ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

TCTATACAGCGACTATCTTGAAGCTGCAGACACGCCTGGGTGGTACTGCGGACCTAACTTCTACACCACAGAAGTCCTCCGCAAGTTTGCCAGGTCACAGgtaaaagcattgttcttaatgctctcaaagtgcccaacgtacggggaagtgaaattgatagttaaattaaatctgttaaatttgcag

Basic information

species	Zea mays
transcript	GRMZM2G110735_T01
intron #	5
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G110735_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os03g52630.2 (Oryza sativa), 5'ss of exon 4

TCTATACAGCGACTATCTTGAAGCTGCAGACACGCCTGGGTGGTACTGCGGACCTAACTTCTACACCACAGAAGTCCTCCGCAAGTTTGCCAGGTCACAGgtaaaagcattgttcttaatgctctcaaagtgcccaacg-tac---ggggaagtgaaattgatagttaaattaaatctgttaaatttgcag
|||||||||||| || || || |||||||| || ||||||||||| || |||||||  |||||||| ||||||||||||||||| ||||| |||||||||||||  |  |||||    |||||||  ||||   ||| | |||    |   |||    |  ||     |   ||| |  || |||||||||
TCTATACAGCGATTACCTGGATGCTGCAGATACACCTGGGTGGTATTGTGGACCTACTTTCTACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAGgtaag-gttttgttgcccatgctcttgaagtagtcaaagctacattagcacagttcggtgaatttgacacccaaaacccttcaatttgcag

upper sequence: GRMZM2G110735_T01 (Zea mays), 5'ss of exon 5
lower sequence: Vv12s0035g02180.t01 (Vitis vinifera), 5'ss of exon 5

TCTATACAGCGACTATCTTGAAGCTGCAGACACGCCTGGGTGGTACTGCGGACCTAACTTCTACACCACAGAAGTCCTCCGCAAGTTTGCCAGGTCACAGgtaaaagc------attgttc--ttaatgctctcaaagtgcccaa-----cgtacggggaagtgaa-attgatagt-taaattaaatctgttaaatttgcag--------------------
 || ||||| || |||||||||||||| ||||| ||||| ||||| || |||||||| |||||  | || |||||||| ||  | ||||||| | | ||||||   |       |||  ||  |||| | | | |  |  |   |     |  | |  | | | || |||| | |    ||  |  ||  ||||||||                        
CCTGTACAGTGATTATCTTGAAGCTGCTGACACCCCTGGATGGTATTGTGGACCTAATTTCTATTCAACTGAAGTCCTGCGTGAATTTGCCAAGACCCAGgtatgcgatatctgattcctcaattaaagttgtgagggaacatgagtctgctcatgtagtaataaatattgttggaaccaacaaggtcacttaaatttttcatatctctgaccttctggcag

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|31353920|gb|CD438277.1|CD438277

EST:     GACCTAACTTCTACACCACAGAAGTCCTCCGCAAGTTTGCCAGGTCACAG                         CTCGACTACATCCTTGGCAAGAACCCATTGAAGATGAGCTACGTTGTGGGT
genomic: GACCTAACTTCTACACCACAGAAGTCCTCCGCAAGTTTGCCAGGTCACAGgtaaaagcat ... aaatttgcagCTCGACTACATCCTTGGCAAGAACCCATTGAAGATGAGCTACGTTGTGGGT

EST: gi|23199797|gb|BU582362.1|BU582362

EST:     GACCTAACTTCTACACCACAGAAGTCCTCCGCAAGTTTGCCAGGTCACAG                         CTCGACTACATCCTTGGCAAGAACCCATTGAAGATGAGCTAC
genomic: GACCTAACTTCTACACCACAGAAGTCCTCCGCAAGTTTGCCAGGTCACAGgtaaaagcat ... aaatttgcagCTCGACTACATCCTTGGCAAGAACCCATTGAAGATGAGCTAC

EST: gi|211316249|gb|FL106351.1|FL106351

EST:     GACCTAACTTCTACACCACAGAAGTCCTCCGCAAGTTTGCCAGGTCACAG                         CTCGACTACATCCTTGGCAAGAACCCATTGAAGATGAGCTACGTTGTGGGT
genomic: GACCTAACTTCTACACCACAGAAGTCCTCCGCAAGTTTGCCAGGTCACAGgtaaaagcat ... aaatttgcagCTCGACTACATCCTTGGCAAGAACCCATTGAAGATGAGCTACGTTGTGGGT

EST: gi|67022056|gb|CO450805.1|CO450805

EST:     ACCTAACTTCTACACCACAGAAGTCCTCCGCNAAGTT-GCCAGGTCACAG                         CTCGACTACATCCTTGGGCAAGAACCCATTGAAGATGAGCTACGTTGTGGG
genomic: ACCTAACTTCTACACCACAGAAGTCCTCCGC-AAGTTTGCCAGGTCACAGgtaaaagcat ... aaatttgcagCTCGACTACATCCTTGG-CAAGAACCCATTGAAGATGAGCTACGTTGTGGG

EST: gi|32938675|gb|CF043494.1|CF043494

EST:     GACCTAACTTCTACACCACAGAAGTCCTCCGCAAGTTTGCCAGGTCACAG                         CTCGACTACATCCTTGGCAAGAACCCATTGAAGATGAGCTACGTTGTGGGT
genomic: GACCTAACTTCTACACCACAGAAGTCCTCCGCAAGTTTGCCAGGTCACAGgtaaaagcat ... aaatttgcagCTCGACTACATCCTTGGCAAGAACCCATTGAAGATGAGCTACGTTGTGGGT

EST: gi|37393645|gb|CF634088.1|CF634088

EST:     GACCTAACTTCTACACCACAGAAGTCCTCCGCAAGTTTGCCAGGTCACAG                         CTCGACTACATCCTTGGCAAGAACCCATTGAAGATGAGCTACGTTGTGGGT
genomic: GACCTAACTTCTACACCACAGAAGTCCTCCGCAAGTTTGCCAGGTCACAGgtaaaagcat ... aaatttgcagCTCGACTACATCCTTGGCAAGAACCCATTGAAGATGAGCTACGTTGTGGGT

EST: gi|94479489|gb|EB708447.1|EB708447

EST:     CGCAAGTTTGCCAGGTCACAG                         CTCGACTACATCCTTGGCAAGAACCCATTGAAGATGAGCTACGTTGGGGGT
genomic: CGCAAGTTTGCCAGGTCACAGgtaaaagcat ... aaatttgcagCTCGACTACATCCTTGGCAAGAACCCATTGAAGATGAGCTACGTTGTGGGT

EST: gi|6020730|gb|AW065538.1|AW065538

EST:     GACCTAACTTCTACACCACAGAAGTCCTCCGCAAGTTTGCCAGGTCACAG                         CTCGACTACATCCTTGGCAAGAACCCATTGAAGATGAGCTACGTTGTGGGT
genomic: GACCTAACTTCTACACCACAGAAGTCCTCCGCAAGTTTGCCAGGTCACAGgtaaaagcat ... aaatttgcagCTCGACTACATCCTTGGCAAGAACCCATTGAAGATGAGCTACGTTGTGGGT

EST: gi|21891489|gb|BQ744702.1|BQ744702

EST:     GACCTAACTTCTACACCACAGAAGTCCTCCGCAAGTTTGCCAGGTCACAG                         CTCGACTACATCCTTGGCAAGAACCCATTGAAGATGAGCTACGTTGTGGGT
genomic: GACCTAACTTCTACACCACAGAAGTCCTCCGCAAGTTTGCCAGGTCACAGgtaaaagcat ... aaatttgcagCTCGACTACATCCTTGGCAAGAACCCATTGAAGATGAGCTACGTTGTGGGT

EST: gi|32939292|gb|CF044111.1|CF044111

EST:     GACCTAACTTCTACACCACAGAAGTCCTCCGCAAGTTTGCCAGGTCACAG                         CTCGACTACATCCTTGGCAAGAACCCATTGAAGATGAGCTACGTTGTGGGT
genomic: GACCTAACTTCTACACCACAGAAGTCCTCCGCAAGTTTGCCAGGTCACAGgtaaaagcat ... aaatttgcagCTCGACTACATCCTTGGCAAGAACCCATTGAAGATGAGCTACGTTGTGGGT

EST: gi|211316245|gb|FL106347.1|FL106347

EST:     GACCTAACTTCTACACCACAGAAGTCCTCCGCAAGTTTGCCAGGTCACAG                         CTCGACTACATCCTTGGCAAGAACCCATTGAAGATGAGCTACGTTGTGGGT
genomic: GACCTAACTTCTACACCACAGAAGTCCTCCGCAAGTTTGCCAGGTCACAGgtaaaagcat ... aaatttgcagCTCGACTACATCCTTGGCAAGAACCCATTGAAGATGAGCTACGTTGTGGGT

EST: gi|211316246|gb|FL106348.1|FL106348

EST:     GACCTAACTTCTACACCACAGAAGTCCTCCGCAAGTTTGCCAGGTCACAG                         CTCGACTACATTCTTGGCAAGAACCCATTGAAGATGAGCTACGTTGTGGGT
genomic: GACCTAACTTCTACACCACAGAAGTCCTCCGCAAGTTTGCCAGGTCACAGgtaaaagcat ... aaatttgcagCTCGACTACATCCTTGGCAAGAACCCATTGAAGATGAGCTACGTTGTGGGT

EST: gi|149026851|gb|EE046205.2|EE046205

EST:     TACACCACAGAAGTCCTCGGCAAGTTTGCCAGGTCACAG                         CTGGACTACATCCTTGGCAAGAACCCATAGAAGATGAGCTACGTTGTGGGT
genomic: TACACCACAGAAGTCCTCCGCAAGTTTGCCAGGTCACAGgtaaaagcat ... aaatttgcagCTCGACTACATCCTTGGCAAGAACCCATTGAAGATGAGCTACGTTGTGGGT

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: 43

TCTATACAGCGACTATCTTGAAGCTGCAGACACGCCTGGGTGGTACTGCGGACCTAACTTCTACACCACAGAAGTCCTCCGCAAGTTTGCCAGGTCACAGgtaaaagcat ... aaatttgcagCTCGACTACATCCTTGGCAAGAACCCATTGAAGATGAGCTACGTTGTGGGTTTCGGAAACAAGTACCCGAAGCGCCCTCATCACAGAGGCGCGTCGATAC

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 120

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 92

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 351

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTATACAGCGACTATCTTGAAGCTGCAGACACGCCTGGGTGGTACTGCGGACCTAACTTCTACACCACAGAAGTCCTCCGCAAGTTTGCCAGGTCACAGgtaaaagcattgttcttaatgctctcaaagtgcccaacgtacggggaagtgaaattgatagttaaattaaatctgttaaatttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT