ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

GATAAGCACAGCATGGAGAAGGACATCGCTGAGTACATAAAGAAGGAGTTCGACAAGAACCACGGCCCAACCTGGCACTGCATCGTCGGCCGCAACTTCGgtattgctctttttcaaaccccttttgggaaccctccttaattagtactgaatgatttcgccagttgtggtcggggtcgggtgtctagtctgatatgctt...

Basic information

species	Zea mays
transcript	GRMZM2G146012_T01
intron #	2
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G146012_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os01g15260.1 (Oryza sativa), 5'ss of exon 2

GATAAGCACAGCATGGAGAAGGACATCGCTGAGTACATAAAGAAGGAGTTCGACAAGAACCACGGCCCAACCTGGCACTGCATCGTCGGCCGCAACTTCGgtattgctctttttcaaaccccttttgggaaccctccttaattagtactgaatgatttcgc-cagttgtggtcggggtcgggtgtctagtctgatatgctt---
|| ||||||| |||||||||||||||||| |||||||| ||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||| | |||| | ||     |  | | |   ||| |  |  ||  |    | |  ||| |  | |        || |     ||||| |||   |    ||   
GAGAAGCACACCATGGAGAAGGACATCGCGGAGTACATCAAGAAGGAGTTCGACAAGAACCACGGCCCTACCTGGCACTGCATCGTCGGCCGCAACTTCGgtactcctctctctc----tctctctcgcctccccctcttcttgctggaaatttctttggtaccgcatcatctggtgatttatgtcttgtcctctcctgttgat

upper sequence: GRMZM2G146012_T01 (Zea mays), 5'ss of exon 2
lower sequence: AT4G15930.1 (Arabidopsis thaliana), 5'ss of exon 2

GATAAGCACAGCATGGAGAAGGACATCGCTGAGTACATAAAGAAGGAGTTCGACAAGAACCACGGCCCAACCTGGCACTGCATCGTCGGCCGCAACTTCGgtattgctctttttcaaaccccttttgggaaccctccttaat-tagtactgaatgatttcgccagttgtggtcggggtcgg--gtgtctagtctgatatgctt
|| ||| ||||  |||||||||| || |||||| | |||||||||||||| |||||||| || ||  | || ||||| ||||| || || |||||||| ||| | | ||  |      |  |  ||   |   ||||||||  | | | |    |||         |  | | |||    |   | |||       |||   |
GAGAAGTACAGTGTGGAGAAGGATATAGCTGAGAATATAAAGAAGGAGTTTGACAAGAAACATGGTGCTACTTGGCATTGCATTGTTGGTCGCAACTTTGgt-tagttccctcctctccttcgctt--aatttctccttaaggtggcatttttcgatgaaaagttctcagttagggaatagtgatttcttagtaagtatatct

upper sequence: GRMZM2G146012_T01 (Zea mays), 5'ss of exon 2
lower sequence: Vv05s0077g02110.t01 (Vitis vinifera), 5'ss of exon 2

GATAAGCACAGCATGGAGAAGGACATCGCTGAGTACATAAAGAAGGAGTTCGACAAGAACCACGGCCCAACCTGGCACTGCATCGTCGGCCGCAACTTCGgtattgctctttt--tcaaaccccttttgggaaccct--ccttaattagtactgaatgatttcgccagttgtggtcggggtcgggtgtctagtctgatatgctt
|| || |||||  |||||||  |||| || ||||| || |||||||||||||| ||||| || || || |||||||| ||||| ||||| ||||| ||||||| | | | |||  |||     ||| |   |    |    | ||||  ||||| ||   ||      |     || | |  ||   |||  | | | ||    
GAGAATCACAGTGTGGAGAAAAACATTGCGGAGTATATCAAGAAGGAGTTCGATAAGAAGCATGGACCTACCTGGCATTGCATTGTCGGTCGCAATTTCGgtaattcccgtttaatcatttttcttataatatatgtaatatcaatttctactggatagattaattgatg--aatcagcggtggtgttctgttgttacatat--

upper sequence: GRMZM2G146012_T01 (Zea mays), 5'ss of exon 2
lower sequence: PP1S335_29V6.1 (Physcomitrella patens), 5'ss of exon 3

GATAAGCACAGCATGGAGAAGGACATCGCTGAGTACATAAAGAAGGAGTTCGACAAGAACCACGGCCCAACCTGGCACTGCATCGTCGGCCGCAACTTCGgtattgctcttttt----caaaccccttttgggaaccctccttaattagtactgaatgatttcgccagttgtggtcggggtcgggtgtctagtctgatatgctt
|| ||| |||   |||| || || || || |  ||||| || ||||||||||| |||||  |    ||||||||||||||||||||||| ||||||||||||     | | |||    |||| | |||||    |  |     | |    |  | | |||    |     || || |   |||  |   | ||      ||   
GACAAGTACAATGTGGAAAAAGATATAGCAGCCTACATCAAAAAGGAGTTCGATAAGAAGTATAATCCAACCTGGCACTGCATCGTCGGGCGCAACTTCGgtgagagtttgttttacgcaaatcacttttttttatgcctagaattctagaaaggaggatagatctgtgagtcgttgaa-tcgaatagatggttattggtg---

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|211413157|gb|FL382742.1|FL382742

EST:     CGACAAGAACCACGGCCCAACCTGGCACTGCATCGTCGGCCGCAACTTCG                         GTTCATACGT-ACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT
genomic: CGACAAGAACCACGGCCCAACCTGGCACTGCATCGTCGGCCGCAACTTCGgtattgctct ... cttgatgcagGTTCATACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT

EST: gi|211322038|gb|FL425800.1|FL425800

EST:     CGACAAGAACCACGGCCCAACCTGGCACTGCATCGTCGGCCGCAACTTCG                         GTTCATACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT
genomic: CGACAAGAACCACGGCCCAACCTGGCACTGCATCGTCGGCCGCAACTTCGgtattgctct ... cttgatgcagGTTCATACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT

EST: gi|50332742|gb|CO527868.1|CO527868

EST:     CGACAAGAACCACGGCCCAACCTGGCACTGCATCGTCGGCCGCAACTTCG                         GTTCATACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT
genomic: CGACAAGAACCACGGCCCAACCTGGCACTGCATCGTCGGCCGCAACTTCGgtattgctct ... cttgatgcagGTTCATACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT

EST: gi|211328079|gb|FL404916.1|FL404916

EST:     CGACAAGAACCACGGCCCAACCTGGCACTGCATCGTCGGCCGCAACTTCG                         GTTCATACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT
genomic: CGACAAGAACCACGGCCCAACCTGGCACTGCATCGTCGGCCGCAACTTCGgtattgctct ... cttgatgcagGTTCATACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT

EST: gi|211147695|gb|FL418238.1|FL418238

EST:     CGACWAGAACCACGGCCCAACCTGGCACTGCATCGTCGGCCGCAACTTCG                         GTTCATACGTGACGCACGAGACAAACTACTTTGTANATTTCTACATCGACT
genomic: CGACAAGAACCACGGCCCAACCTGGCACTGCATCGTCGGCCGCAACTTCGgtattgctct ... cttgatgcagGTTCATACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT

EST: gi|18179580|gb|BM380790.1|BM380790

EST:     CGACAAGAACCACGGCCCAACCTGGCACTGCATCGTCGGCCGCAACTTCG                         GTTCATACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT
genomic: CGACAAGAACCACGGCCCAACCTGGCACTGCATCGTCGGCCGCAACTTCGgtattgctct ... cttgatgcagGTTCATACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT

EST: gi|149055663|gb|EE156369.2|EE156369

EST:     CGACAAGAACCACGGCCCAACCTGGCACTGCATCGTCGGCCGCAACTTCG                         GTTCATACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT
genomic: CGACAAGAACCACGGCCCAACCTGGCACTGCATCGTCGGCCGCAACTTCGgtattgctct ... cttgatgcagGTTCATACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT

EST: gi|211336225|gb|FL371126.1|FL371126

EST:     CGACAAGAACCACGGCCCAACCTGGCACTGCATCGTCGGCCGCAACTTCG                         GTTCATACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT
genomic: CGACAAGAACCACGGCCCAACCTGGCACTGCATCGTCGGCCGCAACTTCGgtattgctct ... cttgatgcagGTTCATACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT

EST: gi|211254929|gb|FL426613.1|FL426613

EST:     CGACAAGAACCACGGCCCAACCTGGCACTGCATCGTCGGCCGCAACTTCG                         GTTCATACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT
genomic: CGACAAGAACCACGGCCCAACCTGGCACTGCATCGTCGGCCGCAACTTCGgtattgctct ... cttgatgcagGTTCATACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT

EST: gi|211068885|gb|FL409569.1|FL409569

EST:     CGACAAGAACCACGGCCCAACCTGGCACTGCATCGTCGGCCGCAACTTCG                         GTTCATACGTGACGCACGAGACAAACTACTTTGTATATTTTCTACATCGAC
genomic: CGACAAGAACCACGGCCCAACCTGGCACTGCATCGTCGGCCGCAACTTCGgtattgctct ... cttgatgcagGTTCATACGTGACGCACGAGACAAACTACTTTGTATATTT-CTACATCGAC

EST: gi|211251155|gb|FL466754.1|FL466754

EST:     GACAAGAACCACGGCCCAACCCTGGCACTGCATCGTCGGCCGCAACTTCG                         GTTCATACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT
genomic: GACAAGAACCACGGCCCAA-CCTGGCACTGCATCGTCGGCCGCAACTTCGgtattgctct ... cttgatgcagGTTCATACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT

EST: gi|211067902|gb|FL369030.1|FL369030

EST:     CGACAAGAACCACGGCCCAACCTGGCACTGCATCGTCGGCCGCAACTTCG                         GTTCATACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT
genomic: CGACAAGAACCACGGCCCAACCTGGCACTGCATCGTCGGCCGCAACTTCGgtattgctct ... cttgatgcagGTTCATACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT

EST: gi|211521197|gb|FL395752.1|FL395752

EST:     CGACAAGAACCACGGCCCAACCTGGCACTGCATCGTCGGCCGCAACTTCG                         GTTCATACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT
genomic: CGACAAGAACCACGGCCCAACCTGGCACTGCATCGTCGGCCGCAACTTCGgtattgctct ... cttgatgcagGTTCATACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT

EST: gi|148959413|gb|EE010777.2|EE010777

EST:     CGACAAGAACCACGGCCCAACCTGGCACTGCATCGTCGGCCGCAACTTCG                         GTTCATACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT
genomic: CGACAAGAACCACGGCCCAACCTGGCACTGCATCGTCGGCCGCAACTTCGgtattgctct ... cttgatgcagGTTCATACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT

EST: gi|211371126|gb|FL382277.1|FL382277

EST:     CGACAAGAACCACGGCCCAACCTGGCACTGCATCGTCGGCCGCAACTTCG                         GTTCATACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT
genomic: CGACAAGAACCACGGCCCAACCTGGCACTGCATCGTCGGCCGCAACTTCGgtattgctct ... cttgatgcagGTTCATACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT

EST: gi|211479243|gb|FL398888.1|FL398888

EST:     CGACAAGAACCACGGCCCAACCTGGCACTGCATCGTCGGCCGCAACTTCG                         GTTCATACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT
genomic: CGACAAGAACCACGGCCCAACCTGGCACTGCATCGTCGGCCGCAACTTCGgtattgctct ... cttgatgcagGTTCATACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT

EST: gi|211159719|gb|FL392770.1|FL392770

EST:     CGACAAGAACCACGGCCCAACCTGGCACTGCATCGTCGGCCGCAACTTCG                         GTTCATACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT
genomic: CGACAAGAACCACGGCCCAACCTGGCACTGCATCGTCGGCCGCAACTTCGgtattgctct ... cttgatgcagGTTCATACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT

EST: gi|211262046|gb|FL417890.1|FL417890

EST:     CGACAAGAACCACGGCCCAACCTGGCACTGCATCGTCGGCCGCAACTTCG                         GTTCATACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT
genomic: CGACAAGAACCACGGCCCAACCTGGCACTGCATCGTCGGCCGCAACTTCGgtattgctct ... cttgatgcagGTTCATACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT

EST: gi|211206828|gb|FL384241.1|FL384241

EST:     CGACAAGAACCACGGCCCAACCTGGCACTGCATCGTCGGCCGCAACTTCG                         GTTCATACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT
genomic: CGACAAGAACCACGGCCCAACCTGGCACTGCATCGTCGGCCGCAACTTCGgtattgctct ... cttgatgcagGTTCATACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT

EST: gi|211294912|gb|FL412765.1|FL412765

EST:     CGACAAGAACCACGGCCCAACCTGGCACTGCATCGTCGGCCGCAACTTCG                         GTTCATACGTW-CGCCCGAGACAAACTACCTTGT
genomic: CGACAAGAACCACGGCCCAACCTGGCACTGCATCGTCGGCCGCAACTTCGgtattgctct ... cttgatgcagGTTCATACGTGACGCACGAGACAAACTACTTTGT

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), 42 (downstream exon)
Score: 170

GATAAGCACAGCATGGAGAAGGACATCGCTGAGTACATAAAGAAGGAGTTCGACAAGAACCACGGCCCAACCTGGCACTGCATCGTCGGCCGCAACTTCGgtattgctct ... cttgatgcagGTTCATACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACTCTAAAGCTGTCTTGCTATTCAAGTCTGGGTGATTGCTCGCAGCCGACGC

Block sizes: 48 (upstream exon), 44 (downstream exon)
Score: 54

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 72

Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 49

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATAAGCACAGCATGGAGAAGGACATCGCTGAGTACATAAAGAAGGAGTTCGACAAGAACCACGGCCCAACCTGGCACTGCATCGTCGGCCGCAACTTCGgtattgctctttttcaaaccccttttgggaaccctccttaattagtactgaatgatttcgccagttgtggtcggggtcgggtgtctagtctgatatgctt

- - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccctcctt