ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

TGTCCTAACTAGCATTGTTCTGATTGGAGGGATGATACCTTACATTTCCGAGACATTTGCCAGAATTCTGTTCCTGAGCAATTCATTGACGTTTATGATGgtatggaattaccagcgcttataattgtaataaaattgtactccctccattttttatttgtcgcgttttagtttaaaaatgaactagcgggcgacaaatattcgagaacggaaggagtataaatttaatagtaaggcatgtttgagaaagtcttacattggtaactctgacttctgatatggcatgttag

Basic information

species	Zea mays
transcript	GRMZM2G082976_T01
intron #	3
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G082976_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os03g63520.1 (Oryza sativa), 5'ss of exon 3

TGTCCTAACTAGCATTGTTCTGATTGGAGGGATGATACCTTACATTTCCGAGACATTTGCCAGAATTCTGTTCCTGAGCAATTCATTGACGTTTATGATGgtatggaattaccagcgcttataattgtaataaaattgtactccctccattttttatttgtcgcgttttagtttaaaaatgaactagcgggcgacaaatattcgagaacggaaggagtataaatttaatagta--aggcatgtttgagaaagtcttacattggtaactctgacttctgatatggcatgttag
|||||| ||| |||||||||||||||| |||||||||||||| ||||| ||||||||||||||||| |||||| |||||||||||||||| |||||||||||| |  ||||               |||  |  ||| ||||       |||||  |||    |    | |||             | |   ||||||| || | ||      ||  | | ||  || |  |    ||    |      ||||      || |||| ||     |||  |||||      ||
TGTCCTGACTGGCATTGTTCTGATTGGTGGGATGATACCTTATATTTCTGAGACATTTGCCAGAATCCTGTTCTTGAGCAATTCATTGACATTTATGATGgtacgagatta---------------gtacaagcattatacttg----gtttttggttttctacaccatcgttaggg---------gtgcaggacaaatcttagggattttctgggctctgaaaatagtcttcttgggtgcatacttagaagttgagttttagtaattcc----tctcgtatggacctgcag

upper sequence: GRMZM2G082976_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv10s0116g00010.t01 (Vitis vinifera), 5'ss of exon 1

TGTCCTAACTAGCATTGTTCTGATTGGAGGGATGATACCTTACATTTCCGAGACATTTGCCAGAATTCTGTTCCTGAGCAATTCATTGACGTTTATGATGgt--atggaattaccagcgcttataattgtaataaaattgtactccctccattttttatttgtcgcgttttagtttaaaaatgaactagcgggcgacaaatattcgagaacggaaggagtataaatttaatagtaaggcatgtttgagaaagtcttacattggtaactctgacttctgatatggcatgttag
|||  ||||  | |||||||| ||||| ||||||||||| ||  | || ||| ||||||| | |||| | |||||||||||||||||||| || ||||||||   |  | ||  |   ||| | |  |  ||  |  || || |   | || |  || |    |   | ||  ||  |        ||    |       | ||  | |                                                                                   
TGTTTTAACGGGGATTGTTCTCATTGGGGGGATGATACCATATGTATCAGAGTCATTTGCAAAAATTATATTCCTGAGCAATTCATTGACATTCATGATGgttagttaatttttctttgctcacacatagaa-gatgttttattggttacagtcattgtgcaacaactgtt--ttggatgtcttgttactctgtttttcctgttgtacag----------------------------------------------------------------------------------

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|37379052|gb|CF626253.1|CF626253

EST:     AGACATTTGCCAGAATTCTGTTCTTGAGCAATTCATTGACGTTTATGATG                         GTTTATGTCTGGAGCAAGCACAATCCTTTCATCCATATGAGCTTTCTGGGC
genomic: AGACATTTGCCAGAATTCTGTTCCTGAGCAATTCATTGACGTTTATGATGgtatggaatt ... ggcatgttagGTTTATGTCTGGAGCAAGCACAATCCTTTCATCCATATGAGCTTTCTGGGC

EST: gi|42491916|gb|CK700962.1|CK700962

EST:     AGACATTTGCCAGAATTCTGTTCCTGAGCAATTCATTGACGTTTATGATG                         GTTTATGTCTGGAGCAAGCACAATCCTTTCATCCATATGAGCTTTCTGGGC
genomic: AGACATTTGCCAGAATTCTGTTCCTGAGCAATTCATTGACGTTTATGATGgtatggaatt ... ggcatgttagGTTTATGTCTGGAGCAAGCACAATCCTTTCATCCATATGAGCTTTCTGGGC

EST: gi|37378913|gb|CF626178.1|CF626178

EST:     ACGTTTATGATG                         GTTTATGTATGGAGCAAGCACAATCCTTTCATCCATATGAGCTTTCTGGGC
genomic: ACGTTTATGATGgtatggaatt ... ggcatgttagGTTTATGTCTGGAGCAAGCACAATCCTTTCATCCATATGAGCTTTCTGGGC

EST: gi|78543826|gb|DV621324.1|DV621324

EST:     AGACATTTGCCAGAATTCTGTTCCTGAGCAATTCATTGACGTTTATGATG                         GTTTATGTCTGGAGCAAGCACAATCCTTTCATCCATATGAGCTTTCTGGGC
genomic: AGACATTTGCCAGAATTCTGTTCCTGAGCAATTCATTGACGTTTATGATGgtatggaatt ... ggcatgttagGTTTATGTCTGGAGCAAGCACAATCCTTTCATCCATATGAGCTTTCTGGGC

EST: gi|88754119|gb|DY538260.1|DY538260

EST:     AGACATTTGCCAGAATTCTGTTCCTGAGCAATTCATTGACGTTTATGATG                         GTTTATGTCTGGAGCAAGCACAATCCTTTCATCCATATGAGCTTTCTGGGC
genomic: AGACATTTGCCAGAATTCTGTTCCTGAGCAATTCATTGACGTTTATGATGgtatggaatt ... ggcatgttagGTTTATGTCTGGAGCAAGCACAATCCTTTCATCCATATGAGCTTTCTGGGC

EST: gi|26457330|gb|CA828913.1|CA828913

EST:     AGACATTTGCCAGAATTCTGTTCCTGAGCAATTCATTGACGTTTATGATG                         GTTTATGTCTGGAGCAAGCACAATCCTTTCATCCATATGAGCTTTCTGGGC
genomic: AGACATTTGCCAGAATTCTGTTCCTGAGCAATTCATTGACGTTTATGATGgtatggaatt ... ggcatgttagGTTTATGTCTGGAGCAAGCACAATCCTTTCATCCATATGAGCTTTCTGGGC

EST: gi|31353782|gb|CD438139.1|CD438139

EST:     AGACATTTGCCAGAATTCTGTTCCTGAGCAATTCATTGACGTTTATGATG                         GTTTATGTCTGGAGCAAGCACAATCCTTTCATCCATATGAGCTTTCTGGGC
genomic: AGACATTTGCCAGAATTCTGTTCCTGAGCAATTCATTGACGTTTATGATGgtatggaatt ... ggcatgttagGTTTATGTCTGGAGCAAGCACAATCCTTTCATCCATATGAGCTTTCTGGGC

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: 47 (upstream exon), 49 (downstream exon)
Score: 113

TGTCCTAACTAGCATTGTTCTGATTGGAGGGATGATACCTTACATTTCCGAGACATTTGCCAGAATTCTGTTCCTGAGCAATTCATTGACGTTTATGATGgtatggaatt ... ggcatgttagGTTTATGTCTGGAGCAAGCACAATCCTTTCATCCATATGAGCTTTCTGGGCCTGTTCACCTTTACGGCTGCATACTTACCATGG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 109

Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 90