ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

TATTGGTTGGATGATGGGACAAAGGATGGACTTGAATTTTCAGCTATTTGAGACAGCAACTCTCTTCATAACAGTGCTTGTGGTAGCATTTATGCTACAGgtaggttcttaaggtggatattaataaaaacttttataaaatgtgtctgttgttgcctgttggtaaggtttattgatgccatcatatggactgtgaaaat...

Basic information

species	Zea mays
transcript	GRMZM2G040017_T02
intron #	10
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G040017_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os04g55940.2 (Oryza sativa), 5'ss of exon 9

TATTGGTTGGATGATGGGACAAAGGATGGACTTGAATTTTCAGCTATTTGAGACAGCAACTCTCTTCATAACAGTGCTTGTGGTAGCATTTATGCTACAGgtaggttcttaaggtggatattaataaaaacttttataaaatgtgtctgtt--gttgcctgttggtaaggtttattgatgccatcatatggactgtgaaaat
 ||||||||||||||||| |||| ||||||||||||||| || ||||| || |||||||| |||||||||||||| || || || |||||||||||||||||||||| ||  |    ||||||| ||  | ||| ||||    || ||| |   |     ||| || | | |  |   ||   |  ||||   || | | ||
CATTGGTTGGATGATGGGGCAAAAGATGGACTTGAATTTCCAACTATTCGAAACAGCAACGCTCTTCATAACAGTACTAGTCGTGGCATTTATGCTACAGgtaggttattgtgtgaaatattaagaattattttgataagggatgcctgcttaatgaagagtttgtcaagct-gtgtttgtttttgtatgccttg-gcacat

upper sequence: GRMZM2G040017_T01 (Zea mays), 5'ss of exon 10
lower sequence: Vv09s0018g01840.t01 (Vitis vinifera), 5'ss of exon 10

TATTGGTTGGATGATGGGACAAAGGATGGACTTGAATTTTCAGCTATTTGAGACAGCAACTCTCTTCATAACAGTGCTTGTGGTAGCATTTATGCTACAGgtaggttcttaaggtggatattaataaaaacttttataaaatgtgtctgttg-ttgcctgt-tggtaaggtttattgatgccatcatatggactgtgaaaat---
| |||||||||| |||||||||   ||||||||||||||||| || |||||||| || |||||||| ||  | ||||| || || ||||||||| | |||||  ||| | ||| |    |||        ||||||      || |  ||   |  ||  | |||  |  | | ||| |    |  | | |    ||   ||   
TGTTGGTTGGATTATGGGACAACCAATGGACTTGAATTTTCAACTCTTTGAGACTGCCACTCTCTTTATCGCGGTGCTAGTAGTGGCATTTATGTTGCAGgtttgttatcaagttcctcatttcc-----cttttagttttggttttggtcaatcaccgatatggacacatatcttgttaattttgtctaggtcttgtgcatcat

upper sequence: GRMZM2G040017_T01 (Zea mays), 5'ss of exon 10
lower sequence: PP1S79_95V6.1 (Physcomitrella patens), 5'ss of exon 10

TATTGGTTGGATGATGGGACAAAGGATGGACTTGAATTTTCAGCTATTTGAGACAGCAACTCTCTTCATAACAGTGCTTGTGGTAGCATTTATGCTACAGgtaggttcttaa------ggtggatattaataaaaact--tttataaa----atgtgtctgttgttgcctgt-tggtaaggtttattgatgccatcatatggactgtgaaaat--------------
 ||||| |||   |||||       |||||| |||||||| | || |||||||| |||||||| ||||||||||| || ||||| || || ||||| || ||  |   | ||       ||   | |   |   |||    | |||||    || |   |    || | ||| || | |    |  |  | |  || | |    |   | ||               
CATTGGATGGCCCATGGGGACCCACATGGACCTGAATTTTGAACTGTTTGAGACGGCAACTCTATTCATAACAGTTCTGGTGGTTGCCTTGATGCTTCAAgtgagaaatcaatcatccagtctctgtctctgttaaccaactaataaatccgatattcttaggtttccttgtgtgctcactcgtgattgttctgtc-tctaattttccataactccgaatgtaccag

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|211272295|gb|FL440029.1|FL440029

EST:     AGACAGCAACTCTCTTCATAACAGTGCTTGTGGTAGCATTTATGCTACAG                         GATGGCACCGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTA
genomic: AGACAGCAACTCTCTTCATAACAGTGCTTGTGGTAGCATTTATGCTACAGgtaggttctt ... ttcgttgcagGATGGGACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTA

EST: gi|149085153|gb|EE174657.2|EE174657

EST:     AGACAGCAACTCTCTTCATAACAGTGCTTGTGGTAGCATTTATGCTACAG                         GATGGGACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATTTA
genomic: AGACAGCAACTCTCTTCATAACAGTGCTTGTGGTAGCATTTATGCTACAGgtaggttctt ... ttcgttgcagGATGGGACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTA

EST: gi|211010290|gb|FL457993.1|FL457993

EST:     AGACAGCAACTCTCTTCATAACAGTGCTTGTGGTAGCATTTATGCTACAG                         GATGGCACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTA
genomic: AGACAGCAACTCTCTTCATAACAGTGCTTGTGGTAGCATTTATGCTACAGgtaggttctt ... ttcgttgcagGATGGGACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTA

EST: gi|91868897|gb|EB400200.1|EB400200

EST:     AGACAGCAACTCTCTTCATAACAGTGCTTGTGGTAGCATTTATGCTACAG                         GATGGGACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTA
genomic: AGACAGCAACTCTCTTCATAACAGTGCTTGTGGTAGCATTTATGCTACAGgtaggttctt ... ttcgttgcagGATGGGACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTA

EST: gi|32837305|gb|CD976983.1|CD976983

EST:     AGACAGCAACTCTCTTCATAACAGTGCTTGTGGTAGCATTTATGCTACAG                         GATGGCACTGCGAACTACTTGAAAGGACTTATGCTGAT
genomic: AGACAGCAACTCTCTTCATAACAGTGCTTGTGGTAGCATTTATGCTACAGgtaggttctt ... ttcgttgcagGATGGGACTGCGAACTACTTGAAAGGACTTATGCTGAT

EST: gi|32836604|gb|CD976282.1|CD976282

EST:     AGACAGCAACTCTCTTCATAACAGTGCTTGTGGTAGCATTTATGCTACAG                         GATGGCACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTA
genomic: AGACAGCAACTCTCTTCATAACAGTGCTTGTGGTAGCATTTATGCTACAGgtaggttctt ... ttcgttgcagGATGGGACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTA

EST: gi|148972711|gb|EE023671.2|EE023671

EST:     AGACAGCAACTCTCTTCATAACAGTGCTTGTGGTAGCATTTATGCTACAG                         GATGGGACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTA
genomic: AGACAGCAACTCTCTTCATAACAGTGCTTGTGGTAGCATTTATGCTACAGgtaggttctt ... ttcgttgcagGATGGGACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTA

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: 47 (upstream exon), 49 (downstream exon)
Score: 139

TATTGGTTGGATGATGGGACAAAGGATGGACTTGAATTTTCAGCTATTTGAGACAGCAACTCTCTTCATAACAGTGCTTGTGGTAGCATTTATGCTACAGgtaggttctt ... ttcgttgcagGATGGGACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTAATAGTTGCTGCCAGTTTCTTTGTTCATGTTGATCCACAATCAA

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 169

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 195