ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

AATTGTTCTCAATGGCCCGCGTGTATGTTGGCAACTTGGATTCACGGGTGACTTCTGGGGAACTCGAAGATGAGTTCCGCGTGTTTGGAGTTCTGCGAAGgtcactttttttcaaactttattcaggttttgtatagatacatttcatagttttttcatgttgtccctcgagccttgaatgattggcaagttaactaaga...

Basic information

species	Zea mays
transcript	GRMZM2G080930_T01
intron #	2
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G080930_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os02g54770.1 (Oryza sativa), 5'ss of exon 2

AATTGTTCTCAATGGCCCGCGTGTATGTTGGCAACTTGGATTCACGGGTGACTTCTGGGGAACTCGAAGATGAGTTCCGCGTGTTTGGAGTTCTGCGAAGgtcacttttt-ttcaaactttattcaggttttgtatagatacatttcatagttttttcatgttgtccctcgagccttgaatgattggcaagttaactaaga
| |||||| | ||||||||| |||||||||||||||||||| | || |||||||| |||||||| ||||||||||| || |||||||||||||||||||||||| ||| |    |  |  | ||     ||  | ||  |   | |  | |||||| |||  ||   |   || ||||  |  ||      |  ||||   
ATTTGTTCACGATGGCCCGCTTGTATGTTGGCAACTTGGATCCCCGAGTGACTTCCGGGGAACTTGAAGATGAGTTTCGTGTGTTTGGAGTTCTGCGAAGgtcagtttctgcctaggcaatttttccacttcatctaattgggtgtt-tggtttttgcattgtgctgcattagtcttgtgtagtttttggatagactagtt

upper sequence: GRMZM2G080930_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA14G17930.4 (Glycine max), 5'ss of exon 2

AATTGTTCTCA-ATGGCCCGCGTGTATGTTGGCAACTTGGATTCACGGGTGACTTCTGGGGAACTCGAAGATGAGTTCCGCGTGTTTGGAGTTCTGCGAAGgtcacttt-----ttttcaaactttat----tcaggttttgtatagatacatttcatagttttttcatgttgtccctcgagccttgaatgattg-gcaagttaactaaga
  || |    | ||| | |||||||||||||| |||||||||||||| || ||     | || |||||||| || |||||||| || |||||| | || |||| | ||       ||| | | ||||     |||  ||   | | ||||| | |  |  | | ||   ||||  |   ||   |||  || ||  ||   ||        
-CTTCTGAAAAGATGTCTCGCGTGTATGTTGGTAACTTGGATTCACGAGTCACCGAGAGAGATCTCGAAGACGAATTCCGCGTTTTCGGAGTTATTCGGAGgtaaattaacacgctttaatattttaccctctcaatttcgttgtggatacttctatttctctgttttggttg--ctatgatttttgtttggttttgctgatt--------

upper sequence: GRMZM2G080930_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA17G29080.2 (Glycine max), 5'ss of exon 2

AATTGTTCTCA-ATGGCCCGCGTGTATGTTGGCAACTTGGATTCACGGGTGACTTCTGGGGAACTCGAAGATGAGTTCCGCGTGTTTGGAGTTCTGCGAAGgtcactttttttcaaactttattcaggttttgtatagatacatttcatagttttttcatgttgtccctcgagccttgaatgattggcaagttaactaaga----
  || |    | ||| | |||||||||||||| |||||||||||||| || ||     | || |||||||| || ||||| || || |||||| | || |||| | ||   |     ||||| |    |||  | |  ||    ||  | | |  ||||  || |   |   |  |  | |||||      ||   |  |     
-CTTCTGAAAAGATGTCTCGCGTGTATGTTGGTAACTTGGATTCACGAGTCACCGAGAGAGATCTCGAAGACGAATTCCGTGTTTTCGGAGTTATTCGGAGgtaaattaactc---gctttaatattatttcctctcaatttcgttt-tggatacttcaatttctaagttttggttgcagtgatttttttttttgtttggctgtt

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|211113501|gb|FL364717.1|FL364717

EST:     ACTTCTGGGGAACTCGAAGATGAGTTCCGTGTGTTTGGAGTTCTGCGAAG                         TGTTTGGATTGCACGTAAACCACCTGGCTTTGCATTTATTGATTTTGACGA
genomic: ACTTCTGGGGAACTCGAAGATGAGTTCCGCGTGTTTGGAGTTCTGCGAAGgtcacttttt ... ctcaatgcagTGTTTGGATTGCACGTAAACCACCTGGCTTTGCATTTATTGATTTTGACGA

EST: gi|211105696|gb|FL316276.1|FL316276

EST:     ACTTCTGGGGAACTCGAAGATGAGTTCCGCGTGTTTGGAGTTCTGCGAAG                         TGTTTGGATTGCACGTAAACCACCTGGCTTTGCATTTATTGATTTTGATGA
genomic: ACTTCTGGGGAACTCGAAGATGAGTTCCGCGTGTTTGGAGTTCTGCGAAGgtcacttttt ... ctcaatgcagTGTTTGGATTGCACGTAAACCACCTGGCTTTGCATTTATTGATTTTGACGA

EST: gi|211260063|gb|FL327809.1|FL327809

EST:     ACTTCTGGGGAACTCGAAGATGAGTTCCGTGTGTTTGGAGTTCTGCGAAG                         TGTTTGGATTGCACGTAAACCACCTGGCTTTGCATTTATTGATTTTGACGA
genomic: ACTTCTGGGGAACTCGAAGATGAGTTCCGCGTGTTTGGAGTTCTGCGAAGgtcacttttt ... ctcaatgcagTGTTTGGATTGCACGTAAACCACCTGGCTTTGCATTTATTGATTTTGACGA

EST: gi|211310251|gb|FL338861.1|FL338861

EST:     ACTTCTGGGGAACTCGAAGATGAGTTCCGCGTGTTTGGAGTTCTGCGAAG                         TGTTTGGATTGCACGTAAACCACCTGGCTTTGCATTTATTGATTTTGACGA
genomic: ACTTCTGGGGAACTCGAAGATGAGTTCCGCGTGTTTGGAGTTCTGCGAAGgtcacttttt ... ctcaatgcagTGTTTGGATTGCACGTAAACCACCTGGCTTTGCATTTATTGATTTTGACGA

EST: gi|18964300|gb|BM660926.1|BM660926

EST:     ACTTCTGGGGAACTCGAAGATGAGTTCCGTGTGTTTGGAGTTCTGCGAAG                         TGTTTGGATTGCACGTAAACCACCTGGCTTTGCATTTATTGATTTTGACGA
genomic: ACTTCTGGGGAACTCGAAGATGAGTTCCGCGTGTTTGGAGTTCTGCGAAGgtcacttttt ... ctcaatgcagTGTTTGGATTGCACGTAAACCACCTGGCTTTGCATTTATTGATTTTGACGA

EST: gi|211158830|gb|FL334283.1|FL334283

EST:     ACTTCTGGGGAACTCGAAGATGAGTTCCGCGTGTTTGGAGTTCTGCGAAG                         TGTTTGGATTGCACGTAAACCACCTGGCTTTGCATTTATTGATTTTGACGA
genomic: ACTTCTGGGGAACTCGAAGATGAGTTCCGCGTGTTTGGAGTTCTGCGAAGgtcacttttt ... ctcaatgcagTGTTTGGATTGCACGTAAACCACCTGGCTTTGCATTTATTGATTTTGACGA

EST: gi|211072623|gb|FL332514.1|FL332514

EST:     ACTTCTGGGGAACTCGAAGATGAGTTCCGCGTGTTTGGAGTTCTGCGAAG                         TGTTTGGATTGCACGTAAACCACCTGGCTTTGCATTTATTGATTTTGACGA
genomic: ACTTCTGGGGAACTCGAAGATGAGTTCCGCGTGTTTGGAGTTCTGCGAAGgtcacttttt ... ctcaatgcagTGTTTGGATTGCACGTAAACCACCTGGCTTTGCATTTATTGATTTTGACGA

EST: gi|211205317|gb|FL316783.1|FL316783

EST:     ACTTCTGGGGAACTCGAAGATGAGTTCCGCGTGTTTGGAGTTCTGCGAAG                         TGTTTGGATTGCACGTAAACCACCTGGCTTTGCATTTATTGATTTTGACGA
genomic: ACTTCTGGGGAACTCGAAGATGAGTTCCGCGTGTTTGGAGTTCTGCGAAGgtcacttttt ... ctcaatgcagTGTTTGGATTGCACGTAAACCACCTGGCTTTGCATTTATTGATTTTGACGA

EST: gi|211375406|gb|FL332329.1|FL332329

EST:     ACTTCTGGGGAACTCGAAGATGAGTTCCGTGTGTTTGGAGTTCTGCGAAG                         TGTTTGGATTGCACGTAAACCACCTGGCTTTGCATTTATTGATTTTGACGA
genomic: ACTTCTGGGGAACTCGAAGATGAGTTCCGCGTGTTTGGAGTTCTGCGAAGgtcacttttt ... ctcaatgcagTGTTTGGATTGCACGTAAACCACCTGGCTTTGCATTTATTGATTTTGACGA

EST: gi|211215612|gb|FL316847.1|FL316847

EST:     ACTTCTGGGGAACTCGAAGATGAGTTCCGTGTGTTTGGAGTTCTGCGAAG                         TGTTTGGATTGCACGTAAACCACCTGGCTTTGCATTTATTGATTTTGACGA
genomic: ACTTCTGGGGAACTCGAAGATGAGTTCCGCGTGTTTGGAGTTCTGCGAAGgtcacttttt ... ctcaatgcagTGTTTGGATTGCACGTAAACCACCTGGCTTTGCATTTATTGATTTTGACGA

EST: gi|211138186|gb|FL349860.1|FL349860

EST:     ACTTCTGGGGAACTCGAAGATGAGTTCCGTGTGTTTGGAGTTCTGCGAAG                         TGTTTGGATTGCACGTAAACCACCTGGCTTTGCATTTATTGATTTTGACGA
genomic: ACTTCTGGGGAACTCGAAGATGAGTTCCGCGTGTTTGGAGTTCTGCGAAGgtcacttttt ... ctcaatgcagTGTTTGGATTGCACGTAAACCACCTGGCTTTGCATTTATTGATTTTGACGA

EST: gi|211274557|gb|FL349470.1|FL349470

EST:     ACTTCTGGGGAACTCGAAGATGAGTTCCGCGTGTTTGGAGTTCTGCGAAG                         TGTTTGGATTGCACGTAAACCACCTGGCTTTGCATTTATTGATTTTGACGA
genomic: ACTTCTGGGGAACTCGAAGATGAGTTCCGCGTGTTTGGAGTTCTGCGAAGgtcacttttt ... ctcaatgcagTGTTTGGATTGCACGTAAACCACCTGGCTTTGCATTTATTGATTTTGACGA

EST: gi|211432430|gb|FL327491.1|FL327491

EST:     ACTTCTGGGGAACTCGAACATGAGTTCCGTGTGTTTGGAGTTCTGCGAAG                         TGTTTGGATTGCACGTAAACCACCTGGCTTTGCATTTATTGATTTTGACGA
genomic: ACTTCTGGGGAACTCGAAGATGAGTTCCGCGTGTTTGGAGTTCTGCGAAGgtcacttttt ... ctcaatgcagTGTTTGGATTGCACGTAAACCACCTGGCTTTGCATTTATTGATTTTGACGA

EST: gi|211416748|gb|FL321413.1|FL321413

EST:     ACTTCTGGGGAACTCGAAGATGAGTTCCGCGTGTTTGGAGTTCTGCGAAG                         TGTTTGGATTGCACGTAAACCACCTGGCTTTGCATTTATTGATTTTGACGA
genomic: ACTTCTGGGGAACTCGAAGATGAGTTCCGCGTGTTTGGAGTTCTGCGAAGgtcacttttt ... ctcaatgcagTGTTTGGATTGCACGTAAACCACCTGGCTTTGCATTTATTGATTTTGACGA

EST: gi|211470387|gb|FL342153.1|FL342153

EST:     ACTTCTGGGGAACTCGAAGATGAGTTCCGCGTGTTTGGAGTTCTGCGAAG                         TGTTTGGATTGCACGTAAACCACCTGGCTTTGCATTTATTGATTTTGACGA
genomic: ACTTCTGGGGAACTCGAAGATGAGTTCCGCGTGTTTGGAGTTCTGCGAAGgtcacttttt ... ctcaatgcagTGTTTGGATTGCACGTAAACCACCTGGCTTTGCATTTATTGATTTTGACGA

EST: gi|211047373|gb|FL359874.1|FL359874

EST:     ACTTCTGGGGAACTCGAAGATGAGTTCCGCGTGTTTGGAGTTCTGCGAAG                         TGTTTGGATTGCACGTAAACCACCTGGCTTTGCATTTRTTGATTTTKACGA
genomic: ACTTCTGGGGAACTCGAAGATGAGTTCCGCGTGTTTGGAGTTCTGCGAAGgtcacttttt ... ctcaatgcagTGTTTGGATTGCACGTAAACCACCTGGCTTTGCATTTATTGATTTTGACGA

EST: gi|211091140|gb|FL328973.1|FL328973

EST:     ACTTCTGGGGAACTCGAACATGAGTTCCGTGTGTTTGGAGTTCTGCGAAG                         TGTTTGGATTGCACGTAAACCACCTGGCTTTGCATTTATTGATTTTGACGA
genomic: ACTTCTGGGGAACTCGAAGATGAGTTCCGCGTGTTTGGAGTTCTGCGAAGgtcacttttt ... ctcaatgcagTGTTTGGATTGCACGTAAACCACCTGGCTTTGCATTTATTGATTTTGACGA

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: 119

AATTGTTCTCAATGGCCCGCGTGTATGTTGGCAACTTGGATTCACGGGTGACTTCTGGGGAACTCGAAGATGAGTTCCGCGTGTTTGGAGTTCTGCGAAGgtcacttttt ... ctcaatgcagTGTTTGGATTGCACGTAAACCACCTGGCTTTGCATTTATTGATTTTGACGACAGGAGGGATGCGGAGGATGCTATTCGTGATCTAGATG

Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 92

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 60

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 79

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATTGTTCTCAATGGCCCGCGTGTATGTTGGCAACTTGGATTCACGGGTGACTTCTGGGGAACTCGAAGATGAGTTCCGCGTGTTTGGAGTTCTGCGAAGgtcactttttttcaaactttattcaggttttgtatagatacatttcatagttttttcatgttgtccctcgagccttgaatgattggcaagttaactaaga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtccctcg