ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

CTGGCTTTTATCCTTTTATGATGCTGCAGTTGATTATTTGTCCACCACAAGGGTTATGCCAAGACTTGTAGAGGTTGTCAAGGGCTCTACTAAAGAGAAGgtaatgttctaaatttgcatgtcatattgtgccactgtaattacgtcagaaaaatgttaacattatgcacaaacttgaag

Basic information

species	Zea mays
transcript	GRMZM2G019999_T01
intron #	6
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G019999_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os07g36470.1 (Oryza sativa), 5'ss of exon 4

CTGGCTTTTATCCTTTTATGATGCTGCAGTTGATTATTTGTCCACCACAAGGGTTATGCCAAGACTTGTAGAGGTTGTCAAGGGCTCTACTAAAGAGAAGgtaatgttctaaat-ttgc----atgtcatattgtgccactgtaattacgtcagaaaaat-gttaacattatgcacaaacttgaag---
|||||||||||||||||||||||| || ||||||||||||||||| |||||||||||||||||||||||||||||||| || || || || ||||||||||| | |||  || | |||      |||| | ||||  ||      ||   ||||||| |   || |  || | |  ||| |    |   
CTGGCTTTTATCCTTTTATGATGCAGCCGTTGATTATTTGTCCACTACAAGGGTTATGCCAAGACTTGTAGAGGTTGTGAAAGGTTCAACAAAAGAGAAGgtgaggtttgaagtattgttgttttgtcgtgttgtcacatctcctttgtatcagaaataccattcatgtttttcctaaaataattgcag

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|78080157|gb|DV508569.1|DV508569

EST:     GGTTATGCCAAGACTTGTAGAGGTTGTCAAGGGCTCTACTAAAGAGAAG                         GTGGTCAGAGTTGTTGTGTTGTCCTTCCGCAATTTGCTGGCAAAGGGTGCA
genomic: GGTTATGCCAAGACTTGTAGAGGTTGTCAAGGGCTCTACTAAAGAGAAGgtaatgttct ... aaacttgaagGTGGTCAGAGTTGTTGTGTTGTCCTTCCGCAATTTGCTGGCAAAGGGTGCA

EST: gi|5847348|gb|AW000427.1|AW000427

EST:     GGGTTATGCCAAGACTTGTAGAGGTTGTCAAGGGCTCTACTAAAGAGAAG                         GTGGTCAGAGTTGTTGTGTTGTCCTTCCGCAATTTGCTGGCAAAGGGTGCA
genomic: GGGTTATGCCAAGACTTGTAGAGGTTGTCAAGGGCTCTACTAAAGAGAAGgtaatgttct ... aaacttgaagGTGGTCAGAGTTGTTGTGTTGTCCTTCCGCAATTTGCTGGCAAAGGGTGCA

EST: gi|60401227|gb|DN234034.1|DN234034

EST:     GGGTTATGCCAAGACTTGTAGAGGTTGTCAAGGGCTCTACTAAAGAGAAG                         GTGGTCAGAGTTGTTGTGTTGTCCTTCCGCAATTTGCTGGCAAAGGGTGCA
genomic: GGGTTATGCCAAGACTTGTAGAGGTTGTCAAGGGCTCTACTAAAGAGAAGgtaatgttct ... aaacttgaagGTGGTCAGAGTTGTTGTGTTGTCCTTCCGCAATTTGCTGGCAAAGGGTGCA

EST: gi|6031414|gb|AW076316.1|AW076316

EST:     GGGTTATGCCAAGACTTGTAGAGGTTGTCAAGGGCTCTACTAAAGAGAAG                         GTGGTCAGAGTTGTTGTGTTGTCCTTCCGCAATTTGCTGGCAAAGGGTGCA
genomic: GGGTTATGCCAAGACTTGTAGAGGTTGTCAAGGGCTCTACTAAAGAGAAGgtaatgttct ... aaacttgaagGTGGTCAGAGTTGTTGTGTTGTCCTTCCGCAATTTGCTGGCAAAGGGTGCA

EST: gi|6020588|gb|AW065621.1|AW065621

EST:     GTCAAGGGCTCTACTAAAGAGAAG                         GTGGTCAGAGTTGTTGTGTTGTCCTTCCGCAATTTGCTGGCAAAGGGTGCA
genomic: GTCAAGGGCTCTACTAAAGAGAAGgtaatgttct ... aaacttgaagGTGGTCAGAGTTGTTGTGTTGTCCTTCCGCAATTTGCTGGCAAAGGGTGCA

EST: gi|18170707|gb|BM340547.1|BM340547

EST:     AGGGCTCTACTAAAGAGAAG                         GTGGTCAGAGTTGTTGTGTTGTCCTTCCGCAATTTGCTGGCAAAGGGTACA
genomic: AGGGCTCTACTAAAGAGAAGgtaatgttct ... aaacttgaagGTGGTCAGAGTTGTTGTGTTGTCCTTCCGCAATTTGCTGGCAAAGGGTGCA

EST: gi|61119705|gb|DN560666.1|DN560666

EST:     GGGTTATGCCAAGACTTGTAGAGGTTGTCAAGGGCTCTACTAAAGAGAAG                         GTGGTCAGAGTTGTTGTGTTGTCCTTCCGCAATTTGCTGGCAAAGGGTGCA
genomic: GGGTTATGCCAAGACTTGTAGAGGTTGTCAAGGGCTCTACTAAAGAGAAGgtaatgttct ... aaacttgaagGTGGTCAGAGTTGTTGTGTTGTCCTTCCGCAATTTGCTGGCAAAGGGTGCA

EST: gi|6194754|gb|AW146858.1|AW146858

EST:     GGGTTATGCCAAGACTTGTAGAGGTTGTCAAGGGCTCTACTAAAGAGAAG                         GTGGTCAGAGTTGTTGTGTTGTCCTTCCGCAATTTGCTGGCAAAGGGTGCA
genomic: GGGTTATGCCAAGACTTGTAGAGGTTGTCAAGGGCTCTACTAAAGAGAAGgtaatgttct ... aaacttgaagGTGGTCAGAGTTGTTGTGTTGTCCTTCCGCAATTTGCTGGCAAAGGGTGCA

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: 244

CTGGCTTTTATCCTTTTATGATGCTGCAGTTGATTATTTGTCCACCACAAGGGTTATGCCAAGACTTGTAGAGGTTGTCAAGGGCTCTACTAAAGAGAAGgtaatgttct ... aaacttgaagGTGGTCAGAGTTGTTGTGTTGTCCTTCCGCAATTTGCTGGCAAAGGGTGCATTTGCTGCCCAGATGATCGATCTTGGATTGCCACAAATGGTACAAAACT

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 267

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 284

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 290

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGGCTTTTATCCTTTTATGATGCTGCAGTTGATTATTTGTCCACCACAAGGGTTATGCCAAGACTTGTAGAGGTTGTCAAGGGCTCTACTAAAGAGAAGgtaatgttctaaatttgcatgtcatattgtgccactgtaattacgtcagaaaaatgttaacattatgcacaaacttgaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA