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

...cttatcacaacttagttttatatactttatgcttgaattgccgttattagctcctggtcgttctagaaattttattattgtcttcatgtggtttgttcagATTGTTAATGGACCTCGCTCTGTAGAATCTCTAAACGACAAGTTTGAAGTATTCTATATCGACTATGGCAACCAAGAGGTGGTTCCCTACAGTCGTCTAC

Basic information

species	Zea mays
transcript	GRMZM2G136296_T01
intron #	15
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G136296_T01 (Zea mays), 3'ss of exon 15
lower sequence: LOC_Os02g32350.1 (Oryza sativa), 3'ss of exon 14

cttatcacaacttagttttatatactttatgcttga-attgccgttattagctcctggtcgttctagaaattttattattgtcttcatgtggtttgttc---agATTGTTAATGGACCTCGC---TCTGTAGAATCTCTAAACGACAAGTTTGAAGTATTCTATATCGACTATGGCAACCAAGAGGTGGTTCCCTACAGTCGTCTAC
   | | ||  |||||  |  |    ||| | |  | ||| |||||  ||| | |||||  |   | | | ||    | | | | ||| |    || ||   ||||||| |||||||||||     |||||  ||||| | |||||||||||||||||||||| || ||||||||||||||||| || ||||| ||||||||     
---aac-cattttagtcctggacttgttaagttgaacattcccgtttctagtttctggttttcaaaaataattaggaagtatatccattttaactgatctgcagATTGTGAATGGACCTCGAGGAGCTGTATCATCTCAAGACGACAAGTTTGAAGTATTCTACATTGACTATGGCAACCAAGAAGTCGTTCCTTACAGTCGCA---

upper sequence: GRMZM2G136296_T01 (Zea mays), 3'ss of exon 15
lower sequence: GLYMA05G33320.1 (Glycine max), 3'ss of exon 15

cttatcacaacttagtt--ttatatactttatgcttgaattgccgttattagctcctggtc-gttctagaaattttattattgtct----tcatgtggt-ttgttcagATTGTTAATGGACCTCGC---TCTGTAGAATCTCTAAACGACAAGTTTGAAGTATTCTATATCGACTATGGCAACCAAGAGGTGGTTCCCTACAGTCGTCTAC
        ||    |||  | | || |   ||  |   | || || |  || | ||| ||| ||||    ||  ||| |  | | |    |  | |||  ||||  || | || |||||||||||     |||| ||||||| |||||||| |||||||||||||||||| || ||||| || ||||| |  || || |||  ||  |   
--------aatagggttgatgagatgcaaaatagtcagagtgtcgcttgtaccacctagtctgttcagtcaaacttacttctttatgaaatggtatggaattgtgtagGTAGTCAATGGACCTCGAGGACCTGTTGAATCTCCAAACGACATGTTTGAAGTATTCTATATTGATTATGGAAATCAAGAAGAAGTACCTTACTCTCAGC---

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|511415|gb|T23393.1|T23393

EST:     AGATAGTCCTCTCACAATTTAGCCTTGACAACTCCTGGAACAGAGCTATG                         ATTGTAAATGGACCTCGCTCTGTAGAATCTCTAAACGACAAGTTTGAAGTA
genomic: AGATAGTCCTCTCACAATTTAGCCTTGACAACTCCTGGAACAGAGCTATGgtatgtcgca ... gtttgttcagATTGTTAATGGACCTCGCTCTGTAGAATCTCTAAACGACAAGTTTGAAGTA

EST: gi|67011396|gb|CO440145.1|CO440145

EST:     AGATAGTCCTCTCACAATTTAGCCTTGACAACTCCTGGAACAGAGCTATG                         ATTGTTAATGGACCTCGCTCTGTAGAATCTCTAAACGACAAGTTTGAAGTA
genomic: AGATAGTCCTCTCACAATTTAGCCTTGACAACTCCTGGAACAGAGCTATGgtatgtcgca ... gtttgttcagATTGTTAATGGACCTCGCTCTGTAGAATCTCTAAACGACAAGTTTGAAGTA

EST: gi|67040223|gb|CO466478.1|CO466478

EST:     AGATAGTCCTCTCACAATTTAGCCTTGACAACTCCTGGAACAGAGCTATG                         ATTGNTAATGGACCTCGC
genomic: AGATAGTCCTCTCACAATTTAGCCTTGACAACTCCTGGAACAGAGCTATGgtatgtcgca ... gtttgttcagATTGTTAATGGACCTCGC

EST: gi|211486828|gb|FL010663.1|FL010663

EST:     AGATAGTCCTCTCACAATTTAGCCTTGACAACTCCTGGAACAGAGCTATG                         ATTGTTAATGGACCTCGCTCTGTAGAATCTCTAAACGACAAGTTTGAAGTA
genomic: AGATAGTCCTCTCACAATTTAGCCTTGACAACTCCTGGAACAGAGCTATGgtatgtcgca ... gtttgttcagATTGTTAATGGACCTCGCTCTGTAGAATCTCTAAACGACAAGTTTGAAGTA

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: 206

GAAACTTAAAGATGCACCAGTCATTGGTGCCTTTAATCCTGTGAAGGGAGAGATAGTCCTCTCACAATTTAGCCTTGACAACTCCTGGAACAGAGCTATGgtatgtcgca ... gtttgttcagATTGTTAATGGACCTCGCTCTGTAGAATCTCTAAACGACAAGTTTGAAGTATTCTATATCGACTATGGCAACCAAGAGGTGGTTCCCTACAGTCGTCTAC

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 261

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 155

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 353

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

attagctcctggtcgttctagaaattttattattgtcttcatgtggtttgttcagATTGTTAATGGACCTCGCTCTGTAGAATCTCTAAACGACAAGTTTGAAGTATTCTATATCGACTATGGCAACCAAGAGGTGGTTCCCTACAGTCGTCTAC

                                              tttgttc  CT-rich tract
               ttctagaaattttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttatcacaacttagttttatatactttatgcttgaattgccgttattagctcctggtcgttctagaaattttattattgtcttcatgtggtttgttcagATTGTTAATGGACCTCGCTCTGTAGAATCTCTAAACGACAAGTTTGAAGTATTCTATATCGACTATGGCAACCAAGAGGTGGTTCCCTACAGTCGTCTAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG