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

gtgtgtacctcttttcttctttcatttccttatattgtctgactccatattagctgtttatgccttgtttactcaatttgttaaaccacacaagtcatttttcatgtcattagccattctgatggtgatgcataaatgatacttgtagGTTGAAAGATTGTTGTCTTCGGAACAGAAGGCTACAGATTATCGAACACCAGATGATGGAGCTGCACCAGATCATCGGCCAACTAATGCTTGTATAAG

Basic information

species	Zea mays
transcript	GRMZM5G823484_T01
intron #	4
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM5G823484_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os12g13590.1 (Oryza sativa), 3'ss of exon 18

gtgtgtacctcttttcttctttcatttccttatattgtctgactccatattagctgtttatgccttgtttactcaat--------ttgttaaaccacacaagtcatttttcatgtcattagccattctga-----tggtgatgcata-------aatgatacttg-tagGTTGAAAGATTGTTGTCTTCGGAACAGAAGGCTACAGATTATCGAACACCAGATGATGGAGCTGCACCAGATCATCGGCCAACTAATGCTTGTATAAG
                    |||  | |  | |  |  | | | |  | |||| ||||| || ||||||   |  |         |     || || | | || | ||||  ||||| |   |||  | |     |||| | |  |        |  | | ||||  |||||||||||||| ||||||| ||||||||||||||||||||||||||||||||||||||||||||||| |||||||| ||||| |||||||| |||||
-------------------gttcgctcctatctcattacaggcacactgttaggtgtttgtgtcttgttagtttgacattcatgatcagcgaatcagatatgttacttttggtgtcactgtgcatcttcaacgtttggttaagtgtgtgcttctatcgttgcttgacagGTTGAAAGATTGCTGTCTTCAGAACAGAAGGCTACAGATTATCGAACACCAGATGATGGAGCTGCACCGGATCATCGACCAACCAATGCTTGCATAAG

upper sequence: GRMZM5G823484_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA07G05160.1 (Glycine max), 3'ss of exon 18

gtgtgtacctcttttcttctttcatttccttatattgtctgactccatattagctgtttatgccttgtttactcaatttgttaaaccacacaagtcatttttcatgtcattagccattctgatggtgatgcataaatgatacttgtagGTTGAAAGATTGTTGTCTTCGGAACAGAAGGCTACAGATTATCGAACACCAGATGATGGAGCTGCACCAGATCATCGGCCAACTAATGCTTGTATAAG
                                |  ||  | |     | |    ||||| | | || | || |||| ||  | ||||         |  |  ||     |||   ||||   |         | ||      | | |||| ||  | ||| | ||  | ||||| |||||||||||||||||| |||| |||||||||   || || || || ||| |||| | ||| || | |||
------------------------------gtttctggttcagggtgtttcctgtgttttttctttttctaatcaagtt--tgaacc-------ctagctcccaaactcttaaatattccact---------ttaaaccccttggcagGTGGAGCGGTTGCTTTCAGCTGAACAAAAGGCTACAGATTATCGATCACCTGATGATGGAATGGCTCCTGACCACCGGGCAACCAGTGCCTGCACAAG

upper sequence: GRMZM5G823484_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA16G01660.1 (Glycine max), 3'ss of exon 18

gtgtgtacctcttttcttctttcatttccttatattgtctgactccatattagctgtttatgccttgtttactcaatttgttaaaccacacaagtcatttttcatgtcattagccattctgatggtgatgcataaatgatacttgtagGTTGAAAGATTGTTGTCTTCGGAACAGAAGGCTACAGATTATCGAACACCAGATGATGGAGCTGCACCAGATCATCGGCCAACTAATGCTTGTATAAG
                                               |  | | |     ||  |  | || |   ||| ||   |    |||||     | |  |     |   | ||| |   |    | | ||      | | |||| ||  | ||| | ||  | ||||| |||||||||||||||||| |||| |||||||||   || || || || ||| |||| | ||| || | |||
--------------------------------------------tttttctggttcagggtgtttcctgtattt--tttctttttcttttcaagtttgaatcctagctcccaa--actcttaaaattccactttaaaccccttggcagGTGGAGCGGTTGCTTTCAGCTGAACAAAAGGCTACAGATTATCGATCACCTGATGATGGAATGGCTCCTGACCACCGGGCAACCAGTGCCTGCACAAG

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|9566477|gb|BE475986.1|BE475986

EST:     CTGCTGCTCACAAAGGACTGCTACAATGTATTGATACTGTTATGTCTGAG                         GTTGAAAGATTGTTGTCTTCAGAACAGAAGGCTACAGATTATCGAACACCA
genomic: CTGCTGCTCACAAAGGACTGCTACAATGTATTGATACTGTTATGTCTGAGgtgtgtacct ... atacttgtagGTTGAAAGATTGTTGTCTTCGGAACAGAAGGCTACAGATTATCGAACACCA

EST: gi|32802642|gb|CD954878.1|CD954878

EST:     CTGCTGCTCACAAAGGACTGCTACAATGTATTGATACTGTTATGTCTGAG                         GTTGAAAGATTGTTGTCTTCAGAACAGAAGGCTACAGATTATCGAACACCA
genomic: CTGCTGCTCACAAAGGACTGCTACAATGTATTGATACTGTTATGTCTGAGgtgtgtacct ... atacttgtagGTTGAAAGATTGTTGTCTTCGGAACAGAAGGCTACAGATTATCGAACACCA

EST: gi|32804847|gb|CD957083.1|CD957083

EST:     CTGCTGCTCACAAAGGACTGCTACAATGTATTGATACTGTCATGTCTGAG                         GTTGAAAGATTGTTGTCTTCAGAACAGAAGGCTACAGATTATCGAACACCA
genomic: CTGCTGCTCACAAAGGACTGCTACAATGTATTGATACTGTTATGTCTGAGgtgtgtacct ... atacttgtagGTTGAAAGATTGTTGTCTTCGGAACAGAAGGCTACAGATTATCGAACACCA

EST: gi|71434510|gb|DR815560.1|DR815560

EST:     CTGCTGCTCACAAAGGACTGCTACAATGTATTGATACTGTTATGTCTGAG                         GTTGAAAGATTGTTGTCTTCGGAACAGAAGGCTACAGATTATCGAACACCA
genomic: CTGCTGCTCACAAAGGACTGCTACAATGTATTGATACTGTTATGTCTGAGgtgtgtacct ... atacttgtagGTTGAAAGATTGTTGTCTTCGGAACAGAAGGCTACAGATTATCGAACACCA

EST: gi|60396240|gb|DN229109.1|DN229109

EST:     ACAATGTATTGATACTGTTATGTCTGAG                         GTTGAAAGATTGTTGTCTTCGGAACAGAAGGCTACAGATTATCGAACACCA
genomic: ACAATGTATTGATACTGTTATGTCTGAGgtgtgtacct ... atacttgtagGTTGAAAGATTGTTGTCTTCGGAACAGAAGGCTACAGATTATCGAACACCA

EST: gi|5847426|gb|AW000505.1|AW000505

EST:     CTGCTGCTCACAAAGGACTGCTACAATGTATTGATACTGTTATGTCTGAG                         GTTGAAAGATTGTTGTCTTCAGAACAGAAGGCTACAGATTATCGAACACCA
genomic: CTGCTGCTCACAAAGGACTGCTACAATGTATTGATACTGTTATGTCTGAGgtgtgtacct ... atacttgtagGTTGAAAGATTGTTGTCTTCGGAACAGAAGGCTACAGATTATCGAACACCA

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: 193

TCATCCGTCTGCTTGTGAAGATATGGGGTCAGCAGTATCAGTAGTTGAGGCTGCTGCTCACAAAGGACTGCTACAATGTATTGATACTGTTATGTCTGAGgtgtgtacct ... atacttgtagGTTGAAAGATTGTTGTCTTCGGAACAGAAGGCTACAGATTATCGAACACCAGATGATGGAGCTGCACCAGATCATCGGCCAACTAATGCTTGTATAAG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 195

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 208

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 164

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

gtcatttttcatgtcattagccattctgatggtgatgcataaatgatacttgtagGTTGAAAGATTGTTGTCTTCGGAACAGAAGGCTACAGATTATCGAACACCAGATGATGGAGCTGCACCAGATCATCGGCCAACTAATGCTTGTATAAG

                       ttctgat  putative branch site (score: 164)
                                      ataaatgata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgtacctcttttcttctttcatttccttatattgtctgactccatattagctgtttatgccttgtttactcaatttgttaaaccacacaagtcatttttcatgtcattagccattctgatggtgatgcataaatgatacttgtagGTTGAAAGATTGTTGTCTTCGGAACAGAAGGCTACAGATTATCGAACACCAGATGATGGAGCTGCACCAGATCATCGGCCAACTAATGCTTGTATAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA