ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

CTGTATGCCAATTACGCCATAGGCAAGGACGTACAGGCGATGAAGGCAGTGGTTGGAGAGGAAGCGCTGTCATCAGAGGACCTGgtaaccctcatgcatgacctgacattgttattcttaaactccttaattattttaagttttaacctcctaatcaactgatctatgaaaaaaatgacag

Basic information

species	Oryza sativa
transcript	LOC_Os01g51380.2
intron #	14
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: LOC_Os01g51380.2 (Oryza sativa), 5'ss of exon 14
lower sequence: PP1S100_117V6.1 (Physcomitrella patens), 5'ss of exon 14

CTGTATGCCAATTACGCCATAGGCAAGGACGTACAGGCGATGAAGGCAGTGGTTGGAGAGGAAGCGCTGTCATCAGAGGACCTGgtaaccctcatgcatga-cctgacattgttatt----cttaaactccttaattatt-ttaagttttaacctcctaatca-------actgatctatgaaaaaaatgacag--------------------------------
 ||||||| ||||| ||||| || ||||| || || || |||||||| || ||||||||||||||  |||| ||||| || |||||| ||||| || ||   ||||  | ||  |      || ||  |  | |||| || || | |     || |  | |         |||   |||||  ||   |    |                                
TTGTATGCTAATTATGCCATTGGAAAGGATGTTCAAGCAATGAAGGCTGTCGTTGGAGAGGAAGCTTTGTCTTCAGAAGATCTGgta-ccctcgtgaatactcctgtgactgcaagcagaactcaatttgttcaatttttatttaatccatgccgctcatttccgtgcatactccgctatgtcaactctatttgttgcttacatcctcacttgttttgttttccag

upper sequence: LOC_Os01g51380.2 (Oryza sativa), 5'ss of exon 14
lower sequence: EFJ13375 (Selaginella moellendorffii), 5'ss of exon 13

CTGTATGCCAATTACGCCATAGGCAAGGACGTACAGGCGATGAAGGCAGTGGTTGGAGAGGAAGCGCTGTCATCAGAGGACCTGgtaaccctcatgcatgacctgacattgttattcttaaactccttaattattttaagttttaacctcctaatcaactgatctatgaaaaaaatgacag
|| ||||| || || ||||| ||||| ||||| || |||||||| || || || ||||| |||||||||||||| || || |||||||  | |  |  |  | |    ||| |     ||   |    || | | ||   |     |                                  
CTCTATGCAAACTATGCCATTGGCAAAGACGTTCAAGCGATGAAAGCTGTCGTGGGAGAAGAAGCGCTGTCATCTGAAGATCTGgtaaagcaccagttttgcttt---ttgatgccagtatgttaaccaactgtgttccttccctgcag--------------------------------

upper sequence: LOC_Os01g51380.2 (Oryza sativa), 5'ss of exon 14
lower sequence: EFJ11911 (Selaginella moellendorffii), 5'ss of exon 13

CTGTATGCCAATTACGCCATAGGCAAGGACGTACAGGCGATGAAGGCAGTGGTTGGAGAGGAAGCGCTGTCATCAGAGGACCTGgtaaccctcatgcatgacctgacattgttattcttaaactccttaattattttaagttttaacctcctaatcaactgatctatgaaaaaaatgacag
|| ||||| || || ||||| ||||| ||||| || |||||||| || || || ||||| |||||||||||||| || || |||||||  | |  |  |  | |    ||| |     ||   |    || | | ||   |     |                                  
CTTTATGCAAACTATGCCATTGGCAAAGACGTTCAAGCGATGAAAGCTGTCGTGGGAGAAGAAGCGCTGTCATCTGAAGATCTGgtaaagcaccagttttgcttt---ttgatgccagtatgttaaccaactgtgttccttccctgcag--------------------------------

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|88840140|gb|CI079594.1|CI079594

EST:     TTGGAGAGGAAGCGCTGTCATCAGAGGACCTG                         CTGTACCTCGAGTTTCTTGACAAGTTCGAGCGGAAGTTCGTGACACAAGGA
genomic: TTGGAGAGGAAGCGCTGTCATCAGAGGACCTGgtaaccctca ... aaaatgacagCTGTACCTCGAGTTTCTTGACAAGTTCGAGCGGAAGTTCGTGACACAAGGA

EST: gi|86541335|gb|CI181541.1|CI181541

EST:     GAGAGGAAGCGCTGTCATCAGAGGACCTG                         CTGTACCTCGAGTTTCTTGACAAGTTCGAGCGGAAGTTCGTGACACAAGGA
genomic: GAGAGGAAGCGCTGTCATCAGAGGACCTGgtaaccctca ... aaaatgacagCTGTACCTCGAGTTTCTTGACAAGTTCGAGCGGAAGTTCGTGACACAAGGA

EST: gi|58687170|gb|CK075857.1|CK075857

EST:     AGGCGATGAAGGCAGTGGTTGGAGAGGAAGCGTTGTCATCAGAGGACCTG                         CTGTACCTCGAGTTTCTTGACAAGTTCGAGCGGAAGTTCGTGACACAAGGA
genomic: AGGCGATGAAGGCAGTGGTTGGAGAGGAAGCGCTGTCATCAGAGGACCTGgtaaccctca ... aaaatgacagCTGTACCTCGAGTTTCTTGACAAGTTCGAGCGGAAGTTCGTGACACAAGGA

EST: gi|86834967|gb|CI346051.1|CI346051

EST:     AGGCGATGAAGGCAGTGGTTGGAGAGGAAGCGCTGTCATCAGAGGACCTG                         CTGTACCTCGAGTTTCTTGACAAGTTCGAGCGGAAGTTCGTGACACAAGGA
genomic: AGGCGATGAAGGCAGTGGTTGGAGAGGAAGCGCTGTCATCAGAGGACCTGgtaaccctca ... aaaatgacagCTGTACCTCGAGTTTCTTGACAAGTTCGAGCGGAAGTTCGTGACACAAGGA

EST: gi|88225844|gb|CI225760.1|CI225760

EST:     AGGCGATGAAGGCAGTGGTTGGAGAGGAAGCGCTGTCATCAGAGGACCTG                         CTGTACCTCGAGTTTCTTGACAAGTTCGAGCGGAAGTTCGTGACACAAGGA
genomic: AGGCGATGAAGGCAGTGGTTGGAGAGGAAGCGCTGTCATCAGAGGACCTGgtaaccctca ... aaaatgacagCTGTACCTCGAGTTTCTTGACAAGTTCGAGCGGAAGTTCGTGACACAAGGA

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 1 RNA-Seqlibrary.

Block sizes: 74 (upstream exon), 60 (downstream exon)
Score: 9

CTGTATGCCAATTACGCCATAGGCAAGGACGTACAGGCGATGAAGGCAGTGGTTGGAGAGGAAGCGCTGTCATCAGAGGACCTGgtaaccctca ... aaaatgacagCTGTACCTCGAGTTTCTTGACAAGTTCGAGCGGAAGTTCGTGACACAAGGAGCATATGACACACGCAACATCTTCCAGTCGCTTGACCTCGCCTGGTCAC

<

<

<

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGTATGCCAATTACGCCATAGGCAAGGACGTACAGGCGATGAAGGCAGTGGTTGGAGAGGAAGCGCTGTCATCAGAGGACCTGgtaaccctcatgcatgacctgacattgttattcttaaactccttaattattttaagttttaacctcctaatcaactgatctatgaaaaaaatgacag

- - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA