ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

CTCTACTTTTGGTGATGGTCTTGAAAGAGAATTACCAGCATGCCTTCCCATACTCGTTGACAGGATGGGTAATGAAATTACAAGACTTACAGCTGTCAAGgtaagtttttgactgcttgcgtttgataccaatacttaattggaggttttaacatcgtgcattgcttgtttatggcatatttaatattaaagaacaaatg...

Basic information

species	Zea mays
transcript	GRMZM2G168629_T05
intron #	17
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G168629_T01 (Zea mays), 5'ss of exon 17
lower sequence: LOC_Os02g07120.1 (Oryza sativa), 5'ss of exon 17

CTCTACTTTTGGTGATGGTCTTGAAAGAGAATTACCAGCATGCCTTCCCATACTCGTTGACAGGATGGGTAATGAAATTACAAGACTTACAGCTGTCAAGgtaagtttttgactgcttgcgt-ttgataccaatacttaattggaggttttaacatcgtgcattgcttgtttatggcatatttaatattaaagaacaaatg--
 |  || ||||||||||||||  |||| ||| | || |||||||||||||| || ||||| || |||||||||||||| || ||||||||||| || |||||||| | | ||||||     |  ||| |   |   ||  ||       |||      | |||| ||| |       |  | |  | || || | ||| |   
ATTCACGTTTGGTGATGGTCTCCAAAGGGAACTGCCGGCATGCCTTCCCATTCTTGTTGATAGAATGGGTAATGAAATAACTAGACTTACAGCAGTTAAGgtaagctatcgactgcacctttactgacagataggattgcttaatctccttattg--attcattacttatgagcactacttgttttctttaaca-caattata

upper sequence: GRMZM2G168629_T01 (Zea mays), 5'ss of exon 17
lower sequence: LOC_Os02g07340.1 (Oryza sativa), 5'ss of exon 13

CTCTACTTTTGGTGATGGTCTTGAAAGAGAATTACCAGCATGCCTTCCCATACTCGTTGACAGGATGGGTAATGAAATTACAAGACTTACAGCTGTCAAGgtaagtttttgactgcttgcgtttgataccaatacttaattggaggttttaacatcg-tgcattgcttgtttatggcatatttaatattaaagaacaaatg---
 || || ||||||||||||||  |||| ||| | || |||||||||||| | || ||||| || |||||||||||||| || ||||||||||| || |||||||| |   ||||||   | |||  |  ||  |    ||||    | |    || | | |||| ||| |       |  | |  | || || | ||| |    
ATCCACGTTTGGTGATGGTCTCCAAAGGGAACTGCCGGCATGCCTTCCCGTTCTTGTTGATAGAATGGGTAATGAAATAACTAGACTTACAGCAGTTAAGgtaagctaccgactgc--acctttactgacag-atagcattgctaatctccttattgattcattacttatgagcactacttgttttctttaaca-caattatgt

upper sequence: GRMZM2G168629_T01 (Zea mays), 5'ss of exon 17
lower sequence: Vv12s0035g01840.t01 (Vitis vinifera), 5'ss of exon 18

CTCTACTTTTGGTGATGGTCTTGAAAGAGAATTACCAGCATGCCTTCCCATACTCGTTGACAGGATGGGTAATGAAATTACAAGACTTACAGCTGTCAAGgtaagtttttg-actgcttg--cgtttgataccaatacttaattggaggttttaacatcgtgcattgcttgtttatggcatatttaat-attaaagaacaaatg
 || || |||||||||   ||   |  ||||||||| |||||||||||  |||| |||||| ||||||| ||||| || ||  ||||||| ||||| |||||  ||||||| |    |||  | | |  |    |       ||   ||  || ||||  | | ||     |      || |  || | |||  |    |    
TTCAACATTTGGTGATAACCTCAGAGCAGAATTACCTGCATGCCTTCCTGTACTTGTTGACCGGATGGGAAATGAGATAACTCGACTTACTGCTGTAAAGgttggtttttgcatctattgaccatatattttttagggcctgtttttggggttgacattttcctttttagatcagaaacagacatattcatttcattgga----

upper sequence: GRMZM2G168629_T01 (Zea mays), 5'ss of exon 17
lower sequence: PP1S337_6V6.1 (Physcomitrella patens), 5'ss of exon 16

CTCTACTTTTGGTGATGGTCTTGAAAGAGAATTACCAGCATGCCTTCCCATACTCGTTGACAGGATGGGTAATGAAATTACAAGACTTACAGCTGTCAAGgtaagtttttgactgcttgcgtttgataccaatacttaattggaggttttaacatcgtgcattgcttgtttatggcatatttaatattaaagaacaaatg-------------------------------------
 || | | |||| |||  |||| | |  ||  |     ||||| | ||  |  |  | ||  |  |  | ||||||||||||||||| |||||||| ||||||||| | | |  |     |   ||        | |  ||   | || ||    ||   |    |     ||||  |  || || || |   |||| |                                      
TTCCATTCTTGGAGATCATCTTAAGAACGAGATGGGCACATGCTTGCCATTGTTGTTAGAGCGATTACGCAATGAAATTACAAGACTCACAGCTGTGAAGgtaagtgtattaacgacactgaacgacgttttgccct--tttctgattctatgtacgcaaacctttatagaatggtttggttgat-tttagccacaagtcttctgaagtttgtttacataattgtgcttgtatgcag

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|18383962|gb|BM417162.1|BM417162

EST:     TACTCGTTGACAGGATGGGTAATGAAATTACAAGACTTACAGCTGTCAAG                         GCATTTTCAGTTATTGCGAATTCACCTCTACGTATTGATCTCTCGTGTGTC
genomic: TACTCGTTGACAGGATGGGTAATGAAATTACAAGACTTACAGCTGTCAAGgtaagttttt ... cacttgacagGCATTTTCAGTTATTGCGAATTCACCTCTACGTATTGATCTCTCGTGTGTC

EST: gi|22489194|gb|BU049130.1|BU049130

EST:     TACTCGTTGACAGGATGGGTAATGAAATTACAAGACTTACAGCTGTCAAG                         GCATTTTCAGTTATTGCGAATTCACCTCTACGTATTGATCTCTCGTGTGTC
genomic: TACTCGTTGACAGGATGGGTAATGAAATTACAAGACTTACAGCTGTCAAGgtaagttttt ... cacttgacagGCATTTTCAGTTATTGCGAATTCACCTCTACGTATTGATCTCTCGTGTGTC

EST: gi|211432450|gb|FL213954.1|FL213954

EST:     TACTCGTTGACAGGATGGGTAATGAAATTACAAGACTTACAGCTGTCAAG                         GCATTTTCAGTTATTGCGAATTCACCTCTACGTATTGATCTCTCGTGTGTC
genomic: TACTCGTTGACAGGATGGGTAATGAAATTACAAGACTTACAGCTGTCAAGgtaagttttt ... cacttgacagGCATTTTCAGTTATTGCGAATTCACCTCTACGTATTGATCTCTCGTGTGTC

EST: gi|87298767|gb|DY470770.1|DY470770

EST:     TACTCGTTGACAGGATGGGTAATGAAATTACAAGACTTACAGCTGTCAAG                         GCATTTTCAGTTATTGCGAATTCACCTCTACGTATTGATCTCTCGTGTGTC
genomic: TACTCGTTGACAGGATGGGTAATGAAATTACAAGACTTACAGCTGTCAAGgtaagttttt ... cacttgacagGCATTTTCAGTTATTGCGAATTCACCTCTACGTATTGATCTCTCGTGTGTC

EST: gi|61118518|gb|DN559479.1|DN559479

EST:     TACTCGTTGACAGGATGGGTAATGAAATTACAAGACTTACAGCTGTCAAG                         GCATTTTCAGTTATTG
genomic: TACTCGTTGACAGGATGGGTAATGAAATTACAAGACTTACAGCTGTCAAGgtaagttttt ... cacttgacagGCATTTTCAGTTATTG

EST: gi|32859371|gb|CD999052.1|CD999052

EST:     TACTCGTTGACAGGATGGGTAATGAAATTACAAGACTTACAGCTGTCAAG                         GCATTTTCAGGTATTGCGAATTCACCTCTACGTATTGATCTCTCGTGTGTC
genomic: TACTCGTTGACAGGATGGGTAATGAAATTACAAGACTTACAGCTGTCAAGgtaagttttt ... cacttgacagGCATTTTCAGTTATTGCGAATTCACCTCTACGTATTGATCTCTCGTGTGTC

EST: gi|211432451|gb|FL213955.1|FL213955

EST:     TACTCGTTGACAGGATGGGTAATGAAATTACAAGACTTACAGCTGTCAAG                         GCATTTTCAGTTATTGCGAATTCACCTCTACGTATTGATCTCTCGTGTGTC
genomic: TACTCGTTGACAGGATGGGTAATGAAATTACAAGACTTACAGCTGTCAAGgtaagttttt ... cacttgacagGCATTTTCAGTTATTGCGAATTCACCTCTACGTATTGATCTCTCGTGTGTC

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: 397

CTCTACTTTTGGTGATGGTCTTGAAAGAGAATTACCAGCATGCCTTCCCATACTCGTTGACAGGATGGGTAATGAAATTACAAGACTTACAGCTGTCAAGgtaagttttt ... cacttgacagGCATTTTCAGTTATTGCGAATTCACCTCTACGTATTGATCTCTCGTGTGTCCTGGATCATGTTGTTTCTGAGCTCACAGCTTTCCTTCGCAAG

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 206

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 184

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 164

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTCTACTTTTGGTGATGGTCTTGAAAGAGAATTACCAGCATGCCTTCCCATACTCGTTGACAGGATGGGTAATGAAATTACAAGACTTACAGCTGTCAAGgtaagtttttgactgcttgcgtttgataccaatacttaattggaggttttaacatcgtgcattgcttgtttatggcatatttaatattaaagaacaaatg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG