ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
PPT, BS, UA-tract

Sequence

atgc intronic sequence ATGC exonic sequence

...ttgggagcttgttattttgcagtttctagattttgtgcatgttaagtatttctactactctcgtatttacttcatggaatctgtgcttatgattttacagGGGACTAGTCGACCTGCACATTATCATGTACTATGGGATGAAAATAAATTTTCTGCGGACAGTTTGCAGTCGTTGACAAACAATCTTTGCTATAC

Basic information

species	Physcomitrella patens
transcript	PP1S7_194V6.1
intron #	16
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: PP1S7_194V6.1 (Physcomitrella patens), 3'ss of exon 16
lower sequence: EFJ24991 (Selaginella moellendorffii), 3'ss of exon 20

ttgggagcttgttattttgcagtttctagattttgtgcatgttaagtatttctactactctcgtatttacttcatggaatctgtgcttatgattttacagGGGACTAGTCGACCTGCACATTATCATGTACTATGGGATGAAAATAAATTTTCTGCGGACAGTTTGCAGTCGTTGACAAACAATCTTTGCTATAC
                                       |   |||          |  ||  | |     | ||||    ||||  |  ||   | ||||| |||||||| || |||||||||||||| || ||||||||||| |  ||  | || ||  |||||||||| || || ||||| || ||||| ||
--------------------------------------gtacgaaggcacagcgtcaacctgat-tgaggctgatgg---ttgtgactgcgaccctgcagGGAACTAGTCGGCCGGCACATTATCATGTGCTTTGGGATGAAAACACTTTCACGGCTGATGGTTTGCAGTCATTAACGAACAACCTATGCTACAC

upper sequence: PP1S7_194V6.1 (Physcomitrella patens), 3'ss of exon 16
lower sequence: EFJ15357 (Selaginella moellendorffii), 3'ss of exon 20

ttgggagcttgttattttgcagtttctagattttgtgcatgttaagtatttctactactctcgtatttacttcatggaatctgtgcttatgattttacagGGGACTAGTCGACCTGCACATTATCATGTACTATGGGATGAAAATAAATTTTCTGCGGACAGTTTGCAGTCGTTGACAAACAATCTTTGCTATAC
                                       |   |||         ||  ||  | |     | ||||     |||  |  ||   ||||||| |||||||| || |||||||||||||| || ||||||||||| |  ||  | || ||  |||||||||| || || ||||| || ||||| ||
--------------------------------------gtacgaaggcacagcgttaacctgat-tgaggctgatgg---tcgtgactgcgaccctacagGGAACTAGTCGGCCGGCACATTATCATGTGCTTTGGGATGAAAACACTTTCACGGCTGATGGTTTGCAGTCATTAACGAACAACCTATGCTACAC

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|162272457|gb|FC449070.1|FC449070

EST:     GTCACCCTACGGAGTTTGACTTTTATCTTTGCAGTCATGCTGGAATTCAG                         GGGACTAGTCGACCTGCACATTATCATGTACTATGGGATGAAAATAAATTT
genomic: GTCACCCTACGGAGTTTGACTTTTATCTTTGCAGTCATGCTGGAATTCAGgttcatatcc ... gattttacagGGGACTAGTCGACCTGCACATTATCATGTACTATGGGATGAAAATAAATTT

EST: gi|162213696|gb|FC390311.1|FC390311

EST:     GTCACCCTACGGAGTTTGACTTTTATCTTTGCAGTCATGCTGGAATTCAG                         GGGACTAGTCGACCTGCACATTATCATGTACTATGGGATGAAAATAAATTT
genomic: GTCACCCTACGGAGTTTGACTTTTATCTTTGCAGTCATGCTGGAATTCAGgttcatatcc ... gattttacagGGGACTAGTCGACCTGCACATTATCATGTACTATGGGATGAAAATAAATTT

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: 18 (upstream exon), 35 (downstream exon)
Score: 4

GGACTGTTGTGGACTCGAAGATTTGTCACCCTACGGAGTTTGACTTTTATCTTTGCAGTCATGCTGGAATTCAGgttcatatcc ... gattttacagGGGACTAGTCGACCTGCACATTATCATGTACTATGGGATGAAAATAAATTTTCTGCGGACAGTTTGCAGTCGTTGACAAACAATCTTTGCTATAC

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atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

gtatttctactactctcgtatttacttcatggaatctgtgcttatgattttacagGGGACTAGTCGACCTGCACATTATCATGTACTATGGGATGAAAATAAATTTTCTGCGGACAGTTTGCAGTCGTTGACAAACAATCTTTGCTATAC