ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GGATACAGCTTTCACAGTTCAAGCCATTGTGGCTACCAACCTTATTGAAGAGTTTGGTCCTACCCTTAAACTAGCACACAACTATATCAAGAATTCACAGgtacagtcgacatgcctttttgtatatattgttcaatcttaggttcatttacagcactgataaatggctgtttaatatgaaag

Basic information

species	Zea mays
transcript	GRMZM2G023798_T02
intron #	7
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G023798_T02 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os02g04710.2 (Oryza sativa), 5'ss of exon 9

GGATACAGCTTTCACAGTTCAAGCCATTGTGGCTACCAACCTTATTGAAGAGTTTGGTCCTACCCTTAAACTAGCACACAACTATATCAAGAATTCACAGgtacagtc----gacatgcctttttgta----tatattgttcaatcttaggttcatttacagcactgataaatggctgtttaatatgaaag
||| |||||||||||||||||||| || ||||||||   ||| |||||||| ||||||||||| ||||||||||||||   ||| || |||||  | ||||| ||  |      ||||     || ||    |||| |  ||||  ||     |  |  ||  ||| |    ||||| ||||   ||||||
GGACACAGCTTTCACAGTTCAAGCTATAGTGGCTACTGGCCTCATTGAAGAATTTGGTCCTACTCTTAAACTAGCACATGGCTACATAAAGAAAACGCAGgtgcatgcctcatgcatgttcccttatacgattatactaatcaacatttcaagccatctcattacttacctgtggct-tttatcctgaaag

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|21331674|gb|BQ487055.1|BQ487055

EST:     AGTTTGGTCCTACCCTTAAACTAGCACACAACTATATCAAGAATTCACAG                         GTTCTTGATGACTGCCCTG
genomic: AGTTTGGTCCTACCCTTAAACTAGCACACAACTATATCAAGAATTCACAGgtacagtcga ... aatatgaaagGTTCTTGATGACTGCCCTG

EST: gi|23199794|gb|BU582359.1|BU582359

EST:     AGTTTGGTCCTACCCTTAAACTAGCACACAACTATATCAAGAATTCACAG                         GTTCTTGATGACTGCCCTGGTGATCTGAATGACTGGTACCGCCACACATCT
genomic: AGTTTGGTCCTACCCTTAAACTAGCACACAACTATATCAAGAATTCACAGgtacagtcga ... aatatgaaagGTTCTTGATGACTGCCCTGGTGATCTGAATGACTGGTACCGCCACACATCT

EST: gi|18659473|gb|BM500356.1|BM500356

EST:     GTTTGGTCCTACCCTTAAACTAGCACACAACTATATCAAGAATTCACAG                         GTTCTTGATGACTGCCCTGGTGATCTGAATGACTGGTACCGCCACACATCT
genomic: GTTTGGTCCTACCCTTAAACTAGCACACAACTATATCAAGAATTCACAGgtacagtcga ... aatatgaaagGTTCTTGATGACTGCCCTGGTGATCTGAATGACTGGTACCGCCACACATCT

EST: gi|87156285|gb|DY401074.1|DY401074

EST:     AGTTTGGTCCTACCCTTAAACTAGCACACAACTATATCAAGAATTCACAG                         GTTCTTGATGACTGCCCTGGTGATCTGAATGACTGGTACCGCCACACATCT
genomic: AGTTTGGTCCTACCCTTAAACTAGCACACAACTATATCAAGAATTCACAGgtacagtcga ... aatatgaaagGTTCTTGATGACTGCCCTGGTGATCTGAATGACTGGTACCGCCACACATCT

EST: gi|26560142|gb|CA832377.1|CA832377

EST:     AGTTTGGTCCTACCCTTAAACTAGCACACAACTATATCAAGAATTCACAG                         GTTCTTGATGACTGCCCTGGTGATCTGAATGACTGGTACCGCCACACATCT
genomic: AGTTTGGTCCTACCCTTAAACTAGCACACAACTATATCAAGAATTCACAGgtacagtcga ... aatatgaaagGTTCTTGATGACTGCCCTGGTGATCTGAATGACTGGTACCGCCACACATCT

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: 235

GGATACAGCTTTCACAGTTCAAGCCATTGTGGCTACCAACCTTATTGAAGAGTTTGGTCCTACCCTTAAACTAGCACACAACTATATCAAGAATTCACAGgtacagtcga ... aatatgaaagGTTCTTGATGACTGCCCTGGTGATCTGAATGACTGGTACCGCCACACATCTAAAGGTGCATGGCCATTCTCAACTGCTGATCATGGTTGGCCTATATCTG

Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 191

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 148