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

...ataccgagtggtccattttgctgccttctatttcagcttatgttatccccatggcttcattgtctgtttaagaaatcctctacatttattctgaatgtagGGCAGCCTTTGTCCATTGGAGTATGCCACAGAAATTGCAAAGGAAGCAGATCAGTACAACGGCTTTAACCTTATATTGGCTGATGTGAACTCAGGAACCA

Basic information

species	Zea mays
transcript	GRMZM2G003057_T01
intron #	2
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G003057_T04 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os04g47680.1 (Oryza sativa), 3'ss of exon 1

ataccgagtggtccattttgctgccttctatttcagcttatgtta--tccccatggcttcattgtctgtttaagaaatcctctacatttat---tctg-aatgtagGGCAGCCTTTGTCCATTGGAGTATGCCACAGAAATTGCAAAGGAAGCAGATCAGTACAACGGCTTTAACCTTATATTGGCTGATGTGAACTCAGGAACCA
  |     || || |    ||| | |  ||  | |||||     |  |   | | |||| ||| |   |  ||    || | ||| |  ||   |||   ||  |||| | ||  ||||| |||||||||||   |||||| || |||||||||||||||||||| |||||||||||| |||||||||||||| | || ||||  |
--attacatgttctaca--gctccttcttagattagcttcctacaattgatccttgcttaattattgat--aatgtttcttttacttcaatgaatctatgatacagGGAAACCAATGTCCGTTGGAGTATGCGGAAGAAATAGCCAAGGAAGCAGATCAGTACAATGGCTTTAACCTTGTATTGGCTGATGTGCAGTCGGGAAATA

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|211484497|gb|FL376552.1|FL376552

EST:     CTCTGATCGGGGCCAAGACCAGAGGACAGCTCCCGGTCAGGTTTCTACAG                         GGCAGCCTTTGTCCATTGGAGTATGCCACAGAAATTGCAAAGGAAGCAGAT
genomic: CTCTGATCGGGGCCAAGACCAGAGGACAGCTCCCGGTCAGGTTTCTACAGgttcggcctt ... ctgaatgtagGGCAGCCTTTGTCCATTGGAGTATGCCACAGAAATTGCAAAGGAAGCAGAT

EST: gi|211394987|gb|FL376971.1|FL376971

EST:     CTCTGATCGGGGCCAAGACCAGAGGACAGCTCCCGGTCAGGTTTCTACAG                         --C--C-TTTGTCCATTGGAGTATGCCACAGAAATTGCAAAGGAAGCAGAT
genomic: CTCTGATCGGGGCCAAGACCAGAGGACAGCTCCCGGTCAGGTTTCTACAGgttcggcctt ... ctgaatgtagGGCAGCCTTTGTCCATTGGAGTATGCCACAGAAATTGCAAAGGAAGCAGAT

EST: gi|211509432|gb|FL413813.1|FL413813

EST:     CTCTGATCGGGGCCAAGACCAGAGGACAGCTCCCGGTCAGGTTTCTACAG                         GGCAGCCTTTGTCCATTGGAGTATGCCACAGAAATTGCAAAGGAAGCAGAT
genomic: CTCTGATCGGGGCCAAGACCAGAGGACAGCTCCCGGTCAGGTTTCTACAGgttcggcctt ... ctgaatgtagGGCAGCCTTTGTCCATTGGAGTATGCCACAGAAATTGCAAAGGAAGCAGAT

EST: gi|211074490|gb|FL413464.1|FL413464

EST:     CTCTGATCGGGGCCAAGACCAGAGGACAGCTCCCGGTCAGGTTTCTACAG                         GGCAGCCTTTGTCCATTGGAGTATGCCACAGAAATTGCAAAGGAAGCAGAT
genomic: CTCTGATCGGGGCCAAGACCAGAGGACAGCTCCCGGTCAGGTTTCTACAGgttcggcctt ... ctgaatgtagGGCAGCCTTTGTCCATTGGAGTATGCCACAGAAATTGCAAAGGAAGCAGAT

EST: gi|211242704|gb|FL378106.1|FL378106

EST:     CTCTGATCGGGGCCAAGACCAGAGGACAGCTCCCGGTCAGGTTTCTACAG                         GGCAGCCTTTGTCCATTGGAGTATGCCACAGAAATTGCAAAGGAAGCAGAT
genomic: CTCTGATCGGGGCCAAGACCAGAGGACAGCTCCCGGTCAGGTTTCTACAGgttcggcctt ... ctgaatgtagGGCAGCCTTTGTCCATTGGAGTATGCCACAGAAATTGCAAAGGAAGCAGAT

EST: gi|211309013|gb|FL381285.1|FL381285

EST:     CTCTGATCGGGGCCAAGACCAGAGGACAGCTCCCGGTCAGGTTTCTACAG                         GGCAGCCTTTGTCCATTGGAGTATGCCACAGAAATTGCAAAGGAAGCAGAT
genomic: CTCTGATCGGGGCCAAGACCAGAGGACAGCTCCCGGTCAGGTTTCTACAGgttcggcctt ... ctgaatgtagGGCAGCCTTTGTCCATTGGAGTATGCCACAGAAATTGCAAAGGAAGCAGAT

EST: gi|211256544|gb|FL390497.1|FL390497

EST:     CTCTGATCGGGGCCAAGACCAGAGGACAGCTCCCGGTCAGGTTTCTACAG                         GGCAGCCTTTGTCCATTGGAGTATGCCACAGAAATTGCAAAGGAAGCAGAT
genomic: CTCTGATCGGGGCCAAGACCAGAGGACAGCTCCCGGTCAGGTTTCTACAGgttcggcctt ... ctgaatgtagGGCAGCCTTTGTCCATTGGAGTATGCCACAGAAATTGCAAAGGAAGCAGAT

EST: gi|211150343|gb|FL403094.1|FL403094

EST:     CTCTGATCGGGGCCAAGACCAGAGGACAGCTCCCGGTCAGGTTTCTACAG                         GGCAGCMTTTGTCCATTGGAGTATGCCACAGAAATTGCAAAGGAAGCAGAT
genomic: CTCTGATCGGGGCCAAGACCAGAGGACAGCTCCCGGTCAGGTTTCTACAGgttcggcctt ... ctgaatgtagGGCAGCCTTTGTCCATTGGAGTATGCCACAGAAATTGCAAAGGAAGCAGAT

EST: gi|93284444|gb|EB676708.1|EB676708

EST:     CTCTGATCGGGGCCAAGACCAGAGGACAGCTCCCGGTCAGGTTTCTACAG                         GGCAGCCTTTGTCCATTGGAGTATGCCACAGAAATTGCAAAGGAAGCAGAT
genomic: CTCTGATCGGGGCCAAGACCAGAGGACAGCTCCCGGTCAGGTTTCTACAGgttcggcctt ... ctgaatgtagGGCAGCCTTTGTCCATTGGAGTATGCCACAGAAATTGCAAAGGAAGCAGAT

EST: gi|211115170|gb|FL372345.1|FL372345

EST:     CTCTGATCGGGGCCAAGACCAGAGGACAGCTCCCGGTCAGGTTTCTACAG                         GGCAGCCTTTGTCCATTGGAGTATGCCACAGAAATTGCAAAGGAAGCAGAT
genomic: CTCTGATCGGGGCCAAGACCAGAGGACAGCTCCCGGTCAGGTTTCTACAGgttcggcctt ... ctgaatgtagGGCAGCCTTTGTCCATTGGAGTATGCCACAGAAATTGCAAAGGAAGCAGAT

EST: gi|149100496|gb|EE186576.2|EE186576

EST:     CTCTGATCGGGGCCAAGACCAGAGGACAGCTCCCGGTCAGGTTTCTACAG                         GGCAGCCTTTGTCCATTGGAGTATGCCACAGAAATTGCAAAGGAAGCAGAT
genomic: CTCTGATCGGGGCCAAGACCAGAGGACAGCTCCCGGTCAGGTTTCTACAGgttcggcctt ... ctgaatgtagGGCAGCCTTTGTCCATTGGAGTATGCCACAGAAATTGCAAAGGAAGCAGAT

EST: gi|211127336|gb|FL391795.1|FL391795

EST:     CTCTGATCGGGGCCAAGACCAGAGGACAGCTCCCGGTCAGGTTTCTACAG                         GGCAGCCTTTGTCCATTGGAGTATGCCACAGAAATTGCAAAGGAAGCAGAT
genomic: CTCTGATCGGGGCCAAGACCAGAGGACAGCTCCCGGTCAGGTTTCTACAGgttcggcctt ... ctgaatgtagGGCAGCCTTTGTCCATTGGAGTATGCCACAGAAATTGCAAAGGAAGCAGAT

EST: gi|211421544|gb|FL418414.1|FL418414

EST:     CTCTGATCGGGGCCAAGACCAGAGGACAGCTCCCGGTCAGGTTTCTACAG                         GGCAGCCTTTGTCCATTGGAGTATGCCACAGAAATTGCAAAGGAAGCAGAT
genomic: CTCTGATCGGGGCCAAGACCAGAGGACAGCTCCCGGTCAGGTTTCTACAGgttcggcctt ... ctgaatgtagGGCAGCCTTTGTCCATTGGAGTATGCCACAGAAATTGCAAAGGAAGCAGAT

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: 45 (upstream exon), 49 (downstream exon)
Score: 40

CACGAGGGATGGTAAGCTCGCCTTCCTGACCAACGTGCGGGAACCCAGCTCTCTGATCGGGGCCAAGACCAGAGGACAGCTCCCGGTCAGGTTTCTACAGgttcggcctt ... ctgaatgtagGGCAGCCTTTGTCCATTGGAGTATGCCACAGAAATTGCAAAGGAAGCAGATCAGTACAACGGCTTTAACCTTATATTGGCTGATGTGAACTCAGGAACCA

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 81

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 80

Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 38

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tccccatggcttcattgtctgtttaagaaatcctctacatttattctgaatgtagGGCAGCCTTTGTCCATTGGAGTATGCCACAGAAATTGCAAAGGAAGCAGATCAGTACAACGGCTTTAACCTTATATTGGCTGATGTGAACTCAGGAACCA

                                       tttattct  CT-rich tract
                     tttaagaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ataccgagtggtccattttgctgccttctatttcagcttatgttatccccatggcttcattgtctgtttaagaaatcctctacatttattctgaatgtagGGCAGCCTTTGTCCATTGGAGTATGCCACAGAAATTGCAAAGGAAGCAGATCAGTACAACGGCTTTAACCTTATATTGGCTGATGTGAACTCAGGAACCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT