCTCATACTATGGACAAACCTGTTTATGTGGCAGCTGAAAGCTACAAGgtaatgcatg ... acttcggcagTTTGCTCGGCTATATCCCTTGGATCAAAAGGACATGACGCCAGCTCACCGA

EST: gi|71328055|gb|DR800674.1|DR800674

EST:     TGGCTCATACTATGGACAAACCTGTTTATGTGGCAGCTGAAAGCTACAAG                         TTTGTTCGGCTATATCCCTTGGATCAAAAGGACATGACGCCAGCTCCCCGC
genomic: TGGCTCATACTATGGACAAACCTGTTTATGTGGCAGCTGAAAGCTACAAGgtaatgcatg ... acttcggcagTTTGCTCGGCTATATCCCTTGGATCAAAAGGACATGACGCCAGCTCACCGA

EST: gi|76282990|gb|DV022558.1|DV022558

EST:     TGGCTCATACTATGGACAAACCTGTTTATGTGGCAGCTGAAAGCTACAAG                         TTTGTTCGGCTATATCCCTTGGATCAAAAGGACATGACGCCAGCTCACCGA
genomic: TGGCTCATACTATGGACAAACCTGTTTATGTGGCAGCTGAAAGCTACAAGgtaatgcatg ... acttcggcagTTTGCTCGGCTATATCCCTTGGATCAAAAGGACATGACGCCAGCTCACCGA

EST: gi|71758051|gb|DR955988.1|DR955988

EST:     TGGCTCATACTATGGACAAACCTGTTTATGTGGCAGCTGAAAGCTACAAG                         TTTGTTCGGCTATATCCCTTGGATCAAAAGGACATGACGCCAGCTCACCGA
genomic: TGGCTCATACTATGGACAAACCTGTTTATGTGGCAGCTGAAAGCTACAAGgtaatgcatg ... acttcggcagTTTGCTCGGCTATATCCCTTGGATCAAAAGGACATGACGCCAGCTCACCGA

EST: gi|78118155|gb|DV536542.1|DV536542

EST:     TGGCTCATACTATGGACAAACCTGTTTATGTGGCAGCTGAAAGCTACAAG                         TTTGCTCGGCTATATCCCTTGGATCAAAAGGACATGACGCCAGCTCCCCGA
genomic: TGGCTCATACTATGGACAAACCTGTTTATGTGGCAGCTGAAAGCTACAAGgtaatgcatg ... acttcggcagTTTGCTCGGCTATATCCCTTGGATCAAAAGGACATGACGCCAGCTCACCGA

EST: gi|78022010|gb|DV490397.1|DV490397

EST:     TGGCTCATACTATGGACAAACCTGTTTATGTGGCAGCTGAAAGCTACAAG                         TTTGCTCGGCTATATCCCTTGGATCAAAAGGACATGACGCCAGCTCACCGA
genomic: TGGCTCATACTATGGACAAACCTGTTTATGTGGCAGCTGAAAGCTACAAGgtaatgcatg ... acttcggcagTTTGCTCGGCTATATCCCTTGGATCAAAAGGACATGACGCCAGCTCACCGA

EST: gi|76928321|gb|DV171574.1|DV171574

EST:     TGGCTCATACTATGGACAAACCTGTTTATGTGGCAGCTGAAAGCTACAAG                         TTTGCTCGGCTATATCCCTTGGATCAAAAGGACATGACGCCAGCTCCCCGC
genomic: TGGCTCATACTATGGACAAACCTGTTTATGTGGCAGCTGAAAGCTACAAGgtaatgcatg ... acttcggcagTTTGCTCGGCTATATCCCTTGGATCAAAAGGACATGACGCCAGCTCACCGA

EST: gi|71762540|gb|DR960477.1|DR960477

EST:     TGGCTCATACTATGGACAAACCTGTTTATGTGGCAGCTGAAAGCTACAAG                         TTTGCTCGGCTATATCCCTTGGATCAAAAGGACATGACGCCAGCTCCCCGA
genomic: TGGCTCATACTATGGACAAACCTGTTTATGTGGCAGCTGAAAGCTACAAGgtaatgcatg ... acttcggcagTTTGCTCGGCTATATCCCTTGGATCAAAAGGACATGACGCCAGCTCACCGA

EST: gi|78105935|gb|DV524353.1|DV524353

EST:     TGGCTCATACTATGGACAAACCTGTTTATGTGGCAGCTGAAAGCTACAAG                         TTTGCTCGGCTATATCCCTTGGATCAAAAGGACATGACGCCAGCTCACCGA
genomic: TGGCTCATACTATGGACAAACCTGTTTATGTGGCAGCTGAAAGCTACAAGgtaatgcatg ... acttcggcagTTTGCTCGGCTATATCCCTTGGATCAAAAGGACATGACGCCAGCTCACCGA

EST: gi|211175941|gb|FL479913.1|FL479913

EST:     TGGCTCATACTATGGACAAACCTGTTTATGTGGCAGCTGAAAGCTACAAG                         TTTGCTCGGCTATATCCCTTGGATCAAAAGGACATGACGCCAGCTCACCGA
genomic: TGGCTCATACTATGGACAAACCTGTTTATGTGGCAGCTGAAAGCTACAAGgtaatgcatg ... acttcggcagTTTGCTCGGCTATATCCCTTGGATCAAAAGGACATGACGCCAGCTCACCGA

EST: gi|50337597|gb|CO532723.1|CO532723

EST:     TGGCTCATACTATGGACAAACCTGTTTATGTGGCAGCTGAAAGCTACAAG                         TTTGCTCGGCTATATCCCTTGGATCAAAAGGACATGACGCCAGCTCACCGA
genomic: TGGCTCATACTATGGACAAACCTGTTTATGTGGCAGCTGAAAGCTACAAGgtaatgcatg ... acttcggcagTTTGCTCGGCTATATCCCTTGGATCAAAAGGACATGACGCCAGCTCACCGA

EST: gi|71769908|gb|DR967845.1|DR967845

EST:     TGGCTCATACTATGGACAAACCTGTTTATGTGGCAGCTGAAAGCTACAAG                         TTTGCTCGGCTATATCCCTTGGATCAAAAGGACATGACGCCAGCTCACCGA
genomic: TGGCTCATACTATGGACAAACCTGTTTATGTGGCAGCTGAAAGCTACAAGgtaatgcatg ... acttcggcagTTTGCTCGGCTATATCCCTTGGATCAAAAGGACATGACGCCAGCTCACCGA

EST: gi|71764897|gb|DR962834.1|DR962834

EST:     TGGCTCATACTATGGACAAACCTGTTTATGTGGCAGCTGAAAGCTACAAG                         TTTGCTCGGCTATATCCCTTGGATCAAAAGGACATGACGCCAGCTCACCGA
genomic: TGGCTCATACTATGGACAAACCTGTTTATGTGGCAGCTGAAAGCTACAAGgtaatgcatg ... acttcggcagTTTGCTCGGCTATATCCCTTGGATCAAAAGGACATGACGCCAGCTCACCGA

EST: gi|6227189|gb|AW155718.1|AW155718

EST:     -GGCTCATACTATGGACAAACCTGTT-ATGTGGCAGCTGAAAGCTACAAG                         TT-GCTCGGCTATATCCC
genomic: TGGCTCATACTATGGACAAACCTGTTTATGTGGCAGCTGAAAGCTACAAGgtaatgcatg ... acttcggcagTTTGCTCGGCTATATCCC

EST: gi|60348428|gb|DN215401.1|DN215401

EST:     TGGCTCATACTATGGACAAACCTGTTTATGTGGCAGCTGAAAGCTACAAG                         TTTGCTCGGCTATATCCCTTGGATCAAAAGGACATGACGCCAGCTCACCGA
genomic: TGGCTCATACTATGGACAAACCTGTTTATGTGGCAGCTGAAAGCTACAAGgtaatgcatg ... acttcggcagTTTGCTCGGCTATATCCCTTGGATCAAAAGGACATGACGCCAGCTCACCGA

EST: gi|211376349|gb|FL146642.1|FL146642

EST:     ACTATGGACAAACCTGTTTATGTGGCAGCTGAAAGCTACAAG                         TTTGCTCGGCTATATCCCTTGGATCAAAAGGACATGACGCCAGCTCACCGA
genomic: ACTATGGACAAACCTGTTTATGTGGCAGCTGAAAGCTACAAGgtaatgcatg ... acttcggcagTTTGCTCGGCTATATCCCTTGGATCAAAAGGACATGACGCCAGCTCACCGA

EST: gi|111990864|gb|EE332311.1|EE332311

EST:     TGGCTCATACTATGGACAAACCTGTTTATGTGGCAGCTGAAAGCTACAAG                         TTTGCTCGGCTATATCCCTTGGATCAAAAGGACATGGCGCCAGCTCACCGA
genomic: TGGCTCATACTATGGACAAACCTGTTTATGTGGCAGCTGAAAGCTACAAGgtaatgcatg ... acttcggcagTTTGCTCGGCTATATCCCTTGGATCAAAAGGACATGACGCCAGCTCACCGA

EST: gi|19351346|gb|BM895878.1|BM895878

EST:     TGGCTCATACTATGGACAAACCTGTTTATGTGGCAGCTGAAAGCTACAAG                         TTTGCTCGGCTATATCCCATGGATCAAAAGGACATGA
genomic: TGGCTCATACTATGGACAAACCTGTTTATGTGGCAGCTGAAAGCTACAAGgtaatgcatg ... acttcggcagTTTGCTCGGCTATATCCCTTGGATCAAAAGGACATGA

EST: gi|89248963|gb|DY620749.1|DY620749

EST:     TGGCAGCTGAAAGCTACAAG                         TTTGCTCTGCTATTTCCCTTGGATCAAAAGGACATGACGCCAGCTCACCGA
genomic: TGGCAGCTGAAAGCTACAAGgtaatgcatg ... acttcggcagTTTGCTCGGCTATATCCCTTGGATCAAAAGGACATGACGCCAGCTCACCGA

EST: gi|31360905|gb|CD445262.1|CD445262

EST:     TGGCTCATACTATGGACAAACCTGTTTATGTGGCAGCTGAAAGCTACAAG                         TTTGCTCGGCTATATCCCTTGGATCAAAAGGACATGACGCCAGCTCCCCGA
genomic: TGGCTCATACTATGGACAAACCTGTTTATGTGGCAGCTGAAAGCTACAAGgtaatgcatg ... acttcggcagTTTGCTCGGCTATATCCCTTGGATCAAAAGGACATGACGCCAGCTCACCGA

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), 48 (downstream exon)
Score: 38

TGAGAGCGGAGGAATAATCAATATGATGGGCACTTATCAGATAGCTCTTGTGGCTCATACTATGGACAAACCTGTTTATGTGGCAGCTGAAAGCTACAAGgtaatgcatg ... acttcggcagTTTGCTCGGCTATATCCCTTGGATCAAAAGGACATGACGCCAGCTCACCGACCAATAGATTTTGGAGTCCCAATACCCATTGGTGTGGAAGTGGAGACAT

Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 34

Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 30

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 29

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAGAGCGGAGGAATAATCAATATGATGGGCACTTATCAGATAGCTCTTGTGGCTCATACTATGGACAAACCTGTTTATGTGGCAGCTGAAAGCTACAAGgtaatgcatgttatgataatgtacttcaataatatattatccttgtttcactcatcttatttctttgcatcattacttttgtaatttaatgaatttggta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA