ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

GTCATTCCAATTGGAGGAATGTTTGCAATGACACTTTGGCTAGGGAACAGTGCGTACCTCTACATATCTGTCGCATTTGCACAGATGTTGAAGGCAATAAgtatgtgtgctaccctcagttttgattgtgaggaaaatatcaggatttgattttgatgaacttaccattgaatgatacag

Basic information

species	Zea mays
transcript	GRMZM2G022793_T01
intron #	4
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G022793_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os08g04110.2 (Oryza sativa), 5'ss of exon 4

GTCATTCCAATTGGAGGAATGTTTGCAATGACACTTTGGCTAGGGAACAGTGCGTACCTCTACATATCTGTCGCATTTGCACAGATGTTGAAGGCAATAAgtatgtgtgctaccctcagttttga-ttgtgagg----------aaaatatcaggatttgattttgatgaacttaccattgaatgat-acag
||||||||||| |||| |||||||||||||||||| ||||||||||||||||| |||||||| |||||||| ||||||||||||||| ||||||| ||||||||||| ||| |  |   | | || |  | |||          |  |  | || || |||| || ||| |||     ||| |  ||   ||
GTCATTCCAATCGGAGCAATGTTTGCAATGACACTCTGGCTAGGGAACAGTGCTTACCTCTATATATCTGTTGCATTTGCACAGATGCTGAAGGCGATAAgtatgtgagctgctttttttatcgagtcataaggttttttttttattaatttagaatatgatgttaatgtactctttgttggaaaattgtag

upper sequence: GRMZM2G022793_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA08G18730.1 (Glycine max), 5'ss of exon 5

GTCATTCCAATTGGAGGAATGTTTGCAATGACACTTTGGCTAGGGAACAGTGCGTACCTCTACATATCTGTCGCATTTGCACAGATGTTGAAGGCAATAAgtatgt----gtgctaccctcagttttgattgtgaggaaaatatcaggatttgattttgatgaacttaccattgaatgatacag------------------------------------------------------------------------
||  | |||||||| |  |||||||||||||| |||||||| || || | ||| ||||| || || ||||| || |||||||| ||| |||||||||| |||| ||    ||| | |  |   || |   |   ||  |  ||||    |    ||  |||  |  ||||| | |   ||  |                                                                         
GTAGTGCCAATTGGGGCCATGTTTGCAATGACTCTTTGGCTGGGAAATACTGCCTACCTGTATATTTCTGTTGCTTTTGCACAAATGCTGAAGGCAATTAgtaagttttagtgatcctgttgtttattgataatagttaggtatctttgtccatttaggat--atctaccaatcaccaatggaaagcataattaccaaatgtgtatcataaggcatttaaaaccatctgatctattggttaatcaacttgccttag

upper sequence: GRMZM2G022793_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA15G40160.1 (Glycine max), 5'ss of exon 4

GTCATTCCAATTGGAGGAATGTTTGCAATGACACTTTGGCTAGGGAACAGTGCGTACCTCTACATATCTGTCGCATTTGCACAGATGTTGAAGGCAATAAgtatgt----gtgctaccctcagttttgattgtgaggaaaatatcaggatttgattttgatgaacttaccattgaatgatacag------------------
||  | |||||||| |  |||||||||||||| |||||||| || || | ||| ||||| || || ||||| || |||||||| ||| |||||||||| |||| ||    ||| | |     ||| |   |   ||  |  ||||    |    || ||||  |  ||||| | |   ||  |                   
GTAGTGCCAATTGGGGCCATGTTTGCAATGACTCTTTGGCTGGGAAATACTGCCTACCTGTATATTTCTGTTGCTTTTGCACAAATGCTGAAGGCAATTAgtaagttttagtgatcctgctggttattgataatagttaggtatctttgtccatttatgat--atctaccaatcaccaatggaaagcataattgctaaatgt

upper sequence: GRMZM2G022793_T01 (Zea mays), 5'ss of exon 4
lower sequence: AT3G14410.1 (Arabidopsis thaliana), 5'ss of exon 4

GTCATTCCAATTGGAGGAATGTTTGCAATGACACTTTGGCTAGGGAACAGTGCGTACCTCTACATATCTGTCGCATTTGCACAGATGTTGAAGGCAATAAgtatgtgtgctaccctcagttttgatt----gtgaggaaaatatcaggatttgat-tttgatgaacttaccattgaatgatacag------------
|| |||||||| || | ||||||||||||||| || ||| | || |||| ||| |||||||||||||| || |||||||| |||||||||||||| ||||||| |    ||   |    | ||| ||     | ||    || |     | | || | |||  |||     |  | ||  | ||             
GTTATTCCAATAGGTGCAATGTTTGCAATGACCCTCTGGTTGGGAAACACTGCCTACCTCTACATATCAGTTGCATTTGCGCAGATGTTGAAGGCTATAAgtaag-aaactgttcatgctcttggttcctcataagtcttatgtttacttcttatatctgactaacaatgtacagtattcttcaaccatacttgcag

upper sequence: GRMZM2G022793_T01 (Zea mays), 5'ss of exon 4
lower sequence: AT1G53660.1 (Arabidopsis thaliana), 5'ss of exon 4

GTCATTCCAATTGGAGGAATGTTTGCAATGACACTTTGGCTAGGGAACAGTGCGTACCTCTACATATCTGTCGCATTTGCACAGATGTTGAAGGCAATAAgtatg----tgtgctaccctcagttttgattgtgaggaaaatatcaggatttgattttgatgaact-taccattgaatgatacag
|| |||||||| || | ||||||||||||||| || ||| |||| |||| ||| || ||||||||| |||| |||||| | || |||||||| || || |||| |    |  |||   |    | |   ||| |    |  ||| |   || |||  | | |||   ||   ||| |        
GTTATTCCAATAGGTGCAATGTTTGCAATGACTCTATGGTTAGGAAACACTGCTTATCTCTACATAACTGTTGCATTTTCCCAAATGTTGAAAGCCATCAgtaagaacttaagctcttcctgatctcatttgcgtt--acttataaattttagataatcaagaatcatatttttgcag-------

upper sequence: GRMZM2G022793_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv15s0046g00460.t01 (Vitis vinifera), 5'ss of exon 4

GTCATTCCAATTGGAGGAATGTTTGCAATGACACTTTGGCTAGGGAACAGTGCGTACCTCTACATATCTGTCGCATTTGCACAGATGTTGAAGGCAATAAgtatgtg--tgctaccct-cagttttgattgtgaggaaaatatcaggatttgattttgatgaacttaccattgaatgatacag------------------
|| || || ||||| | ||  ||||||||||| |||||||| || |||| ||| ||||| || || ||||| ||||||||||| |||||||||||||| |||| ||   ||| |  || |  |||    | |       | |  || || |    || ||||      | || | || |||||                  
GTGATCCCTATTGGTGCAACATTTGCAATGACTCTTTGGCTGGGAAACACTGCTTACCTGTATATTTCTGTTGCATTTGCACAAATGTTGAAGGCAATTAgtaagttcttgcaattcttctatttcatctatctttctgacaagag-atctatacttaatgataaatactttaattgctacagcttcaaaatctatatcaa

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|91053683|gb|EB164101.1|EB164101

EST:     TGCGTACCTCTACATATCTGTCGCATTTGCACAGATGTTGAAGGCAATAA                         TGCCTGTAGCCGTGTTTCTTCTGGGAGCAGCATTTGGCCTGGAAGAAATGA
genomic: TGCGTACCTCTACATATCTGTCGCATTTGCACAGATGTTGAAGGCAATAAgtatgtgtgc ... aatgatacagTGCCTGTAGCCGTGTTTCTTCTGGGAGCAGCATTTGGCCTGGAAGAAATGA

EST: gi|148949951|gb|EC895462.2|EC895462

EST:     TGCGTACCTCTACATATCTGTCGCATTTGCACAGATGTTGAAGGCAATAA                         TGCCTGTAGCCGTGTTTCTTCTGGGAGCAGCATTTGGCCTGGAAGAAATGA
genomic: TGCGTACCTCTACATATCTGTCGCATTTGCACAGATGTTGAAGGCAATAAgtatgtgtgc ... aatgatacagTGCCTGTAGCCGTGTTTCTTCTGGGAGCAGCATTTGGCCTGGAAGAAATGA

EST: gi|148958042|gb|EC904220.2|EC904220

EST:     TGCGTACCTCTACATATCTGTCGCATTTGCACAGATGTTGAAGGCAATAA                         TGCCTGTAGCCGTGTTTCTTCTGGGAGCAGCATTTGGCCTGGAAGAAATGA
genomic: TGCGTACCTCTACATATCTGTCGCATTTGCACAGATGTTGAAGGCAATAAgtatgtgtgc ... aatgatacagTGCCTGTAGCCGTGTTTCTTCTGGGAGCAGCATTTGGCCTGGAAGAAATGA

EST: gi|211529569|gb|FL022744.1|FL022744

EST:     TGCGTACCTCTACATATCTGTCGCATTTGCACAGATGTTGAAGGCAATAA                         TGCCTGTAGCCGTGTTTCTTCTGGGAGCAGCATTTGGCCTGGAAGAAATGA
genomic: TGCGTACCTCTACATATCTGTCGCATTTGCACAGATGTTGAAGGCAATAAgtatgtgtgc ... aatgatacagTGCCTGTAGCCGTGTTTCTTCTGGGAGCAGCATTTGGCCTGGAAGAAATGA

EST: gi|31351537|gb|CD435894.1|CD435894

EST:     TGCGTACCTCTACATATCTGTCGCATTTGCACAGATGTTGAAGGCAATAA                         TGCCTGTAGCCGTGTTTCTTCTGGGAGCAGCATTTGGCCTGGAAGAAATGA
genomic: TGCGTACCTCTACATATCTGTCGCATTTGCACAGATGTTGAAGGCAATAAgtatgtgtgc ... aatgatacagTGCCTGTAGCCGTGTTTCTTCTGGGAGCAGCATTTGGCCTGGAAGAAATGA

EST: gi|211234820|gb|FL436043.1|FL436043

EST:     TGCGTACCTCTACATATCTGTCGCATTTGCACAGATGTTGAAGGCAATAA                         TGCCTGTAGCCGTGTTTCTTCTGGGAGCAGCATTTGGCCTGGAAGAAATGA
genomic: TGCGTACCTCTACATATCTGTCGCATTTGCACAGATGTTGAAGGCAATAAgtatgtgtgc ... aatgatacagTGCCTGTAGCCGTGTTTCTTCTGGGAGCAGCATTTGGCCTGGAAGAAATGA

EST: gi|89252538|gb|DY624324.1|DY624324

EST:     TGCGTACCTCTACATATCTGTCGCATTTGCACAGATGTTGAAGGCAATAA                         TGCCTGTAGCCGTGTTTCTTCTGGGAGCAGCATTTGGCCTGGAAGAAATGA
genomic: TGCGTACCTCTACATATCTGTCGCATTTGCACAGATGTTGAAGGCAATAAgtatgtgtgc ... aatgatacagTGCCTGTAGCCGTGTTTCTTCTGGGAGCAGCATTTGGCCTGGAAGAAATGA

EST: gi|211529568|gb|FL022743.1|FL022743

EST:     TGCGTACCTCTACATATCTGTCGCATTTGCACAGATGTTGAAGGCAATAA                         TGCCTGTAGCCGTGTTTCTTCTGGGAGCAGCATT-GGCCT
genomic: TGCGTACCTCTACATATCTGTCGCATTTGCACAGATGTTGAAGGCAATAAgtatgtgtgc ... aatgatacagTGCCTGTAGCCGTGTTTCTTCTGGGAGCAGCATTTGGCCT

EST: gi|30307221|gb|CD001894.1|CD001894

EST:     TGCGTACCTCTACATATCTGTCGCATTTGCACAGATGTTGAAGGCAATAA                         TGCCTGTAGCCGTGTTTCTTCTGGGAGCAGCATTTGGCCTGGAAGAAATGA
genomic: TGCGTACCTCTACATATCTGTCGCATTTGCACAGATGTTGAAGGCAATAAgtatgtgtgc ... aatgatacagTGCCTGTAGCCGTGTTTCTTCTGGGAGCAGCATTTGGCCTGGAAGAAATGA

EST: gi|67023288|gb|CO452037.1|CO452037

EST:     TGCGTACCTCTACATATCTGTCGCATTTGCACAGATGTTGAAGGCAATAA                         TGCCTGTAGCTGTGTTTCTTCTGGGAGCAGCATTTGGCCTGGAAGAAATGA
genomic: TGCGTACCTCTACATATCTGTCGCATTTGCACAGATGTTGAAGGCAATAAgtatgtgtgc ... aatgatacagTGCCTGTAGCCGTGTTTCTTCTGGGAGCAGCATTTGGCCTGGAAGAAATGA

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), 43 (downstream exon)
Score: 42

GTCATTCCAATTGGAGGAATGTTTGCAATGACACTTTGGCTAGGGAACAGTGCGTACCTCTACATATCTGTCGCATTTGCACAGATGTTGAAGGCAATAAgtatgtgtgc ... aatgatacagTGCCTGTAGCCGTGTTTCTTCTGGGAGCAGCATTTGGCCTGGAAGAAATGAGCTATAAAATGCTTTCTATCATGTCTGTCATCAGTGTTGGAGTTATTGT

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 74

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 51

Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 68

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCATTCCAATTGGAGGAATGTTTGCAATGACACTTTGGCTAGGGAACAGTGCGTACCTCTACATATCTGTCGCATTTGCACAGATGTTGAAGGCAATAAgtatgtgtgctaccctcagttttgattgtgaggaaaatatcaggatttgattttgatgaacttaccattgaatgatacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG