ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
PPT, BS, UA-tract

Sequence

atgc intronic sequence ATGC exonic sequence

gtaagtaaacttgtcttatagaaaagaatagaaataaaccaacctacctcccaacctctcctgatgtagtttgtctgtcccgtttcagATGATACGGCAATGTTCTGGGGTGTAAAGTTCTACAATGATTTGCTGATGCAAGCCGGCAAACTTGGGAATGTGCAATCAGAACTGCTTCTCCGCAAGGA

Basic information

species	Zea mays
transcript	GRMZM2G071970_T01
intron #	5
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G071970_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os05g32110.3 (Oryza sativa), 3'ss of exon 3

------------gtaagtaaacttgtcttatagaaaagaatagaaataaaccaac-----------ctacctcccaacctctc---------ctgatgtagtttgtctgtcccgtttcagATGATACGGCAATGTTCTGGGGTGTAAAGTTCTACAATGATTTGCTGATGCAAGCCGGCAAACTTGGGAATGTGCAATCAGAACTGCTTCTCCGCAAGGA
              ||       |   ||||  || | ||| | | |  ||                || ||| |   |||||         |||||| ||||| |   | |  ||| ||||||||| || ||||||||||| || |||||||| || |||||||| |||||||| ||   |||||| ||||  || |||||||| ||||| || |||||
gtaagtcaatttacaaactgttctcctttatttaagaaaattggagtgcacttgtaatacgttcctttatctctctctctctctctctttctctgatgaagtttattccttctattttagATGATACTGCGATGTTCTGGGGAGTTAAGTTCTATAACGATTTGCTCATGCAAGCTGGTCCACTTGGAAATGCACAGTCAGAACTTCTTCTGCGTAAGGA

upper sequence: GRMZM2G071970_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA13G06660.1 (Glycine max), 3'ss of exon 5

------gtaagtaaacttgtcttatagaaa-agaatagaaataaaccaacctacctcccaacctctcctgatg-tagtttgtct--gtcccgttt--cagATGATACGGCAATGTTCTGGGGTGTAAAGTTCTACAATGATTTGCTGATGCAAGCCGGCAAACTTGGGAATGTGCAATCAGAACTGCTTCTCCGCAAGGA
       ||| |  |   |    |||     |   | | |||| | ||       |    |     |   ||| |  ||  |||  ||  | |||   ||||||||| |||||| | |||||  | ||||||||||||||||| || |||||||| |||   ||||| ||||| |||||||| || ||  || | |||||
gtcataataactgcatgagcaacatattcttattttcgcaatagaacatgtattttgtggaggcaccaaaatgattattgatctaagttacttttaatagATGATACAGCAATGCTTTGGGGACTTAAGTTCTACAATGATTTTCTCATGCAAGCTGGCCCTCTTGGTAATGTACAATCAGAGCTACTATTCAGAAAGGA

upper sequence: GRMZM2G071970_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA19G04210.1 (Glycine max), 3'ss of exon 6

---------------gtaa-gtaaacttgtctt-atagaaaagaatagaaataaaccaacctacctcccaacctctcctgatgtagtttgtctgtcccgtttcagATGATACGGCAATGTTCTGGGGTGTAAAGTTCTACAATGATTTGCTGATGCAAGCCGGCAAACTTGGGAATGTGCAATCAGAACTGCTTCTCCGCAAGGA
               | ||  ||  ||| | || |    ||| || |   ||      |    |  |  ||    |  |||| ||  ||   |      |  |||||||||| |||||| | ||||| || ||||||||||||||||| || |||||||| |||   ||||| ||||| ||||||||||| ||  || | |||||
tcataaactgtatgagcaacatattcttattttcaccataaataacatgtatttttgtagaggcgccaaaatgattattgatctaagttacttt-----taacagATGATACAGCAATGCTTTGGGGAGTTAAGTTCTACAATGATTTTCTCATGCAAGCTGGCCCTCTTGGTAATGTACAATCAGAACTACTATTCAGAAAGGA

upper sequence: GRMZM2G071970_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA02G35400.1 (Glycine max), 3'ss of exon 5

--------------gtaagtaaacttgtcttat----agaaaagaatagaaataaaccaacctacctcccaacctctcctgatgtagtttgtctgtcccgtttcagATGATACGGCAATGTTCTGGGGTGTAAAGTTCTACAATGATTTGCTGATGCAAGCCGGCAAACTTGGGAATGTGCAATCAGAACTGCTTCTCCGCAAGGA
               | || ||     ||||||      || |||| |   ||          ||  |  ||    |  |||| ||  ||   |      |   ||||||||| |||||| | |||||  | ||||||||||||||||| || |||||||| |||   ||||| ||||| |||||||| || ||  || | |||||
gtcataataactgcatgagcaacacattcttattttcgcaatagaacatgtattttgtggag-acaccaaaatgattattgatctaagttacttt-----taatagATGATACAGCAATGCTTTGGGGACTTAAGTTCTACAATGATTTTCTCATGCAAGCTGGCCCTCTTGGTAATGTACAATCAGAGCTACTATTCAGAAAGGA

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|76932301|gb|DV172999.1|DV172999

EST:     GTTGTTCAGCTTCAACTACAAACCACTTACTCCATATGGGGGTGGCATAA                         ATGATACGGCAATGTTCTGGGGTGTAAAGTTCTACAATGATTTGCTGATGC
genomic: GTTGTTCAGCTTCAACTACAAACCACTTACTCCATATGGGGGTGGCATAAgtaagtaaac ... cccgtttcagATGATACGGCAATGTTCTGGGGTGTAAAGTTCTACAATGATTTGCTGATGC

EST: gi|211075812|gb|FL010798.1|FL010798

EST:     TACAAACCACTTACTCCATATGGGGGTGGCATAA                         ATGATACGGCAATGTTCTGGGGTGTAAAATTCTACAATGATTTGCTGATGC
genomic: TACAAACCACTTACTCCATATGGGGGTGGCATAAgtaagtaaac ... cccgtttcagATGATACGGCAATGTTCTGGGGTGTAAAGTTCTACAATGATTTGCTGATGC

EST: gi|14190873|gb|BG833103.1|BG833103

EST:     GTTGTTCAGCTTCAACTACAAGCCACTTACTCCATATGGGGGTGGCATAA                         ATGATACGGCAATGTTCTGGGGTGTAAAATTCTACAATGATTTGCTGATGC
genomic: GTTGTTCAGCTTCAACTACAAACCACTTACTCCATATGGGGGTGGCATAAgtaagtaaac ... cccgtttcagATGATACGGCAATGTTCTGGGGTGTAAAGTTCTACAATGATTTGCTGATGC

EST: gi|32938804|gb|CF043623.1|CF043623

EST:     GTTGTTCAGCTTCAACTACAAACCACTTACTCCATATGGGGGTGGCATAA                         ATGATACGGCAATGTTCTGGGGTGTAAAATTCTACAATGATTTGCTGATGC
genomic: GTTGTTCAGCTTCAACTACAAACCACTTACTCCATATGGGGGTGGCATAAgtaagtaaac ... cccgtttcagATGATACGGCAATGTTCTGGGGTGTAAAGTTCTACAATGATTTGCTGATGC

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), 48 (downstream exon)
Score: 88

ACACAGTGGAACTTAGTTGCTCAGCATCCAAACTTTGATAATATCACTCAGTTGTTCAGCTTCAACTACAAACCACTTACTCCATATGGGGGTGGCATAAgtaagtaaac ... cccgtttcagATGATACGGCAATGTTCTGGGGTGTAAAGTTCTACAATGATTTGCTGATGCAAGCCGGCAAACTTGGGAATGTGCAATCAGAACTGCTTCTCCGCAAGGA

Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 71

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 89

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 226

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ataaaccaacctacctcccaacctctcctgatgtagtttgtctgtcccgtttcagATGATACGGCAATGTTCTGGGGTGTAAAGTTCTACAATGATTTGCTGATGCAAGCCGGCAAACTTGGGAATGTGCAATCAGAACTGCTTCTCCGCAAGGA