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

...tcttcacttttgacatatttctgctttgaaagatcatttttatgaattataccatcaaagctacatgcttatgccttatgtttttggttactcctttcagAGGTTAGCAACCAGATGTTGGAACTGTATGAGCAAAACCGTGTTCAACCACCACCATCACAAGGCAATGATACTGAAGGCAGTTCTGCAAGTGTTGCGAA

Basic information

species	Zea mays
transcript	AC233979.1_FGT009
intron #	5
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: AC233979.1_FGT009 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA20G02860.1 (Glycine max), 3'ss of exon 6

-tcttcacttttgaca-tatttctgctttgaaagatcatttttatgaattatac-catcaaagctacatgcttatgccttatgtttttggttactcctttcagAGGTTAGCAACCAGATGTTGGAACTGTATGAGCAAAACCGTGTTCAACCACCACCATCACAAGGCAATGATACTGAAGGCAGTTCTGCAAGTGTTGCGAA------
   || | |  |   | || ||   |  ||     || ||||       | ||  | ||       | | || |   ||| ||  |    ||    ||| ||||||||||||| || ||||||||||| |||||||| ||      |  ||  |||||| |||| || | |||    ||||| ||| ||| | |               
cagtttattgctatgagtagtttaacaatgggctgtccttttgtgtgtctgtatgcttctgtatatccttctcagttcttgtgggt---attttctcttgcagAGGTTAGCAATCAAATGTTGGAACTCTATGAGCAGAA------TAGACTTCCACCAGCACAGGGAAGTGAAGTAGAAGGAAGTGCTGGAGGAACAAGAGCTGCTTC

upper sequence: AC233979.1_FGT009 (Zea mays), 3'ss of exon 5
lower sequence: Vv00s0125g00270.t01 (Vitis vinifera), 3'ss of exon 5

-tcttcacttttgacatatttctgctttgaaagatcatttttatgaattataccatcaaagctacatgcttatgccttatgtttttggttactc--ctttcagAGGTTAGCAACCAGATGTTGGAACTGTATGAGCAAAACCGTGTTCAACCACCACCATCACAAGGCAATGATACTGAAGGCAGTTCTGCAAGTGTTGCGAA------
  | |     |||   | ||||     ||         ||||  |  || | |     || ||   ||  | | ||| |  || | ||||| |   ||| ||||| ||||||| || |||||||||||||||||||||||| | ||       || ||| | ||||| | ||| |  ||||  |   |     |||     ||      
gccatgggcattgc--tgtttcattcatggggctgtccttttgcgtcttcttcgggtgaacctttttggatttccctaacattat-ggttatttgtcttgcagAGATTAGCAATCAAATGTTGGAACTGTATGAGCAAAACAGAGT------GCCTCCACCTCAAGGGAGTGAAATGGAAGTTAACGCCAGTGGTGGACTAAACCATAG

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|71331945|gb|DR802861.1|DR802861

EST:     GGTGGCAAGAGTTTGATGTAACTCCGTGGCAGCTGGAAG                         AGGTTAGCAACCAGATGTTGGAACTGTATGAGCAAAACCGTGTTCAACCAC
genomic: GGTGGCAAGAGTTTGATGTAACTCCGTGGCAGCTGGAAGgttggtctct ... ctcctttcagAGGTTAGCAACCAGATGTTGGAACTGTATGAGCAAAACCGTGTTCAACCAC

EST: gi|211118455|gb|FL397818.1|FL397818

EST:     CGAGAAGGTCTGGTGGCAAGAGTTTGATGTAACTCCGTGGCAGCTGGAAG                         AGGTTAGCAACCAGATGTTGGAACTGTATGAGCAAAACCGTGTTCAACCAC
genomic: CGAGAAGGTCTGGTGGCAAGAGTTTGATGTAACTCCGTGGCAGCTGGAAGgttggtctct ... ctcctttcagAGGTTAGCAACCAGATGTTGGAACTGTATGAGCAAAACCGTGTTCAACCAC

EST: gi|116826111|gb|EC869868.1|EC869868

EST:     CGAGAAGGTCTGGTGGCAAGAGTTTGATGTAACTCCGTGGCAGCTGGAAG                         AGGTCTAGCAACCAGATGTTGGAACTGTATGAGCAAAACCGTGTTCAACCA
genomic: CGAGAAGGTCTGGTGGCAAGAGTTTGATGTAACTCCGTGGCAGCTGGAAGgttggtctct ... ctcctttcagAGGT-TAGCAACCAGATGTTGGAACTGTATGAGCAAAACCGTGTTCAACCA

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: 271

GCAATCTTCCTCGCTGCGAAGTTTCTCAAAGTCAAGCTTCCATCAGATGGCGAGAAGGTCTGGTGGCAAGAGTTTGATGTAACTCCGTGGCAGCTGGAAGgttggtctct ... ctcctttcagAGGTTAGCAACCAGATGTTGGAACTGTATGAGCAAAACCGTGTTCAACCACCACCATCACAAGGCAATGATACTGAAGGCAGTTCTGCAAGTGTTGCGAA

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

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 253

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 171

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

attataccatcaaagctacatgcttatgccttatgtttttggttactcctttcagAGGTTAGCAACCAGATGTTGGAACTGTATGAGCAAAACCGTGTTCAACCACCACCATCACAAGGCAATGATACTGAAGGCAGTTCTGCAAGTGTTGCGAA

                                          ttactcctttc  CT-rich tract
                              ttatgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcttcacttttgacatatttctgctttgaaagatcatttttatgaattataccatcaaagctacatgcttatgccttatgtttttggttactcctttcagAGGTTAGCAACCAGATGTTGGAACTGTATGAGCAAAACCGTGTTCAACCACCACCATCACAAGGCAATGATACTGAAGGCAGTTCTGCAAGTGTTGCGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - ttctgct
- - - - - - - - - - - - - - - - - - - - - - - - - - catcaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tacatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcctta