ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

ACTGGCTTTGCACATGGCTGCTGAGGCAAACAATCCGTATTTCCGCCTAGGTTACAACAGCTTGGGTGCATTTGCCACAATCAACCACTTGCATTTCCAGgtagagtacatgcccatgtagcaggttaagtctgctgtctctgacgctcaagctaattacgtgtagcaattgcgttcaaagaagtcaatgccgttgagag...

Basic information

species	Physcomitrella patens
transcript	PP1S9_179V6.1
intron #	5
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: PP1S9_179V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: GLYMA02G46230.1 (Glycine max), 5'ss of exon 5

ACTGGCTTTGCACATGGCTGCTGAGGCAAACAATCCGTATTTCCGCCTAGGTTACAACAGCTTGGGTGCATTTGCCACAATCAACCACTTGCATTTCCAGgtagagtacatgcccatgtagcaggttaagtctgctgtctctgacgctcaagctaattacgtgtagcaattgcgttcaaagaagtcaatgccgttgagag
 || ||  | || ||||| |  || ||  | ||||| ||||| ||  | |||||||||||||||||||| ||||| || ||||||||  | || |||||||||  | | |      | || ||     | |  |   | | ||| | |   | |  |||  | ||  |||    ||  ||   |   ||   |  |    
CCTTGCACTTCAGATGGCAGTGGAAGCCGATAATCCTTATTTTCGATTGGGTTACAACAGCTTGGGTGCTTTTGCAACTATCAACCATCTTCACTTCCAGgtactggatactgaattatacca---ctaataggtcatgt-tgatgattccgttgtttaattctacaaatctgattgcaatttggtgattttgcag----

upper sequence: PP1S9_179V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: GLYMA08G43200.1 (Glycine max), 5'ss of exon 6

ACTGGCTTTGCACATGGCTGCTGAGGCAAACAATCCGTATTTCCGCCTAGGTTACAACAGCTTGGGTGCATTTGCCACAATCAACCACTTGCATTTCCAGgtagagtacatgcccatgtagcaggttaagtctgctgt-ctctgacgctcaagctaatta----cgtgtagcaattgcgttcaaagaagtcaatgccgttgagag----------------------------
 || ||  | || ||||| ||||| || |  ||||| |||||  |  | |||||||||||||||||||||||||| || || |||||  | || || ||||||     |||  |||   | |  |  |   ||||  | |  |     | | | | ||||    | |||   |||     || |       |      || | |                             
GCTTGCACTTCAAATGGCCGCTGAAGCTAGGAATCCATATTTTAGGTTGGGTTACAACAGCTTGGGTGCATTTGCAACCATTAACCATCTCCACTTTCAGgta---cgcattaccaatcaactcgagatcactgcaatgcaatattctttatgttgattattggcttgttagaatccttatctagtgttctagcagtattcaaattgacattttttgattttgacgaactcag

upper sequence: PP1S9_179V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: GLYMA18G10430.1 (Glycine max), 5'ss of exon 5

ACTGGCTTTGCACATGGCTGCTGAGGCAAACAATCCGTATTTCCGCCTAGGTTACAACAGCTTGGGTGCATTTGCCACAATCAACCACTTGCATTTCCAGgtag--agtacatgcccatgtagca--ggttaagtctgctgtctctgacgctcaagctaattacgtgtagcaatt-gcgttcaa--agaagtcaa--tgccgttgagag----------------
 || ||  | || ||||| | ||| ||||  ||||| |||||  |  | |||||||||||||||||||||||||| || || |||||  | || || ||||||   | |||    | |      |    |  | |   || |   | | | | |   || |  | |||   |||| | |||| |  || | ||||  || | ||  | |                
GCTTGCACTTCAAATGGCAGTTGAAGCAAGGAATCCATATTTTAGGTTGGGTTACAACAGCTTGGGTGCATTTGCAACCATTAACCATCTCCACTTTCAGgtactcattactgatcaactcgagatcactgcaatgcactattcttcatgttga--ttattggcttgtttgaattagtgttctagcagtattcaaattgacattttgtgattttgacaaacccag

upper sequence: PP1S9_179V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: AT4G26850.1 (Arabidopsis thaliana), 5'ss of exon 5

ACTGGCTTTGCACATGGCTGCTGAGGCAAACAATCCGTATTTCCGCCTAGGTTACAACAGCTTGGGTGCATTTGCCACAATCAACCACTTGCATTTCCAGgtagagtacatgcccatgtagcaggttaagtctgctgtctctgacgctcaagctaattacgtgtagcaattgcgttcaaagaagtcaatgccgttgagag
 || ||  | |||||||||||||||||    ||||| || ||| | || |||||||||||||||||||| |||||||| ||||| ||  | || || ||||||   ||        ||   || |   |  ||  |  | ||   |||||    |  |   |||    ||||  ||    |   |   |   |   | ||
GCTTGCAGTTCACATGGCTGCTGAGGCTGCTAATCCATACTTCAGACTCGGTTACAACAGCTTGGGTGCTTTTGCCACTATCAATCATCTCCACTTTCAGgta---tatccaaaagtgatccaagcataaccttttcaccct--tgctcatctaagatgtttgttctgattgttttggtggtgattgtttttggaaacag

upper sequence: PP1S9_179V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: Vv19s0090g01000.t01 (Vitis vinifera), 5'ss of exon 5

ACTGGCTTTGCACATGGCTGCTGAGGCAAACAATCCGTATTTCCGCCTAGGTTACAACAGCTTGGGTGCATTTGCCACAATCAACCACTTGCATTTCCAGgtagagtacatgcccatgtagcaggttaagtctgctgtctctgacgctcaagctaattacgtgtagcaattgcgttcaaagaagtcaatgccgttgagag
 || ||  |  |||||||||  || |||   ||||| ||||||||  | |||||||||||||||||||||||||| || ||||||||| | || || |||||    | |   | ||  |   |  |  | ||      || | |   |    | | |      |   |  ||  ||| |  |  |  |||          
GCTTGCCCTTGACATGGCTGTGGAAGCAGGAAATCCATATTTCCGGTTGGGTTACAACAGCTTGGGTGCATTTGCTACCATCAACCACCTTCACTTTCAGgtttctttccacctcacctttgaactgcaatcattgtactataaaattggctccattggttaatgaaatatgaattccataactttcatggtaacag---

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|162152165|gb|FC328755.1|FC328755

EST:     GTT-CAACAGCTTGGGTGCATTTGCCACAATCAACCACTTGCATTTCCAG                         GCCTACTATCTGGCAGCTCCCTTTCCGATTGAAAGAGCACCTACTGTGCGA
genomic: GTTACAACAGCTTGGGTGCATTTGCCACAATCAACCACTTGCATTTCCAGgtagagtaca ... ggacttgcagGCCTACTATCTGGCAGCTCCCTTTCCGATTGAAAGAGCACCTACTGTGCGA

EST: gi|19783742|gb|BQ040061.1|BQ040061

EST:     GTTACAACAGCTTGGGTGCATTTGCCACAATCAACCACTTGCATTTCCAG                         GCCTACTATCTGGCAGCTCCCTTTCCGATTGAAAGAGCACCTACTGTGCGA
genomic: GTTACAACAGCTTGGGTGCATTTGCCACAATCAACCACTTGCATTTCCAGgtagagtaca ... ggacttgcagGCCTACTATCTGGCAGCTCCCTTTCCGATTGAAAGAGCACCTACTGTGCGA

EST: gi|100439484|gb|BY961956.1|BY961956

EST:     GTTACAACAGCTTGGGTGCATTTGCCACAATCAACCACTTGCATTTCCAG                         GCCTACTATCTGGCAGCTCCCTTTCCGATTGAAAGAGCACCTACTGTGCGA
genomic: GTTACAACAGCTTGGGTGCATTTGCCACAATCAACCACTTGCATTTCCAGgtagagtaca ... ggacttgcagGCCTACTATCTGGCAGCTCCCTTTCCGATTGAAAGAGCACCTACTGTGCGA

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 1 RNA-Seqlibrary.

Block sizes: 35 (upstream exon), 35 (downstream exon)
Score: 130

ACTGGCTTTGCACATGGCTGCTGAGGCAAACAATCCGTATTTCCGCCTAGGTTACAACAGCTTGGGTGCATTTGCCACAATCAACCACTTGCATTTCCAGgtagagtaca ... ggacttgcagGCCTACTATCTGGCAGCTCCCTTTCCGATTGAAAGAGCACCTACTGTGCGAATCCCCTACGGCAGAAAGAAAGGTGGTGTCAAAGTGTACGAGCTTACCG