ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

GTAAAGCAAATGGTTGTTGCTACACTTGCGGAGTCAGGAATGAATCTTTTAGATGAGGTCATAGAGAGCATCATTGATAAGgtgtgctgagatatttgtattgacatacttgtctggctatttccttttcatgtagagcccttgtggacttataagaaaatcatgaaaacaatgtgtggag...

Basic information

species	Zea mays
transcript	GRMZM2G112672_T02
intron #	6
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G112672_T02 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os03g42840.1 (Oryza sativa), 5'ss of exon 6

GTAAAGCAAATGGTTGTTGCTACACTTGCGGAGTCAGGAATGAATCTTTTAGATGAGGTCATAGAGAGCATCATTGATAAGgtgtgc-tgagatatttgtattgacatacttgtctggctatttccttttcatgtagagcccttgtggacttataa-gaaaatcatgaaaacaatgtgtggag-
|| ||||||||||||||||| |||||||| ||||| |||||||||||||  ||||| ||||||||||||||||||||||||||   | |||| | |||   |  || ||    |||||  ||    ||||||||   | |  ||    | | || | ||  |||||     |  | | ||    
GTTAAGCAAATGGTTGTTGCAACACTTGCTGAGTCGGGAATGAATCTTTCGGATGAAGTCATAGAGAGCATCATTGATAAGgtaaacatgagttgtttacttcaacgtatcaatctggggatagttttttcatg---atcatttaatcaatcatgatgagcatcattttccctttttatgctct

upper sequence: GRMZM2G112672_T02 (Zea mays), 5'ss of exon 6
lower sequence: Vv00s1569g00020.t01 (Vitis vinifera), 5'ss of exon 6

GTAAAGCAAATGGTTGTTGCTACACTTGCGGAGTCAGGAATGAATCTTTTAGATGAGGTCATAGAGAGCATCATTGATAAGgtgtgctgagatatttgtattgacatacttgtctggctatttccttttcatgtagagcccttgtggacttataagaaaatcatgaaaacaatgtgtggag--------------
|| ||||| ||||| || ||||| ||||| || || || |||||||||| |||||| || ||||| || |||||||||||||||  || |   ||||| ||  |     |  | |  |||||| ||| | |||        | || ||  || ||    ||| |||  ||| |   |                  
GTCAAGCAGATGGTAGTGGCTACGCTTGCTGAATCTGGCATGAATCTTTCAGATGATGTAATAGAAAGTATCATTGATAAGgtgctctca---atttg-atcaa-----tcattttactatttgcttcttatg--acatattggtagatgtacaa---catcttgagcacattccctcagaatttcataccacca

upper sequence: GRMZM2G112672_T02 (Zea mays), 5'ss of exon 6
lower sequence: Vv19s0015g01070.t01 (Vitis vinifera), 5'ss of exon 6

GTAAAGCAAATGGTTGTTGCTACACTTGCGGAGTCAGGAATGAATCTTTTAGATGAGGTCATAGAGAGCATCATTGATAAGgtgtgctgagatatttgtattgacatacttgtc----tggctatttccttttcatgtagagcccttgtggacttataagaaaatcatgaaaacaatgtgtggag
|| ||||||||||| || || |||||||| || || || ||||||||||  ||||| || ||||| || |||||||| ||||||  |    |      | |||||  | ||  |    ||   | |  ||  |||  |  | ||        |  ||    ||   |||     |   |      
GTGAAGCAAATGGTAGTGGCCACACTTGCTGAATCTGGTATGAATCTTTCGGATGATGTTATAGAAAGTATCATTGACAAGgtgctccctcaaccccat-ttgactcatttaacatcttgtacagtatctgatcacctctaaccacccatttcacatgtttaatggatggtgtaagcatcca---

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|5846848|gb|AI999931.1|AI999931

EST:     AGTCAGGAATGAATCTTTTAGATGAGGTCATAGAGAGCATCATTGATAAG                         ACTTTTGAGGAGGCAGACACAAAGCATGATGGGAAAATTGACAAAGAAGAA
genomic: AGTCAGGAATGAATCTTTTAGATGAGGTCATAGAGAGCATCATTGATAAGgtgtgctgag ... tttctaaaagACTTTTGAGGAGGCAGACACAAAGCATGATGGGAAAATTGACAAAGAAGAA

EST: gi|211265415|gb|FL346370.1|FL346370

EST:     AGTCAGGAATGAATCTTTTAGATGAGGTCATAGAGAGCATCATTGATAAG                         ACTTTTGAGGAGGCAGACACAAAGCATGATGGGAAAATTGACAAAGAAGAA
genomic: AGTCAGGAATGAATCTTTTAGATGAGGTCATAGAGAGCATCATTGATAAGgtgtgctgag ... tttctaaaagACTTTTGAGGAGGCAGACACAAAGCATGATGGGAAAATTGACAAAGAAGAA

EST: gi|31360067|gb|CD444424.1|CD444424

EST:     AGTCAGGAATGAATCTTTTAGATGAGGTCATAGAGAGCATCATTGATAAG                         ACTTTTGAGGAGGCAGACACAAAGCATGATGGGAAAATTGACAAAGAAGAA
genomic: AGTCAGGAATGAATCTTTTAGATGAGGTCATAGAGAGCATCATTGATAAGgtgtgctgag ... tttctaaaagACTTTTGAGGAGGCAGACACAAAGCATGATGGGAAAATTGACAAAGAAGAA

EST: gi|5525520|gb|AI861413.1|AI861413

EST:     AGTCAGGAATGAATCTTTTAGATGAGGTCATAGAGAGCATCATTGATAAG                         ACTTTTGAGGAGGCAGACACAAAGCATGATGGGAAAATTGACAAAGAAGAA
genomic: AGTCAGGAATGAATCTTTTAGATGAGGTCATAGAGAGCATCATTGATAAGgtgtgctgag ... tttctaaaagACTTTTGAGGAGGCAGACACAAAGCATGATGGGAAAATTGACAAAGAAGAA

EST: gi|60354409|gb|DN221382.1|DN221382

EST:     AGTCAGGAATGAATCTTTTAGATGAGGTCATAGAGAGCATCATTGATAAG                         ACTTTTGAGGAGGCAGACACAAAGCATGATGGGAAAATTGACAAAGAAGAA
genomic: AGTCAGGAATGAATCTTTTAGATGAGGTCATAGAGAGCATCATTGATAAGgtgtgctgag ... tttctaaaagACTTTTGAGGAGGCAGACACAAAGCATGATGGGAAAATTGACAAAGAAGAA

EST: gi|8930139|gb|BE224783.1|BE224783

EST:     AGTCAGGAATGAATCTTTTAGATGAGGTCATAGAGAGCATCATTGATAAG                         ACTTTTGAGGAGGCAGACACAAAGCATGATGGGAAAATTGACAAAGAAGAA
genomic: AGTCAGGAATGAATCTTTTAGATGAGGTCATAGAGAGCATCATTGATAAGgtgtgctgag ... tttctaaaagACTTTTGAGGAGGCAGACACAAAGCATGATGGGAAAATTGACAAAGAAGAA

EST: gi|6194508|gb|AW146612.1|AW146612

EST:     AGTCAGGAATGAATCTTTTAGATGAGGTCATAGAGAGCATCATTGATAAG                         ACTTTTGAGGAGGCAGACACAAAGCATGATGGGAAAATTGACAAAGAAGAA
genomic: AGTCAGGAATGAATCTTTTAGATGAGGTCATAGAGAGCATCATTGATAAGgtgtgctgag ... tttctaaaagACTTTTGAGGAGGCAGACACAAAGCATGATGGGAAAATTGACAAAGAAGAA

EST: gi|78021323|gb|DV489710.1|DV489710

EST:     AGTCAGGAATGAATCTTTTAGATGAGGTCATAGAGAGCATCATTGATAAG                         ACTTTTGAGGAGGCAGACACAAAGCATGATGGGAAAATTGACAAAGAAGAA
genomic: AGTCAGGAATGAATCTTTTAGATGAGGTCATAGAGAGCATCATTGATAAGgtgtgctgag ... tttctaaaagACTTTTGAGGAGGCAGACACAAAGCATGATGGGAAAATTGACAAAGAAGAA

EST: gi|211071789|gb|FK958795.1|FK958795

EST:     AGTCAGGAATGAATCTTTTAGATGAGGTCATAGAGAGCATCATTGATAAG                         ACTTTTGAGGAGGCAGACACAAAGCATGATGGGAAAATTGACAAAGAAGAA
genomic: AGTCAGGAATGAATCTTTTAGATGAGGTCATAGAGAGCATCATTGATAAGgtgtgctgag ... tttctaaaagACTTTTGAGGAGGCAGACACAAAGCATGATGGGAAAATTGACAAAGAAGAA

EST: gi|5770153|gb|AI973327.1|AI973327

EST:     AGTCAGGAATGAATCTTTTAGATGAGGTCATAGAGAGCATCATTGATAAG                         ACTTTTGAGGAGGCAGACACAAAGCATGATGGGAAAATTGACAAAGAAGAA
genomic: AGTCAGGAATGAATCTTTTAGATGAGGTCATAGAGAGCATCATTGATAAGgtgtgctgag ... tttctaaaagACTTTTGAGGAGGCAGACACAAAGCATGATGGGAAAATTGACAAAGAAGAA

EST: gi|9952360|gb|BE638943.1|BE638943

EST:     AGTCAGGAATGAATCTTTTAGATGAGGTCATAGAGAGCATCATTGATAAG                         ACTTTTGAGGAGGCAGACACAAAGCATGATGGGAAAATTGACAAAGAAGAA
genomic: AGTCAGGAATGAATCTTTTAGATGAGGTCATAGAGAGCATCATTGATAAGgtgtgctgag ... tttctaaaagACTTTTGAGGAGGCAGACACAAAGCATGATGGGAAAATTGACAAAGAAGAA

EST: gi|211483288|gb|FL326631.1|FL326631

EST:     AGTCAGGAATGAATCTTTTARATGAGGTCATAGAGAGCATCATTGATAAG                         ACTTTTGAGGAGGCAGACACAAAGCATGATGGGAAAATTGACAAAGAAGAA
genomic: AGTCAGGAATGAATCTTTTAGATGAGGTCATAGAGAGCATCATTGATAAGgtgtgctgag ... tttctaaaagACTTTTGAGGAGGCAGACACAAAGCATGATGGGAAAATTGACAAAGAAGAA

EST: gi|211071790|gb|FK958796.1|FK958796

EST:     GTCAGGAATGAATCTTTTAGATGAGGTCATAGAGAGCATCATTTGATAAG                         ACTTTTGAGGAGGCAGACACAAAGCATGATGGGAAAATTGACAAAGAAGA
genomic: GTCAGGAATGAATCTTTTAGATGAGGTCATAGAGAGCATCATT-GATAAGgtgtgctgag ... tttctaaaagACTTTTGAGGAGGCAGACACAAAGCATGATGGGAAAATTGACAAAGAAGA

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: 205

GTAAAGCAAATGGTTGTTGCTACACTTGCGGAGTCAGGAATGAATCTTTTAGATGAGGTCATAGAGAGCATCATTGATAAGgtgtgctgag ... tttctaaaagACTTTTGAGGAGGCAGACACAAAGCATGATGGGAAAATTGACAAAGAAGAATGGCGCAATTTAGTAGTGAGGCATCCCTCTTTATTGAAGAACATGACAC

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 254

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 256

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 201

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTAAAGCAAATGGTTGTTGCTACACTTGCGGAGTCAGGAATGAATCTTTTAGATGAGGTCATAGAGAGCATCATTGATAAGgtgtgctgagatatttgtattgacatacttgtctggctatttccttttcatgtagagcccttgtggacttataagaaaatcatgaaaacaatgtgtggag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aagaaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaaacaa