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

gtttgacttcatttctttcgttttcacccaatattcgttagtcattccagtaaatgtgtgttacgatgttataacacaagttaaaaccactggcattttcagGTTTTGCCTACAATTGTGAAGCTTTTTGCCTCTAATGACCGAGCTATCCGAGTTAGCCTTTTGCAGCACATAGATCAGTTTGGGGAGTCATTGACAGCTC

Basic information

species	Oryza sativa
transcript	LOC_Os01g60440.1
intron #	10
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: LOC_Os01g60440.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G098078_T04 (Zea mays), 3'ss of exon 10

gtttgacttcatttctttcgttttcacccaatattcgttagtcattccagtaaatgtgtgttacgatgttataacacaagttaaaaccactggcattttcagGTTTTGCCTACAATTGTGAAGCTTTTTGCCTCTAATGACCGAGCTATCCGAGTTAGCCTTTTGCAGCACATAGATCAGTTTGGGGAGTCATTGACAGCTC
               |  | ||||| |    ||||      | |   | |   |||  |  |    |  | | | | ||   | ||   | |   ||||||||| ||||| || ||||| |||||||||||||| |||||||||||||||||||   | |||||||| |||||||||||||||||||| ||| || | ||||
--------------gtgacattttctctacttatt--gcgattaacactgcttatgaattatcaagtaatctgatataatagagaatgccggctcttttcagGTCTTGCCAACTATTGTCAAGCTTTTTGCCTCCAATGACCGAGCTATCCGAGCATGTCTTTTGCACCACATAGATCAGTTTGGGGAATCAATGTCTGCTC

upper sequence: LOC_Os01g60440.1 (Oryza sativa), 3'ss of exon 10
lower sequence: AC218972.3_FGT001 (Zea mays), 3'ss of exon 10

gtttgacttcatttctttcgttttcacccaatattcgttagtcattccagtaaatgtgtgttacgatgttataacacaagttaaaaccactggca-ttttcagGTTTTGCCTACAATTGTGAAGCTTTTTGCCTCTAATGACCGAGCTATCCGAGTTAGCCTTTTGCAGCACATAGATCAGTTTGGGGAGTCATTGACAGCTC
                 |    ||  | |  || |  |||    |   | |   | || | ||  | ||  |   |  | |  | |   |||||  ||||||||| ||||| || ||||| |||||||||||||| |||||||||||||||||||   | |||||||| |||||| ||||||||||||| ||| || ||||||
----------------gtgaccttttctc--tacttattatggttaatactgcttatgagctatcaagtagtctgattattagagaatgctggcccttttcagGTCTTGCCAACTATTGTCAAGCTTTTTGCCTCCAATGACCGAGCTATCCGAGCATGTCTTTTGCATCACATAAATCAGTTTGGGGAATCAATGTCAGCTC

upper sequence: LOC_Os01g60440.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA20G36180.1 (Glycine max), 3'ss of exon 10

-----------gtttgac---ttcatttctttcgttttcacccaatattcgttagtcattccagtaaatgtgtgttacgatg-ttataacacaagttaaaacc--actggcattttcagGTTTTGCCTACAATTGTGAAGCTTTTTGCCTCTAATGACCGAGCTATCCGAGTTAGCCTTTTGCAGCACATAGATCAGTTTGGGGAGTCATTGACAGCTC
            ||  ||   || ||      | |||||  |     ||| |  |    |  | |   | | | | || | | ||    | || | |   |    | |    | |  ||||  | || |||||||| || |||||||| || |||||||||||||| |||||| ||||| | || || || ||||||||||||||||||||  |||| |
gtgtataacaacttcaacacctttatgatgccccttttctactttctttcatacggtgcttgattctctctctctaaccaggatttcttctcatgcttgtattggatttcactatatagGTGCTTCCAACAATTGTTAAACTTTTTGCATCCAATGACCGAGCTATTCGAGTTGGCCTTCTTCAACATATTGATCAGTTTGGGGAGTCATTATCAGCAC

upper sequence: LOC_Os01g60440.1 (Oryza sativa), 3'ss of exon 10
lower sequence: AT2G40730.1 (Arabidopsis thaliana), 3'ss of exon 10

gtttgacttcatttctttcgttttcacccaatattcgttagtcattccagtaa---atgtgtgttacgatgttataacacaa-gttaaaaccactggcattttcagGTTTTGCCTACAATTGTGAAGCTTTTTGCCTCTAATGACCGAGCTATCCGAGTTAGCCTTTTGCAGCACATAGATCAGTTTGGGGAGTCATTGACAGCTC
|||||        |  |   |||      || |  |  ||  || |||| |     |||| |  |     |||||     || | ||   ||  |     ||| ||||  | || |||||||| ||||||||||| || ||||| ||||||||| |||||   |||||||| ||  | ||||| ||||| || ||| || | |  |
gtttgttcagccatgctaaatttctgtttaa-acgctctatacactccaatgctgtatgtatacttttcagttattgtctaaaggtactcccttttatgattttagGTACTACCAACAATTGTCAAGCTTTTTGCTTCCAATGATCGAGCTATCAGAGTTTCTCTTTTGCAACATGTTGATCAATTTGGAGAATCAATGTCTGGGC

upper sequence: LOC_Os01g60440.1 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv13s0067g03110.t01 (Vitis vinifera), 3'ss of exon 10

---------------------------------------------gtttgactt-catttctttcgttttcacccaatattcgttagtcattccagtaaatgtgtgttacgatgttataacacaagttaaaacc--actggcattttcagGTTTTGCCTACAATTGTGAAGCTTTTTGCCTCTAATGACCGAGCTATCCGAGTTAGCCTTTTGCAGCACATAGATCAGTTTGGGGAGTCATTGACAGCTC
                                              ||| | |  || |  |||  | ||  |   || |   |   |  ||     |  | ||| || | |   | | |        ||  ||  | |   || | |||||  | || ||||||||||| ||||| ||||| ||||||||||| || |||||| | ||  ||||||| || ||||||| ||||||||||||  | || |
gtcatactcttttgagtacctcatgtaaacttattatgttggcatttttaattaacaataattttatcttt-ctttatgtgtttagatgcttatctcatttctgtttttctaaaatttgatgttgtcaaactcctcatttttatatacagGTACTTCCGACAATTGTGAAACTTTTCGCCTCAAATGACCGAGCCATTCGAGTTGGTCTCCTGCAGCATATTGATCAGTATGGGGAGTCATTATCTGCAC

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|29623603|gb|CB628614.1|CB628614

EST:     TATTGTTGAAGATGGGTTCCTGGCTTCCAGCTGACCAATTTAGTGCAAAG                         GTTTTGCCTACAATTGTGAAGCTTTTTGCCTCTAATGACCGAGCTATCCGA
genomic: TATTGTTGAAGATGGGTTCCTGGCTTCCAGCTGACCAATTTAGTGCAAAGgtttgacttc ... gcattttcagGTTTTGCCTACAATTGTGAAGCTTTTTGCCTCTAATGACCGAGCTATCCGA

EST: gi|58683845|gb|CK072532.1|CK072532

EST:     TATTGTTGAAGATGGGTTCCTGGCTTCCAGCTGACCAATTTAGTGCAAAG                         GTTTTGGCTACAATTGTGAAGCTTTTTGGCTCTAATGACCGAGCTATCCGA
genomic: TATTGTTGAAGATGGGTTCCTGGCTTCCAGCTGACCAATTTAGTGCAAAGgtttgacttc ... gcattttcagGTTTTGCCTACAATTGTGAAGCTTTTTGCCTCTAATGACCGAGCTATCCGA

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 1 RNA-Seqlibrary.

Block sizes: 74 (upstream exon), 69 (downstream exon)
Score: 30

GCTGGCATCTGCTCTTGAGTTTGGTTCAGCTGCTGCACCAGCCTTGGTTGTATTGTTGAAGATGGGTTCCTGGCTTCCAGCTGACCAATTTAGTGCAAAGgtttgacttc ... gcattttcagGTTTTGCCTACAATTGTGAAGCTTTTTGCCTCTAATGACCGAGCTATCCGAGTTAGCCTTTTGCAGCACATAGATCAGTTTGGGGAGTCATTGACAGCTC

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atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

cagtaaatgtgtgttacgatgttataacacaagttaaaaccactggcattttcagGTTTTGCCTACAATTGTGAAGCTTTTTGCCTCTAATGACCGAGCTATCCGAGTTAGCCTTTTGCAGCACATAGATCAGTTTGGGGAGTCATTGACAGCTC

                     ttataac  putative branch site (score: 30)
                                              cattttc  putative PPT
                  atgttataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgacttcatttctttcgttttcacccaatattcgttagtcattccagtaaatgtgtgttacgatgttataacacaagttaaaaccactggcattttcagGTTTTGCCTACAATTGTGAAGCTTTTTGCCTCTAATGACCGAGCTATCCGAGTTAGCCTTTTGCAGCACATAGATCAGTTTGGGGAGTCATTGACAGCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC