ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

TTTACAATCAAAAGGGGAGTTGGGACTGATACGTGTGTTAGCGTTAACTATGACGACTTTGTTAATGATGTTGAAGTGGGCGACATGCTCCTTGTAGATGgtatgctgatatttacattccttttctgttagaaaataagactacataaccccctgaactattaatatttgggtctactttaacccagaacctacataac...

Basic information

species	Zea mays
transcript	GRMZM2G152686_T01
intron #	3
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G152686_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g47080.1 (Oryza sativa), 5'ss of exon 3

TTTACAATCAAAAGGGGAGTTGGGACTGATACGTGTGTTAGCGTTAACTATGACGACTTTGTTAATGATGTTGAAGTGGGCGACATGCTCCTTGTAGATGgtatgctgatatttacattccttttctgttagaaaataagactacataaccccctgaactattaatat--ttgggtctactttaacccaga--acctacataac
|| ||||| || || |||||||||||||| || |||||||||||||||||||| ||||||||||||||||| |||||||| ||||||||||| ||||||||||||  ||||||      ||| |  | ||  ||  ||    |   |      |  |   |   ||||  |||  |  ||| ||| | | |  ||  ||     
TTCACAATTAAGAGAGGAGTTGGGACTGAGACATGTGTTAGCGTTAACTATGATGACTTTGTTAATGATGTAGAAGTGGGTGACATGCTCCTCGTAGATGgtatgtggatattccttcccctctaatcttt-aacttacttttgtctcctttgcatagacacacatatgattgtattcactgtaagcaaaacaactcactc---

upper sequence: GRMZM2G152686_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA10G37210.1 (Glycine max), 5'ss of exon 3

TTTACAATCAAAAGGGGAGTTGGGACTGATACGTGTGTTAGCGTTAACTATGACGACTTTGTTAATGATGTTGAAGTGGGCGACATGCTCCTTGTAGATGgtatgctgat-atttacattccttttctgttagaaaataagactacataaccccctgaactattaatatttgggtctactttaacccagaacctacataac-----
||||| |||   ||||| ||||| ||||     |||||||| || ||||||||||| || || |||||||| || ||||| |||||||| ||||| |||||||||   |  |  ||  |        |||| ||||   | |  |  |      ||     ||| |||       | ||   | |   | ||  |  ||       
TTTACCATCCGGAGGGGTGTTGGAACTGCAGATTGTGTTAGTGTGAACTATGACGATTTCGTCAATGATGTGGATGTGGGGGACATGCTTCTTGTTGATGgtatggcaaccaactaattggtaaaagtgtttgaaatataaaaaatgtgttttgctcgtggattgata-----agccacca-agcatgggactaatttattatttt

upper sequence: GRMZM2G152686_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA20G30430.1 (Glycine max), 5'ss of exon 3

TTTACAATCAAAAGGGGAGTTGGGACTGATACGTGTGTTAGCGTTAACTATGACGACTTTGTTAATGATGTTGAAGTGGGCGACATGCTCCTTGTAGATGgtatgctgatatttacattccttttc-tgttagaaaataagactacataaccccctgaactattaatatttgggtctactttaacccagaacctacataac
||||| |||   ||||| ||||| ||||     |||||||| || ||||||||||| || || |||||||| || ||||| |||||||| ||||| |||||||||   |       |||  |     |||| ||||   | || |  |      ||      || |||         || |    | |     | | |   
TTTACCATCCGGAGGGGTGTTGGAACTGCAGATTGTGTTAGTGTGAACTATGACGATTTCGTCAATGATGTGGATGTGGGAGACATGCTTCTTGTTGATGgtatggcaaccaactgattggtaaaaatgtttgaaatataaacaatttgttatgctcgtgggttgataagccaccaaacatgggactaatttattctttt-

upper sequence: GRMZM2G152686_T01 (Zea mays), 5'ss of exon 3
lower sequence: AT5G52920.1 (Arabidopsis thaliana), 5'ss of exon 3

TTTACAATCAAAAGGGGAGTTGGGACTGATACGTGTGTTAGCGTTAACTATGACGACTTTGTTAATGATGTTGAAGTGGGCGACATGCTCCTTGTAGATGgtatgctgatatttacattccttttctgttagaaaataagactacataaccccct---gaactattaatatttgggtctactttaacccagaacctacataac
||||||||  | || |||||  | ||    |  ||||| || ||||||||||| || || |||||||| || |||| ||| |||||||| ||||| |||||||||   || ||   |||   | |      |    ||   || | | |  |  |    |  |||| ||    |  | |||| |     ||            
TTTACAATTGAGAGAGGAGTCAGCACACCAAGTTGTGTCAGTGTTAACTATGATGATTTCGTTAATGACGTGGAAGCGGGTGACATGCTTCTTGTTGATGgtatgtacatcttattatttggtgtacaa-gggttttacatctgctttagtcttttccaatatattgatggc-gcttttactatgttgtag------------

upper sequence: GRMZM2G152686_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv16s0050g02180.t01 (Vitis vinifera), 5'ss of exon 3

TTTACAATCAAAAGGGGAGTTGGGACTGATACGTGTGTTAGCGTTAACTATGACGACTTTGTTAATGATGTTGAAGTGGGCGACATGCTCCTTGTAGATGgtatgctgatatttacattccttttctgttagaaaataagactacataaccccctgaactattaatatt---tgggtctactttaacccagaacctacat-aac--
|| |||||  |||| || |||||||| |     |||||||| ||||||||||| || ||||| |||||||| ||| ||||||||||||| || || |||||||   ||| |    |||   |||||||| | | ||  ||  |   ||    |||      || |  ||   |  || |  |    | |  | |||  || |||  
TTCACAATTCAAAGAGGCGTTGGGACAGCAGATTGTGTTAGTGTTAACTATGATGATTTTGTCAATGATGTAGAAATGGGCGACATGCTTCTCGTGGATGgta---tgaaac---catgttttttctgtcatacaaataggttttgtagtaacctctttcctttactttccatcagtttgttcacccacttatcctcaattaactt

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|148961971|gb|EE012768.2|EE012768

EST:     TGACGACTTTGTTAATGATGTTGAAGTGGGCGACATGCTCCTTGTAGATG                         GAGGAATGATGTCATTCTTGGTCAAATCAAAAACTGAAGATTCTGTGAAAT
genomic: TGACGACTTTGTTAATGATGTTGAAGTGGGCGACATGCTCCTTGTAGATGgtatgctgat ... caatttttagGAGGAATGATGTCATTCTTGGTCAAATCAAAAACTGAAGATTCTGTGAAAT

EST: gi|148957677|gb|EC903791.2|EC903791

EST:     TGACGACTTTGTTAATGATGTTGAAGTGGGCGACATGCTCCTTGTAGATG                         GAGGAATGATGTC
genomic: TGACGACTTTGTTAATGATGTTGAAGTGGGCGACATGCTCCTTGTAGATGgtatgctgat ... caatttttagGAGGAATGATGTC

EST: gi|148934386|gb|EC878416.2|EC878416

EST:     TGACGACTTTGTTAATGATGTTGAAGTGGGCGACATGCTCCCTGTAAATG                         GAGGAATGATGTCATTCTTGGTCAAATCAAAAAC
genomic: TGACGACTTTGTTAATGATGTTGAAGTGGGCGACATGCTCCTTGTAGATGgtatgctgat ... caatttttagGAGGAATGATGTCATTCTTGGTCAAATCAAAAAC

EST: gi|5296084|gb|AI782959.1|AI782959

EST:     TGACGACTTTGTTAATGATGTTGAAGTGGGCGACATGCTCCTTGTAGATG                         GAGGAATGATGTCATTCTTGGTCAAATCAAAAACTGAAGATTCTGTGAAAT
genomic: TGACGACTTTGTTAATGATGTTGAAGTGGGCGACATGCTCCTTGTAGATGgtatgctgat ... caatttttagGAGGAATGATGTCATTCTTGGTCAAATCAAAAACTGAAGATTCTGTGAAAT

EST: gi|71426208|gb|DR807258.1|DR807258

EST:     TGACGACTTTGTTAATGATGTTGAAGTGGGCGACATGCTCCTTGTAGATG                         GAGGAATGATGTCATTCTTGGTCAAATCAAAAACTGAAGATTCTGTGAAAT
genomic: TGACGACTTTGTTAATGATGTTGAAGTGGGCGACATGCTCCTTGTAGATGgtatgctgat ... caatttttagGAGGAATGATGTCATTCTTGGTCAAATCAAAAACTGAAGATTCTGTGAAAT

EST: gi|67041095|gb|CO467350.1|CO467350

EST:     TGACGACTTTGTTAATGATGTTGAAGTGGGCGACATGCTCCTTGTAGATG                         GAGGAATGATGTCATTCTTGGGTCAA-TCAAAAACTGAAGATTCTGTGAAA
genomic: TGACGACTTTGTTAATGATGTTGAAGTGGGCGACATGCTCCTTGTAGATGgtatgctgat ... caatttttagGAGGAATGATGTCATTCTTGG-TCAAATCAAAAACTGAAGATTCTGTGAAA

EST: gi|211141481|gb|FL154590.1|FL154590

EST:     TGTTAATGATGTTGAAGTGGGCGACATGCTCCTTGTAGATG                         GAGGAATGATGTCATTCTTGGTCAAATCAAAAACTGAAGATTCTGTGAAAT
genomic: TGTTAATGATGTTGAAGTGGGCGACATGCTCCTTGTAGATGgtatgctgat ... caatttttagGAGGAATGATGTCATTCTTGGTCAAATCAAAAACTGAAGATTCTGTGAAAT

EST: gi|67025561|gb|CO454310.1|CO454310

EST:     TGACGACTTTGTTAATGATGTTGAAGTGGGCGACATGCTCCTTGTAGATG                         GAGGAATGATGTCATTCTTGGTCAAATCAAAAACTGAAGATTCTGTGAAAT
genomic: TGACGACTTTGTTAATGATGTTGAAGTGGGCGACATGCTCCTTGTAGATGgtatgctgat ... caatttttagGAGGAATGATGTCATTCTTGGTCAAATCAAAAACTGAAGATTCTGTGAAAT

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), 48 (downstream exon)
Score: 196

TTTACAATCAAAAGGGGAGTTGGGACTGATACGTGTGTTAGCGTTAACTATGACGACTTTGTTAATGATGTTGAAGTGGGCGACATGCTCCTTGTAGATGgtatgctgat ... caatttttagGAGGAATGATGTCATTCTTGGTCAAATCAAAAACTGAAGATTCTGTGAAATGTGAAGTTATTGACGGTGGTGAATTGAAATCTAGGCGCCATCTGAATGT

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 154

Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 98

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 434

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTACAATCAAAAGGGGAGTTGGGACTGATACGTGTGTTAGCGTTAACTATGACGACTTTGTTAATGATGTTGAAGTGGGCGACATGCTCCTTGTAGATGgtatgctgatatttacattccttttctgttagaaaataagactacataaccccctgaactattaatatttgggtctactttaacccagaacctacataac

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaaataa