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

...gccaacttggcaagttggttttgattatttatctgatttgtgtatcagtgtatatgtggatggcaccctatatcttatatctgttgatgttgatatttagGATCTGAAGAAAAAGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAACAAAAGAGAACGGGTGTGTTGGCTTTCAGTCTTTCTGCTCCTTTTGCCAG

Basic information

species	Zea mays
transcript	GRMZM2G174730_T02
intron #	2
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G174730_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os05g42330.2 (Oryza sativa), 3'ss of exon 2

gccaa--cttggcaagttggttttgatta-tttatctgatttgtgtatcagtgtatatgtggatggcaccctatatcttatatctgttgatgttgatatttagGATCTGAAGAAAAAGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAACAAAAGAGAACGGGTGTGTTGGCTTTCAGTCTTTCTGCTCCTTTTGCCAG
|  |   |||      |    | ||   | || || | |    | | |  || | | | ||||||   || ||| ||||  |||  ||  | ||   ||||||||| |||||||||||||||||||||||||||| ||||| ||||| ||||||||||||||| ||                                     
gttattcctttatttataacatctgccaagttaatttcaggcat-tcttggtttgtttttggatgattccttatgtcttgcatccatt--tctttgaatttagGATTTGAAGAAAAAGGAGAAAGAACTCCAGGCAATGGAAGCTGAACTAAACAAAAGAGAAAGG-------------------------------------

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|211137750|gb|FL292365.1|FL292365

EST:     ATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAG                         GATCTGAAGAAAAAGGAGAAAGA
genomic: ATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAGgtacttataa ... tgatatttagGATCTGAAGAAAAAGGAGAAAGA

EST: gi|91876331|gb|EB406288.1|EB406288

EST:     ATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAG                         GATCTGAAGAAAAAGGAGAAAGAACTCCAGGCTATGGAGG
genomic: ATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAGgtacttataa ... tgatatttagGATCTGAAGAAAAAGGAGAAAGAACTCCAGGCTATGGAGG

EST: gi|149015443|gb|EE045301.2|EE045301

EST:     ATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAG                         GATCTGAAGAAAAAGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAAC
genomic: ATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAGgtacttataa ... tgatatttagGATCTGAAGAAAAAGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAAC

EST: gi|211137751|gb|FL292366.1|FL292366

EST:     ATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAG                         GATCTGAAGAAAAAGGAGAAAGA
genomic: ATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAGgtacttataa ... tgatatttagGATCTGAAGAAAAAGGAGAAAGA

EST: gi|211138689|gb|FL292372.1|FL292372

EST:     ATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAG                         GATCTGAAGAAAAAGGAGAAAGA
genomic: ATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAGgtacttataa ... tgatatttagGATCTGAAGAAAAAGGAGAAAGA

EST: gi|211138692|gb|FL292375.1|FL292375

EST:     ATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAG                         GATCTGAAGAAAAAGGAGAAAGA
genomic: ATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAGgtacttataa ... tgatatttagGATCTGAAGAAAAAGGAGAAAGA

EST: gi|211138694|gb|FL292377.1|FL292377

EST:     ATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAG                         GATCTGAAGAAAAAGGAGAAAGA
genomic: ATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAGgtacttataa ... tgatatttagGATCTGAAGAAAAAGGAGAAAGA

EST: gi|211138693|gb|FL292376.1|FL292376

EST:     ATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAG                         GATCTGAAGAAAAAGGAGAAAGA
genomic: ATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAGgtacttataa ... tgatatttagGATCTGAAGAAAAAGGAGAAAGA

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: 288

GGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAGgtacttataa ... tgatatttagGATCTGAAGAAAAAGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAACAAAAGAGAACGGGTGTGTTGGCTTTCAGTCTTTCTGCTCCTTTTGCCAG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 233

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 117

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 417

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

cagtgtatatgtggatggcaccctatatcttatatctgttgatgttgatatttagGATCTGAAGAAAAAGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAACAAAAGAGAACGGGTGTGTTGGCTTTCAGTCTTTCTGCTCCTTTTGCCAG

                                          tgttgat  putative branch site (score: 417)
                       tatatcttatatct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gccaacttggcaagttggttttgattatttatctgatttgtgtatcagtgtatatgtggatggcaccctatatcttatatctgttgatgttgatatttagGATCTGAAGAAAAAGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAACAAAAGAGAACGGGTGTGTTGGCTTTCAGTCTTTCTGCTCCTTTTGCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - -tgatttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - -gtggatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgat