ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

TGGTGGCTTGCGAGAGTTGATTGTTGGGAAGGATGATGAGATCCTGAAAACAGAAACAAGAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATACAGgtagcttcatacagtggaagacacgtaactgtagatccatgcttttctcaaactcttgtgaaagtgctaactctatagtttgattgatctgtggctttcctatgcag

Basic information

species	Zea mays
transcript	GRMZM2G047219_T01
intron #	6
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G047219_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os05g01970.1 (Oryza sativa), 5'ss of exon 6

TGGTGGCTTGCGAGAGTTGATTGTTGGGAAGGATGATGAGATCCTGAAAACAGAAACAAGAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATACAGgtagcttcata-cagtggaagacacgtaactgtagatccatgcttttctcaaactcttgtgaaagtgctaactctatagtttgattgatctgtggctttcctatgcag
||||||  |||| |||||| ||||||||||||||||||||||| |||| |||||||||| ||||||  |||| || |||||||||||||||||  |||||||| ||||| | | ||||| |||| || |||||  ||  |  || | |||      || || |  | | |  |||   || |    || |  ||  |   |||     
TGGTGGTGTGCGGGAGTTGCTTGTTGGGAAGGATGATGAGATCTTGAAGACAGAAACAAAAACTATTACCAGAGCAGATGTTGCAGAAGTTTGTTTACAGgtaccttcacaactgtggatgacatgttactgttcat--aatctctgctcggtgaattttgcatctaccatgtctgatgtctccgagaacaatg-ttaatcta-----

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|17931616|gb|BM268576.1|BM268576

EST:     CAGAAACAAGAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATACAG                         GCATTGCTATTCGAAGAGTCAAAGTTTAAGGCATTTGATCTGGCATCAAAA
genomic: CAGAAACAAGAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATACAGgtagcttcat ... tcctatgcagGCATTGCTATTCGAAGAGTCAAAGTTTAAGGCATTTGATCTGGCATCAAAA

EST: gi|94473462|gb|EB702420.1|EB702420

EST:     CAGAAACAAGAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATACAG                         GCATTGCTATTCGAAGAGTCAAAGTTTAAGGCATTTGATCTGGCATCAAAA
genomic: CAGAAACAAGAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATACAGgtagcttcat ... tcctatgcagGCATTGCTATTCGAAGAGTCAAAGTTTAAGGCATTTGATCTGGCATCAAAA

EST: gi|148966373|gb|EE017367.2|EE017367

EST:     CAGAAACAAGAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATCCAG                         GCATTGCTATTCGAAGAGTCAAAGTTTAAGGCATTTGATCTGGCATCAAAA
genomic: CAGAAACAAGAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATACAGgtagcttcat ... tcctatgcagGCATTGCTATTCGAAGAGTCAAAGTTTAAGGCATTTGATCTGGCATCAAAA

EST: gi|13381992|gb|BG458667.1|BG458667

EST:     CAGAAACAAGAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATACAG                         GCATTGCTATTCGAAGAGTCAAAGTTTAAGGCATTTGATCTGGCATCAAAA
genomic: CAGAAACAAGAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATACAGgtagcttcat ... tcctatgcagGCATTGCTATTCGAAGAGTCAAAGTTTAAGGCATTTGATCTGGCATCAAAA

EST: gi|211140552|gb|FL174090.1|FL174090

EST:     CAGAAACAAGAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATACAG                         GCATTGCTATTCGAAGAGTCAAAGTTTAAGGCATTTGATCTGGCATCAAAA
genomic: CAGAAACAAGAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATACAGgtagcttcat ... tcctatgcagGCATTGCTATTCGAAGAGTCAAAGTTTAAGGCATTTGATCTGGCATCAAAA

EST: gi|16380015|gb|BI993261.1|BI993261

EST:     CAGAAACAAGAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATACAG                         GCATTGCTATTCGAAGAGTCAAAGTTTAAGGCATTTGATCTGGCATCAAAA
genomic: CAGAAACAAGAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATACAGgtagcttcat ... tcctatgcagGCATTGCTATTCGAAGAGTCAAAGTTTAAGGCATTTGATCTGGCATCAAAA

EST: gi|148955762|gb|EC901460.2|EC901460

EST:     CAGAAACAAGAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATACAG                         GCATTGCTATTCGAAGAGTCAAAGTTTAAGGCATTTGATCTGGCATCAAAA
genomic: CAGAAACAAGAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATACAGgtagcttcat ... tcctatgcagGCATTGCTATTCGAAGAGTCAAAGTTTAAGGCATTTGATCTGGCATCAAAA

EST: gi|32940932|gb|CF045751.1|CF045751

EST:     CAGAAACAAGAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATACAG                         GCATTGCTATTCGAAGAGTCAAAGTTTAAGGCATTTGATCTGGCATCAAAA
genomic: CAGAAACAAGAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATACAGgtagcttcat ... tcctatgcagGCATTGCTATTCGAAGAGTCAAAGTTTAAGGCATTTGATCTGGCATCAAAA

EST: gi|211028260|gb|FL437885.1|FL437885

EST:     CAGAAMCAAGAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATACAG                         GCATTGCTATTCGAAGAGTCAAAGTTTAAGGCATTTGATCTGGCATCAAAA
genomic: CAGAAACAAGAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATACAGgtagcttcat ... tcctatgcagGCATTGCTATTCGAAGAGTCAAAGTTTAAGGCATTTGATCTGGCATCAAAA

EST: gi|89762676|gb|DY690164.1|DY690164

EST:     CAGAAACAAGAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATACAG                         GCATTGCTATTCGAAGAGTCAAAGTTTAAGGCATTTTATCTGGCATCAA
genomic: CAGAAACAAGAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATACAGgtagcttcat ... tcctatgcagGCATTGCTATTCGAAGAGTCAAAGTTTAAGGCATTTGATCTGGCATCAA

EST: gi|5706289|gb|AI942065.1|AI942065

EST:     CAGAAACAAGAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATACAG                         GCATTGCTATTCGAAGAGTCAAAGTTTAAGGCATTTGATCTGGCATCAAAA
genomic: CAGAAACAAGAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATACAGgtagcttcat ... tcctatgcagGCATTGCTATTCGAAGAGTCAAAGTTTAAGGCATTTGATCTGGCATCAAAA

EST: gi|74243387|gb|DT651301.1|DT651301

EST:     CAGAAACAAGAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATACAG                         GCATTGCTATTCGAAGAGTCAAAGTTTAAGGCATTTGATCTGGCATCAAAA
genomic: CAGAAACAAGAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATACAGgtagcttcat ... tcctatgcagGCATTGCTATTCGAAGAGTCAAAGTTTAAGGCATTTGATCTGGCATCAAAA

EST: gi|16919596|gb|BM074268.1|BM074268

EST:     CAGAAACAAGAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATACAG                         GCATTGCTATTCGAAGAGTCAAAGTTTAAGGCATTTGATCTGGCATCAAAA
genomic: CAGAAACAAGAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATACAGgtagcttcat ... tcctatgcagGCATTGCTATTCGAAGAGTCAAAGTTTAAGGCATTTGATCTGGCATCAAAA

EST: gi|6742502|gb|AW313317.1|AW313317

EST:     CAGAAACAAGAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATACAG                         GCATTGCTATTCGAAGAGTCAAAGTTTAAGGCATTTGATCTGGCATCAAAA
genomic: CAGAAACAAGAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATACAGgtagcttcat ... tcctatgcagGCATTGCTATTCGAAGAGTCAAAGTTTAAGGCATTTGATCTGGCATCAAAA

EST: gi|91055640|gb|EB166058.1|EB166058

EST:     CAGAAACA-GAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATACAG                         GCATTGCTATTCGAAGAGTCAAAAGTT-AAGGCATTTGATCTGCCATCAAA
genomic: CAGAAACAAGAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATACAGgtagcttcat ... tcctatgcagGCATTGCTATTCGAAGAGTCAAA-GTTTAAGGCATTTGATCTGGCATCAAA

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: 48 (upstream exon), 48 (downstream exon)
Score: 64

TGGTGGCTTGCGAGAGTTGATTGTTGGGAAGGATGATGAGATCCTGAAAACAGAAACAAGAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATACAGgtagcttcat ... tcctatgcagGCATTGCTATTCGAAGAGTCAAAGTTTAAGGCATTTGATCTGGCATCAAAACCAGAAGGTGAAGGGACGCCAACTACAGACTTTAGGGCACTTTTTGCAC

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 458

Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 25

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 174

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGTGGCTTGCGAGAGTTGATTGTTGGGAAGGATGATGAGATCCTGAAAACAGAAACAAGAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATACAGgtagcttcatacagtggaagacacgtaactgtagatccatgcttttctcaaactcttgtgaaagtgctaactctatagtttgattgatctgtggctttcctatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT