ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

CTTGTTAAGAAGCTTGCCAAGAAGTACCATGCTTTTTTGGCATCAGAGACCATCATCAAGCAAATTCCCCGTCTCCTTGGTCCTGGTCTCAACAAGGCAGgcaagtagtccgtttctgacatgactgttactttgcgtgccaagctgtagcatgcaatgcagtgttgtctcatatttctgtatgtagttttgcatgataa...

Basic information

species	Zea mays
transcript	GRMZM2G181194_T02
intron #	1
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G181194_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os08g44450.3 (Oryza sativa), 5'ss of exon 1

CTTGTTAAGAAGCTTGCCAAGAAGTACCATGCTTTTTTGGCATCAGAGACCATCATCAAGCAAATTCCCCGTCTCCTTGGTCCTGGTCTCAACAAGGCAGgcaagtagtccgttt-ctgacatgactgttactttgcgtgccaagctgtagcatgcaatgcagtgttgtctcatatttctgtatgtagttttgcatgataa-
|| |||||||||||||||||||||||||||||||| || ||||||||| ||||||||||||| ||||| |||||||||||||||||||||||||||||||||||||| ||| ||| |||||||   || |  ||   | |   || | |    |  || | ||||    ||  | |||||   |||||||||| ||  ||| 
CTGGTTAAGAAGCTTGCCAAGAAGTACCATGCTTTCTTAGCATCAGAGGCCATCATCAAGCAGATTCCTCGTCTCCTTGGTCCTGGTCTCAACAAGGCAGgcaagtattccattttctgacattcttgctttttcttg-gtgtagttctgaattttaacg-agtgcatgctagtttttcttggtgtagttttgaattctaat

upper sequence: GRMZM2G181194_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os08g44380.2 (Oryza sativa), 5'ss of exon 4

CTTGTTAAGAAGCTTGCCAAGAAGTACCATGCTTTTTTGGCATCAGAGACCATCATCAAGCAAATTCCCCGTCTCCTTGGTCCTGGTCTCAACAAGGCAGgcaagtagtccgttt-ctgacatgactgttactttgcgtgccaagctgtagcatgcaatgcagtgttgtctcatatttctgtatgtagttttgcatgataa--
||||| ||||||||||||||||||||||||||||| || ||||||||| ||||||||||||| || ||||||||||||||||||||||| ||||||||||||||||  ||| ||| ||||||||  || | |||    |    | || |    || ||| |  |||| | |||| |   |||||| |  |||  ||  |    
CTTGTGAAGAAGCTTGCCAAGAAGTACCATGCTTTCTTAGCATCAGAGGCCATCATCAAGCAGATCCCCCGTCTCCTTGGTCCTGGTCTAAACAAGGCAGgcaagtcttccattttctgacatgcttgct-cttcttttcatgatctttgttttg-aatacc-tgttttttcatgtacttgtatgcacatttcaattttttgg

upper sequence: GRMZM2G181194_T01 (Zea mays), 5'ss of exon 4
lower sequence: EDP07503 (Chlamydomonas reinhardtii), 5'ss of exon 3

CTTGTTAAGAAGC--TTGCCAAGAAG-TACCATGCTTTTTTGGCATCAGA--GACCATCATCAAGCAAATTCCCCGTCTCCTTGGTCCTGGTCTCAACAAGGCAGgcaagtagtccgtttctgacatgactgttactttgcgtgccaagctgtagcatgcaatgcagtgttgtctcatatttctgtatgtagttttgcatgataa--
    ||  ||  |  |   |||| || | ||  |  |  | |||  | |   || ||    |  |||| ||||| |   |  |   |  |  |        |  ||  ||     |       ||     ||         |       | |  ||| |||  |  |  |  || |  | | | ||    ||  ||| || ||    
----TTCGGACTCCGTCATCAAGCAGATTCCCCGTCTGCTGGGCCCCGGTCTGAACAAGGCCG-GCAAGTTCCCTGCTCCTATCAACAAGAACCTGGAGGAGATGgtgagcga--caaacgcaacgcccttgggttggcagggatgggacgggggcaggcagggtgggctgctcactgactgcagtggtaagggttgaattatggca

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|5713971|gb|AI943956.1|AI943956

EST:     CATCATCAAGCAAATTCCCCGTCTCCTTGGTCCTGGTCTCAACAAGGCAG                         GCAAGTTCCCCACTCTGGTCACTCACCAGGAATCCCTGGAATCCAAGGTGA
genomic: CATCATCAAGCAAATTCCCCGTCTCCTTGGTCCTGGTCTCAACAAGGCAGgcaagtagtc ... actcctgcagGCAAGTTCCCCACTCTGGTCACTCACCAGGAATCCCTGGAATCCAAGGTGA

EST: gi|32943776|gb|CF048595.1|CF048595

EST:     CATCATCAAGCAAACTCCCCGTCTCCTTGGTCCTGGTCTCAACAAGGCAG                         GCAAGTTCCCCACTCTGGTCACTCACCAGGAATCCCTGGAATCCAAGGTGA
genomic: CATCATCAAGCAAATTCCCCGTCTCCTTGGTCCTGGTCTCAACAAGGCAGgcaagtagtc ... actcctgcagGCAAGTTCCCCACTCTGGTCACTCACCAGGAATCCCTGGAATCCAAGGTGA

EST: gi|32841275|gb|CD980956.1|CD980956

EST:     CATCATCAAGCAAATTCCCCGTCTCCTTGGTCCTGGTCTCAACAAGGCAG                         GCAAGTTCCCCACTCTGGTCACTCACCAGGAATCCCTGGAATCCAAGGTGA
genomic: CATCATCAAGCAAATTCCCCGTCTCCTTGGTCCTGGTCTCAACAAGGCAGgcaagtagtc ... actcctgcagGCAAGTTCCCCACTCTGGTCACTCACCAGGAATCCCTGGAATCCAAGGTGA

EST: gi|32930778|gb|CF035590.1|CF035590

EST:     CATCATCAAGCAAATTCCCCGTCTCCTTGGTCCTGGTCTCAACAAGGCAG                         GCAAGTTCCCCACTCTGGTCACTCACCAGGAATCCCTGGAATCCAAGGTGA
genomic: CATCATCAAGCAAATTCCCCGTCTCCTTGGTCCTGGTCTCAACAAGGCAGgcaagtagtc ... actcctgcagGCAAGTTCCCCACTCTGGTCACTCACCAGGAATCCCTGGAATCCAAGGTGA

EST: gi|60347511|gb|DN214484.1|DN214484

EST:     CATCATCAAGCAAATTCCCCGTCTCCTTGGTCCTGGTCTCAACAAGGCAG                         GCAAGTTCCCCACTCTGGTCACTCACCAGGAATCCCTGGAATCCAAGGTGA
genomic: CATCATCAAGCAAATTCCCCGTCTCCTTGGTCCTGGTCTCAACAAGGCAGgcaagtagtc ... actcctgcagGCAAGTTCCCCACTCTGGTCACTCACCAGGAATCCCTGGAATCCAAGGTGA

EST: gi|211379030|gb|FL141076.1|FL141076

EST:     CATCWTCAAGCAAATTCCCCGTCTCCTTGGTCCTGGTCTCAACAAGGCAG                         GCAAGTTCCCCACTCTGGTCACTCACCAGGAATCCCTGGAATCCAAGGTGA
genomic: CATCATCAAGCAAATTCCCCGTCTCCTTGGTCCTGGTCTCAACAAGGCAGgcaagtagtc ... actcctgcagGCAAGTTCCCCACTCTGGTCACTCACCAGGAATCCCTGGAATCCAAGGTGA

EST: gi|19769382|gb|BQ034103.1|BQ034103

EST:     CATCATCAAGCAAATTCCCCGTCTCCTTGGTCCTGGTCTCAACAAGGCAG                         GCAAGTTCCCCACTCTGGTCACTCGCCAGGAATCCCTGGAATCCAAGGTGA
genomic: CATCATCAAGCAAATTCCCCGTCTCCTTGGTCCTGGTCTCAACAAGGCAGgcaagtagtc ... actcctgcagGCAAGTTCCCCACTCTGGTCACTCACCAGGAATCCCTGGAATCCAAGGTGA

EST: gi|211268446|gb|FL141046.1|FL141046

EST:     CWTCWTCAAGCAAATTCCCCGTCTCCTTGGTCCTGGTCTCAACAAGGCAG                         GCAAGTTCCCCACTCTGGTCACTCACCAGGAATCCCTGGAATCCAAGGTGA
genomic: CATCATCAAGCAAATTCCCCGTCTCCTTGGTCCTGGTCTCAACAAGGCAGgcaagtagtc ... actcctgcagGCAAGTTCCCCACTCTGGTCACTCACCAGGAATCCCTGGAATCCAAGGTGA

EST: gi|60358826|gb|DN225799.1|DN225799

EST:     CATCATCAAGCAAATTCCCCGTCTCCTTGGTCCTGGTCTCAACAAGGCAG                         GCAAGTTCCCCACTCTGGTCACTCACCAGGAATCCCTGGAATCCAAGGTGA
genomic: CATCATCAAGCAAATTCCCCGTCTCCTTGGTCCTGGTCTCAACAAGGCAGgcaagtagtc ... actcctgcagGCAAGTTCCCCACTCTGGTCACTCACCAGGAATCCCTGGAATCCAAGGTGA

EST: gi|84977553|gb|DW475975.1|DW475975

EST:     CATCATCAAGCAAATTCCCCGTCTCCTTGGTCCTGGTCTCAACAAGGCAG                         GCAAGTTCCCCACTCTGGTCACTCACCAGGAATCCCTGGAATCCAAGGTGA
genomic: CATCATCAAGCAAATTCCCCGTCTCCTTGGTCCTGGTCTCAACAAGGCAGgcaagtagtc ... actcctgcagGCAAGTTCCCCACTCTGGTCACTCACCAGGAATCCCTGGAATCCAAGGTGA

EST: gi|15323558|gb|BI478780.1|BI478780

EST:     CATCATCAAGCAAATTCCCCGTCTCCTTGGTCCTGGTCTCAACAAGGCAG                         GCAAGTTCCCCACTCTGGTCACTCACCAGGAATCCCTGGAATCCAAGGTGA
genomic: CATCATCAAGCAAATTCCCCGTCTCCTTGGTCCTGGTCTCAACAAGGCAGgcaagtagtc ... actcctgcagGCAAGTTCCCCACTCTGGTCACTCACCAGGAATCCCTGGAATCCAAGGTGA

EST: gi|211263568|gb|FL141014.1|FL141014

EST:     CATCWTCAAGCAAATTCCCCGTCTCCTTGGTCCTGGTCTCAACAAGGCAG                         GCAAGTTCCCCACTCTGGTCACTCACCAGGAATCCCTGGAATCCAAGGTGA
genomic: CATCATCAAGCAAATTCCCCGTCTCCTTGGTCCTGGTCTCAACAAGGCAGgcaagtagtc ... actcctgcagGCAAGTTCCCCACTCTGGTCACTCACCAGGAATCCCTGGAATCCAAGGTGA

EST: gi|6865330|gb|AW360680.1|AW360680

EST:     CATCATCAAGCAAATTCCCCGTCTCCTTGGTCCTGGTCTCAACAAGGCAG                         GCAAGTTCCCCACTCTGGTCACTCACCAGGAATCCCTGGAATCCAAGGTGA
genomic: CATCATCAAGCAAATTCCCCGTCTCCTTGGTCCTGGTCTCAACAAGGCAGgcaagtagtc ... actcctgcagGCAAGTTCCCCACTCTGGTCACTCACCAGGAATCCCTGGAATCCAAGGTGA

EST: gi|60345300|gb|DN212273.1|DN212273

EST:     CATCATCAAGCAAATTCCCCGTCTCCTTGGTCCTGGTCTCAACAAGGCAG                         GCAAGTTCCCCACTCTGGTCACTCACCAGGAATCCCTGGAATCCAAGGTGA
genomic: CATCATCAAGCAAATTCCCCGTCTCCTTGGTCCTGGTCTCAACAAGGCAGgcaagtagtc ... actcctgcagGCAAGTTCCCCACTCTGGTCACTCACCAGGAATCCCTGGAATCCAAGGTGA

EST: gi|60357767|gb|DN224740.1|DN224740

EST:     CATCATCAAGCAAATTCCCCGTCTCCTTGGTCCTGGTCTCAACAAGGCAG                         GCAAGTTCCCCACTCTGGTCACTCACCAGGAATCCCTGGAATCCAAGGTGA
genomic: CATCATCAAGCAAATTCCCCGTCTCCTTGGTCCTGGTCTCAACAAGGCAGgcaagtagtc ... actcctgcagGCAAGTTCCCCACTCTGGTCACTCACCAGGAATCCCTGGAATCCAAGGTGA

EST: gi|60396150|gb|DN229019.1|DN229019

EST:     CATCATCAAGCAAATTCCCCGTCTCCTTGGTCCTGGTCTCAACAAGGCAG                         GCAAGTTCCCCACTCTGGTCACTCACCAGGAATCCCTGGAATCCAAGGTGA
genomic: CATCATCAAGCAAATTCCCCGTCTCCTTGGTCCTGGTCTCAACAAGGCAGgcaagtagtc ... actcctgcagGCAAGTTCCCCACTCTGGTCACTCACCAGGAATCCCTGGAATCCAAGGTGA

EST: gi|32934673|gb|CF039485.1|CF039485

EST:     CATCATCAAGCAAATTCCCCGTCTCCTTGGTCCTGGTCTCAACAAGGCAG                         GCAAGTTCCCCACTCTGGTCACTCACCAGGAATCCCTGGAATCCAAGGTGA
genomic: CATCATCAAGCAAATTCCCCGTCTCCTTGGTCCTGGTCTCAACAAGGCAGgcaagtagtc ... actcctgcagGCAAGTTCCCCACTCTGGTCACTCACCAGGAATCCCTGGAATCCAAGGTGA

EST: gi|33093601|gb|CF053595.1|CF053595

EST:     CATCATCAAGCAAATTCCCCGTCTCCCTGGTCCTGGTCTCAACAAGGCAG                         GCAAGTTCCCCACTCTGGTCACTCACCAGGAAT-CCTGGAATCCAAGGTGA
genomic: CATCATCAAGCAAATTCCCCGTCTCCTTGGTCCTGGTCTCAACAAGGCAGgcaagtagtc ... actcctgcagGCAAGTTCCCCACTCTGGTCACTCACCAGGAATCCCTGGAATCCAAGGTGA

EST: gi|32930672|gb|CF035484.1|CF035484

EST:     CATCATCAAGCAAATTCCCCGTCTCCTTGGTCCTGGTCTCAACAAGACAG                         GCAAGTTCCCCACTCTGGTCACTCACCAGGAATCCCTGGAATCCAAGGTGA
genomic: CATCATCAAGCAAATTCCCCGTCTCCTTGGTCCTGGTCTCAACAAGGCAGgcaagtagtc ... actcctgcagGCAAGTTCCCCACTCTGGTCACTCACCAGGAATCCCTGGAATCCAAGGTGA

EST: gi|12973327|gb|BG268425.1|BG268425

EST:     CATCATCAAGCAAATTCCCCGTCTCCTTGGTCCTGGTCTCAACAAGGCAG                         GCAAGTTCCCCACTCTGGTCACTCACCAGGAATCCCTGGAATCCAAGGTGA
genomic: CATCATCAAGCAAATTCCCCGTCTCCTTGGTCCTGGTCTCAACAAGGCAGgcaagtagtc ... actcctgcagGCAAGTTCCCCACTCTGGTCACTCACCAGGAATCCCTGGAATCCAAGGTGA

EST: gi|211242318|gb|FL469539.1|FL469539

EST:     CATCATCAAGCAAATTCCCCGTCTCCTTGGTCCTGGTCTCAACAAGGCAG                         GCAAGTTCCCCACTCTGGTCACTCACCAGGAATCCCTGGAATCCAAGGTGA
genomic: CATCATCAAGCAAATTCCCCGTCTCCTTGGTCCTGGTCTCAACAAGGCAGgcaagtagtc ... actcctgcagGCAAGTTCCCCACTCTGGTCACTCACCAGGAATCCCTGGAATCCAAGGTGA

EST: gi|5018419|gb|AI714612.1|AI714612

EST:     CATCATCAAGCAAATTCCCCGTCTCCTTGGTCCTGGTCTCAACAAGGCAG                         GCAAGTTCCCCACTCTGGTCACTCACCAGGAATCCCTGGAATCCAAGGTGA
genomic: CATCATCAAGCAAATTCCCCGTCTCCTTGGTCCTGGTCTCAACAAGGCAGgcaagtagtc ... actcctgcagGCAAGTTCCCCACTCTGGTCACTCACCAGGAATCCCTGGAATCCAAGGTGA

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: 354

CTTGTTAAGAAGCTTGCCAAGAAGTACCATGCTTTTTTGGCATCAGAGACCATCATCAAGCAAATTCCCCGTCTCCTTGGTCCTGGTCTCAACAAGGCAGgcaagtagtc ... actcctgcagGCAAGTTCCCCACTCTGGTCACTCACCAGGAATCCCTGGAATCCAAGGTGAATGAGACGAAGGCTACAGTCAAGTTTCAACTGAAGAAAGTCCTTTGCAT

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 268

Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 261

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 206

Putative cis-regulatory sequences

atgc	intron	ATGC	exonic elements by Pertea et al.
ATGC	exon	atgc	putative intronic elements
		ATGC	putative exonic elements identified for retained introns

        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTGTTAAGAAGCTTGCCAAGAAGTACCATGCTTTTTTGGCATCAGAGACCATCATCAAGCAAATTCCCCGTCTCCTTGGTCCTGGTCTCAACAAGGCAGgcaagtagtccgtttctgacatgactgttactttgcgtgccaagctgtagcatgcaatgcagtgttgtctcatatttctgtatgtagttttgcatgataa

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA