ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
PPT, BS, UA-tract
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

...gtttgtacatgattaggtcctgtgctatctgttaaacatttgtctatggaacattgtccaaataacacttgcgatctggaatgtgaatcctatttttcagATCACATACCACTTTTTCCATTGGAAGAAAGGAACACCTTTTGCTGATGACCAGGGAATGTACAACACATTGACTTGGTGGGAACAAATGGACAATGGCA

Basic information

species	Zea mays
transcript	GRMZM2G151009_T01
intron #	1
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G151009_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g45180.1 (Oryza sativa), 3'ss of exon 1

--gtttgtacatgattaggtcctgtgctatctgttaaacatttgtctatgga-acattgtccaaataacacttgcgatctggaatgtgaatcctatttttcagATCACATACCACTTTTTCCATTGGAAGAAAGGAACACCTTTTGCTGATGACCAGGGAATGTACAACACATTGACTTGGTGGGAACAAATGGACAATGGCA
    || |   ||  |      |    | ||| |  | |||  |   ||    ||  |||||||  |   |   |    | ||||   |||| ||| ||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||
actattctctttgcattttcgttagcatttctctatagcatcggatgatacctaccgtgtccaatgatttcccacttaatcgaat---aatcttatgtttcagATCACATACCACTTTTTCCATTGGAAGAAGGGAACACCTTTTGCTGATGACCAGGGAATGTACAACACATTGACTTGGTGGGAGCAAATGGACAATGGCA

upper sequence: GRMZM2G151009_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA16G02540.1 (Glycine max), 3'ss of exon 1

-gtttgtacatgattaggtcctgtgctatc--tgttaa---acatttgtctatggaacattgtccaaataacacttgcgatctggaatgtgaatcctatttttcagATCACATACCACTTTTTCCATTGGAAGAAAGGAACACCTTTTGCTGATGACCAGGGAATGTACAACACATTGACTTGGTGGGAACAAATGGACAATGGCA
 | || || || | ||  |  | ||  |    ||||||   |  ||    ||    |  || || | ||  | |||      | || | ||  |  | |   |||| | ||||| |||||||| || |||||||||||||| || ||||| || ||||| || || ||||| | ||||||||||||||| ||  | |||||||| |
aggttataaattaatattttgtttgtaaatattgttaatggatgttaaaataatttaacttctctacatggcgctta----attgattatg--ttgtgtccatcagGTAACATATCACTTTTTTCACTGGAAGAAAGGAACTCCATTTGCGGAGGACCAAGGGATCTACAATAGATTGACTTGGTGGGAGCAGGTAGACAATGGAA

upper sequence: GRMZM2G151009_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA07G05940.1 (Glycine max), 3'ss of exon 1

gtttgtacatgattaggtcctgtgctatctgttaaacatttgtctatggaacattgtccaaataacacttgcgatctggaatg------tgaatcctatttttcagATCACATACCACTTTTTCCATTGGAAGAAAGGAACACCTTTTGCTGATGACCAGGGAATGTACAACACATTGACTTGGTGGGAACAAATGGACAATGGCA
      |  | || |  |  | || | | ||| |||   ||||  |||||   |    ||| | |   |  | |  |||  |       |   |  | |   |||| | ||||| |||||||| || |||||||||||||| || ||||| || ||||| || || ||||| | ||||||||||||||| ||  | |||||||| |
-----caggttataaattaatctgttgtttgt-aaattattgttaatggatgctaaaacaatttaacttctctaaatggcctaattgattatgttgtgtccatcagGTAACATATCACTTTTTTCACTGGAAGAAAGGAACTCCATTTGCAGAGGACCAAGGGATCTACAATAGATTGACTTGGTGGGAGCAGGTAGACAATGGAA

upper sequence: GRMZM2G151009_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA16G01830.1 (Glycine max), 3'ss of exon 1

gtttgtacatgattaggtcctgtgctatctgttaaacatttgtctatggaacattgtccaaataacacttgcgatctggaatg------tgaatcctatttttcagATCACATACCACTTTTTCCATTGGAAGAAAGGAACACCTTTTGCTGATGACCAGGGAATGTACAACACATTGACTTGGTGGGAACAAATGGACAATGGCA
      |  | || |  |  | |  | | ||| ||| ||| ||  |||||   |     || | |   |  | |  |||  |       |   |  | |   |||| | |||||  ||||||| || |||||||||||||| || ||||| || ||||| || || ||||| | ||||||||||||||| ||  | |||||||| |
----tcaggttataaattaatattttgtttgt-aaatatt-gttaatggatgttaaaataatttaacttctctacatggcttaattgattatgttgtgtccatcagGTAACATATGACTTTTTTCACTGGAAGAAAGGAACTCCGTTTGCAGAGGACCAAGGGATCTACAATAGATTGACTTGGTGGGAGCAGGTAGACAATGGAA

upper sequence: GRMZM2G151009_T01 (Zea mays), 3'ss of exon 1
lower sequence: AT5G42000.2 (Arabidopsis thaliana), 3'ss of exon 1

gtttgtacatgattaggtcctgtgctatctgttaaacatttgtctatggaacattgtccaaataacacttgcgatctggaatgtgaatcctatttttcagATCACATACCACTTTTTCCATTGGAAGAAAGGAACACCTTTTGCTGATGACCAGGGAATGTACAACACATTGACTTGGTGGGAACAAATGGACAATGGCA
           ||||   ||  |    || | |  | ||||    || |    || || | ||     |||   | | || | |   |  | ||||  || |||| || || |  |||||||||||||| |||||||| ||||  ||||| || ||| | || || | |||||||||||||||||| || || |||||||
---------gtattattcccgatctcctccgatcca-atttcgaaattgttggtt-tctagat-----ttgaatttttgagttt---ttttgttttctagGTCACGTATCATTCCTTCCATTGGAAGAAGGGAACACCATTTGGAGATGATCAAGGAGTCTATAATAGATTGACTTGGTGGGAACAGATTGATAATGGCA

upper sequence: GRMZM2G151009_T01 (Zea mays), 3'ss of exon 1
lower sequence: AT1G01230.1 (Arabidopsis thaliana), 3'ss of exon 1

-gtttgtacatgattaggtcctgtgctatctgttaaacatttgtctatggaacattgtccaaataacacttgcgatctggaat--gtgaatcctatttttcagATCACATACCACTTTTTCCATTGGAAGAAAGGAACACCTTTTGCTGATGACCAGGGAATGTACAACACATTGACTTGGTGGGAACAAATGGACAATGGCA
 |    | | |||||     |    | |  | | |   | ||    ||    | ||    ||||   |  |  ||   | |||  ||| ||  |  || |||| | || || |||   ||||| |||| ||||||||| |||||||| |||||||| ||||| |||||    || ||||||||||||||||||||||||||  
tggcattgcttgattg---tcaaaaccaaatttaatctaatttctaattactctttaggaaaatgtgatgtctgagtagaaatttgtggatatttgttgtcagGTAACGTATCACAGCTTCCACTGGATGAAAGGAACTCCTTTTGCAGATGACCAAGGAATCTACAATGGTTTAACTTGGTGGGAACAAATGGACAATGGTC

upper sequence: GRMZM2G151009_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv15s0046g00140.t01 (Vitis vinifera), 3'ss of exon 1

gtttgtacatgattaggtcctgtgctatctgttaaacatttgtctatggaacattgtccaaataacacttgcgatctggaatgtgaatcctatttttcagATCACATACCACTTTTTCCATTGGAAGAAAGGAACACCTTTTGCTGATGACCAGGGAATGTACAACACATTGACTTGGTGGGAACAAATGGACAATGGCA
||||||  ||  |      ||||     ||     |   |    ||    || || |         |    |    ||    |        |   || || |||| || ||||| |||||||||||||||||||| ||||||||||| ||||||||||| ||||| |  ||||| |||||||| || || |||||||| |
gtttgtttatcttctttgtctgtatacccttcctgatgctacattagattactttatatcctctctatgacctgattgaggagcatgcttcacactttagGTCACCTATCACTTCTTCCATTGGAAGAAAGGAACTCCTTTTGCTGAAGACCAGGGAATCTACAATAGGTTGACGTGGTGGGAGCAGATAGACAATGGAA

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|211256578|gb|FL391908.1|FL391908

EST:     GCTGCACCCCTGGCACCGCGTGGACCGTCGTCAACCTCTTCCACTTCGCG                         ATCACATACCACTTTTTCCATTGAAAGAAAGGAACACCTTTTGCTGATGAC
genomic: GCTGCACCCCTGGCACCGCGTGGACCGTCGTCAACCTCTTCCACTTCGCGgtaactgcct ... tatttttcagATCACATACCACTTTTTCCATTGGAAGAAAGGAACACCTTTTGCTGATGAC

EST: gi|87157542|gb|DY402331.1|DY402331

EST:     GCTGCACCCCTGGCACCGCGTGGACCGTCGTCAACCTCTTCCACTTCGCG                         ATCACATACCACTTTTTCCATTGGAAGAAAGGAACACCTTTTGCTGATGAC
genomic: GCTGCACCCCTGGCACCGCGTGGACCGTCGTCAACCTCTTCCACTTCGCGgtaactgcct ... tatttttcagATCACATACCACTTTTTCCATTGGAAGAAAGGAACACCTTTTGCTGATGAC

EST: gi|211403609|gb|FL421570.1|FL421570

EST:     GCTGCACCCCTGGCACCGCGTGGACCGTCGTCAACCTCTTCCACTTCGCG                         ATCACATACCACTTTTTCCATTGGAAGAAAGGAACACCTTTTGCTGATGAC
genomic: GCTGCACCCCTGGCACCGCGTGGACCGTCGTCAACCTCTTCCACTTCGCGgtaactgcct ... tatttttcagATCACATACCACTTTTTCCATTGGAAGAAAGGAACACCTTTTGCTGATGAC

EST: gi|16925050|gb|BM078118.1|BM078118

EST:     GCTGCACCCCTGGCACCGCGTGGACCGTCGTCAACCTCTTCCACTTCGCG                         ATCACATACCACTTTTTCCATTGGAAGAAAGGAACACCTTTTGCTGATGAC
genomic: GCTGCACCCCTGGCACCGCGTGGACCGTCGTCAACCTCTTCCACTTCGCGgtaactgcct ... tatttttcagATCACATACCACTTTTTCCATTGGAAGAAAGGAACACCTTTTGCTGATGAC

EST: gi|101401475|gb|EB822417.1|EB822417

EST:     GCTGCACCCCTGGCACCGCGTGGACCGTCGTCAACCTCTTCCACTTCGCG                         ATCACATACCACTTTTTCCATTGGAAGAAAGGAACACCTTTTGCTGATGAC
genomic: GCTGCACCCCTGGCACCGCGTGGACCGTCGTCAACCTCTTCCACTTCGCGgtaactgcct ... tatttttcagATCACATACCACTTTTTCCATTGGAAGAAAGGAACACCTTTTGCTGATGAC

EST: gi|18174920|gb|BM350308.1|BM350308

EST:     GCTGCACCCCTGGCACCGCGTGGACCGTCGTCAACCTCTTCCACTTCGCG                         ATCACATACCACTTTTTCCATTGGAAGAAAGGAACACCTTTTGCTGATGAC
genomic: GCTGCACCCCTGGCACCGCGTGGACCGTCGTCAACCTCTTCCACTTCGCGgtaactgcct ... tatttttcagATCACATACCACTTTTTCCATTGGAAGAAAGGAACACCTTTTGCTGATGAC

EST: gi|211461438|gb|FL402432.1|FL402432

EST:     CTGCACCCCTGGCACCGCGTGGMACCGTCGTCAACCTCTTCCACTTCGCG                         ATCACATACCACTTTTTCCATTGGAAGAAAGGAACACCTTTT
genomic: CTGCACCCCTGGCACCGCGTGG-ACCGTCGTCAACCTCTTCCACTTCGCGgtaactgcct ... tatttttcagATCACATACCACTTTTTCCATTGGAAGAAAGGAACACCTTTT

EST: gi|26558414|gb|CA830649.1|CA830649

EST:     GCTGCACCCCTGGCACCGCGTGGACCGTCGTCAACCTCTTCCACTTCGCG                         ATCACATACCACTTTTTCCATTGGAAGAAAGGAACACCTTTTGCTGATGAC
genomic: GCTGCACCCCTGGCACCGCGTGGACCGTCGTCAACCTCTTCCACTTCGCGgtaactgcct ... tatttttcagATCACATACCACTTTTTCCATTGGAAGAAAGGAACACCTTTTGCTGATGAC

EST: gi|32919445|gb|CF024257.1|CF024257

EST:     GCTGCACCCCTGGCACCGCGTGGACCGTCGTCAACCTCTTCCACTTCGCG                         ATCACATACCACTTTTTCCATTGGAAGAAAGGAACACCTTTTGCTGATGAC
genomic: GCTGCACCCCTGGCACCGCGTGGACCGTCGTCAACCTCTTCCACTTCGCGgtaactgcct ... tatttttcagATCACATACCACTTTTTCCATTGGAAGAAAGGAACACCTTTTGCTGATGAC

EST: gi|71763891|gb|DR961828.1|DR961828

EST:     GCTGCACCCCTGGCACCGCGTGGACCGTCGTCAACCTCTTCCACTTCGCG                         ATCACATACCACTTTTTCCATTGGAAGAAAGGAACACCTTTTGCTGATGAC
genomic: GCTGCACCCCTGGCACCGCGTGGACCGTCGTCAACCTCTTCCACTTCGCGgtaactgcct ... tatttttcagATCACATACCACTTTTTCCATTGGAAGAAAGGAACACCTTTTGCTGATGAC

EST: gi|211416053|gb|FL407182.1|FL407182

EST:     GCTGCACCCCTGGCACCGCGTGGACCGTCGTCAACCTCTTCCACTTCGCG                         ATCACATACCACTTTTTCCATTGGAA
genomic: GCTGCACCCCTGGCACCGCGTGGACCGTCGTCAACCTCTTCCACTTCGCGgtaactgcct ... tatttttcagATCACATACCACTTTTTCCATTGGAA

EST: gi|18176788|gb|BM351721.1|BM351721

EST:     GCTGCACCCCTGGCACCGCGTGGACCGTCGTCAACCTCTTCCACTTCGCG                         ATCACATACCACTTTTTCCATTGGAAGAAAGGAACACCTTTTGCTGATGAC
genomic: GCTGCACCCCTGGCACCGCGTGGACCGTCGTCAACCTCTTCCACTTCGCGgtaactgcct ... tatttttcagATCACATACCACTTTTTCCATTGGAAGAAAGGAACACCTTTTGCTGATGAC

EST: gi|71441911|gb|DR822961.1|DR822961

EST:     GCTGCACCCCTGGCACCGCGTGGACCGTCGTCAACCTCTTCCACTTCGCG                         ATCACATACCACTTTTTCCATTGGAAGAAAGGAACACCTTTTGCTGATGAC
genomic: GCTGCACCCCTGGCACCGCGTGGACCGTCGTCAACCTCTTCCACTTCGCGgtaactgcct ... tatttttcagATCACATACCACTTTTTCCATTGGAAGAAAGGAACACCTTTTGCTGATGAC

EST: gi|22546072|gb|BU098393.1|BU098393

EST:     GCTGCACCCCTGGCACCGCGTGGACCGTCGTCAACCTCTTCCACTTCGCG                         ATCACATACCACTTTTTCCATTGGAAGAAAGGAACACCTTTTGCTGATGAC
genomic: GCTGCACCCCTGGCACCGCGTGGACCGTCGTCAACCTCTTCCACTTCGCGgtaactgcct ... tatttttcagATCACATACCACTTTTTCCATTGGAAGAAAGGAACACCTTTTGCTGATGAC

EST: gi|60343697|gb|DN210670.1|DN210670

EST:     GCTGCACCCCTGGCACCGCGTGGACCGTCGTCAACCTCTTCCACTTCGCG                         ATCACATACCACTTTTTCCATTGGAAGAAAGGAACACCTTTTGCTGATGAC
genomic: GCTGCACCCCTGGCACCGCGTGGACCGTCGTCAACCTCTTCCACTTCGCGgtaactgcct ... tatttttcagATCACATACCACTTTTTCCATTGGAAGAAAGGAACACCTTTTGCTGATGAC

EST: gi|71763892|gb|DR961829.1|DR961829

EST:     GCTGCACCCCTGGCACCGCGTGGACCGTCGTCAACCTCTTCCACTTCGCG                         ATCACATACCACTTTTTCCATTGGAAGAAAGGAACACCTTTTGCTGATGAC
genomic: GCTGCACCCCTGGCACCGCGTGGACCGTCGTCAACCTCTTCCACTTCGCGgtaactgcct ... tatttttcagATCACATACCACTTTTTCCATTGGAAGAAAGGAACACCTTTTGCTGATGAC

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: 137

CTACATCATCATCGTCTTCTTCTCCTGGCTCCTCGTCCTCTCCGTCTTTGGCTGCACCCCTGGCACCGCGTGGACCGTCGTCAACCTCTTCCACTTCGCGgtaactgcct ... tatttttcagATCACATACCACTTTTTCCATTGGAAGAAAGGAACACCTTTTGCTGATGACCAGGGAATGTACAACACATTGACTTGGTGGGAACAAATGGACAATGGCA

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 381

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 367

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 216

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

atggaacattgtccaaataacacttgcgatctggaatgtgaatcctatttttcagATCACATACCACTTTTTCCATTGGAAGAAAGGAACACCTTTTGCTGATGACCAGGGAATGTACAACACATTGACTTGGTGGGAACAAATGGACAATGGCA

              aaataac  putative branch site (score: 216)
                                          tcctatttttc  putative PPT
                                             tatttttca  TA-rich tract

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtacatgattaggtcctgtgctatctgttaaacatttgtctatggaacattgtccaaataacacttgcgatctggaatgtgaatcctatttttcagATCACATACCACTTTTTCCATTGGAAGAAAGGAACACCTTTTGCTGATGACCAGGGAATGTACAACACATTGACTTGGTGGGAACAAATGGACAATGGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG