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

gtaacacaatgataccacgaaacttagtttctttaccctttttttgctctatttactattggtccatcttgtttcactgtgcctcactttattttgaattttcagGAAACAGCTCTTAATCATGTGAAAACAGCTGGCCTTCTTGGAGATGGTTTTGGCGCCACACCAGAGATGAGCAAACGAAACTTGATCTGGGTTGTCAGCA

Basic information

species	Zea mays
transcript	GRMZM5G829544_T01
intron #	2
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM5G829544_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os11g43820.1 (Oryza sativa), 3'ss of exon 2

gtaacacaatgataccacgaaacttagtttctttaccctttttttgctctatttactattggtccatcttgtttcactgtgcctcactttattttgaatttt-cagGAAACAGCTCTTAATCATGTGAAAACAGCTGGCCTTCTTGGAGATGGTTTTGGCGCCACACCAGAGATGAGCAAACGAAACTTGATCTGGGTTGTCAGCA
||||     ||      |     |||||||  || | | |||     |   |||  ||| | | ||| |   |       ||      ||||||  |||||| ||||||||||||||||| |||||||  || ||||| |||||||||||||||||||| || ||||| |||||||||||||| |||||||| |||||||||||||
gtaagtggttgcacattctgtttttagttttatttctcatttcagcat---tttgttatagattcatatgtctctttcaagctggcaattatttaaaattttgcagGAAACAGCTCTTAACCATGTGAGGACTGCTGGTCTTCTTGGAGATGGTTTTGGGGCTACACCGGAGATGAGCAAACGGAACTTGATATGGGTTGTCAGCA

upper sequence: GRMZM5G829544_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g43090.4 (Oryza sativa), 3'ss of exon 3

gtaacacaatgataccacgaaacttagtttctttaccctttttttgctctatttactattggtccatcttgtttcactgtgcctcactttattttgaatttt-cagGAAACAGCTCTTAATCATGTGAAAACAGCTGGCCTTCTTGGAGATGGTTTTGGCGCCACACCAGAGATGAGCAAACGAAACTTGATCTGGGTTGTCAGCA
||||     ||      |     |||||||| || | | |||     |   |||  ||| | | | | |   |       ||      ||||||  |||||| |||||||| |||||||| ||||| |  || ||||| |||||||||||||||||||| || ||||| |||||||||||||| |||||||| |||||||||||||
gtaagtggttgcacattctgtttttagtttcatttctcatttcagcat---tttgttatagattcgtatgtctctttcaagctggcaattatttaaaattttgcagGAAACGGCTCTTAACCATGTAAGGACTGCTGGTCTTCTTGGAGATGGTTTTGGGGCTACACCGGAGATGAGCAAACGGAACTTGATATGGGTTGTCAGCA

upper sequence: GRMZM5G829544_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os06g05130.1 (Oryza sativa), 3'ss of exon 2

gtaacacaatgataccacgaaacttagtttctttacccttttttt-gctctatttactattggtccatcttgtttcactgtgc-ctcactttattttgaa--ttttcagGAAACAGCTCTTAATCATGTGAAAACAGCTGGCCTTCTTGGAGATGGTTTTGGCGCCACACCAGAGATGAGCAAACGAAACTTGATCTGGGTTGTCAGCA
         |||||| | | | ||  | | ||||| | ||| ||  |   | || ||||||||| |||  |||| |   |    || ||| || ||||||  ||| |||||||||||||| || ||||||||||| ||||| ||  | || ||||||||||| || || || |||||||||||||| ||||| || |||||||||||||
--------gtgatacaatggagctatgctgctttagcttttcttccgtatttttcactattggtacattatgtt-cgtggcatactaactgtaatttgaagctttgcagGAAACAGCTCTGAACCATGTGAAAACTGCTGGTCTCTTAGGTGATGGTTTTGGTGCTACGCCGGAGATGAGCAAACGGAACTTAATATGGGTTGTCAGCA

upper sequence: GRMZM5G829544_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA05G08060.3 (Glycine max), 3'ss of exon 2

-------------------------------------------------gtaacacaatgataccacgaaacttagtttctttaccctttttttgctctatttactattggt-ccatcttgtt-tcactgtgc---ctcactttattttgaatttt----------cagGAAACAGCTCTTAATCATGTGAAAACAGCTGGCCTTCTTGGAGATGGTTTTGGCGCCACACCAGAGATGAGCAAACGAAACTTGATCTGGGTTGTCAGCA
                                                  |      |  |    | |    ||  |||  | ||  |  ||    |  || ||    |  |  |||  |||| | ||| | |   ||   ||||| |  | | ||          |||||||| || ||||||||||| ||||  ||||| |||||||| ||||| |||||  |||| ||||| ||| |||||   |||||||| ||||| || |   
gtaagtccgtcctcatacaagtgaatctttatgatcttcagagatgagtatgctttgactaagatagggctgtttatttagtcactgtaattcaatttcatatatagataatatcattctgttgttacttttcatactatatttatatcaactatttgcttaacaacagGAAACTGCACTTAATCATGTTAAAAGTGCTGGGCTTCTTGGTGATGGCTTTGGTTCCACGCCAGAAATGTGCAAAAAGAACTTGATATGGGTGGTTACTC

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|148991050|gb|EE032494.2|EE032494

EST:     TTGGTGCCGATCGTACGGCTTCTATAGAGACATTAATGAATCATTTACAG                         GAAACAGCTCTTAATCATGTGAAAACAGCTGGCCTTCTTGGAGATGGTTTT
genomic: TTGGTGCCGATCGTACGGCTTCTATAGAGACATTAATGAATCATTTACAGgtaacacaat ... gaattttcagGAAACAGCTCTTAATCATGTGAAAACAGCTGGCCTTCTTGGAGATGGTTTT

EST: gi|76909772|gb|DV163527.1|DV163527

EST:     TTGGTGCCGATCGTACGGCTTCTATAGAGACATTATTGAATCATTTACAG                         GAAACAGCTCTTAATCATGTGAAAACAGCTGGCCTTCTTGGGAGATGGTTT
genomic: TTGGTGCCGATCGTACGGCTTCTATAGAGACATTAATGAATCATTTACAGgtaacacaat ... gaattttcagGAAACAGCTCTTAATCATGTGAAAACAGCTGGCCTTCTTGG-AGATGGTTT

EST: gi|76019085|gb|DT946255.1|DT946255

EST:     TTGGTGCCGATCGTACGGCTTCTATAGAGACATTAATGAATCATTTACAG                         GAAACAGCTCTTAATCATGTGAAAACAGCTGGCCTTCTTGGAGATGGTTTT
genomic: TTGGTGCCGATCGTACGGCTTCTATAGAGACATTAATGAATCATTTACAGgtaacacaat ... gaattttcagGAAACAGCTCTTAATCATGTGAAAACAGCTGGCCTTCTTGGAGATGGTTTT

EST: gi|149057529|gb|EE156667.2|EE156667

EST:     TTGGTGCCGATCGTACGGCTTCTATAGAGACATTAATGAATCATTTACAG                         GAAACAGCTCTTAATCATGTGAAAACAGCTGGCCTTCT
genomic: TTGGTGCCGATCGTACGGCTTCTATAGAGACATTAATGAATCATTTACAGgtaacacaat ... gaattttcagGAAACAGCTCTTAATCATGTGAAAACAGCTGGCCTTCT

EST: gi|101390157|gb|EB817011.1|EB817011

EST:     TTGGTGCCGATCGTACGGCTTCTATAGAGACATTAATGAATCATTTACAG                         GAAACAGCTCTTAATCATGTGAAAACAGCTGGCCTTCTTGGAGATGGGTTT
genomic: TTGGTGCCGATCGTACGGCTTCTATAGAGACATTAATGAATCATTTACAGgtaacacaat ... gaattttcagGAAACAGCTCTTAATCATGTGAAAACAGCTGGCCTTCTTGGAGATGG-TTT

EST: gi|148959868|gb|EE153103.2|EE153103

EST:     TTGGTGCCGATCGTACGGCTTCTATAGAGACATTAATGAATCATTTACAG                         GGAACAGCTCTTAATCATGTGAAAACAGCT
genomic: TTGGTGCCGATCGTACGGCTTCTATAGAGACATTAATGAATCATTTACAGgtaacacaat ... gaattttcagGAAACAGCTCTTAATCATGTGAAAACAGCT

EST: gi|12045510|gb|BF727649.1|BF727649

EST:     TTGGTGCCGATCGTACGGCTTCTATAGAGACATTAATGAATCATTTACAG                         GAAACAGCTCTTAATCATGTGAAAACAGCTGGCCTTCTTGGAGATGGTTTT
genomic: TTGGTGCCGATCGTACGGCTTCTATAGAGACATTAATGAATCATTTACAGgtaacacaat ... gaattttcagGAAACAGCTCTTAATCATGTGAAAACAGCTGGCCTTCTTGGAGATGGTTTT

EST: gi|149080297|gb|EE169321.2|EE169321

EST:     TTGGTGCCGATCGTACGGCTTCTATAGAGACATTAATGAATCATTTACAG                         GAAACAGCTCTTAATCATGTGAAAACAGCTGGCCTTCTTGGAGATGGTTTT
genomic: TTGGTGCCGATCGTACGGCTTCTATAGAGACATTAATGAATCATTTACAGgtaacacaat ... gaattttcagGAAACAGCTCTTAATCATGTGAAAACAGCTGGCCTTCTTGGAGATGGTTTT

EST: gi|6137960|gb|AW134414.1|AW134414

EST:     TTGGTGCCGATCGTACGGCTTCTATAGAGACATTAATGAATCATTTACAG                         GAAACAGCTCTTAATCATGTGAAAACAGCTGGCCTTCTTGGAGATGGTTTT
genomic: TTGGTGCCGATCGTACGGCTTCTATAGAGACATTAATGAATCATTTACAGgtaacacaat ... gaattttcagGAAACAGCTCTTAATCATGTGAAAACAGCTGGCCTTCTTGGAGATGGTTTT

EST: gi|211372077|gb|FL076465.1|FL076465

EST:     GCCGATCGTACGGCTTCTATAGAGACATTAATGAATCATTTACAG                         GAAACAGCTCTTAATCATGTGAAAACAGCTGGCCTTCTTGGAGATGGTTTT
genomic: GCCGATCGTACGGCTTCTATAGAGACATTAATGAATCATTTACAGgtaacacaat ... gaattttcagGAAACAGCTCTTAATCATGTGAAAACAGCTGGCCTTCTTGGAGATGGTTTT

EST: gi|78179128|gb|DV549501.1|DV549501

EST:     TTGGTGCCGATCGTACGGCTTCTATAGAGACATTAATGAATCATTTACAG                         GAAACAGCTCTTAATCATGTGAAAACAGCTGGCCTTCTTGGAGATGGTTTT
genomic: TTGGTGCCGATCGTACGGCTTCTATAGAGACATTAATGAATCATTTACAGgtaacacaat ... gaattttcagGAAACAGCTCTTAATCATGTGAAAACAGCTGGCCTTCTTGGAGATGGTTTT

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: 47 (upstream exon), 49 (downstream exon)
Score: 72

TCAGGATGGGCTGGTTTTTAGGCAAAACTTCTGGATTCGGTCCTATGAGATTGGTGCCGATCGTACGGCTTCTATAGAGACATTAATGAATCATTTACAGgtaacacaat ... gaattttcagGAAACAGCTCTTAATCATGTGAAAACAGCTGGCCTTCTTGGAGATGGTTTTGGCGCCACACCAGAGATGAGCAAACGAAACTTGATCTGGGTTGTCAGCA

Block sizes: 45 (upstream exon), 47 (downstream exon)
Score: 27

Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 27

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 56

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

atttactattggtccatcttgtttcactgtgcctcactttattttgaattttcagGAAACAGCTCTTAATCATGTGAAAACAGCTGGCCTTCTTGGAGATGGTTTTGGCGCCACACCAGAGATGAGCAAACGAAACTTGATCTGGGTTGTCAGCA

                              gcctcac  putative branch site (score: 56)
                                                ttttc  putative PPT
                                   actttattttgaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacacaatgataccacgaaacttagtttctttaccctttttttgctctatttactattggtccatcttgtttcactgtgcctcactttattttgaattttcagGAAACAGCTCTTAATCATGTGAAAACAGCTGGCCTTCTTGGAGATGGTTTTGGCGCCACACCAGAGATGAGCAAACGAAACTTGATCTGGGTTGTCAGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG