ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

CGCACTGGGTCCCGAGGTCAGGTGACCCAAGTTCGTGTTAAGTTTCTGGATGATCAAAATCGACTCATTATGCGCAATGTGAAGGGGCCAGTGCGTGAAGgtacagagtcctggaacttttgtcatgttcttctctaacccaccatggtgtgatctccatcatattgaagcttcttttatattcaaggatctttcagggg...

Basic information

species	Physcomitrella patens
transcript	PP1S41_71V6.1
intron #	2
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: PP1S41_71V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: EFJ30111 (Selaginella moellendorffii), 5'ss of exon 2

CGCACTGGGTCCCGAGGTCAGGTGACCCAAGTTCGTGTTAAGTTTCTGGATGATCAAAATCGACTCATTATGCGCAATGTGAAGGGGCCAGTGCGTGAAGgtacagagtcctggaacttttgtcatgttcttctctaacccaccatggtgtgatctccatcatattgaagcttcttttatattcaaggatctttcagggg
 | || || || || || || ||||||||||| || || ||||| ||||| || || ||||| ||||| ||||||||||| ||||||||  | || |||||||   ||  || ||             || |||| | |  | |   |  ||||||        |||  |||  |||  | |  |               
AGGACGGGATCTCGCGGGCAAGTGACCCAAGTCCGGGTGAAGTTCCTGGACGACCAGAATCGTCTCATCATGCGCAATGTCAAGGGGCCGATCCGCGAAGgta---agctctcga-------------tcctctcgatcgaatcgaagattgatct--------ttggggctaatttcttgtgtag--------------

upper sequence: PP1S41_71V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: EFJ08290 (Selaginella moellendorffii), 5'ss of exon 2

CGCACTGGGTCCCGAGGTCAGGTGACCCAAGTTCGTGTTAAGTTTCTGGATGATCAAAATCGACTCATTATGCGCAATGTGAAGGGGCCAGTGCGTGAAGgtacagagtcctggaacttttgtcatgttcttctctaacccaccatggtgtgatctccatcatattgaagcttcttttatattcaaggatctttcagggg
 | || || || || || || ||||||||||| || || ||||| ||||| || || ||||| ||||| ||||||||||| ||||||||  | || |||||||   ||  || ||             || |||| | |  | |   |  ||||||       |    |  ||||| | ||                   
AGGACGGGATCTCGCGGGCAAGTGACCCAAGTCCGGGTGAAGTTCCTGGACGACCAGAATCGTCTCATCATGCGCAATGTCAAGGGGCCGATCCGCGAAGgta---agctctcga-------------tcctctcgatcgaatcgaagattgatctttggggca----aatttcttgtgtag------------------

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|162236258|gb|FC412014.1|FC412014

EST:     TGATCAAAATCGACTCATTATGCGCAATGTGAAGGGGCCAGTGCGTGAAG                         GTGACATCCTGACTCTCCTGGAGTCTGAGAGAGAGGCTAGGAGGCTGCGGT
genomic: TGATCAAAATCGACTCATTATGCGCAATGTGAAGGGGCCAGTGCGTGAAGgtacagagtc ... ttgtatacagGTGACATCCTGACTCTCCTGGAGTCTGAGAGAGAGGCTAGGAGGCTGCGGT

EST: gi|15727821|gb|BI740480.1|BI740480

EST:     TGATCAAAATCGACTCATTATGCGCAATGTGAAGGGGCCAGTGCGTGAAG                         GTGACATCCTGACTCTCCTGGAGTCTGAGAGAGAGGCTAGGAGGCTGCGGT
genomic: TGATCAAAATCGACTCATTATGCGCAATGTGAAGGGGCCAGTGCGTGAAGgtacagagtc ... ttgtatacagGTGACATCCTGACTCTCCTGGAGTCTGAGAGAGAGGCTAGGAGGCTGCGGT

EST: gi|67695413|gb|BJ955646.1|BJ955646

EST:     TGATCAAAATCGACTCATTATGCGCAATGTGAAGGGGCCAGTGCGTGAAG                         GTGACATCCTGACTCTCCTGGAGTCTGAGAGAGAGGCTAGGAGGCTGCGGT
genomic: TGATCAAAATCGACTCATTATGCGCAATGTGAAGGGGCCAGTGCGTGAAGgtacagagtc ... ttgtatacagGTGACATCCTGACTCTCCTGGAGTCTGAGAGAGAGGCTAGGAGGCTGCGGT

EST: gi|15727930|gb|BI740534.1|BI740534

EST:     TGATCAAAATCGACTCATTATGCGCAATGTGAAGGGGCCAGTGCGTGAAG                         GTGACATCCTGACTCTCCTGGAGTCTGAGAGAGAGGCTAGGAGGCTGCGGT
genomic: TGATCAAAATCGACTCATTATGCGCAATGTGAAGGGGCCAGTGCGTGAAGgtacagagtc ... ttgtatacagGTGACATCCTGACTCTCCTGGAGTCTGAGAGAGAGGCTAGGAGGCTGCGGT

EST: gi|67572047|gb|BJ944871.1|BJ944871

EST:     TGATCAAAATCGACTCATTATGCGCAATGTGAAGGGGCCAGTGCGTGAAG                         GTGACATCCTGACTCTCCTGGAGTCTGAGAGAGAGGCTAGGAGGCTGCGGT
genomic: TGATCAAAATCGACTCATTATGCGCAATGTGAAGGGGCCAGTGCGTGAAGgtacagagtc ... ttgtatacagGTGACATCCTGACTCTCCTGGAGTCTGAGAGAGAGGCTAGGAGGCTGCGGT

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-Seq library.

Block sizes: 32 (upstream exon), 35 (downstream exon)
Score: 8