ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

CGTGCCCTCTTTCAAGATCTACGGCGGCGTCGCGGGGCTCTACGACTACGGACCCCCAGGTTGCGCTGTCAAAGCTAACGTCCTCGCATTCTGGCGCCAGgtactgtactacctactactacacccgcagatggatactgaactagctagctctctcaatacttggcacgttcgaggcaaaggcggcacatttttcagtt...

Basic information

species	Zea mays
transcript	GRMZM2G171688_T01
intron #	1
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G171688_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os04g32650.1 (Oryza sativa), 5'ss of exon 1

CGTGCCCTCTTTCAAGATCTACGGCGGCGTCGCGGGGCTCTACGACTACGGACCCCCAGGTTGCGCTGTCAAAGCTAACGTCCTCGCATTCTGGCGCCAGgtactgtactacctactactacacccgcagatggatactgaactagctagctctctcaatacttggcacgttcgag-gcaaaggcggcacatttttcagtt--
||| || || |||||||||||||||||||||||||| |||||||||||||| || || || ||||| ||||| || ||||||||||| ||||||||||||||  |   |  || ||  |  |||    |   |  | ||       ||     ||    || | |      | ||  |     | |||  |||||   | |  
CGTCCCGTCCTTCAAGATCTACGGCGGCGTCGCGGGCCTCTACGACTACGGCCCTCCCGGCTGCGCCGTCAAGGCCAACGTCCTCGCCTTCTGGCGCCAGgttatccccc-cccacccccccactactacccg--tgcttcttcttcttctcttcggtgtagtagtagtagtagattgggggagtggccaattttcggggtgg

upper sequence: GRMZM2G171688_T01 (Zea mays), 5'ss of exon 1
lower sequence: Vv01s0150g00150.t01 (Vitis vinifera), 5'ss of exon 1

CGTGCCCTCTTTCAAGATCTACGGCGGCGTCGCGGGGCTCTACGACTACGGACCCCCAGGTTGCGCTGTCAAAGCTAACGTCCTCGCATTCTGGCGCCAGgtactgtactacctactactacacccgcagatggatactgaactagctagctctctcaatacttggcacgttcgaggcaaaggcggcacatttttcagtt-
| | || ||||||||||||||| |||||||||| || || |||||||||||||| || || ||||| ||||| || ||||||||||| |||||||| ||||||     |  |    |   | | |        | | || ||||    |   |  |   |  ||  ||  || |             |  ||     |   
CATTCCTTCTTTCAAGATCTACCGCGGCGTCGCTGGACTTTACGACTACGGACCGCCGGGATGCGCCGTCAAGGCCAACGTCCTCGCTTTCTGGCGTCAGgtatgcagcggcagtgtcggagatcgattcgcagtttct-aactgatcaaacccatatttcgtttacaaattgggactgtgaatcttaatttgaattgcaa

upper sequence: GRMZM2G171688_T01 (Zea mays), 5'ss of exon 1
lower sequence: EFJ16329 (Selaginella moellendorffii), 5'ss of exon 1

CGTGCCCTCTTTCAAGATCTACGGCGGCGTCGCGGGGCTCTACGACTACGGACCCCCAGGTTGCGCTGTCAAAGCTAACGTCCTCGCATTCTGGCGCCAGgtactgtactacctactactacacccgcagatggatactgaacta-gctagctctctcaatacttggcacgttcgaggcaaaggcggcacatttttcagtt
|||    ||||||||||||||||| |||||||||||  | | ||| || || || ||||| |  || ||||| | ||||||| |    || |||| |||||||   ||        ||  | |||    |||         ||   | |   |||| ||                                          
CGTCAAGTCTTTCAAGATCTACGGTGGCGTCGCGGGATTGTTCGATTATGGCCCTCCAGGCTCGGCCGTCAAGGATAACGTCTTGAGCTTTTGGCACCAGgtaaaatatcgagctttaaaaaacc-atggataatcttcttacggtgttctttctcgcag-----------------------------------------

upper sequence: GRMZM2G171688_T01 (Zea mays), 5'ss of exon 1
lower sequence: EFJ17803 (Selaginella moellendorffii), 5'ss of exon 1

CGTGCCCTCTTTCAAGATCTACGGCGGCGTCGCGGGGCTCTACGACTACGGACCCCCAGGTTGCGCTGTCAAAGCTAACGTCCTCGCATTCTGGCGCCAGgtactgtactacctactactacacccgcagatggatactgaactagctagctctctcaatacttggcacgttcgaggcaaaggcggcacatttttcagtt
|||    ||||||||||||||||| |||||||||||  | | ||| || || || ||||| |  || ||||| | ||||||| |    || |||| |||||||   ||        ||  | |||     |||||||   | ||   ||  | | ||  |   | |||                                
CGTCAAGTCTTTCAAGATCTACGGTGGCGTCGCGGGATTGTTCGATTATGGCCCTCCAGGCTCGGCCGTCAAGGATAACGTCTTGAGCTTTTGGCACCAGgtaaaatatcgagctttaaaaaacc-----atggata---atcttcttacatttttc--tttctcgcag-------------------------------

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|94479283|gb|EB708241.1|EB708241

EST:     CCCCCCAGGTTGCGCTGTCAAAGCTAACGTCCCTCGCATTCTGGCGCCAG                         CATTTTGTATTGGAGGAAGGGATGCTTGAGGTTGACTGTCCATGTGTGACG
genomic: CCCCC-AGGTTGCGCTGTCAAAGCTAACGTCC-TCGCATTCTGGCGCCAGgtactgtact ... cctttattagCATTTTGTATTGGAGGAAGGGATGCTTGAGGTTGACTGTCCATGTGTGACG

EST: gi|211372632|gb|FK983004.1|FK983004

EST:     GACCCCCAGGTTGCGCTGTCAAAGCTAACGTCCTCGCATTCTGGCGCCAG                         CATTTTGTATTGGAGGAAGGGATGCTTGAGGTTGACTGTCCATGTGTGACG
genomic: GACCCCCAGGTTGCGCTGTCAAAGCTAACGTCCTCGCATTCTGGCGCCAGgtactgtact ... cctttattagCATTTTGTATTGGAGGAAGGGATGCTTGAGGTTGACTGTCCATGTGTGACG

EST: gi|149109533|gb|EE190251.2|EE190251

EST:     GACCCCCAGGTTGCGCTGTCAAAGCTAACGTCCTCCCATTCTGGCGCCAG                         CATTTTGTATTGGAGGAAGGGATGCTTGAGGTTGACTGTCCATGTGTGACG
genomic: GACCCCCAGGTTGCGCTGTCAAAGCTAACGTCCTCGCATTCTGGCGCCAGgtactgtact ... cctttattagCATTTTGTATTGGAGGAAGGGATGCTTGAGGTTGACTGTCCATGTGTGACG

EST: gi|211372631|gb|FK983003.1|FK983003

EST:     GACCCCCAGGTTGCGCTGTCAAAGCTAACGTCCTCGCATTCTGGCGCCAG                         CATTTTGTATTGGAGGAAGGGATGCTTGAGGTTGACTGTCCATGTGTGACG
genomic: GACCCCCAGGTTGCGCTGTCAAAGCTAACGTCCTCGCATTCTGGCGCCAGgtactgtact ... cctttattagCATTTTGTATTGGAGGAAGGGATGCTTGAGGTTGACTGTCCATGTGTGACG

EST: gi|211372630|gb|FK983002.1|FK983002

EST:     GACCCCCAGGTTGCGCTGTCAAAGCTAACGTCCTCGCATTCTGGCGCCAG                         CATTTTGTATTGGAGGAAGGGATGCTTGAGGTTGACTGTCCATGTGTGACG
genomic: GACCCCCAGGTTGCGCTGTCAAAGCTAACGTCCTCGCATTCTGGCGCCAGgtactgtact ... cctttattagCATTTTGTATTGGAGGAAGGGATGCTTGAGGTTGACTGTCCATGTGTGACG

EST: gi|211375301|gb|FK983022.1|FK983022

EST:     GACCCCCAGGNTGCGCTGTCAAAGCTAACGTCCTCGCATTCTGGCGCCAG                         CATTTTGTATTGNAGGAAGGGATGCTTTGAGGT-GACTGTCCATGTGTGAC
genomic: GACCCCCAGGTTGCGCTGTCAAAGCTAACGTCCTCGCATTCTGGCGCCAGgtactgtact ... cctttattagCATTTTGTATTGGAGGAAGGGATGCTT-GAGGTTGACTGTCCATGTGTGAC

EST: gi|148931620|gb|EC874748.2|EC874748

EST:     GACCCCCAGGTTGCGCTGTCAAAGCTAACGTCCTCGCATTCTGGCGCCAG                         CATTTTGTATTGGAGGAAGGGATGCTTGAGGTTGACTGTCCATGTGTGACG
genomic: GACCCCCAGGTTGCGCTGTCAAAGCTAACGTCCTCGCATTCTGGCGCCAGgtactgtact ... cctttattagCATTTTGTATTGGAGGAAGGGATGCTTGAGGTTGACTGTCCATGTGTGACG

EST: gi|148972573|gb|EE023537.2|EE023537

EST:     GACCCCCAGGTTGCGCTGTCAAAGCTAACGTCCTCGCATTCTGGCGCCAG                         CATTTTGTATTGGAGGAAGGGATGCTTGAGGTTGACTGTCCATGTGTGACG
genomic: GACCCCCAGGTTGCGCTGTCAAAGCTAACGTCCTCGCATTCTGGCGCCAGgtactgtact ... cctttattagCATTTTGTATTGGAGGAAGGGATGCTTGAGGTTGACTGTCCATGTGTGACG

EST: gi|148943086|gb|EC888140.2|EC888140

EST:     GACCCCCAGGTTGCGCTGTCAAAGCTAACGTCCTCGCATTCTGGCGCCAG                         CATTTTGTATTGGAGGAAGGGATGCTTGAGGTTGACTGTCCATGTGTGACG
genomic: GACCCCCAGGTTGCGCTGTCAAAGCTAACGTCCTCGCATTCTGGCGCCAGgtactgtact ... cctttattagCATTTTGTATTGGAGGAAGGGATGCTTGAGGTTGACTGTCCATGTGTGACG

EST: gi|148960536|gb|EE011141.2|EE011141

EST:     GACCCCCAGGTTGCGCTGTCAAAGCTAACGTCCTCGCATTCTGGCGCCAG                         CATTTTGTATTGGAGGAAGGGATGCTTGAGGTTGACTGTCCATGTGTGACG
genomic: GACCCCCAGGTTGCGCTGTCAAAGCTAACGTCCTCGCATTCTGGCGCCAGgtactgtact ... cctttattagCATTTTGTATTGGAGGAAGGGATGCTTGAGGTTGACTGTCCATGTGTGACG

EST: gi|211375296|gb|FK983017.1|FK983017

EST:     GACCCCCAGGTTGCGCTGTCAAAGCTAACGTCCTCGCATTCTGGCGCCAG                         CATTTTGTATTGGAGGAAGGGATGCTTGAGGTTGACTGTCCATGTGTGACG
genomic: GACCCCCAGGTTGCGCTGTCAAAGCTAACGTCCTCGCATTCTGGCGCCAGgtactgtact ... cctttattagCATTTTGTATTGGAGGAAGGGATGCTTGAGGTTGACTGTCCATGTGTGACG

EST: gi|211375295|gb|FK983016.1|FK983016

EST:     GACCCCCAGGTTGCGCTGTCAAAGCTAACGTCCTCGCATTCTGGCGCCAG                         CATTTTGTATTGGAGGAAGGGATGCTTGAGGTTGACTGTCCATGTGTGACG
genomic: GACCCCCAGGTTGCGCTGTCAAAGCTAACGTCCTCGCATTCTGGCGCCAGgtactgtact ... cctttattagCATTTTGTATTGGAGGAAGGGATGCTTGAGGTTGACTGTCCATGTGTGACG

EST: gi|211375289|gb|FK983010.1|FK983010

EST:     GACCCCCAGGTTGCGCTGTCAAAGCTAACGTCCTCGCATTCTGGCGCCAG                         CATTTTGTATTGGAGGAAAGGATGCTTGAGGTTGACTGTCCATGTGTGACG
genomic: GACCCCCAGGTTGCGCTGTCAAAGCTAACGTCCTCGCATTCTGGCGCCAGgtactgtact ... cctttattagCATTTTGTATTGGAGGAAGGGATGCTTGAGGTTGACTGTCCATGTGTGACG

EST: gi|211375294|gb|FK983015.1|FK983015

EST:     GACCCCCAGGTTGCGCTGTCAAAGCTAACGTCCTCGCATTCTGGCGCCAG                         CATTTTGTATTGGAGGAAGGGATGCTTGAGGTTGACTGTCCATGTGTGACG
genomic: GACCCCCAGGTTGCGCTGTCAAAGCTAACGTCCTCGCATTCTGGCGCCAGgtactgtact ... cctttattagCATTTTGTATTGGAGGAAGGGATGCTTGAGGTTGACTGTCCATGTGTGACG

EST: gi|211375297|gb|FK983018.1|FK983018

EST:     GACCCCCAGGTTGCGCTGTCAAAGCTAACGTCCTCGCATTCTGGCGCCAG                         CATTTTGTATTGGAGGAAGGGATGCTTGAGGTTGACTGTCCATGTGTGACG
genomic: GACCCCCAGGTTGCGCTGTCAAAGCTAACGTCCTCGCATTCTGGCGCCAGgtactgtact ... cctttattagCATTTTGTATTGGAGGAAGGGATGCTTGAGGTTGACTGTCCATGTGTGACG

EST: gi|148973607|gb|EE024715.2|EE024715

EST:     GACCCCCAGGTTGCGCTGTCAAAGCTAACGTCCTCGCATTCTGGCGCCAG                         CATTTTGTATTGGAGGAAGGGATGCTTGAGGTTGACTGTCCATGTGTGACG
genomic: GACCCCCAGGTTGCGCTGTCAAAGCTAACGTCCTCGCATTCTGGCGCCAGgtactgtact ... cctttattagCATTTTGTATTGGAGGAAGGGATGCTTGAGGTTGACTGTCCATGTGTGACG

EST: gi|47961805|gb|CN844514.1|CN844514

EST:     GACCCCCAGGTTGCGCTGTCAAAGCTAACGTCCTCGCATTCTGGCGCCAG                         CATTTTGTATTGGAGGAAGGGATGCTTGAGGTTGACTGTCCATGTGTGACG
genomic: GACCCCCAGGTTGCGCTGTCAAAGCTAACGTCCTCGCATTCTGGCGCCAGgtactgtact ... cctttattagCATTTTGTATTGGAGGAAGGGATGCTTGAGGTTGACTGTCCATGTGTGACG

EST: gi|211372634|gb|FK983006.1|FK983006

EST:     GACCCCCAGGTTGCGCTGTCAAAGCTAACGTCCTCGCATTCTGGCGCCAG                         CATTTTGTATTGGAGGAAGGGATGCTTGAGGTTGACTGTCCATGTGTGACG
genomic: GACCCCCAGGTTGCGCTGTCAAAGCTAACGTCCTCGCATTCTGGCGCCAGgtactgtact ... cctttattagCATTTTGTATTGGAGGAAGGGATGCTTGAGGTTGACTGTCCATGTGTGACG

EST: gi|60339809|gb|DN206782.1|DN206782

EST:     GACCCCCAGGTTGCGCTGTCAAAGCTAACGTCCTCGCATTCTGGCGCCAG                         CATTTTGTATTGGAGGAAGGGATGCTTGAGGTTGACTGTCCATGTGTGACG
genomic: GACCCCCAGGTTGCGCTGTCAAAGCTAACGTCCTCGCATTCTGGCGCCAGgtactgtact ... cctttattagCATTTTGTATTGGAGGAAGGGATGCTTGAGGTTGACTGTCCATGTGTGACG

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: 45 (upstream exon), 49 (downstream exon)
Score: 151

CGTGCCCTCTTTCAAGATCTACGGCGGCGTCGCGGGGCTCTACGACTACGGACCCCCAGGTTGCGCTGTCAAAGCTAACGTCCTCGCATTCTGGCGCCAGgtactgtact ... cctttattagCATTTTGTATTGGAGGAAGGGATGCTTGAGGTTGACTGTCCATGTGTGACGCCAGAAGTTGTCTTGAAAGCCTCTGGACATGTTGATAAATTTACAGACT

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 123

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 109

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 111

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGTGCCCTCTTTCAAGATCTACGGCGGCGTCGCGGGGCTCTACGACTACGGACCCCCAGGTTGCGCTGTCAAAGCTAACGTCCTCGCATTCTGGCGCCAGgtactgtactacctactactacacccgcagatggatactgaactagctagctctctcaatacttggcacgttcgaggcaaaggcggcacatttttcagtt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cacccgc
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