ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

CATGCTTGGTCTTGGAGAGACTGATGAAGAGGTGAAACAAGCCATGATGGATCTACGGGCAATTGGTGTTGACATCCTTACTTTGGGACAGTACTTGCAGgttagctcaatacacacaggacctattgaatctagatatcatgccatcccatcttcctgtaattaacaatttgatatcacag

Basic information

species	Zea mays
transcript	GRMZM2G101698_T01
intron #	5
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G101698_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os01g56310.1 (Oryza sativa), 5'ss of exon 5

CATGCTTGGTCTTGGAGAGACTGATGAAGAGGTGAAACAAGCCATGATGGATCTACGGGCAATTGGTGTTGACATCCTTACTTTGGGACAGTACTTGCAGgttagctcaatacacacaggacctattgaatctagatatcatgccatcccatcttcctgtaattaacaatttgatatcacag
|||||||||||||||||||||||| || |||||||||||||||||||| ||  || |||| ||||||||||| ||| | ||  |||| ||||| |||||||||||| || ||| |||   | | |||        ||| |  | ||  |  |  | |   ||  | |   ||||| | ||||
CATGCTTGGTCTTGGAGAGACTGACGAGGAGGTGAAACAAGCCATGATTGACTTAAGGGCCATTGGTGTTGATATCTTGACACTGGGCCAGTATTTGCAGgttagcccagtac-cactttatc-attagtcaagaataactggtcagtctttgatgca--aaccatctgcttgatcttacag

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|32859726|gb|CD999407.1|CD999407

EST:     ATCTACGGGCAATTGGTGTTGACATCCTTACTTTGGGACAGTACTTGCAG                         CCATCAGAAAGACATCTAACAGTAAGAGAGTATGTGACTCCCCAAAAGTTC
genomic: ATCTACGGGCAATTGGTGTTGACATCCTTACTTTGGGACAGTACTTGCAGgttagctcaa ... gatatcacagCCATCAGAAAGACATCTAACAGTAAGAGAGTATGTGACTCCCCAAAAGTTC

EST: gi|211319523|gb|FK953030.1|FK953030

EST:     ATCTACGGGCAATTGGTGTTGACATCCTTACTTTGGGACAGTACTTGCAG                         CCATCAGAAAGACATCTAACAGTAAGAGAGTATGTGACTCCC
genomic: ATCTACGGGCAATTGGTGTTGACATCCTTACTTTGGGACAGTACTTGCAGgttagctcaa ... gatatcacagCCATCAGAAAGACATCTAACAGTAAGAGAGTATGTGACTCCC

EST: gi|211317505|gb|FK953025.1|FK953025

EST:     ATCTACGGGCAATTGGTGTTGACATCCTTACTTTGGGACAGTACTTGCAG                         CCATCAGAAAGACATCTAACAGTAAGAGAGTATGTGACTCCCCAAAAAGTT
genomic: ATCTACGGGCAATTGGTGTTGACATCCTTACTTTGGGACAGTACTTGCAGgttagctcaa ... gatatcacagCCATCAGAAAGACATCTAACAGTAAGAGAGTATGTGACTCCCCAAAA-GTT

EST: gi|60341912|gb|DN208885.1|DN208885

EST:     ATCTACGGGCAATTGGTGTTGACATCCTTACTTTGGGACAGTACTTGCAG                         CCATCAGAAAGACATCTAACAGTAAGAGAGTATGTGACTCCCCAAAAGTTC
genomic: ATCTACGGGCAATTGGTGTTGACATCCTTACTTTGGGACAGTACTTGCAGgttagctcaa ... gatatcacagCCATCAGAAAGACATCTAACAGTAAGAGAGTATGTGACTCCCCAAAAGTTC

EST: gi|149001280|gb|EE038563.2|EE038563

EST:     GGGCAATTGGTGTTGACATCCTTACTTTGGGACAGTACTTGCAG                         CCATCAGAAAGACATCTAACAGTAAGAGAGTATGTGACTCCCCAAAAGTTC
genomic: GGGCAATTGGTGTTGACATCCTTACTTTGGGACAGTACTTGCAGgttagctcaa ... gatatcacagCCATCAGAAAGACATCTAACAGTAAGAGAGTATGTGACTCCCCAAAAGTTC

EST: gi|211319532|gb|FK953032.1|FK953032

EST:     ATCTACGGGCAATTGGTGTTGACATCCTTACTTTGGGACAGTACTTGCAG                         CCATCAGAAAGACATCTAACAGTAAGAGAGTATGTGACTCCCCAAAAGTTC
genomic: ATCTACGGGCAATTGGTGTTGACATCCTTACTTTGGGACAGTACTTGCAGgttagctcaa ... gatatcacagCCATCAGAAAGACATCTAACAGTAAGAGAGTATGTGACTCCCCAAAAGTTC

EST: gi|71324728|gb|DR799070.1|DR799070

EST:     ATCTACGGGCAATTGGTGTTGACATCCTTACTTTGGGACAGTACTTGCAG                         CCATCAGAAAGACATCTAACAGTAAGAGAGTATGTGACTCCCCAAAAGTTC
genomic: ATCTACGGGCAATTGGTGTTGACATCCTTACTTTGGGACAGTACTTGCAGgttagctcaa ... gatatcacagCCATCAGAAAGACATCTAACAGTAAGAGAGTATGTGACTCCCCAAAAGTTC

EST: gi|33466996|gb|CF244045.1|CF244045

EST:     ATTTACGGGCAATTGGTGTTGACATCCTTACTTTGGGACAGTACTTGCAG                         CCATCAGAAAGACATCTAACAGTAAGAGAGTATGTGACTCCCCAAAAGTTC
genomic: ATCTACGGGCAATTGGTGTTGACATCCTTACTTTGGGACAGTACTTGCAGgttagctcaa ... gatatcacagCCATCAGAAAGACATCTAACAGTAAGAGAGTATGTGACTCCCCAAAAGTTC

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 3 RNA-Seq libraries.

Block sizes: 49 (upstream exon), 37 (downstream exon)
Score: 3

CATGCTTGGTCTTGGAGAGACTGATGAAGAGGTGAAACAAGCCATGATGGATCTACGGGCAATTGGTGTTGACATCCTTACTTTGGGACAGTACTTGCAGgttagctcaa ... gatatcacagCCATCAGAAAGACATCTAACAGTAAGAGAGTATGTGACTCCCCAAAAGTTCCAATTTTGGAAGGAGTATGGAGAATCGGTGGGTTTCCGATATGTTGCTA

Block sizes: 49 (upstream exon), 39 (downstream exon)
Score: 5