ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

GCAAGGATGAACCATCCTAAAGGGTTCACTGTGGACGATAGGGGCAACATTTATGTTGCAGACGGCATGAACATGGCAATACGAAAAATCAGTGATACAGgtaagctaaaatggcccattctgaggtagttcacatggcattgtctggtcccccagttccccttctgtttgttctatgttttttcatggagctcctcctt...

Basic information

species	Zea mays
transcript	GRMZM2G020943_T01
intron #	4
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G020943_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os06g15820.1 (Oryza sativa), 5'ss of exon 4

GCAAGGATGAACCATCCTAAAGGGTTCACTGTGGACGATAGGGGCAACATTTATGTTGCAGACGGCATGAACATGGCAATACGAAAAATCAGTGATACAGgtaagctaaaatggcccat-tctgaggtagtt-cacatggcattgtctggtcccccagttccccttctgtttgttctatgttttttcatggagctcctcctt
|| | |||||||||||| || || || || |||||||||||||| ||||||||||||||||| |  ||||| ||||||||| |||| ||||||||||||||||||||||| || | | | | || ||| ||| ||||||  | |||||||||||| ||   ||  | |||||| | | || ||||   || | ||| ||   
GCGAAGATGAACCATCCGAAGGGATTTACAGTGGACGATAGGGGAAACATTTATGTTGCAGATGCTATGAATATGGCAATAAGAAAGATCAGTGATACAGgtaagctaaagtgtctcttatatggggttgttgcacatgatactgtctggtccccaagcatcc--tatgtttgctatttggttttcattgtaactcttcagc

upper sequence: GRMZM2G020943_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv01s0026g00330.t01 (Vitis vinifera), 5'ss of exon 4

GCAAGGATGAACCATCCTAAAGGGTTCACTGTGGACGATAGGGGCAACATTTATGTTGCAGACGGCATGAACATGGCAATACGAAAAATCAGTGATACAGgtaagctaaaatggcccattctgaggtagttcacatggcattgtctggtcccccagttccccttctgtttgttctatgttttttcatggagctcctcctt---
||||||||||| ||||| || ||| | |||||||| || || || |||||||||||||||||   | |||| ||||| ||  | || || |||||| |||||||    |||||        | | | ||  |   ||   ||  || |  |    || |||       |  ||   ||||   | |||   ||     |    
GCAAGGATGAATCATCCGAAGGGGCTTACTGTGGATGACAGAGGAAACATTTATGTTGCAGATACCTTGAATATGGCCATCAGGAAGATAAGTGATGCAGgtaaatgcaaatgaggatgagtaatgcaggcc---tgtattttgcttgagcatatgtacccagaagaatattttcctgttcactgatgtcccttaagttaagg

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|149005168|gb|EE039704.2|EE039704

EST:     TTATGTTGCAGACGGCATGAACATGGCAATACGAAAAATCAGTGATACAG                         GGGTTACAACCATTGCTGGGGGAAAATCAATTAGAGGAGGGCACATAGATG
genomic: TTATGTTGCAGACGGCATGAACATGGCAATACGAAAAATCAGTGATACAGgtaagctaaa ... taatattcagGGGTTACAACCATTGCTGGGGGAAAATCAATTAGAGGAGGGCACATAGATG

EST: gi|78114597|gb|DV532985.1|DV532985

EST:     TTATGTTGCAGACGGCATGAACATGGCAATACGAAAAATCAGTGATACAG                         GGGTTACAACCATTGCTGGGGGAAAATCAATTAGAGGAGGGCACATAGATG
genomic: TTATGTTGCAGACGGCATGAACATGGCAATACGAAAAATCAGTGATACAGgtaagctaaa ... taatattcagGGGTTACAACCATTGCTGGGGGAAAATCAATTAGAGGAGGGCACATAGATG

EST: gi|76912974|gb|DV164954.1|DV164954

EST:     TTATGTTGCAGACGGCATGAACATGGCAATACGAAAAATCAGTGATACAG                         GGGTTACAACCATTGCTGGGGGAAAATCAATTAGAGGAGGGCACATAGATG
genomic: TTATGTTGCAGACGGCATGAACATGGCAATACGAAAAATCAGTGATACAGgtaagctaaa ... taatattcagGGGTTACAACCATTGCTGGGGGAAAATCAATTAGAGGAGGGCACATAGATG

EST: gi|31360064|gb|CD444421.1|CD444421

EST:     TTATGTTGCAGACGGCATGAACATGGCAATACGAAAAATCAGTGATACAG                         GGGTTACAACCATTGCTGGGGGAGAATCAATTAGAGGAGGGCACATAGATG
genomic: TTATGTTGCAGACGGCATGAACATGGCAATACGAAAAATCAGTGATACAGgtaagctaaa ... taatattcagGGGTTACAACCATTGCTGGGGGAAAATCAATTAGAGGAGGGCACATAGATG

EST: gi|149099000|gb|EE185013.2|EE185013

EST:     TTATGTTGCAGACGGCATGAACATGGCAATACGAAAAATCAGTGATACAG                         GGGTTACAACCATTGCTGGGGGAAAATCAATTAGAGGAGGGCACATAGATG
genomic: TTATGTTGCAGACGGCATGAACATGGCAATACGAAAAATCAGTGATACAGgtaagctaaa ... taatattcagGGGTTACAACCATTGCTGGGGGAAAATCAATTAGAGGAGGGCACATAGATG

EST: gi|148958537|gb|EC904780.2|EC904780

EST:     TTATGTTGCAGACGGCATGAACATGGCAATACGAAAAATCAGTGATACAG                         GGGTTACAACCATTGCTGGGGGAAAATCAATTAGAGGAGGGCACATAGATG
genomic: TTATGTTGCAGACGGCATGAACATGGCAATACGAAAAATCAGTGATACAGgtaagctaaa ... taatattcagGGGTTACAACCATTGCTGGGGGAAAATCAATTAGAGGAGGGCACATAGATG

EST: gi|6021074|gb|AW066002.1|AW066002

EST:     TTATGTTGCAGACGGCATGAACATGGCAATACGAAAAATCAGTGATACAG                         GGGTTACAACCATTGCTGGGGGAAAATCAATTAGAGGAGGGCACATAGATG
genomic: TTATGTTGCAGACGGCATGAACATGGCAATACGAAAAATCAGTGATACAGgtaagctaaa ... taatattcagGGGTTACAACCATTGCTGGGGGAAAATCAATTAGAGGAGGGCACATAGATG

EST: gi|32940716|gb|CF045535.1|CF045535

EST:     TTATGTTGCAGACGGCATGAACATGGCAATACGAAAAATCAGTGATACAG                         GGGTTACAACCATTGCTGAGGGAAAATCAATTAGAGGAGGGCACATAGATG
genomic: TTATGTTGCAGACGGCATGAACATGGCAATACGAAAAATCAGTGATACAGgtaagctaaa ... taatattcagGGGTTACAACCATTGCTGGGGGAAAATCAATTAGAGGAGGGCACATAGATG

EST: gi|89759931|gb|DY688587.1|DY688587

EST:     TTATGTTGCAGACGGCATGAACATGGCAATACGAAAAATCAGTGATACAG                         GGGTTACAACCATTGCTGGGGGAAAATCAATTAGAGGAGGGCACATAGA
genomic: TTATGTTGCAGACGGCATGAACATGGCAATACGAAAAATCAGTGATACAGgtaagctaaa ... taatattcagGGGTTACAACCATTGCTGGGGGAAAATCAATTAGAGGAGGGCACATAGA

EST: gi|74241599|gb|DT649513.1|DT649513

EST:     TTATGTTGCAGACGGCATGAACATGGCAATACGAAAAATCAGTGATACAG                         GGGTTACAACCATTGCTGGGGGAAAATCAATTAGAGGAGGGCACATAGATG
genomic: TTATGTTGCAGACGGCATGAACATGGCAATACGAAAAATCAGTGATACAGgtaagctaaa ... taatattcagGGGTTACAACCATTGCTGGGGGAAAATCAATTAGAGGAGGGCACATAGATG

EST: gi|71325268|gb|DR799321.1|DR799321

EST:     TTATGTTGCAGACGGCATGAACATGGCAATACGAAAAATCAGTGATACAG                         GGGTTACAACCATTGCTGGGGGAAAATCAATTAGAGGAGGGCACATAGATG
genomic: TTATGTTGCAGACGGCATGAACATGGCAATACGAAAAATCAGTGATACAGgtaagctaaa ... taatattcagGGGTTACAACCATTGCTGGGGGAAAATCAATTAGAGGAGGGCACATAGATG

EST: gi|211162233|gb|FL114511.1|FL114511

EST:     TATNGT-GCAGACGGCATGAACATGGCAATACGAAAA-TCAGTGATACAG                         GGGTTACCACCATTG
genomic: TAT-GTTGCAGACGGCATGAACATGGCAATACGAAAAATCAGTGATACAGgtaagctaaa ... taatattcagGGGTTACAACCATTG

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), 49 (downstream exon)
Score: 22

GCAAGGATGAACCATCCTAAAGGGTTCACTGTGGACGATAGGGGCAACATTTATGTTGCAGACGGCATGAACATGGCAATACGAAAAATCAGTGATACAGgtaagctaaa ... taatattcagGGGTTACAACCATTGCTGGGGGAAAATCAATTAGAGGAGGGCACATAGATGGGCCCAGTGATGATGCAAAATTCTCAACTGATTTTGAAATCAAGTACAT

Block sizes: 48 (upstream exon), 36 (downstream exon)
Score: 9

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 8

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 13

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAAGGATGAACCATCCTAAAGGGTTCACTGTGGACGATAGGGGCAACATTTATGTTGCAGACGGCATGAACATGGCAATACGAAAAATCAGTGATACAGgtaagctaaaatggcccattctgaggtagttcacatggcattgtctggtcccccagttccccttctgtttgttctatgttttttcatggagctcctcctt

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