ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GGTGTCAACAAGCATGAGTTTGCCATCAAAAGCTGGTTTAAAGAACAATAAACATGGTCCTAACGATCGTGGTTCTAATGTGGGCAAACCTGTGTCCCAAgtatgcatcacatcttttttttgtctctgtggataatgatattgataccagttttctaactatgattctccactatcag

Basic information

species	Zea mays
transcript	GRMZM2G009849_T03
intron #	12
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G009849_T01 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os01g60040.2 (Oryza sativa), 5'ss of exon 31

GGTGTCAACAAGCATGAGTTTGCCATCAAAAGCTGGTTTAAAGAACAATAAACATGGTCCTAACGATCGTGGTTCTAATGTGGGCAAACCTGTGTCCCAAgtatgcatcacatcttttttttgtctctgtggataatgatattgataccagttttctaactatgattctccactatcag
|||  ||||||||||||| ||||| |||||||| |||| ||||||||| ||||||||||| || ||||| || ||||||||  ||||| | || || |||||| |       | |  ||  ||| | ||||  |  ||| | ||||  |  ||| || | | |  || |    ||||||
GGTAACAACAAGCATGAGCTTGCCTTCAAAAGCAGGTTCAAAGAACAACAAACATGGTCCAAATGATCGCGGATCTAATGTTAGCAAAGCGGTATCTCAAgtacg-------tttccttgctgtttatgtgattgttgaaaatgattgccttttcctgattgttgttttttgttatcag

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|17970269|gb|BM277032.1|BM277032

EST:     AACATGGTCCTAACGATCGTGGTTCTAATGTGGGCAAACCTGTGTCCCAA                         AGAGGACTTCCACAGAGAGCATCTGTTACTATGGTTTCTACTCAAGATTCT
genomic: AACATGGTCCTAACGATCGTGGTTCTAATGTGGGCAAACCTGTGTCCCAAgtatgcatca ... ccactatcagAGAGGACTTCCACAGAGAGCATCTGTTACTATGGTTTCTACTCAAGATTCT

EST: gi|22491327|gb|BU051250.1|BU051250

EST:     AACATGGTCCTAACGATCGTGGTTCTAATGTGGGCAAACCTGTGTCCCAA                         AGAGGACTTCCACAGAGAGCATCTGTTACTATGGTTTCTACTCAAGATTCT
genomic: AACATGGTCCTAACGATCGTGGTTCTAATGTGGGCAAACCTGTGTCCCAAgtatgcatca ... ccactatcagAGAGGACTTCCACAGAGAGCATCTGTTACTATGGTTTCTACTCAAGATTCT

EST: gi|19351752|gb|BM896284.1|BM896284

EST:     AACATGGTCCTAACGATCGTGGTTCTAATGTGGGCAAACCTGTGTCCCAA                         AGAGGACTTCCACAGAGAGCATCTGTTACTATGGTTTCTACTCAAGATTCT
genomic: AACATGGTCCTAACGATCGTGGTTCTAATGTGGGCAAACCTGTGTCCCAAgtatgcatca ... ccactatcagAGAGGACTTCCACAGAGAGCATCTGTTACTATGGTTTCTACTCAAGATTCT

EST: gi|87153866|gb|DY398655.1|DY398655

EST:     AACATGGTCCTAACGATCGTGGTTCTAATGTGGGCAAACCTGTGTCCCAA                         AGAGGACTTCCACAGAGAGCATCTGTTACTATGGTTTCTACTCAAGATTCT
genomic: AACATGGTCCTAACGATCGTGGTTCTAATGTGGGCAAACCTGTGTCCCAAgtatgcatca ... ccactatcagAGAGGACTTCCACAGAGAGCATCTGTTACTATGGTTTCTACTCAAGATTCT

EST: gi|22489504|gb|BU049427.1|BU049427

EST:     ACATGGTCC-ACACGATCGTGGTTCTAATGTGGGCAAACCTGTGTCCCAA                         AGAGGACTTCC-CAGAGAGCATCTGTTACTATGGTTTC
genomic: ACATGGTCCTA-ACGATCGTGGTTCTAATGTGGGCAAACCTGTGTCCCAAgtatgcatca ... ccactatcagAGAGGACTTCCACAGAGAGCATCTGTTACTATGGTTTC

EST: gi|87153811|gb|DY398600.1|DY398600

EST:     AACATGGTCCTAACGATCGTGGTTCTAATGTGGGCAAACCTGTGTCCCAA                         AGAGGACTTCCACAGAGAGCATCTGTTACTATGGTTTCTACTCAAGATTCT
genomic: AACATGGTCCTAACGATCGTGGTTCTAATGTGGGCAAACCTGTGTCCCAAgtatgcatca ... ccactatcagAGAGGACTTCCACAGAGAGCATCTGTTACTATGGTTTCTACTCAAGATTCT

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: 208

GGTGTCAACAAGCATGAGTTTGCCATCAAAAGCTGGTTTAAAGAACAATAAACATGGTCCTAACGATCGTGGTTCTAATGTGGGCAAACCTGTGTCCCAAgtatgcatca ... ccactatcagAGAGGACTTCCACAGAGAGCATCTGTTACTATGGTTTCTACTCAAGATTCTTCTCAATCCCAGGCATTATTTAACATAAAGGACTCAAACAAG

Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 39

Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 47