ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

TCAACGGGCAGCTGGAATTCTACAATGTTGATGAACTAGAGACAATGGCAACAGGAGAGCATTTTATGGCAACAGATATCATGTGGGATCCAACTGGGAGgtgagctagtcactggttttagaaatttcctgattcaacatactgactggtattacataatatagttaaaaatacctaatccagttgacacttgcagatc...

Basic information

species	Zea mays
transcript	GRMZM2G174757_T01
intron #	9
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G174757_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os10g41960.1 (Oryza sativa), 5'ss of exon 9

TCAACGGGCAGCTGGAATTCTACAATGTTGATGAACTAGAGACAATGGCAACAGGAGAGCATTTTATGGCAACAGATATCATGTGGGATCCAACTGGGAGgtgagctagtcactggttttagaaatttcctgat-tcaacatactgactggtattacataatat---agttaaaaatacctaatccagttgacacttgcagatc
| || ||||||||||| || |||||||||||||| || ||||| |||||||| || || ||||| ||||| || || || ||||||||||| ||||| |||| |||   | ||| | |   |||||||   |   ||| |||    ||||| | |  || || |   | ||  ||| ||| | |    |   | ||   | |  
TTAATGGGCAGCTGGAGTTTTACAATGTTGATGAGCTTGAGACGATGGCAACGGGTGAACATTTCATGGCTACTGACATTATGTGGGATCCTACTGGAAGgtaagcctat-acttggtcaggaaatttgtagtcctcaccatgac-actggcactttattatgtcaaattttcaaaaaccaagtatcatatgccctacgaaa--

upper sequence: GRMZM2G174757_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA07G14870.1 (Glycine max), 5'ss of exon 9

TCAACGGGCAGCTGGAATTCTACAATGTTGATGAACTAGAGACAATGGCAACAGGAGAGCATTTTATGGCAACAGATATCATGTGGGATCCAACTGGGAGgtgagctagtcactggttttagaaat----ttcctgatt----caacatactgactggtattacataatat-agttaaaaat---acctaatccagttgacacttgca-gatc--------------------------------------------------------------------------------
|||| || ||| ||||||| ||||| ||||||||||| || || ||||| || |  || ||||||||||||||||||||    |||||||||||||| ||||         |   |  | || |||    || || ||     ||   ||  |  |  | ||   ||| || |||| |||||   |  ||     ||   ||  ||   |||                                                                                 
TCAATGGACAGTTGGAATTTTACAACGTTGATGAACTTGAAACCATGGCTACTGCTGAACATTTTATGGCAACAGATATTGAATGGGATCCAACTGGAAGgtatatggtctatctgaatgagtaatgatattgctaataaaggcagtttataggttaatcttttgtaaaatcagtttaaaattgtatttacctttgtcatcatgtgtttgataattgcaattttactgaaaaagtgcttatggttggtttcttaattatcccaagcttatattgctttctctttatactgtag

upper sequence: GRMZM2G174757_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA04G06080.1 (Glycine max), 5'ss of exon 13

TCAACGGGCAGCTGGAATTCTACAATGTTGATGAACTAGAGACAATGGCAACAGGAGAGCATTTTATGGCAACAGATATCATGTGGGATCCAACTGGGAGgtgagctagtcactggttttagaaat----ttcctgatt----caacatactgactggtattacataatat-agttaaaaat---acctaatccagttgaca-----cttgcagatc----------------------------------------------------------------------------
|||| || ||| ||||||| ||||| |||||||||||  | || ||||| || |  || ||||||||||||||||||||    |||||||||||||| ||||         |   |  | |  |||    || || ||     || |  |  |  |  | ||   ||| || |||  |||||   |  ||    |||   ||      |||    |                                                                             
TCAATGGACAGTTGGAATTTTACAACGTTGATGAACTTAAAACCATGGCTACTGCTGAACATTTTATGGCAACAGATATTGAATGGGATCCAACTGGAAGgtatatggtctatctgaatgaataatgatattgctaataaaggcagctcataggttaatcttttgtaaaatcagtctaaaattgtatttaccttagtcatcaaagtgtttggtatttgccacttcactgaaaaagtacttattatggtttgttaattatcccaagcttatattgctttctctttatgccgcag

upper sequence: GRMZM2G174757_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA03G00470.1 (Glycine max), 5'ss of exon 9

TCAACGGGCAGCTGGAATTCTACAATGTTGATGAACTAGAGACAATGGCAACAGGAGAGCATTTTATGGCAACAGATATCATGTGGGATCCAACTGGGAGgtgagctagtcactggttttagaaat----ttcctgatt----caacatactgactggtattacataatat-agttaaaaat---acctaatccagttgacacttg-cagatc--------------------------------------------------------------------------------
|||| || ||| ||||||| ||||| ||||||||||| || || ||||| || |  || ||||||||||||||||||||    |||||||||||||| ||||         |   |  | || |||    || || ||     ||    |  |  |  | ||   ||| || |||| |||||   |  ||    |||    |  || | |||                                                                                 
TCAATGGACAGTTGGAATTTTACAACGTTGATGAACTTGAAACCATGGCTACTGCTGAACATTTTATGGCAACAGATATTGAATGGGATCCAACTGGAAGgtatatggtctatctgaatgagtaatgatattgctaataaaggcagttcataggttaatcttttgtaaaatcagtttaaaattgtatttaccttagtcattaagtgtctgatttttgccactttactgaaaaagtgcttattgttggtttgttaattatcccaagcttatattgctttctctttatatggcag

upper sequence: GRMZM2G174757_T01 (Zea mays), 5'ss of exon 9
lower sequence: PP1S138_36V6.1 (Physcomitrella patens), 5'ss of exon 8

TCAACGGGCAGCTGGAATTCTACAATGTTGATGAACTAGAGACAATGGCAACAGGAGAGCATTTTATGGCAACAGATATCATGTGGGATCCAACTGGGAGgtgagctag---tcactggt----tttagaaatttcctgattcaacat--actgactggtatta--cataatatagttaaaaatacctaatcca-gttgacacttgcagatc-----------------------------------------------------------
 ||| || ||||| || ||||||||||| ||||| || ||||||||||| ||||  ||||| |||||||| || ||| ||   |||||||| ||||| |||  ||  |       |||||    |||||  |  |  ||  | |   |  | ||| || |  |     |  | |   | |  | ||  ||  |   |  ||  |  |  |||                                                           
ACAATGGTCAGCTTGAGTTCTACAATGTGGATGACCTGGAGACAATGGCGACAGCTGAGCACTTTATGGCCACGGATGTCGACTGGGATCCTACTGGCAGgcaagtgaaagtctcctggtgttgtttagggaactgttgtctgattttgaagtgaatgtttctggttttgttgtgaattaccacactaaagacgtatcaactttaactaatctattgctgggcatttttttgggtcggctagtaatattgggtgttcccattgttctgcag

upper sequence: GRMZM2G174757_T01 (Zea mays), 5'ss of exon 9
lower sequence: EFJ12681 (Selaginella moellendorffii), 5'ss of exon 9

TCAACGGGCAGCTGGAATTCTACAATGTTGATGAACTAGAGACAATGGCAACAGGAGAGCATTTTATGGCAACAGATATCATGTGGGATCCAACTGGGAGgtgagctagtcactggttttagaaatttcctgattcaacatactgactggtattacataatatagttaaaaatacctaatccagttgacacttgcagatc
  ||||||||||| || ||||||||||||||||| || || || |||||||| | ||||||||| |||||||| ||| |    ||||||||  |||| |||| ||||          ||  ||||    || || |     ||||   | |   |                                             
ATAACGGGCAGCTCGAGTTCTACAATGTTGATGATCTCGAAACTATGGCAACGGCAGAGCATTTCATGGCAACTGATGTGGATTGGGATCCCGCTGGAAGgtaagct---------cttctgaaacgaacttatccttaccactggtcgtttgcag--------------------------------------------

upper sequence: GRMZM2G174757_T01 (Zea mays), 5'ss of exon 9
lower sequence: EFJ13839 (Selaginella moellendorffii), 5'ss of exon 9

TCAACGGGCAGCTGGAATTCTACAATGTTGATGAACTAGAGACAATGGCAACAGGAGAGCATTTTATGGCAACAGATATCATGTGGGATCCAACTGGGAGgtgagctagtcactggttttagaaatttcctgattcaacatactgactggtattacataatatagttaaaaatacctaatccagttgacacttgcagatc
  ||||||||||| || ||||||||||||||||| || ||||| |||||||| | ||||||||| |||||||| ||| |    ||||||||  |||| |||| ||||          ||  ||||    || || |     || |   | |   |                                             
ATAACGGGCAGCTCGAGTTCTACAATGTTGATGATCTCGAGACTATGGCAACGGCAGAGCATTTCATGGCAACTGATGTGGATTGGGATCCCGCTGGAAGgtaagct---------cttctgaaacgaacttatccttaccaccggtcgtttgcag--------------------------------------------

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|76289751|gb|DV029319.1|DV029319

EST:     ACAGGAGAGCATTTTATGGCAACAGATATCATGTGGGATCCAACTGGGAG                         ATATCTCGCGACTGCAGTTACCTCAGTTCATGAAATGGAGAATGGCTTT
genomic: ACAGGAGAGCATTTTATGGCAACAGATATCATGTGGGATCCAACTGGGAGgtgagctagt ... ttttgtccagATATCTCGCGACTGCAGTTACCTCAGTTCATGAAATGGAGAATGGCTTT

EST: gi|32929764|gb|CF034576.1|CF034576

EST:     ACAGGAGAGCATTTTATGGCAACAGATATCATGTGGGATCCAACTGGGAG                         ATATCTCGCGACTGCAGTTGCCTCAGTTCATGAAATGGAGAATGGCTTTCA
genomic: ACAGGAGAGCATTTTATGGCAACAGATATCATGTGGGATCCAACTGGGAGgtgagctagt ... ttttgtccagATATCTCGCGACTGCAGTTACCTCAGTTCATGAAATGGAGAATGGCTTTCA

EST: gi|6994119|gb|AW453333.1|AW453333

EST:     ACAGGAGAGCATTTTATGGCAACAGATATCATGTGGGATCCAACTGGGAG                         ATATCTCGCGACTGCAGTTACCTCAGTTCATGAAATGGAGAATGGCTTTCA
genomic: ACAGGAGAGCATTTTATGGCAACAGATATCATGTGGGATCCAACTGGGAGgtgagctagt ... ttttgtccagATATCTCGCGACTGCAGTTACCTCAGTTCATGAAATGGAGAATGGCTTTCA

EST: gi|6564113|gb|AW231735.1|AW231735

EST:     ACAGGAGAGCATTTTATGGCAACAGATATCATGTGGGATCCAACTGGGAG                         ATATCTCGCGACTGCAGTTACCTCAGTTCATGAAATGGAGAATGGCTTTCA
genomic: ACAGGAGAGCATTTTATGGCAACAGATATCATGTGGGATCCAACTGGGAGgtgagctagt ... ttttgtccagATATCTCGCGACTGCAGTTACCTCAGTTCATGAAATGGAGAATGGCTTTCA

EST: gi|32929752|gb|CF034564.1|CF034564

EST:     ACAGGAGAGCATTTTATGGCAACAGATATCATGTGGGATCCAACTGGGAG                         ATATCTCGCGACTGCAGTTACCTCAGTTCATGAAATGGAGAATGGCTTTCA
genomic: ACAGGAGAGCATTTTATGGCAACAGATATCATGTGGGATCCAACTGGGAGgtgagctagt ... ttttgtccagATATCTCGCGACTGCAGTTACCTCAGTTCATGAAATGGAGAATGGCTTTCA

EST: gi|149098248|gb|EE184214.2|EE184214

EST:     ACAGGAGAGCATTTTATGGCAACAGATATCATGTGGGATCCAACTGGGAG                         ATATCTCGCGACTGCAGTTACCTCAGTTCATGAAATGGAGAATGGCTTTCA
genomic: ACAGGAGAGCATTTTATGGCAACAGATATCATGTGGGATCCAACTGGGAGgtgagctagt ... ttttgtccagATATCTCGCGACTGCAGTTACCTCAGTTCATGAAATGGAGAATGGCTTTCA

EST: gi|21843249|gb|BQ703830.1|BQ703830

EST:     ACAGGAGAGCATTTTATGGCAACAGATATCATGTGGGATCCAACTGGGAG                         ATATCTCGCGACTGCAGTTACCTCAGTTCATGAAATGGAGAATGGCTTTCA
genomic: ACAGGAGAGCATTTTATGGCAACAGATATCATGTGGGATCCAACTGGGAGgtgagctagt ... ttttgtccagATATCTCGCGACTGCAGTTACCTCAGTTCATGAAATGGAGAATGGCTTTCA

EST: gi|32928528|gb|CF033340.1|CF033340

EST:     ACAGGAGAGCATTTTATGGCAACAGATATCATGTGGGATCCAACTGGGAG                         ATATCTCGCGACTGCAGTTACCTCAGTTCATGAAATGGAGAATGGCTTTCA
genomic: ACAGGAGAGCATTTTATGGCAACAGATATCATGTGGGATCCAACTGGGAGgtgagctagt ... ttttgtccagATATCTCGCGACTGCAGTTACCTCAGTTCATGAAATGGAGAATGGCTTTCA

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: 48 (upstream exon), 49 (downstream exon)
Score: 311

TCAACGGGCAGCTGGAATTCTACAATGTTGATGAACTAGAGACAATGGCAACAGGAGAGCATTTTATGGCAACAGATATCATGTGGGATCCAACTGGGAGgtgagctagt ... ttttgtccagATATCTCGCGACTGCAGTTACCTCAGTTCATGAAATGGAGAATGGCTTTCAAATATGGTCCTTCAGTGGCAAGCATCTTTACAAGGTGTCAAAGGATCAT

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 281

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 199

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 195

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCAACGGGCAGCTGGAATTCTACAATGTTGATGAACTAGAGACAATGGCAACAGGAGAGCATTTTATGGCAACAGATATCATGTGGGATCCAACTGGGAGgtgagctagtcactggttttagaaatttcctgattcaacatactgactggtattacataatatagttaaaaatacctaatccagttgacacttgcagatc

- - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaatac