ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

gtgagaggagttcgatcggtctgctccgcgcaatgcggcgggcgaagacttatcttctccttattttccggcgccggccgggccttggatcgtccttgctgatcatctccgtttcggtgcgcttcttcttcttcctcctcctcctccttcggtcgcggaaacgccatggatggatggattgggacgggctagcagGAGTACGTGCGGAGCTCGAGAGGCGTGCAGCTCTTCACCTGCGGCTGGCTGCCCGCTGCCGCATCGCCCAAGGCGCTCGTCTTCCTCTGCCACG

Basic information

species	Zea mays
transcript	GRMZM2G080320_T03
intron #	1
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G080320_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g21300.1 (Oryza sativa), 3'ss of exon 1

gtgagaggagttcgatcggtctgctccgcgcaatgcggcgggcgaagacttatcttctccttattttccggcgccggccgggccttggatcgtccttgctgatcatctccgtttcggtgcgcttcttcttcttcctcctcctcctccttcggtcgcggaaacgccatggatggatggattgggacgggctagcagGAGTACGTGCGGAGCTCGAGAGGCGTGCAGCTCTTCACCTGCGGCTGGCTGCCCGCTGCCGCATCGCCCAAGGCGCTCGTCTTCCTCTGCCACG
                                                                        |   |||| || | | || |    || |    |||    |  |  |      | |  |   |||      | | |||| |         ||||||||||||||||         ||  |||||||||||||||||| ||||||||| ||||||||||||||||||||||||||||||||     | ||||||||||| |||||||||||||||||||
------------------------------------------------------------------------gtgagccgcgcttcgcattgcatctgtt--ctatcgttttcccattttctcgcgtactgaacctgacatgcattcttccg-------ggcgccatggatggatgg---------ggggagcagGAGTACGTGCGGAACTCGAGAGGGGTGCAGCTCTTCACCTGCGGCTGGCTGCCCGCCAAAACGTCGCCCAAGGCCCTCGTCTTCCTCTGCCACG

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|101386310|gb|EB815175.1|EB815175

EST:     GCGGCCACGCCTNNNNNNNNNNNNNNGACATGGAGGTCGAATACCACGAG                         GAGTACGTGCGGAGCTCGAGAGGCGTGCAGCTCTTCACCTGCGGCTGGCTG
genomic: GCGGCCACGCCTCGCGCGCGCGCGCGGACATGGAGGTCGAATACCACGAGgtgagaggag ... gggctagcagGAGTACGTGCGGAGCTCGAGAGGCGTGCAGCTCTTCACCTGCGGCTGGCTG

EST: gi|76933105|gb|DV173322.1|DV173322

EST:     GCGGCCACGCCTNNNNNNNNNNNNNNGACATGGAGGTCGAATACCACGAG                         GAGTACGTGCGGAGCTCGAGAGGCGTGCAGCTCTTCACCTGCGGCTGGCTG
genomic: GCGGCCACGCCTCGCGCGCGCGCGCGGACATGGAGGTCGAATACCACGAGgtgagaggag ... gggctagcagGAGTACGTGCGGAGCTCGAGAGGCGTGCAGCTCTTCACCTGCGGCTGGCTG

EST: gi|76937527|gb|DV175177.1|DV175177

EST:     GACATGGAGGTCGAATACCACGAG                         GAGTACGTGCGGAGCTCGAGAGGCGTGCAGCTCTTCACCTGCGGCTGGCTG
genomic: GACATGGAGGTCGAATACCACGAGgtgagaggag ... gggctagcagGAGTACGTGCGGAGCTCGAGAGGCGTGCAGCTCTTCACCTGCGGCTGGCTG

EST: gi|71442135|gb|DR823185.1|DR823185

EST:     GCGGCCACGCCTNNNNNNNNNNNNNNGACATGGAGGTCGAATACCACGAG                         GAGTACGTGCGGAGCTCGAGAGGCGTGCAGCTCTTCACCTGCGGCTGGCTG
genomic: GCGGCCACGCCTCGCGCGCGCGCGCGGACATGGAGGTCGAATACCACGAGgtgagaggag ... gggctagcagGAGTACGTGCGGAGCTCGAGAGGCGTGCAGCTCTTCACCTGCGGCTGGCTG

EST: gi|71324668|gb|DR799031.1|DR799031

EST:     GCGGCCACGCCTNNNNNNNNNNNNNNGACATGGAGGTCGAATACCACGAG                         GAGTACGTGCGGAGCTCGAGAGGCGTGCAGCTCTTCACCTGCGGCTGGCTG
genomic: GCGGCCACGCCTCGCGCGCGCGCGCGGACATGGAGGTCGAATACCACGAGgtgagaggag ... gggctagcagGAGTACGTGCGGAGCTCGAGAGGCGTGCAGCTCTTCACCTGCGGCTGGCTG

EST: gi|88756708|gb|DY540849.1|DY540849

EST:     GCGGCCACGCCTNNNNNNNNNNNNNNGACATGGAGGTCGAATACCACGAG                         GAGTACGTGCGGAGCTCGAGAGGCGTGCAGCTCTTCACCTGCGGCTGGCTG
genomic: GCGGCCACGCCTCGCGCGCGCGCGCGGACATGGAGGTCGAATACCACGAGgtgagaggag ... gggctagcagGAGTACGTGCGGAGCTCGAGAGGCGTGCAGCTCTTCACCTGCGGCTGGCTG

EST: gi|76016400|gb|DT943570.1|DT943570

EST:     GCGGCCACGCCTNNNNNNNNNNNNNNGACATGGAGGTCGAATACCACGAGCAG                       
genomic: GCGGCCACGCCTCGCGCGCGCGCGCGGACATGGAGGTCGAATACCAC--G-AGgtgagaggag ... gggctagc

EST: gi|148949770|gb|EC895253.2|EC895253

EST:     GACATGGAGGTCGAATACCACGAG                         GAGTACGTGCGGAGCTCGAGAGGCGTGCAGCTCTTCACCTGCGGCTGGCTG
genomic: GACATGGAGGTCGAATACCACGAGgtgagaggag ... gggctagcagGAGTACGTGCGGAGCTCGAGAGGCGTGCAGCTCTTCACCTGCGGCTGGCTG

EST: gi|149075325|gb|EE163832.2|EE163832

EST:     GCGGCCACGCCTNNNNNNNNNNNNNNGACATGGAGGTCGAATACCACGAG                         GAGTACGTGCGGAGCTCGAGAGGCGTGCAGCTCTTCACCTGCGGCTGGCTG
genomic: GCGGCCACGCCTCGCGCGCGCGCGCGGACATGGAGGTCGAATACCACGAGgtgagaggag ... gggctagcagGAGTACGTGCGGAGCTCGAGAGGCGTGCAGCTCTTCACCTGCGGCTGGCTG

EST: gi|50331619|gb|CO526745.1|CO526745

EST:     GCGGCCACGCCTNNNNNNNNNNNNNNGACATGGAGGTCGAATACCACGAG                         GAGTACGTGCGGAGCTCGAGAGGCGTGCAGCTCTTCACCTGCGGCTGGCTG
genomic: GCGGCCACGCCTCGCGCGCGCGCGCGGACATGGAGGTCGAATACCACGAGgtgagaggag ... gggctagcagGAGTACGTGCGGAGCTCGAGAGGCGTGCAGCTCTTCACCTGCGGCTGGCTG

EST: gi|50335883|gb|CO531009.1|CO531009

EST:     GCGGCCACGCCTNNNNNNNNNNNNNNGACATGGAGGTCGAATACCACGAG                         GAGTACGTGCGGAGCTCGAGAGGCGTGCAGCTCTTCACCTGCGGCTGGCTG
genomic: GCGGCCACGCCTCGCGCGCGCGCGCGGACATGGAGGTCGAATACCACGAGgtgagaggag ... gggctagcagGAGTACGTGCGGAGCTCGAGAGGCGTGCAGCTCTTCACCTGCGGCTGGCTG

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), 49 (downstream exon)
Score: 50

GCGCCGGCGCTGTAGTGTGCAGCCCTCCTCCTGGATCTCTGCACCCTTCGGCGGCCACGCCTCGCGCGCGCGCGCGGACATGGAGGTCGAATACCACGAGgtgagaggag ... gggctagcagGAGTACGTGCGGAGCTCGAGAGGCGTGCAGCTCTTCACCTGCGGCTGGCTGCCCGCTGCCGCATCGCCCAAGGCGCTCGTCTTCCTCTGCCACG

Block sizes: 49 (upstream exon), 36 (downstream exon)
Score: 4

Block sizes: 41 (upstream exon), 25 (downstream exon)
Score: 4