ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
PPT, BS, UA-tract

Sequence

atgc intronic sequence ATGC exonic sequence

gtacatttctaccagtatatattggtacttccaccctattagttatatttctgtgttactaagttatgattttatgatgtagATCCTGGCCCTTTAGTACAGCTGGGCTGCGGAACAGTCTCTGGAGCGCTAGGAGCGACATGCGTTTATCCTTTACAAGTCATCAGAACAAG

Basic information

species	Zea mays
transcript	GRMZM2G180971_T01
intron #	2
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G180971_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g10740.1 (Oryza sativa), 3'ss of exon 2

gtacatttctaccagta---tatattggtacttccaccctattagttatatttctgtgttactaagttatgattttatgatgtagATCCTGGCCCTTTAGTACAGCTGGGCTGCGGAACAGTCTCTGGAGCGCTAGGAGCGACATGCGTTTATCCTTTACAAGTCATCAGAACAAG
||| | | |   ||  |   | | ||   |   |   ||| | | || |   |   | |  ||||  ||| || || | ||| ||||||||| |||||||| || || || || || |||||||| ||||| |||||||| ||||| ||||| ||||| |||||||||||||||||
gtaaactccgtgcaaaaaattctgtttacatcacagtcctctcaattttcaattgatttcgctaaagtataatctttt-atgcagATCCTGGTCCTTTAGTCCAACTAGGTTGTGGGACAGTCTCAGGAGCTCTAGGAGCAACATGTGTTTACCCTTTGCAAGTCATCAGAACAAG

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|6653802|gb|AW267207.1|AW267207

EST:     TTATGAAACACTGAAAGAAATGTCCAGGACATATGTCCTCGTGGACAAAG                         ATCCTGGCCCTTTAGTACAGCTGGGCTGCGGAACAGTCTCTGGAGCGCTAG
genomic: TTATGAAACACTGAAAGAAATGTCCAGGACATATGCCCTCGTGGACAAAGgtacatttct ... tatgatgtagATCCTGGCCCTTTAGTACAGCTGGGCTGCGGAACAGTCTCTGGAGCGCTAG

EST: gi|71323059|gb|DR798203.1|DR798203

EST:     TTATGAAACACTGAAAGAAATGTCCAGGACATATGCCCTCGTGGACAAAG                         ATCCTGGCCCTTTAGTACAGCTGGGCTGCGGAACAGTCTCTGGAGCGCTAG
genomic: TTATGAAACACTGAAAGAAATGTCCAGGACATATGCCCTCGTGGACAAAGgtacatttct ... tatgatgtagATCCTGGCCCTTTAGTACAGCTGGGCTGCGGAACAGTCTCTGGAGCGCTAG

EST: gi|78544099|gb|DV621597.1|DV621597

EST:     TTATGAAACACTGAAAGAAATGTCCAGGACATATGTCCTCGTGGACAAAG                         ATCCTGGCCCTTTAGTACAGCTGGGCTGCGGAACAGTCTCTGGAGCGCTAG
genomic: TTATGAAACACTGAAAGAAATGTCCAGGACATATGCCCTCGTGGACAAAGgtacatttct ... tatgatgtagATCCTGGCCCTTTAGTACAGCTGGGCTGCGGAACAGTCTCTGGAGCGCTAG

EST: gi|149001456|gb|EE038757.2|EE038757

EST:     TTATGAAACACTGAAAGAAATGTCCAGGACATATGCCCTCGTGGACAAAG                         ATCCTGGCCCTTTAGTACAGCTGGGCTGCGGAACAGTCTCTGGAGCGCTAG
genomic: TTATGAAACACTGAAAGAAATGTCCAGGACATATGCCCTCGTGGACAAAGgtacatttct ... tatgatgtagATCCTGGCCCTTTAGTACAGCTGGGCTGCGGAACAGTCTCTGGAGCGCTAG

EST: gi|20336906|gb|BQ172536.1|BQ172536

EST:     TTATGAAACACTGAAAGAAATGTCCAGGACATATGTCCTCGTGGACAAAG                         ATCCTGGCCCTTTAGTACAGCTGGGCTGCGGAACAGTCTCTGGAGCGCTAG
genomic: TTATGAAACACTGAAAGAAATGTCCAGGACATATGCCCTCGTGGACAAAGgtacatttct ... tatgatgtagATCCTGGCCCTTTAGTACAGCTGGGCTGCGGAACAGTCTCTGGAGCGCTAG

EST: gi|88747876|gb|DY532017.1|DY532017

EST:     GGACATATGCCCTCGTGGACAAAG                         ATCCTGGCCCTTTAGTACAGCTGGGGTGCGGAACAGTTTTTGGAGCGCTAG
genomic: GGACATATGCCCTCGTGGACAAAGgtacatttct ... tatgatgtagATCCTGGCCCTTTAGTACAGCTGGGCTGCGGAACAGTCTCTGGAGCGCTAG

EST: gi|211451242|gb|FL460011.1|FL460011

EST:     AAAGAAATGTCCAGGACATATGCCYTCGTGGACAAAG                         ATCCTGGCCCTTTAGTACAGCTGGGCTGCGGAACAAGTCTCTGGAGCGCTA
genomic: AAAGAAATGTCCAGGACATATGCCCTCGTGGACAAAGgtacatttct ... tatgatgtagATCCTGGCCCTTTAGTACAGCTGGGCTGCGGAAC-AGTCTCTGGAGCGCTA

EST: gi|149107568|gb|EE189450.2|EE189450

EST:     TTATGAAACACTGAAAGAAATGTCCAGGACATATGCCCTCGTGGACAAAG                         ATCCTGGCCCTTTAGTACAGCTGGGCTGCGGAACAGTTTCTGGAGCGCTAG
genomic: TTATGAAACACTGAAAGAAATGTCCAGGACATATGCCCTCGTGGACAAAGgtacatttct ... tatgatgtagATCCTGGCCCTTTAGTACAGCTGGGCTGCGGAACAGTCTCTGGAGCGCTAG

EST: gi|60394866|gb|DN227735.1|DN227735

EST:     TTATGAAACACTGAAAGAAATGTCCAGGACATATGCCCTCGTGGACAAAG                         ATCCTGGCCCTTTAGTACAGCTGGGCTGCGGAACAGTCTCTGGAGCGCTAG
genomic: TTATGAAACACTGAAAGAAATGTCCAGGACATATGCCCTCGTGGACAAAGgtacatttct ... tatgatgtagATCCTGGCCCTTTAGTACAGCTGGGCTGCGGAACAGTCTCTGGAGCGCTAG

EST: gi|88748965|gb|DY533106.1|DY533106

EST:     TTATGAAACACTGAAAGAAATGTCCAGGACATATGCCCTCGTGGACAAAG                         ATCCTGGCCCTTTAGTACAGCTGGGCTGCGGAACAGTCTCTGGAGCGCTAG
genomic: TTATGAAACACTGAAAGAAATGTCCAGGACATATGCCCTCGTGGACAAAGgtacatttct ... tatgatgtagATCCTGGCCCTTTAGTACAGCTGGGCTGCGGAACAGTCTCTGGAGCGCTAG

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: 45 (upstream exon), 49 (downstream exon)
Score: 68

GTTCCATCATTGCTTGGCATGGTCCCTTATGCTGGAATTGATCTTACTGTTTATGAAACACTGAAAGAAATGTCCAGGACATATGCCCTCGTGGACAAAGgtacatttct ... tatgatgtagATCCTGGCCCTTTAGTACAGCTGGGCTGCGGAACAGTCTCTGGAGCGCTAGGAGCGACATGCGTTTATCCTTTACAAGTCATCAGAACAAG

Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 35

Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 38

Block sizes: 45 (upstream exon), 36 (downstream exon)
Score: 17

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

cttccaccctattagttatatttctgtgttactaagttatgattttatgatgtagATCCTGGCCCTTTAGTACAGCTGGGCTGCGGAACAGTCTCTGGAGCGCTAGGAGCGACATGCGTTTATCCTTTACAAGTCATCAGAACAAG