ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

GGTAGAGAAGCTCCCCAATGATCTGGAAGGAATGGAGTCCTCAATGGAGAAGCTTTACATTCTTATTGATGAGATCTACAAATACGTCGATGATGTTGTGgtacggatctctctctctctcactcactctcctgcatctgtttttttctattttattttgatttatttggacgcgggtgagtaacctccatatgacattgaag

Basic information

species	Zea mays
transcript	GRMZM2G098153_T01
intron #	4
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G098153_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os05g01450.1 (Oryza sativa), 5'ss of exon 4

GGTAGAGAAGCTCCCCAATGATCTGGAAGGAATGGAGTCCTCAATGGAGAAGCTTTACATTCTTATTGATGAGATCTACAAATACGTCGATGATGTTGTGgtacggatctctctctctctcactcactctcctgcatctgtttttttctattttattttgatttatttggacgcgggtgagtaacctccatatgacattgaag
 || |||||||||||||||||||||||||||||||| ||||| ||||| ||||| ||  | |||||||| |||||||||||||| || |||||||| |||||| | | || |         | || ||    |     | | |  | |  | |||    |  || ||    | |     ||                      
TGTGGAGAAGCTCCCCAATGATCTGGAAGGAATGGAATCCTCCATGGAAAAGCTGTATGTCCTTATTGACGAGATCTACAAATATGTTGATGATGTCGTGgtaagaaccttttggggcaaaattctcttattt---cttatgtagtgcagtgttaaaaaggctttttccacccctatgtag----------------------

upper sequence: GRMZM2G098153_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA18G03340.1 (Glycine max), 5'ss of exon 4

-GGTAGAGAAGCTCCCCAATGATCTGGAAGGAATGGAGTCCTCAATGGAGAAGCTTTACATTCTTATTGATGAGATCTACAAATACGTCGATGATGTTGTGgtacgg-atctctctctctctcactcactctcctgcatctgtttttttctattttattttgatttatttggacgcgggtgagtaacctccatatgacattgaag
  || || ||  | |||   ||| | ||||| |||||  | |||||| |  | ||     |  | |||||||| ||||||||||| || || ||||||||||||||  ||   |  ||   | | || ||| |||    || |    || |||| |  | | |||| |    ||                               
CAGTTGACAAAATTCCCTCAGATTTAGAAGGGATGGAAGCATCAATGCAACATCTGCTAGTCTTGATTGATGACATCTACAAATATGTTGACGATGTTGTggtacgatattgttgccttctttaatctctcgccttgtcctctgagattgtattattatataatttttcaacaca------------------------------

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|76286915|gb|DV026483.1|DV026483

EST:     AGCTTTACATTCTTATTGATGAGATCTACAAATACGTCGATGATGTTGTG                         GGGGGACGCGTGGCACCTGATAACAAAATCGGAAG
genomic: AGCTTTACATTCTTATTGATGAGATCTACAAATACGTCGATGATGTTGTGgtacggatct ... gacattgaagGAAGGACGCGTGGCACCTGATAACAGAATCGGAAG

EST: gi|60394964|gb|DN227833.1|DN227833

EST:     AGCTTTACATTCTTATTGATGAGATCTACAAATACGTCGATGATGTTGTG                         GAAGGACGCGTGGCACCTGATAACAGAATCGGAAGGTTGGTCTCTGAATCT
genomic: AGCTTTACATTCTTATTGATGAGATCTACAAATACGTCGATGATGTTGTGgtacggatct ... gacattgaagGAAGGACGCGTGGCACCTGATAACAGAATCGGAAGGTTGGTCTCTGAATCT

EST: gi|71439970|gb|DR821020.1|DR821020

EST:     AGCTTTACATTCTTATTGATGAGATCTACAAATACGTCGATGATGTTGTG                         GAAGGACGCGTGGCACCTGATAACAGAATCGGAAGGTTGGTCTCTGAATCT
genomic: AGCTTTACATTCTTATTGATGAGATCTACAAATACGTCGATGATGTTGTGgtacggatct ... gacattgaagGAAGGACGCGTGGCACCTGATAACAGAATCGGAAGGTTGGTCTCTGAATCT

EST: gi|67015095|gb|CO443844.1|CO443844

EST:     AGCTTTACATTCTTATTGATGAGATCTACAAATACGTCGATGATGTTGTG                         GAAGGACGCGTGGCACCTGATAACAGAATCGGAAGGTTGGTCTCTGAATCT
genomic: AGCTTTACATTCTTATTGATGAGATCTACAAATACGTCGATGATGTTGTGgtacggatct ... gacattgaagGAAGGACGCGTGGCACCTGATAACAGAATCGGAAGGTTGGTCTCTGAATCT

EST: gi|71439969|gb|DR821019.1|DR821019

EST:     AGCTTTACATTCTTATTGATGAGATCTACAAATACGTCGATGATGTTGTG                         GAAGGACGCGTGGCACCTGATAACAGAATCGGAAGGTTGGTTTCTGAATCT
genomic: AGCTTTACATTCTTATTGATGAGATCTACAAATACGTCGATGATGTTGTGgtacggatct ... gacattgaagGAAGGACGCGTGGCACCTGATAACAGAATCGGAAGGTTGGTCTCTGAATCT

EST: gi|16919791|gb|BM074356.1|BM074356

EST:     AGCTTTACATTCTTATTGATGAGATCTACAAATACGTCGATGATGTTG-G                         GAAGGACGCGTGGCACCTGATAACAGAATCGGAAGGTTGGTCTCTGAATCT
genomic: AGCTTTACATTCTTATTGATGAGATCTACAAATACGTCGATGATGTTGTGgtacggatct ... gacattgaagGAAGGACGCGTGGCACCTGATAACAGAATCGGAAGGTTGGTCTCTGAATCT

EST: gi|37399477|gb|CF637068.1|CF637068

EST:     AGCTTTACATTCTTATTGATGAGATCTACAAATACGTCGATGATGTTGTG                         GAAGGACGCGTGGCACCTGATAACAGAATCGGAAGGTTGGTCTCTGAATCT
genomic: AGCTTTACATTCTTATTGATGAGATCTACAAATACGTCGATGATGTTGTGgtacggatct ... gacattgaagGAAGGACGCGTGGCACCTGATAACAGAATCGGAAGGTTGGTCTCTGAATCT

EST: gi|74240762|gb|DT648676.1|DT648676

EST:     AGCTTTACATTCTTATTGATGAGATCTACAAATACGTCGATGATGTTGTG                         GAAGGACGCGTGGCACCTGATAACAGAATCGGAAGGTTGGTCTCTGAATCT
genomic: AGCTTTACATTCTTATTGATGAGATCTACAAATACGTCGATGATGTTGTGgtacggatct ... gacattgaagGAAGGACGCGTGGCACCTGATAACAGAATCGGAAGGTTGGTCTCTGAATCT

EST: gi|15499459|gb|BI595972.1|BI595972

EST:     AGCTTTACATTCTTATTGATGAGATCTACAAATACGTCGATGATGTTGTG                         GAAGGACGCGTGGCACCTGATAACAGAATCGGAAGGTTGGTCTCTGAATCT
genomic: AGCTTTACATTCTTATTGATGAGATCTACAAATACGTCGATGATGTTGTGgtacggatct ... gacattgaagGAAGGACGCGTGGCACCTGATAACAGAATCGGAAGGTTGGTCTCTGAATCT

EST: gi|60358158|gb|DN225131.1|DN225131

EST:     AGCTTTACATTCTTATTGATGAGATCTACAAATACGTCGATGATGTTGTG                         GAAGGACGCGTGGCACCTGATAACAGAATCGGAAGGTTGGTCTCTGAATCT
genomic: AGCTTTACATTCTTATTGATGAGATCTACAAATACGTCGATGATGTTGTGgtacggatct ... gacattgaagGAAGGACGCGTGGCACCTGATAACAGAATCGGAAGGTTGGTCTCTGAATCT

EST: gi|87152453|gb|DY397242.1|DY397242

EST:     AGCTTTACATTCTTATTGATGAGATCTACAAATACGTCGATGATGTTGTG                         GAAAGACGCGTGGCACCTGATAACAGAAT
genomic: AGCTTTACATTCTTATTGATGAGATCTACAAATACGTCGATGATGTTGTGgtacggatct ... gacattgaagGAAGGACGCGTGGCACCTGATAACAGAAT

EST: gi|6526821|gb|AW216090.1|AW216090

EST:     AGCTTTACATTCTTATTGATGAGATCTACAAATACGTCGATGATGTTGTG                         GAAGGACGCGTGGCACCTGATAACAGAATCGGAAGGTTGGTCTCTGAATCT
genomic: AGCTTTACATTCTTATTGATGAGATCTACAAATACGTCGATGATGTTGTGgtacggatct ... gacattgaagGAAGGACGCGTGGCACCTGATAACAGAATCGGAAGGTTGGTCTCTGAATCT

EST: gi|19822328|gb|BQ048352.1|BQ048352

EST:     AGCTTTACATTCTTATTGATGAGATCTACAAATACGTCGATGATGTTGTG                         GAAGGACGCGTGGCACCTGATAACAGAATCGGAAGGTTGGTCTCTGAATCT
genomic: AGCTTTACATTCTTATTGATGAGATCTACAAATACGTCGATGATGTTGTGgtacggatct ... gacattgaagGAAGGACGCGTGGCACCTGATAACAGAATCGGAAGGTTGGTCTCTGAATCT

EST: gi|6057055|gb|AW091460.1|AW091460

EST:     TTATTGATGAGATCTACAAATACGTCGATGATGTTGTG                         GAAGGACGCGTGGCCCCTGATACCAGAATCGGAAGGTTGGTCTCTGAATCT
genomic: TTATTGATGAGATCTACAAATACGTCGATGATGTTGTGgtacggatct ... gacattgaagGAAGGACGCGTGGCACCTGATAACAGAATCGGAAGGTTGGTCTCTGAATCT

EST: gi|78091175|gb|DV519549.1|DV519549

EST:     AGCTTTACATTCTTATTGATGAGATCTACAAATACGTCGATGATGTTGTG                         GAAGGACGCGTGGCACCTGATAACAGAATCGGAAGGTTGGTCTCTGAATCT
genomic: AGCTTTACATTCTTATTGATGAGATCTACAAATACGTCGATGATGTTGTGgtacggatct ... gacattgaagGAAGGACGCGTGGCACCTGATAACAGAATCGGAAGGTTGGTCTCTGAATCT

EST: gi|93015004|gb|EB640524.1|EB640524

EST:     AGCTTTACATTCTTATTGATGAGATCTACAAATACGTCGATGATGTTGTG                         GAAGGACGCGTGGCACCTGATAACAGAATCGGAAGGTTGGTCTCTGAATCT
genomic: AGCTTTACATTCTTATTGATGAGATCTACAAATACGTCGATGATGTTGTGgtacggatct ... gacattgaagGAAGGACGCGTGGCACCTGATAACAGAATCGGAAGGTTGGTCTCTGAATCT

EST: gi|76284328|gb|DV023896.1|DV023896

EST:     AGCTTTACATTCTTATTGATGAGATCTACAAATACGTCGATGATGTTGTG                         GAAGGACGCGTGGCACCTGATAACAGAATCGGAAGGTTGGTCTCTGAATCT
genomic: AGCTTTACATTCTTATTGATGAGATCTACAAATACGTCGATGATGTTGTGgtacggatct ... gacattgaagGAAGGACGCGTGGCACCTGATAACAGAATCGGAAGGTTGGTCTCTGAATCT

EST: gi|101384548|gb|EB814319.1|EB814319

EST:     AGCTTTACATTCTTATTGATGAGATCTACAAATACGTCGATGATGTTGTG                         GAGGGACGCGTGGCACCTGATAACAGAATCGGAAGGTTGGTCTCTGAATCT
genomic: AGCTTTACATTCTTATTGATGAGATCTACAAATACGTCGATGATGTTGTGgtacggatct ... gacattgaagGAAGGACGCGTGGCACCTGATAACAGAATCGGAAGGTTGGTCTCTGAATCT

EST: gi|83278726|gb|DV942734.1|DV942734

EST:     AGCTTTACATTCTTATTGATGAGATCTACAAATACGTCGATGATGTTGTG                         GAAGGACGCGTGGCACCTGATAACAGAATCGGAAGGTTGGTCTCTGAATCT
genomic: AGCTTTACATTCTTATTGATGAGATCTACAAATACGTCGATGATGTTGTGgtacggatct ... gacattgaagGAAGGACGCGTGGCACCTGATAACAGAATCGGAAGGTTGGTCTCTGAATCT

EST: gi|67011620|gb|CO440369.1|CO440369

EST:     AGCTTTACATTCTTATTGATGAGATCTACAAATACGTCGATGATGTTGTG                         GAAGGACGCGTGGCACCTGATAACAGAATCGGAAGGCTGGTCTCTGAATCT
genomic: AGCTTTACATTCTTATTGATGAGATCTACAAATACGTCGATGATGTTGTGgtacggatct ... gacattgaagGAAGGACGCGTGGCACCTGATAACAGAATCGGAAGGTTGGTCTCTGAATCT

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: 124

GGTAGAGAAGCTCCCCAATGATCTGGAAGGAATGGAGTCCTCAATGGAGAAGCTTTACATTCTTATTGATGAGATCTACAAATACGTCGATGATGTTGTGgtacggatct ... gacattgaagGAAGGACGCGTGGCACCTGATAACAGAATCGGAAGGTTGGTCTCTGAATCTGTTGCTTCAATGCCGAAATTGTCCCCAGCTGCTTTCGATAAGCTTTTCA

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 137

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 143

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 140

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTAGAGAAGCTCCCCAATGATCTGGAAGGAATGGAGTCCTCAATGGAGAAGCTTTACATTCTTATTGATGAGATCTACAAATACGTCGATGATGTTGTGgtacggatctctctctctctcactcactctcctgcatctgtttttttctattttattttgatttatttggacgcgggtgagtaacctccatatgacattgaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC