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

...ttcccaactttccagcctgatttttttgcattttggtttatttttcattctgctggttactaacattttatttgcaccaatgccttcctcgtctttgtagCTTGTCAATCCTGCCTATCAATCTCTTCTAGGTCACTTACACACTAGAACTTTAGAAGCATTTAAGGAGTACTTTGGCAAGGCCCTAGAAAAGGAGGGAT

Basic information

species	Zea mays
transcript	AC196426.3_FGT007
intron #	13
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: AC196426.3_FGT007 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os01g39310.3 (Oryza sativa), 3'ss of exon 14

ttcccaactttccagcc-tgatttttttgcatt-ttggtttattt-ttcattctgctggttactaacattt-tatttgcaccaatgccttcctcgtctttgtagCTTGTCAATCCTGCCTATCAATCTCTTCTAGGTCACTTACACACTAGAACTTTAGAAGCATTTAAGGAGTACTTTGGCAAGGCCCTAGAAAAGGAGGGAT
   | |  |||  ||   |  || ||     || || ||  |||| || | |    |  |||     |||| |  ||  |||||||  ||||| | |||| ||||||||||| ||||| || |||  | || | | ||| ||||  |||||||||||||||| ||||||||||| ||||| |||| |||||||||||||||| |
--actatttttttagttgttcttgttccatgttattagtgcatttatttactgatattattatcttgatttgttcttataccaatgt-ttccttgccttt-tagCTTGTCAACCCTGCATACCAAAATATTTTGGATCATTTACGGACTAGAACTTTAGAAGTATTTAAGGAGTCCTTTGACAAGTCCCTAGAAAAGGAGGGTT

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|15053846|gb|BI359391.1|BI359391

EST:     TCTAAACTGTTACAG                         CTTGTCAATCCTGCCTATCAATCTCTTCTAGGTCACTTACACACTAGAACT
genomic: TCTAAACTGTTACAGgttcggtcgt ... gtctttgtagCTTGTCAATCCTGCCTATCAATCTCTTCTAGGTCACTTACACACTAGAACT

EST: gi|211454906|gb|FK967300.1|FK967300

EST:     AAGGTGTCAGAAGCTCGAAAAGACAACAACTTGAGTCTAAACTGTTACAG                         CTTGTCAATCCTGCCT
genomic: AAGGTGTCAGAAGCTCGAAAAGACAACAACTTGAGTCTAAACTGTTACAGgttcggtcgt ... gtctttgtagCTTGTCAATCCTGCCT

EST: gi|211454909|gb|FK967303.1|FK967303

EST:     AAGGTGTCANAAGCTCGAAAAGACAACAACTTGAGTCTAAACTGTTACAG                         CTTGNCAATCCTGCCTATCAATCTC
genomic: AAGGTGTCAGAAGCTCGAAAAGACAACAACTTGAGTCTAAACTGTTACAGgttcggtcgt ... gtctttgtagCTTGTCAATCCTGCCTATCAATCTC

EST: gi|211454913|gb|FK967307.1|FK967307

EST:     AAGGTGTCAGAAGCTCGAAAAGACAACAACTTGAGTCTAAACTGTTACAG                         CTTGTCAATCCTGCCTATCA
genomic: AAGGTGTCAGAAGCTCGAAAAGACAACAACTTGAGTCTAAACTGTTACAGgttcggtcgt ... gtctttgtagCTTGTCAATCCTGCCTATCA

EST: gi|211043097|gb|FK967328.1|FK967328

EST:     AAGGTGTCAGAAGCTCGAAAAGACAACAACTTGAGTCTAAACTGTTACAG                         CTTGTCAATCCTGCCTATCAAT
genomic: AAGGTGTCAGAAGCTCGAAAAGACAACAACTTGAGTCTAAACTGTTACAGgttcggtcgt ... gtctttgtagCTTGTCAATCCTGCCTATCAAT

EST: gi|211457040|gb|FK967318.1|FK967318

EST:     AAGGTGTCAGAAGCTCGAAAAGACAACAACTTGAGTCTAAACTGTTACAG                         CTTGTCAATCCTGCCTATCAATCTCTTCT
genomic: AAGGTGTCAGAAGCTCGAAAAGACAACAACTTGAGTCTAAACTGTTACAGgttcggtcgt ... gtctttgtagCTTGTCAATCCTGCCTATCAATCTCTTCT

EST: gi|211457046|gb|FK967324.1|FK967324

EST:     AAGGTGTCAGAAGCTCGAAAAGACAACAACTTGAGTCTAAACTGTTACAG                         CTTGTCAATCCTGCCTATCAATCTCTTCTAGGTCACTTAC
genomic: AAGGTGTCAGAAGCTCGAAAAGACAACAACTTGAGTCTAAACTGTTACAGgttcggtcgt ... gtctttgtagCTTGTCAATCCTGCCTATCAATCTCTTCTAGGTCACTTAC

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: 46 (upstream exon), 48 (downstream exon)
Score: 146

GTATGACATGGAGGCTATTTATTTTGATGAAGGTGTCAGAAGCTCGAAAAGACAACAACTTGAGTCTAAACTGTTACAGgttcggtcgt ... gtctttgtagCTTGTCAATCCTGCCTATCAATCTCTTCTAGGTCACTTACACACTAGAACTTTAGAAGCATTTAAGGAGTACTTTGGCAAGGCCCTAGAAAAGGAGGGAT

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 166

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 182

Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 223

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

cattctgctggttactaacattttatttgcaccaatgccttcctcgtctttgtagCTTGTCAATCCTGCCTATCAATCTCTTCTAGGTCACTTACACACTAGAACTTTAGAAGCATTTAAGGAGTACTTTGGCAAGGCCCTAGAAAAGGAGGGAT

            tactaac  putative branch site (score: 223)
                                   tgccttcctcgtcttt  putative PPT
           ttactaacattttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcccaactttccagcctgatttttttgcattttggtttatttttcattctgctggttactaacattttatttgcaccaatgccttcctcgtctttgtagCTTGTCAATCCTGCCTATCAATCTCTTCTAGGTCACTTACACACTAGAACTTTAGAAGCATTTAAGGAGTACTTTGGCAAGGCCCTAGAAAAGGAGGGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - ctgattt
- - - - - - - - - - - - -ttgcatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgcacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgccttc