ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
PPT, BS, UA-tract
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

gtaagcttggttcctcttaacagtgtacacacataaggcattttccatttgttctttttggtccattctcatcttgcatttaatttttgttgatccacagGCCTGGTAAGTTTCCCTTGGCTATTGTTTTGGCGCCAACAAGAGAACTTGCAAAACAGGTTGAGAGGGAGTTCCTTGATTCCTCCCCTTTGGAAACACTA

Basic information

species	Zea mays
transcript	GRMZM2G107984_T02
intron #	2
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G107984_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os12g41715.1 (Oryza sativa), 3'ss of exon 2

gtaagcttggttcctcttaacagtgtacacacataaggcattttccatttgttc-tttttggtccattctcatcttgcatttaatttttgttgatccacagGCCTGGTAAGTTTCCCTTGGCTATTGTTTTGGCGCCAACAAGAGAACTTGCAAAACAGGTTGAGAGGGAGTTCCTTGATTCCTCCCCTTTGGAAACACTA
||||| || | |||| ||  |    || |    |        | | ||| |||  ||  |  |   || |    |  | ||| |   ||      | |||| |||||||| ||||||||||||||||||||||| |||||||||||||| || ||||| ||||||||||| ||   |||||| |||  | |||||||  | 
gtaagttttggtcctattgtcttcatatatttttttctttactactattggtttgttcctctttgttttttgggtaacctttgagcctttggatgcaacagCCCTGGTAAATTTCCCTTGGCTATTGTTTTGGCCCCAACAAGAGAACTCGCGAAACAAGTTGAGAGGGAATTTTCTGATTCTTCCAATGTGGAAACGATC

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|149061229|gb|EE157494.2|EE157494

EST:     TTTGGAATCCCCATAATGGATGCAATTATCCGCCACAACGAGAAGTACAA                         GCCTGGTAAGTTTCCCTTGGCTATTGTTTTGGCGCCAACAAGAGAACTTGC
genomic: TTTGGAATCCCCATAATGGATGCAATTATCCGCCACAACGAGAAGTACAAgtaagcttgg ... tgatccacagGCCTGGTAAGTTTCCCTTGGCTATTGTTTTGGCGCCAACAAGAGAACTTGC

EST: gi|211281261|gb|FL322092.1|FL322092

EST:     TTTGGAATCCCCATAATGGATGCAATTATCCGCCACAACGAGAAGTACAA                         GCCTGGTAAGTTTCCCTTGGCCATTGTTTTGGCGCC
genomic: TTTGGAATCCCCATAATGGATGCAATTATCCGCCACAACGAGAAGTACAAgtaagcttgg ... tgatccacagGCCTGGTAAGTTTCCCTTGGCTATTGTTTTGGCGCC

EST: gi|149089755|gb|EE179029.2|EE179029

EST:     TTTGGAATCCCCATAATGGATGCAATTATCCGCCACAACGAGAAGTACAA                         GCCTGGTAAGTTTCCCTTGGCTATTGTTTTGGCGCCAACAAGAGAACTTGC
genomic: TTTGGAATCCCCATAATGGATGCAATTATCCGCCACAACGAGAAGTACAAgtaagcttgg ... tgatccacagGCCTGGTAAGTTTCCCTTGGCTATTGTTTTGGCGCCAACAAGAGAACTTGC

EST: gi|14191123|gb|BG833353.1|BG833353

EST:     TTTGGAATCCCCATAATGGATGCAATTATCCGCCACAACGAGAAGTACAA                         GCCTGGTAAGTTTCCCTTGGCTATTGTTTTGGCGCCAACAAGAGAACTTGC
genomic: TTTGGAATCCCCATAATGGATGCAATTATCCGCCACAACGAGAAGTACAAgtaagcttgg ... tgatccacagGCCTGGTAAGTTTCCCTTGGCTATTGTTTTGGCGCCAACAAGAGAACTTGC

EST: gi|211017399|gb|FL066295.1|FL066295

EST:     TTTGGAATCCCCATAATGGATGCAATTATCCGCCACAACGAGAAGTACAA                         GCCTGGTAAGTTTCCCTTGGCCATTGTTTTGGCGCCAACAAGAGAACTTGC
genomic: TTTGGAATCCCCATAATGGATGCAATTATCCGCCACAACGAGAAGTACAAgtaagcttgg ... tgatccacagGCCTGGTAAGTTTCCCTTGGCTATTGTTTTGGCGCCAACAAGAGAACTTGC

EST: gi|71304548|gb|DR788393.1|DR788393

EST:     GAGAAGTACAA                         GCCTGGTAAGTTTCCCTTGGCTATTGTTTTGGCGCCAACAAGAGAACTTGC
genomic: GAGAAGTACAAgtaagcttgg ... tgatccacagGCCTGGTAAGTTTCCCTTGGCTATTGTTTTGGCGCCAACAAGAGAACTTGC

EST: gi|14191124|gb|BG833354.1|BG833354

EST:     TTTGGAATCCCCATAATGGATGCAATTATCCGCCACAACGAGAAGTACAA                         GCCTGGTAAGTTTCCCTTGGCTATTGTTTTGGCGCCAACAAGAGAACTTGC
genomic: TTTGGAATCCCCATAATGGATGCAATTATCCGCCACAACGAGAAGTACAAgtaagcttgg ... tgatccacagGCCTGGTAAGTTTCCCTTGGCTATTGTTTTGGCGCCAACAAGAGAACTTGC

EST: gi|211017398|gb|FL066294.1|FL066294

EST:     TTTGGAATCCCCATAATGGATGCAATTATCCGCCACAACGAGAAGTACAA                         GCCTGGTAAGTTTCCCTTGGCCATTGTTTTGGCGCCAACAAGAGAACTTGC
genomic: TTTGGAATCCCCATAATGGATGCAATTATCCGCCACAACGAGAAGTACAAgtaagcttgg ... tgatccacagGCCTGGTAAGTTTCCCTTGGCTATTGTTTTGGCGCCAACAAGAGAACTTGC

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: 342

GAAGGGACATGGTTGGCCGTGCCAAAACTGGGACTGGTAAAACTTTGGCATTTGGAATCCCCATAATGGATGCAATTATCCGCCACAACGAGAAGTACAAgtaagcttgg ... tgatccacagGCCTGGTAAGTTTCCCTTGGCTATTGTTTTGGCGCCAACAAGAGAACTTGCAAAACAGGTTGAGAGGGAGTTCCTTGATTCCTCCCCTTTGGAAACACTA

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 106

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 185

Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 149

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

catttgttctttttggtccattctcatcttgcatttaatttttgttgatccacagGCCTGGTAAGTTTCCCTTGGCTATTGTTTTGGCGCCAACAAGAGAACTTGCAAAACAGGTTGAGAGGGAGTTCCTTGATTCCTCCCCTTTGGAAACACTA

                                          tgttgat  putative branch site (score: 149)
                                      tttttgtt  CT-rich tract
                                atttaatttttgttga  TA-rich tract

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcttggttcctcttaacagtgtacacacataaggcattttccatttgttctttttggtccattctcatcttgcatttaatttttgttgatccacagGCCTGGTAAGTTTCCCTTGGCTATTGTTTTGGCGCCAACAAGAGAACTTGCAAAACAGGTTGAGAGGGAGTTCCTTGATTCCTCCCCTTTGGAAACACTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG