ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

CATACTCGAGGTCCATTGTGGGTGCTTCCCTAGAGGTGATCCAGAAGAAGAGGGCTGAGAAGCCCGAGGTCCGCGATGCTGCTAGAGAAGCTGCTCTTCGgtatgcttgtcgattttataataaaataaagccatcatttgtgcctatgacagtggtaactgtctgttggcctaaccaacaaaatctctgagtgacatttaacagaaacacaatagatacagatgcttgatatcaggctcatttgaacacccactgacacctttgcag

Basic information

species	Zea mays
transcript	GRMZM2G110328_T04
intron #	4
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G110328_T04 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os05g40820.3 (Oryza sativa), 5'ss of exon 5

CATACTCGAGGTCCATTGTGGGTGCTTCCCTAGAGGTGATCCAGAAGAAGAGGGCTGAGAAGCCCGAGGTCCGCGATGCTGCTAGAGAAGCTGCTCTTCGgtatgcttgtcgattttataataaa-ataaagccatcatttgtgcctatgacagtggtaactgtctgttggcctaaccaacaaaatctctgagtgacatttaacagaaacacaatagatacagatgcttgatatcaggctcatttgaacacccactgacacctttgcag
||||||| ||||| ||||| ||||||||  | || || ||||| |||||||| ||||| ||||| || || || |||||||||||||||||||||||||||||||||  |    |  || ||    ||  || | |  ||  ||  |   |||   ||| |   |  | |     | ||     | ||||   ||   |  |                                                                   
CATACTCTAGGTCAATTGTTGGTGCTTCGTTGGAAGTCATCCAAAAGAAGAGAGCTGAAAAGCCTGAAGTTCGTGATGCTGCTAGAGAAGCTGCTCTTCGgtatgctctttccctgaatgattgccatttagac-tggttactggttccaacaa-agtatccacccatggaatagaacattgcca-ctctatatgggttacat------------------------------------------------------------------

upper sequence: GRMZM2G110328_T04 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA03G34700.1 (Glycine max), 5'ss of exon 4

CATACTCGAGGTCCATTGTGGGTGCTTCCCTAGAGGTGATCCAGAAGAAGAGGGCTGAGAAGCCCGAGGTCCGCGATGCTGCTAGAGAAGCTGCTCTTCGgtatgcttgtcgattttataataaaataaagccatcatttgtgcctatgacagtggtaactgtctgttggcctaaccaacaaaatctctgagtgacatttaacagaaacacaatagatacagatgcttgatatcaggctcatttgaacacccactgacacctttgcag
| ||||| ||||||||||| |||||  | || || || |||||||| ||||| ||||||||||| || || || ||||| ||||| |||||||||||||||| || || ||  | ||    |      |       |||||    | ||    || ||  |   |||      || ||         |    | |    | |                                                                  
CTTACTCTAGGTCCATTGTTGGTGCCACTCTGGAAGTTATCCAGAAAAAGAGAGCTGAGAAGCCAGAAGTTCGAGATGCAGCTAGGGAAGCTGCTCTTCGgtgtgtttttctttatttgtttctgcctactttcggatttgcttttctggatttgtta--tagatgtgcatacaatcacgttctcagccatttaattcctta------------------------------------------------------------------

upper sequence: GRMZM2G110328_T04 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA19G37370.1 (Glycine max), 5'ss of exon 4

CATACTCGAGGTCCATTGTGGGTGCTTCCCTAGAGGTGATCCAGAAGAAGAGGGCTGAGAAGCCCGAGGTCCGCGATGCTGCTAGAGAAGCTGCTCTTCGgtatgcttgtcgattttataataaaataaagccatcatttgtgcctatgacagtggtaactgtctgttggcctaaccaacaaaatctctgagtgacatttaacagaaacacaatagatacagatgcttgatatcaggctcatttgaacacccactgacacctttgcag
| ||||| ||||||||||| |||||  || | || || |||||||| ||||| ||||||||||| || || || ||||| ||||| |||||||||||||||| || ||    |||||||       |   |||  | |||||   |       |||      | |    |  ||   ||  | || ||| ||   ||||||                                                                   
CTTACTCTAGGTCCATTGTTGGTGCGACCTTGGAAGTAATCCAGAAAAAGAGAGCTGAGAAGCCAGAAGTTCGAGATGCAGCTAGGGAAGCTGCTCTTCGgtgtgttttc--attttattt---gtttctgcctacttttgtatttgcatttttggatttgttatagatgtgtacataatcacat-tctcagc--catttattttctt------------------------------------------------------------

upper sequence: GRMZM2G110328_T04 (Zea mays), 5'ss of exon 4
lower sequence: AT3G53020.1 (Arabidopsis thaliana), 5'ss of exon 4

CATACTCGAGGTCCATTGTGGGTGCTTCCCTAGAGGTGATCCAGAAGAAGAGGGCTGAGAAGCCCGAGGTCCGCGATGCTGCTAGAGAAGCTGCTCTTCGgtatgcttgtcgattttataataaaataaagccatcatttgtgcctatgacagtggtaactgtctgttggcctaaccaacaaaatctctgagtgacatttaacagaaacacaatagatacagatgcttgatatcaggctcatttgaacacccactgacacctttgcag
||||||| ||||||||||| |||||| || | || || || ||||||||||| ||||||||||| || || || ||||| || || ||||||||||| ||||  | ||      | | |        ||| |   ||  |  |  ||  | |||  ||        ||| | |||  ||   | | |     ||  ||| |||| | |                                                            
CATACTCAAGGTCCATTGTTGGTGCTACCTTGGAAGTAATTCAGAAGAAGAGAGCTGAGAAGCCTGAAGTTCGTGATGCAGCCAGGGAAGCTGCTCTGCGgttagttttctccctctgt-------caaatcatccaactaggattaaaatagttatat-------ttgacttaataaatgtattgtgatgatg--attcaacaaacag-----------------------------------------------------------

upper sequence: GRMZM2G110328_T04 (Zea mays), 5'ss of exon 4
lower sequence: EDP02103 (Chlamydomonas reinhardtii), 5'ss of exon 2

CATACTCGAGGTCCATTGTGGGTGCTTCCCTAGAGGTGATCCAGAAGAAGAGGGCTGAGAAGCCCGAGGTCCGCGATGCTGCTAGAGAAGCTGCTCTTCGgtatgctt--gtcgattttataataaaataaagccatcatttgtgcctatgacagtggtaactgtctgttggcctaaccaacaaaatctctgagtgacatttaacagaaacacaatagatacagatgcttgatatcaggctcatttgaacacccactgacacctttgcag
           ||||| |||||  | || || |||||||||||||||||| |||| |||||||||||||||||| | ||     | || |||||  | ||  | | |   || | |||||         || |||    |  |||     ||  | || |   | ||  |||   ||  ||    ||    ||| |          | |   |   ||| |    ||                                           
----------CTCCATCGTGGGCACCTCGCTGGAGGTGATCCAGAAGAAGCGGGCGGAGAAGCCCGAGGTCCGCCAGGCCAGCCGTGAGGCTGCCATCCGTGAGGTTAAGgtgggttttagcgcgcggcaatgccgggctgggtg-----gagcggggcagaaggct--tgg---aattaagggcatgctggaggg-------gggggagtgccgcagagaggagtg-------------------------------------------

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|8103338|gb|AW927981.1|AW927981

EST:     CTGAGAAGCCCGAGGTCCGCGATGCTGCTAGAGAAGCTGCTCTTCG                         TGAGATCAAGGAGCGCATCAAGAAGACCAAGGATGAGAAGAAGGCGAAAAA
genomic: CTGAGAAGCCCGAGGTCCGCGATGCTGCTAGAGAAGCTGCTCTTCGgtatgcttgt ... acctttgcagTGAGATCAAGGAGCGCATCAAGAAGACCAAGGATGAGAAGAAGGCGAAAAA

EST: gi|76281134|gb|DV020702.1|DV020702

EST:     AGGGCTGAGAAGCCCGAGGTCCGCGATGCTGCTAGAGAAGCTGCTTTTCG                         TGAGATCAAGGAGCGCATCAAGAAGACCAAGGATGAGAAGAAGGCGAAAAA
genomic: AGGGCTGAGAAGCCCGAGGTCCGCGATGCTGCTAGAGAAGCTGCTCTTCGgtatgcttgt ... acctttgcagTGAGATCAAGGAGCGCATCAAGAAGACCAAGGATGAGAAGAAGGCGAAAAA

EST: gi|31357325|gb|CD441682.1|CD441682

EST:     AGGGCTGAGAAGCCCGAGGTCCGCGATGCTGCTAGAGAAGCTGCTCTTCG                         CGAGATCAAGGAGCGCATCAAGAAGACCAAGGATGAGAAGAAGGCGAAAAA
genomic: AGGGCTGAGAAGCCCGAGGTCCGCGATGCTGCTAGAGAAGCTGCTCTTCGgtatgcttgt ... acctttgcagTGAGATCAAGGAGCGCATCAAGAAGACCAAGGATGAGAAGAAGGCGAAAAA

EST: gi|12046861|gb|BF728987.1|BF728987

EST:     AGGGCTGAGAAGCCCGAGGTCCGCGATGCTGCTAGAGAAGCTGCTCTTCG                         TGAGATCAAGGAGCGCATCAAGAAGACCAAGGATGAGAAGAAGGCGAAAAA
genomic: AGGGCTGAGAAGCCCGAGGTCCGCGATGCTGCTAGAGAAGCTGCTCTTCGgtatgcttgt ... acctttgcagTGAGATCAAGGAGCGCATCAAGAAGACCAAGGATGAGAAGAAGGCGAAAAA

EST: gi|71419243|gb|DR804694.1|DR804694

EST:     AGGGCTGAGAAGCCCGAGGTCCGCGATGCTGCTAGAGAAGCTGCTCTTCG                         TGAGATCAAGGAGCGCATCAAGAAGACCAAGGATGAGAAGAAGGCGAAAAA
genomic: AGGGCTGAGAAGCCCGAGGTCCGCGATGCTGCTAGAGAAGCTGCTCTTCGgtatgcttgt ... acctttgcagTGAGATCAAGGAGCGCATCAAGAAGACCAAGGATGAGAAGAAGGCGAAAAA

EST: gi|76281135|gb|DV020703.1|DV020703

EST:     AGGGCTGAGAAGCCCGAGGTCCGCGATGCTGCTAGAGAAGCTGCTCTTCG                         TGAGATCAAGGAGCGCATCAAGAAGACCAAGGATGAGAAGAAGGCGAAAAA
genomic: AGGGCTGAGAAGCCCGAGGTCCGCGATGCTGCTAGAGAAGCTGCTCTTCGgtatgcttgt ... acctttgcagTGAGATCAAGGAGCGCATCAAGAAGACCAAGGATGAGAAGAAGGCGAAAAA

EST: gi|18181413|gb|BM382623.1|BM382623

EST:     GCGATGCTGCTAGAGAAGCTGCTCTTCG                         TGAGATCAAGGAGCGCATCAAGAAGACCAAGGATGAGAAGAAGGCGAAAAA
genomic: GCGATGCTGCTAGAGAAGCTGCTCTTCGgtatgcttgt ... acctttgcagTGAGATCAAGGAGCGCATCAAGAAGACCAAGGATGAGAAGAAGGCGAAAAA

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: 1043

CATACTCGAGGTCCATTGTGGGTGCTTCCCTAGAGGTGATCCAGAAGAAGAGGGCTGAGAAGCCCGAGGTCCGCGATGCTGCTAGAGAAGCTGCTCTTCGgtatgcttgt ... acctttgcagTGAGATCAAGGAGCGCATCAAGAAGACCAAGGATGAGAAGAAGGCGAAAAAGGCTGAGGTGACCAAGTCCCAGAAGGCACAGACGAAGGGAGCGGTCCAG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 918

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 932

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 557

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATACTCGAGGTCCATTGTGGGTGCTTCCCTAGAGGTGATCCAGAAGAAGAGGGCTGAGAAGCCCGAGGTCCGCGATGCTGCTAGAGAAGCTGCTCTTCGgtatgcttgtcgattttataataaaataaagccatcatttgtgcctatgacagtggtaactgtctgttggcctaaccaacaaaatctctgagtgacatttaacagaaacacaatagatacagatgcttgatatcaggctcatttgaacacccactgacacctttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT