ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

AAACCCCAGGCTGCCGTTGATAAAACTCTTGACAGCAAGGTTTTCAAAGGATGGGTTGAAACTGACAATCCGTGGACATCTGATGACGAGACTGATAATAgtaatttatctttgccttgatctagtttattgcacattctttgattcttatttatcatcattcatgatgattatcaaattgctgtattgttttcag

Basic information

species	Zea mays
transcript	GRMZM2G108115_T01
intron #	3
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G108115_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os03g52340.2 (Oryza sativa), 5'ss of exon 3

AAACCCCAGGCTGCCGTTGATAAAACTCTTGACAGCAAGGTTTTCAAAGGATGGGTTGAAACTGACAATCCGTGGACATCTGATGACGAGACTGATAATAgtaat-ttatctttgccttgatctagtttattgcacattctttgattcttatttatcatcattcatgatgattatcaaattgctgtattgttttcag
||||| |||||| | ||||||| ||| |||||   ||||||||||||||||||| ||||||| |||||||| ||||||| ||| || |||||||||||| ||||  || | ||||| |   | |||| |||||       ||||  | || ||||| |  ||   |||   ||    ||       ||  ||| |||
AAACCACAGGCTACTGTTGATAGAACCCTTGATGCCAAGGTTTTCAAAGGATGGATTGAAACCGACAATCCATGGACATATGACGATGAGACTGATAATGgtaaagttgtttttgcatccttttagtatattgtgtcccttttgtgtgttctttattactatatgtgacagttgctgaaaaaa-acatcattt-cag

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|211489776|gb|FL012897.1|FL012897

EST:     GGGTTGAAACTGACAATCCGTGGACATCTGGATGACGAGACTGATAAATA                         ATGAGATGACTT
genomic: GG-TTGAAACTGACAATCCGTGGACATCTG-ATGACGAGACTGATAA-TAgtaatttatc ... ttgttttcagATGAGATGACTT

EST: gi|5847356|gb|AW000435.1|AW000435

EST:     AT-GGTTGAAACTGACAATCCGTGGACATCTGATGACGAGACTGATAATA                         ATGAGATGACTTACGTGAATCTTCAACTGAATCCTGAACGATACACTGGCT
genomic: ATGGGTTGAAACTGACAATCCGTGGACATCTGATGACGAGACTGATAATAgtaatttatc ... ttgttttcagATGAGATGACTTACGTGAATCTTCAACTGAATCCTGAACGATACACTGGCT

EST: gi|149060174|gb|EE157144.2|EE157144

EST:     ATGGGTTGAAACTGACAATCCGTGGACATCTGATGACGAGACTGATAATA                         ATGAGATGACTTACGTGAATCTT
genomic: ATGGGTTGAAACTGACAATCCGTGGACATCTGATGACGAGACTGATAATAgtaatttatc ... ttgttttcagATGAGATGACTTACGTGAATCTT

EST: gi|32865873|gb|CF005555.1|CF005555

EST:     ATGGGTTGAAACTGACAATCCGTGGACATCTGATGACGAGACTGATAATA                         ATGAGATGACTTACGTGAATCTTCAACTGAATCCTGAACGATACACT
genomic: ATGGGTTGAAACTGACAATCCGTGGACATCTGATGACGAGACTGATAATAgtaatttatc ... ttgttttcagATGAGATGACTTACGTGAATCTTCAACTGAATCCTGAACGATACACT

EST: gi|50338345|gb|CO533471.1|CO533471

EST:     ATGGGTTGAAACTGACAATCCGTGGACATCTGATGACGAGACTGATAATA                         ATGAGATGACTTACGTGAATCTTCAACTGAATCCTGAACGATACACTGGCT
genomic: ATGGGTTGAAACTGACAATCCGTGGACATCTGATGACGAGACTGATAATAgtaatttatc ... ttgttttcagATGAGATGACTTACGTGAATCTTCAACTGAATCCTGAACGATACACTGGCT

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), 48 (downstream exon)
Score: 135

AAACCCCAGGCTGCCGTTGATAAAACTCTTGACAGCAAGGTTTTCAAAGGATGGGTTGAAACTGACAATCCGTGGACATCTGATGACGAGACTGATAATAgtaatttatc ... ttgttttcagATGAGATGACTTACGTGAATCTTCAACTGAATCCTGAACGATACACTGGCTATACTGGTGATTCAGCAAGAAGAATATGGGACGCTATTTACAAAGAGAA

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 211

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 183