ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GAGCAAATGTCATGCTAGGTGGTAAAAGACACAGCCTGGGGATGTCATTTTATGAGCCAACTGTAGTAGGGAATGTCAGCAATGATATGCTTCTTTTCAGgtaaactttacagttggaccttagcaatttcaatcaaaccttgatatagtgcatatattctactttcatgtgcgaataaatagtcttacattgagcaactgtctgacacttcaaagttgttaacatcttttttcatttcag

Basic information

species	Zea mays
transcript	GRMZM2G128114_T02
intron #	16
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G128114_T01 (Zea mays), 5'ss of exon 16
lower sequence: LOC_Os02g07760.1 (Oryza sativa), 5'ss of exon 16

GAGCAAATGTCATGCTAGGTGGTAAAAGACACAGCCTGGGGATGTCATTTTATGAGCCAACTGTAGTAGGGAATGTCAGCAATGATATGCTTCTTTTCAGgtaaactttacagttggaccttagcaatttcaatcaaaccttgatatagtgcatatattctactttcatgtgcgaataaatagtcttacattgagcaactgtctgacact----tcaaagttgttaaca-tcttttttcatttcag
|||||||  ||||||| ||||||||||| |||||||| ||||||||||| ||||||||||||||||||||||| |||||||||||||||||||||||||||||   || | |             ||||   ||   |||||  | ||||||||||  | ||| ||||||  |||| ||||  ||   ||||||| || | | |||||      |   ||||  ||||| ||   |||   |||||
GAGCAAACATCATGCTTGGTGGTAAAAGGCACAGCCTTGGGATGTCATTCTATGAGCCAACTGTAGTAGGGAACGTCAGCAATGATATGCTTCTTTTCAGgtagggttcaaa-------------aattgtgatttgaccttattttagtgcatatgctttaccttcatg--cgaagaaatgttcaatcattgagaaattctttgacatccttgttctagtttctaacaatcacatttggcttcag

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|194717149|gb|FK934302.1|FK934302

EST:     TATGAGCCAACTGTAGTAGGGAATGTCAGCAACGATATGCTTCTTTTCAG                         AGAAGAAGTTTTTGGTCCAGTTGCACCCCTTATACCGTTCAAAACTGAGGA
genomic: TATGAGCCAACTGTAGTAGGGAATGTCAGCAATGATATGCTTCTTTTCAGgtaaacttta ... ttcatttcagAGAAGAAGTTTTTGGTCCAGTTGCACCCCTTATACCATTCAAAACTGAGGA

EST: gi|84980453|gb|DW530802.1|DW530802

EST:     TATGAGCCAACTGTAGTAGGGAATGTCAGCAATGATATGCTTCTTTTCAG                         AGAAGAAGTTTTTGGTCCAGTTGCACCCCTTATACCATTCAAAACTGAGGA
genomic: TATGAGCCAACTGTAGTAGGGAATGTCAGCAATGATATGCTTCTTTTCAGgtaaacttta ... ttcatttcagAGAAGAAGTTTTTGGTCCAGTTGCACCCCTTATACCATTCAAAACTGAGGA

EST: gi|78107120|gb|DV525538.1|DV525538

EST:     AATGTCAGCAATGATATGCTTCTTTTCAG                         AGAAGAAGTTTTTGGTCCAGTTGCACCCCTTATACCATTCAAAACTGAGGA
genomic: AATGTCAGCAATGATATGCTTCTTTTCAGgtaaacttta ... ttcatttcagAGAAGAAGTTTTTGGTCCAGTTGCACCCCTTATACCATTCAAAACTGAGGA

EST: gi|149000517|gb|EE037699.2|EE037699

EST:     TATGAGCCAACTGTAGTAGGGAATGTCAGCAATGATATGCTTCTTTTCAG                         AGAAGAAGTTTTTGGTCCAGTTGCACCCCTTATACCATTCAAAACTGAGGA
genomic: TATGAGCCAACTGTAGTAGGGAATGTCAGCAATGATATGCTTCTTTTCAGgtaaacttta ... ttcatttcagAGAAGAAGTTTTTGGTCCAGTTGCACCCCTTATACCATTCAAAACTGAGGA

EST: gi|32856352|gb|CD996033.1|CD996033

EST:     TATGAGCCAACTGTAGTAGGGAATGGCAGCAATGATATGCTTCTTTTCAG                         AGAAGAAGTTTTTGGTCCAGTTGCACCCCTTATACCATTCAAAACTGAGGA
genomic: TATGAGCCAACTGTAGTAGGGAATGTCAGCAATGATATGCTTCTTTTCAGgtaaacttta ... ttcatttcagAGAAGAAGTTTTTGGTCCAGTTGCACCCCTTATACCATTCAAAACTGAGGA

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: 48 (upstream exon), 49 (downstream exon)
Score: 221

GAGCAAATGTCATGCTAGGTGGTAAAAGACACAGCCTGGGGATGTCATTTTATGAGCCAACTGTAGTAGGGAATGTCAGCAATGATATGCTTCTTTTCAGgtaaacttta ... ttcatttcagAGAAGAAGTTTTTGGTCCAGTTGCACCCCTTATACCATTCAAAACTGAGGAAGAAGCAGTCCATATGGCCAACGATACAAACGCAG

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 257

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 265