ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

CATGGTTTCTTACTTGCCTGCAAGAGTTTGCTGAGTTTGCCATAAGTTTGGATAAGCAGAACAATGTTCCCCCTGAAAAATCACTGAAGCTTCCCTACAAgtaagagtttttgcaaatctatttgtttcataatcctcatgtttatgtgccctggctagtcttgtcattcatgccatagttattgagactaaactggaca...

Basic information

species	Zea mays
transcript	GRMZM2G092112_T01
intron #	9
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G092112_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os01g48920.1 (Oryza sativa), 5'ss of exon 9

CATGGTTTCTTACTTGCCTGCAAGAGTTTGCTGAGTTTGCCATAAGTTTGGATAAGCAGAACAATGTTCCCCCTGAAAAATCACTGAAGCTTCCCTACAAgtaagagtttttgcaaatctatt-tgtttcataatcctcatgtttatgtgc-cctggctagtcttgtcattcatgccatagttatt-gagactaaactggaca
|||||||||| || ||||||||||| ||||||||||| || || || ||||||||  |||||||||| || ||||| || ||| | ||||| || |||||||||||  | || ||| | |||  |  |   | |   |     ||  || |   |   ||      |         |||  |||   |  || | |||     
CATGGTTTCTAACCTGCCTGCAAGATTTTGCTGAGTTCGCTATTAGCTTGGATAAAGAGAACAATGTACCACCTGAGAAGTCATTAAAGCTCCCATACAAgtaagatatatttcaactttatggtactgtgttacttttgaaattgagtacattttattatatgaattgcatggttcatgcttacaagttacaacacttc---

upper sequence: GRMZM2G092112_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os03g44200.2 (Oryza sativa), 5'ss of exon 10

CATGGTTTCTTACTTGCCTGCAAGAGTTTGCTGAGTTTGCCATAAGTTTGGATAAGCAGAACAATGTTCCCCCTGAAAAATCACTGAAGCTTCCCTACAAgtaagagtttttgcaaatctatttgtttcataatcctcatgtttatg--tgccctggctagtcttgtcattcatgcca-tagttattgagactaaactggaca
|||||||||| |||||| ||||||| |||||||| |||||  | |||||||||||  |||||||||| || ||||| || ||| ||||||| || || |||||||  || |||||| | |   | |   || |||     || ||||  |  | ||| |  |  |   |  ||    |    | |||||   | | ||     
CATGGTTTCTGACTTGCTTGCAAGAATTTGCTGATTTTGCTGTTAGTTTGGATAAAGAGAACAATGTACCACCTGACAAGTCATTGAAGCTCCCATATAAgtaagttttattgcaacttt-cctatactatgatctcttagtatatgaattgcatggttcatgctaagacacaaattagccatcattgaacatcacctaag--

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|166484756|gb|EG311660.1|EG311660

EST:     GAAAAATCACTGAAGCTTCCCTACAA                         GATTGATGGTGACAAAGTAGGGAGCCACACGATCGTCCTTAGTTTCAATAA
genomic: GAAAAATCACTGAAGCTTCCCTACAAgtaagagttt ... catttcacagGATTGATGGTGACAAAGTAGGGAGCCACACGATCGTCCTTAGTTTCAATAA

EST: gi|32914777|gb|CF019589.1|CF019589

EST:     GATAAGCAGAACAATGTTCCCCCTGAAAAATCACTGAAGCTTCCCTACAA                         GATTGATGGTGACAAAGTAGGGAGCCACACGATCGTCCTTAGTTTCAATAA
genomic: GATAAGCAGAACAATGTTCCCCCTGAAAAATCACTGAAGCTTCCCTACAAgtaagagttt ... catttcacagGATTGATGGTGACAAAGTAGGGAGCCACACGATCGTCCTTAGTTTCAATAA

EST: gi|50327434|gb|CO522560.1|CO522560

EST:     GATAAGCAGAACAATGTTCCCCCTGAAAAATCACTGAAGCTTCCCTACAA                         GATTGATGGTGACAAAGTAGGGAGCCACACGATCGTCCTTAGTTTCAATAA
genomic: GATAAGCAGAACAATGTTCCCCCTGAAAAATCACTGAAGCTTCCCTACAAgtaagagttt ... catttcacagGATTGATGGTGACAAAGTAGGGAGCCACACGATCGTCCTTAGTTTCAATAA

EST: gi|71764422|gb|DR962359.1|DR962359

EST:     GATAAGCAGAACAATGTTCCCCCTGAAAAATCACTGAAGCTTCCCTACAA                         GATTGATGGTGACAAAGTAGGGAGCCACACGATCGTCCTTAGTTTCAATAA
genomic: GATAAGCAGAACAATGTTCCCCCTGAAAAATCACTGAAGCTTCCCTACAAgtaagagttt ... catttcacagGATTGATGGTGACAAAGTAGGGAGCCACACGATCGTCCTTAGTTTCAATAA

EST: gi|86471374|gb|DY237744.1|DY237744

EST:     GATAAGCAGAACAATGTTCCCCCTGAAAAATCACTGAAGCTTCCCTACAA                         GATTGATGGTGACAAAGTAGGGAGCCACACGATCGTCCTTAGTTTCAATAA
genomic: GATAAGCAGAACAATGTTCCCCCTGAAAAATCACTGAAGCTTCCCTACAAgtaagagttt ... catttcacagGATTGATGGTGACAAAGTAGGGAGCCACACGATCGTCCTTAGTTTCAATAA

EST: gi|74242756|gb|DT650670.1|DT650670

EST:     GATAAGCAGAACAATGTTCCCCCTGAAAAATCACTGAAGCTTCCCTACAA                         GATTGATGGTGACAAAGTAGGGAGCCACACGATCGTCCTTAGTTTCAATAA
genomic: GATAAGCAGAACAATGTTCCCCCTGAAAAATCACTGAAGCTTCCCTACAAgtaagagttt ... catttcacagGATTGATGGTGACAAAGTAGGGAGCCACACGATCGTCCTTAGTTTCAATAA

EST: gi|29545091|gb|CB605269.1|CB605269

EST:     GATAAGCAGAACAATGTTCCCCCTGAAAAATCACTGAAGCTTCCCTACAA                         GATTGATGGTGACAAAGTAGGGAGCCACACGATCGTCCTTAGTTTCAATAA
genomic: GATAAGCAGAACAATGTTCCCCCTGAAAAATCACTGAAGCTTCCCTACAAgtaagagttt ... catttcacagGATTGATGGTGACAAAGTAGGGAGCCACACGATCGTCCTTAGTTTCAATAA

EST: gi|113692214|gb|DW843223.1|DW843223

EST:     AAAAATTCACTGAAGCTTCCCTACAA                         GATTGATGGTGACAAAGTAGGGAGCCACACGATCGTCCTTAGTTTCAATAA
genomic: AAAAA-TCACTGAAGCTTCCCTACAAgtaagagttt ... catttcacagGATTGATGGTGACAAAGTAGGGAGCCACACGATCGTCCTTAGTTTCAATAA

EST: gi|24767878|gb|CA403013.1|CA403013

EST:     GATAAGCAGAACAATGTTCCCCCTGAAAAATCACTGAAGCTTCCCTACAA                         GATTGATGGTGACAAAGTAGGGAGCCACACGATCGTCCTTAGTTTCAATAA
genomic: GATAAGCAGAACAATGTTCCCCCTGAAAAATCACTGAAGCTTCCCTACAAgtaagagttt ... catttcacagGATTGATGGTGACAAAGTAGGGAGCCACACGATCGTCCTTAGTTTCAATAA

EST: gi|40303501|gb|CK347888.1|CK347888

EST:     GATAAGCAGAACAATGTTCCCCCTGAAAAATCACTGTAGCTTCCCTACAA                         GATTGATGTTGACAAAGTAGGGAGCCACACGATCGTCCTTAGTTTCAATAA
genomic: GATAAGCAGAACAATGTTCCCCCTGAAAAATCACTGAAGCTTCCCTACAAgtaagagttt ... catttcacagGATTGATGGTGACAAAGTAGGGAGCCACACGATCGTCCTTAGTTTCAATAA

EST: gi|211504091|gb|FL041160.1|FL041160

EST:     GATAAGCAGAACAATGTTCCCCCTGAAAAATCACTGAAGCTTCCCTACAA                         GATTGATGGTGACAAAGTAGGGAGCCACACGATCGTCCTTAGTTTCAATAA
genomic: GATAAGCAGAACAATGTTCCCCCTGAAAAATCACTGAAGCTTCCCTACAAgtaagagttt ... catttcacagGATTGATGGTGACAAAGTAGGGAGCCACACGATCGTCCTTAGTTTCAATAA

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: 135

CATGGTTTCTTACTTGCCTGCAAGAGTTTGCTGAGTTTGCCATAAGTTTGGATAAGCAGAACAATGTTCCCCCTGAAAAATCACTGAAGCTTCCCTACAAgtaagagttt ... catttcacagGATTGATGGTGACAAAGTAGGGAGCCACACGATCGTCCTTAGTTTCAATAAGAATGAAAACTGGACCAAGGCTCTAAAGTACATGCTGTGCAATCTGAAG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 125

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 106

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 152

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATGGTTTCTTACTTGCCTGCAAGAGTTTGCTGAGTTTGCCATAAGTTTGGATAAGCAGAACAATGTTCCCCCTGAAAAATCACTGAAGCTTCCCTACAAgtaagagtttttgcaaatctatttgtttcataatcctcatgtttatgtgccctggctagtcttgtcattcatgccatagttattgagactaaactggaca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC