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

gtaagtacattccatctgttccacctttatgtttacaatcatatttatgttaatggtatttttgggtatcctttgtccagCGGTTATCTTGCACCTGAGTATGCCATGAGAGGTCATATGACTGAGAAAGTTGATGTCTTTGCATTTGGCGTGGTCTTATTGGAGACTTTAGCTGGACGG

Basic information

species	Oryza sativa
transcript	LOC_Os04g52600.1
intron #	22
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: LOC_Os04g52600.1 (Oryza sativa), 3'ss of exon 22
lower sequence: GRMZM2G031536_T01 (Zea mays), 3'ss of exon 7

gtaagtacatt-ccatct-gttccacctttatgt-----ttacaatcatatttatgttaatggtatttttgggtatcctttgtccagCGGTTATCTTGCACCTGAGTATGCCATGAGAGGTCATATGACTGAGAAAGTTGATGTCTTTGCATTTGGCGTGGTCTTATTGGAGACTTTAGCTGGACGG
||||||||||| |||||| || ||   |  | ||     |||   ||| || |    |||||  | |||   |  || | |||  || |||||||||||||||||||| |||||||||||||||||||| |||||||||||||| |||||||||||| ||||| |||||||||| ||||| ||| | 
gtaagtacatttccatcttgtgccttttacaagtgcatattattttcacatgtgaactaatgccaatttcttgc-tcttctgtgaagTGGTTATCTTGCACCTGAGTACGCCATGAGAGGTCATATGACCGAGAAAGTTGATGTGTTTGCATTTGGCATGGTCATATTGGAGACCTTAGCCGGAAGA

upper sequence: LOC_Os04g52600.1 (Oryza sativa), 3'ss of exon 22
lower sequence: GRMZM2G126858_T02 (Zea mays), 3'ss of exon 20

----------gtaagta-cattccatctgttccacctttatgtttacaatcatatttatgttaatggtatttttgggtatcctttgtcc-----agCGGTTATCTTGCACCTGAGTATGCCATGAGAGGTCATATGACTGAGAAAGTTGATGTCTTTGCATTTGGCGTGGTCTTATTGGAGACTTTAGCTGGACGG
            | ||  |   |||| ||||  |   ||| |||| || | || | |  | |||||| | ||     |  | ||  |       || || |||||| |||||||||| |||||||||||||| |||||||||||||||||| | ||||| ||||| |||||| | ||||||| | | |||||| ||
gtaagggcatacatgtctccccccatatgtttaataatta-gtttccactaatgtctgagctaatggaagttccttttcactttgatttcttgaagTGGCTATCTTTCACCTGAGTACGCCATGAGAGGTCACATGACTGAGAAAGTTGATATTTTTGCTTTTGGTGTGGTCATGTTGGAGATTATTGCTGGAAGG

upper sequence: LOC_Os04g52600.1 (Oryza sativa), 3'ss of exon 22
lower sequence: GRMZM2G126858_T01 (Zea mays), 3'ss of exon 20

----------gtaagta-cattccatctgttccacctttatgtttacaatcatatttatgttaatggtatttttgggtatcctttgtcc-----agCGGTTATCTTGCACCTGAGTATGCCATGAGAGGTCATATGACTGAGAAAGTTGATGTCTTTGCATTTGGCGTGGTCTTATTGGAGACTTTAGCTGGACGG---------------------------------------------------
            | ||  |   |||| ||||  |   ||| |||| || | || | |  | |||||| | ||     |  | ||  |       || || |||||| |||||||||| |||||||||||||| |||||||||||||||||| | ||||| ||||| |||||| | ||||||| | | |||||| ||                                                   
gtaagggcatacatgtctccccccatatgtttaataatta-gtttccactaatgtctgagctaatggaagttccttttcactttgatttcttgaagtggctatctttcacctgagtacgccatgagaggtcacatgactgagaaagttgatatttttgcttttggtgtggtcatgttggagATTATTGCTGGAAGGCCGAACTATGATGGTAAGCTTGACCAAGACATGGCTTATCTTTTAGAATGG

upper sequence: LOC_Os04g52600.1 (Oryza sativa), 3'ss of exon 22
lower sequence: GRMZM2G155837_T02 (Zea mays), 3'ss of exon 18

gtaagtacattccatctgttccacctttatgt-----ttacaatcatatttatgttaatggtatttttgggtatcctttgtccagCGGTTATCTTGCACCTGAGTATGCCATGAGAGGTCATATGACTGAGAAAGTTGATGTCTTTGCATTTGGCGTGGTCTTATTGGAGACTTTAGCTGGACGG
|||||| |||| |     | || ||| ||        |||   ||| || |  | |  ||  | |||      || | |||  || |||||||||||||| ||||| |||||||| ||||||||||| |||||||||||||| ||||||||||| |||||| ||||||||||| |||||||| ||
gtaagtgcatttccatattgcctcctctacacccaagttattttcaaatgtgagctggtgtcaatttcttac-tcttctgtgaagTGGTTATCTTGCACCCGAGTACGCCATGAGGGGTCATATGACCGAGAAAGTTGATGTGTTTGCATTTGGAGTGGTCATATTGGAGACTCTAGCTGGAAGG

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|29661696|gb|CB657971.1|CB657971

EST:     CTTTATGATGACAAGAAGACGCATGTCAGCACGANAGTTGCTGGTACATT                         CGGTTATCTTGCACCTGAGTATGCCATGAGAGGTCATATGACTGAGAAAGT
genomic: CTTTATGATGACAAGAAGACGCATGTCAGCACGAAAGTTGCTGGTACATTgtaagtacat ... ctttgtccagCGGTTATCTTGCACCTGAGTATGCCATGAGAGGTCATATGACTGAGAAAGT

EST: gi|86901791|gb|CI298438.1|CI298438

EST:     CTTTATGATGACAAGAAGACGCATGTCAGCACGAAAGTTGCTGGTACATT                         CGGTTATCTTGCACCTGAGTATGCCATGAGAGGTCATATGACTGAGAA
genomic: CTTTATGATGACAAGAAGACGCATGTCAGCACGAAAGTTGCTGGTACATTgtaagtacat ... ctttgtccagCGGTTATCTTGCACCTGAGTATGCCATGAGAGGTCATATGACTGAGAA

EST: gi|29680824|gb|CB677099.1|CB677099

EST:     CTTTATGATGACAAGAAGACGCATGTCAGCACGAAAGTTGCTGGTACATT                         CGGTTATCTTGCACCTGAGTATGCCATGAGAGGTCATATGACTGAGAAAGT
genomic: CTTTATGATGACAAGAAGACGCATGTCAGCACGAAAGTTGCTGGTACATTgtaagtacat ... ctttgtccagCGGTTATCTTGCACCTGAGTATGCCATGAGAGGTCATATGACTGAGAAAGT

EST: gi|29661697|gb|CB657972.1|CB657972

EST:     TGATGACAAGAAGACGCATGTCAGCACGAAAGTTGCTGGTACATT                         CGGTTATCTTGCACCTGAGTATGCCATGAGAGGTCATATGACTGAGAAAGT
genomic: TGATGACAAGAAGACGCATGTCAGCACGAAAGTTGCTGGTACATTgtaagtacat ... ctttgtccagCGGTTATCTTGCACCTGAGTATGCCATGAGAGGTCATATGACTGAGAAAGT

EST: gi|29661052|gb|CB657327.1|CB657327

EST:     CTTTATGATGACAAGAAGACGCATGTCAGCACGAAAGTTGCTGGTACATT                         CGGTTATCTTGCACCTGAGTATGCCATGAGAGGTCATATGACTGAGAAAGT
genomic: CTTTATGATGACAAGAAGACGCATGTCAGCACGAAAGTTGCTGGTACATTgtaagtacat ... ctttgtccagCGGTTATCTTGCACCTGAGTATGCCATGAGAGGTCATATGACTGAGAAAGT

EST: gi|58592421|gb|CF990729.1|CF990729

EST:     GACGC-TGTCAGCACGAAAGTTGCTGGTACATT                         CGGTTATCTTGCACCTGAGTATGCCATGAGAGGTCATATTACTGAGAAAGT
genomic: GACGCATGTCAGCACGAAAGTTGCTGGTACATTgtaagtacat ... ctttgtccagCGGTTATCTTGCACCTGAGTATGCCATGAGAGGTCATATGACTGAGAAAGT

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: 37 (upstream exon), 42 (downstream exon)
Score: 4

TACTTGACGCCAATCTCAATCCTAAGATCTCAGATTTTGGGCTAGCCAAACTTTATGATGACAAGAAGACGCATGTCAGCACGAAAGTTGCTGGTACATTgtaagtacat ... ctttgtccagCGGTTATCTTGCACCTGAGTATGCCATGAGAGGTCATATGACTGAGAAAGTTGATGTCTTTGCATTTGGCGTGGTCTTATTGGAGACTTTAGCTGGACGG

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atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tttatgtttacaatcatatttatgttaatggtatttttgggtatcctttgtccagCGGTTATCTTGCACCTGAGTATGCCATGAGAGGTCATATGACTGAGAAAGTTGATGTCTTTGCATTTGGCGTGGTCTTATTGGAGACTTTAGCTGGACGG

                      tgttaat  putative branch site (score: 4)
                                           tcctttgtcc  putative PPT
           aatcatatttatgtta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtacattccatctgttccacctttatgtttacaatcatatttatgttaatggtatttttgggtatcctttgtccagCGGTTATCTTGCACCTGAGTATGCCATGAGAGGTCATATGACTGAGAAAGTTGATGTCTTTGCATTTGGCGTGGTCTTATTGGAGACTTTAGCTGGACGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA