ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

GTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAACGGCTCCCTGAGGCCACAATTGGTGGAGgtatgtgatatcttcatctgacaaactttgttactgtgttctctctgtccctagcttatatcctacaatcacataagattgcagtactctgatgcttttttggcattcttgcag

Basic information

species	Zea mays
transcript	GRMZM2G140689_T01
intron #	7
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G140689_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os06g06410.2 (Oryza sativa), 5'ss of exon 8

GTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAACGGCTCCCTGAGGCCACAATTGGTGGAGgta-tgtgatatcttcatctgacaaactttgttac-tgtgttctctctgtccct-agcttatatcctacaatcacataagattgcagtactctgatgcttttttggcattcttgcag
||||||||||||||||||||||| |||||  | || ||||| ||||||||||| |||||||| || ||||| || ||||||| |||  | | | |   || ||  || | | |  |  ||  ||| |||   | | ||  || | |  |        | ||| |  || | | ||||                   
GTTCCTGGTGTTCCAATCATGTATATCACTCGGCACAGGTACTCGATAGAACGACTCCCTGAAGCTACAATCGGAGGAGgtaatgtattttgtgctggtggcagtctctatcaaatccgtcttctatgttaatcatctcctacctttaacctgaggcacatttcgata-tgtaatgcag-----------------

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|19769624|gb|BQ034345.1|BQ034345

EST:     AAGACATAGGTATTCGATAGAACGGCTCCCTGAGGCCACAATTGGTGGAG                         CACCAAGAATCTGATCGGTGCAGACATGAGATGTTCTGGGATGTAATACTA
genomic: AAGACATAGGTATTCGATAGAACGGCTCCCTGAGGCCACAATTGGTGGAGgtatgtgata ... attcttgcagCACCAAGAATCTGATCGGTGCAGACATGAGATGTTCTGGGATGTAATACTA

EST: gi|89252677|gb|DY624463.1|DY624463

EST:     AAGACATAGGTATTCGATAGAACGGCTCCCTGAGGCCACAATTGGGGGAG                         CACCAAGAATCTGATCGGTGCAGACATGAGATGTTCTGGGATGTAATACTA
genomic: AAGACATAGGTATTCGATAGAACGGCTCCCTGAGGCCACAATTGGTGGAGgtatgtgata ... attcttgcagCACCAAGAATCTGATCGGTGCAGACATGAGATGTTCTGGGATGTAATACTA

EST: gi|19770099|gb|BQ034820.1|BQ034820

EST:     AAGACATAGGTATTCGATAGAACGGCTCCCTGAGGCCACAATTGGTGGAG                         CACCAAGAATCTGATCGGTGCAGACATGAGATGTTCTGGGATGTAATACTA
genomic: AAGACATAGGTATTCGATAGAACGGCTCCCTGAGGCCACAATTGGTGGAGgtatgtgata ... attcttgcagCACCAAGAATCTGATCGGTGCAGACATGAGATGTTCTGGGATGTAATACTA

EST: gi|211091999|gb|FL476412.1|FL476412

EST:     AAGACATAGGTATTCGATAGAACGGCTCCCTGAGGCCACAATTGGTGGAG                         CACCAAGAATCTGATCGGTGCAGACATGAGATGTTCTGGGATGTAATACTA
genomic: AAGACATAGGTATTCGATAGAACGGCTCCCTGAGGCCACAATTGGTGGAGgtatgtgata ... attcttgcagCACCAAGAATCTGATCGGTGCAGACATGAGATGTTCTGGGATGTAATACTA

EST: gi|19436894|gb|BM953304.1|BM953304

EST:     AAGACATAGGTATTCGATAGAACGGCTCCCTGAGGCCACAATTGGTGGAG                         CACCAAGAATCTGATCGGTGCAGACATGAGATGTTCTGGGATGTAATACTA
genomic: AAGACATAGGTATTCGATAGAACGGCTCCCTGAGGCCACAATTGGTGGAGgtatgtgata ... attcttgcagCACCAAGAATCTGATCGGTGCAGACATGAGATGTTCTGGGATGTAATACTA

EST: gi|37383195|gb|CF628588.1|CF628588

EST:     AAGACATAGGTATTCGATAGAACGGCTCCCTGAGGCCACAATTGGTGGAG                         CACCAAGAATCTGATCGGTGCAGACATGAGATGTTCTGGGATGTAATACTA
genomic: AAGACATAGGTATTCGATAGAACGGCTCCCTGAGGCCACAATTGGTGGAGgtatgtgata ... attcttgcagCACCAAGAATCTGATCGGTGCAGACATGAGATGTTCTGGGATGTAATACTA

EST: gi|19057702|gb|BM736369.1|BM736369

EST:     AAGACATAGGTATTCGATAGAACGGCTCCCTGAGGCCACAATTGGTGGAG                         CACCAAGAATCTGATCGGTGCAGACATGAGATGTTCTGGGATGTAATACTA
genomic: AAGACATAGGTATTCGATAGAACGGCTCCCTGAGGCCACAATTGGTGGAGgtatgtgata ... attcttgcagCACCAAGAATCTGATCGGTGCAGACATGAGATGTTCTGGGATGTAATACTA

EST: gi|78083854|gb|DV512247.1|DV512247

EST:     AAGACATAGGTATTCGATAGAACGGCTCCCTGAGGCCACAATTGGTGGAG                         CACCAAGAATCTGATCGGTGCAGACATGAGATGTTCTGGGATGTAATACTA
genomic: AAGACATAGGTATTCGATAGAACGGCTCCCTGAGGCCACAATTGGTGGAGgtatgtgata ... attcttgcagCACCAAGAATCTGATCGGTGCAGACATGAGATGTTCTGGGATGTAATACTA

EST: gi|19436893|gb|BM953303.1|BM953303

EST:     AAGACATAGGTATTCGATAGAACGGCTCCCTGAGGCCACAATTGGTGGAG                         CACCAAGAATCTGATCGGTGCAGACATGAG
genomic: AAGACATAGGTATTCGATAGAACGGCTCCCTGAGGCCACAATTGGTGGAGgtatgtgata ... attcttgcagCACCAAGAATCTGATCGGTGCAGACATGAG

EST: gi|50330326|gb|CO525452.1|CO525452

EST:     AAGACATAGGTATTCGATAGAACGGCTCCCTGAGGCCACAATTGGTGGAG                         CACCAAGAATCTGATCGGTGCAGACATGAGATGTTTTGGGATGTAATACTA
genomic: AAGACATAGGTATTCGATAGAACGGCTCCCTGAGGCCACAATTGGTGGAGgtatgtgata ... attcttgcagCACCAAGAATCTGATCGGTGCAGACATGAGATGTTCTGGGATGTAATACTA

EST: gi|5649962|gb|AI920322.1|AI920322

EST:     AAGACATAGGTATTCGATAGAACGGCTCCCTGAGGCCACAATTGGTGGAG                         CACCAAGAATCTGATCGGTGCAGACATGAGATGTTCTGGGATGTAATACT
genomic: AAGACATAGGTATTCGATAGAACGGCTCCCTGAGGCCACAATTGGTGGAGgtatgtgata ... attcttgcagCACCAAGAATCTGATCGGTGCAGACATGAGATGTTCTGGGATGTAATACT

EST: gi|19057549|gb|BM736231.1|BM736231

EST:     AAGACATAGGTATTCGATAGAACGGCTCCCTGAGGCCACAATTGGTGGAG                         CACCAAGAATCTGATCGGTGCAGACATGAGATGTTCTGGGATGTAATACTA
genomic: AAGACATAGGTATTCGATAGAACGGCTCCCTGAGGCCACAATTGGTGGAGgtatgtgata ... attcttgcagCACCAAGAATCTGATCGGTGCAGACATGAGATGTTCTGGGATGTAATACTA

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: 46 (upstream exon), 49 (downstream exon)
Score: 176

GTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAACGGCTCCCTGAGGCCACAATTGGTGGAGgtatgtgata ... attcttgcagCACCAAGAATCTGATCGGTGCAGACATGAGATGTTCTGGGATGTAATACTATGGCGGTACTTGTCCATCTGACCAAGTCACTATTTCATGTTTCAGTCCA

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 103

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 156

Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 103

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAACGGCTCCCTGAGGCCACAATTGGTGGAGgtatgtgatatcttcatctgacaaactttgttactgtgttctctctgtccctagcttatatcctacaatcacataagattgcagtactctgatgcttttttggcattcttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG