ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GAGATTGATAGATCCTCAAGGGAAACCACCCGGAGTGATGGGCTGGTGGCCTTCTCGTGCAGTCACGTTCCTTGAGAACCATGACACCGGATCAACGCAGgtttgcactctatctaccattctagacttgatctatttggtaaccgtaagtatctagttagataattttagtcctgtatgctacaaaccactacaatcgtcgtccttgagtacttgacatgaccctgatagtgccatacgttactgttttcag

Basic information

species	Physcomitrella patens
transcript	PP1S342_20V6.1
intron #	15
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: PP1S342_20V6.1 (Physcomitrella patens), 5'ss of exon 15
lower sequence: GLYMA08G26860.1 (Glycine max), 5'ss of exon 10

GAGATTGATAGATCCTCAAGGGAAACCACCCGGAGTGATGGGCTGGTGGCCTTCTCGTGCAGTCACGTTCCTTGAGAACCATGACACCGGATCAACGCAGgtttgcactctatctaccattctagacttgatctatttggtaaccgtaagtatctagttagataattttagtcctgtatgctacaaaccactacaatcgtcgtccttgagtacttgacatgaccctgatagtgccatacgttactgttttcag
|||| ||||||||||||||||||||||| | ||||||||||| |||||| |||||||||| || || ||||| ||||||||||| ||||| || || || || || ||||| |||     |||   ||  |   |      |  | || || | |  || |||   |||    ||  |  || |||     ||         |||                                                
GAGACTGATAGATCCTCAAGGGAAACCAACAGGAGTGATGGGATGGTGGGCTTCTCGTGCTGTTACATTCCTAGAGAACCATGATACCGGGTCCACACAAgtatgaactctctctctttctct---ctccacacacgca-cactcatatgtttatcttttgattcatttgactct-cacact-caagtacttatgggaaatttccc-----------------------------------------------

upper sequence: PP1S342_20V6.1 (Physcomitrella patens), 5'ss of exon 15
lower sequence: Vv14s0068g00420.t01 (Vitis vinifera), 5'ss of exon 12

GAGATTGATAGATCCTCAAGGGAAACCACCCGGAGTGATGGGCTGGTGGCCTTCTCGTGCAGTCACGTTCCTTGAGAACCATGACACCGGATCAACGCAGgtttgcactctatctaccattctagacttgatctatttg-gtaaccgtaagtatctagttagataattttagtcctgtatgctacaaaccactacaatcgtcgtccttgagtacttgacatgaccctgatagtgccatacgttactgttttcag
||| ||||||||||||||||| |||||| | |||||  |||| ||||||||||| || || ||||| ||  | || |||||||| || || ||||| ||||||  | |||| |||  |  |||     | |   |  ||   |  |  |   |   | | |  | || |  |   |||||   | |||  |  |  ||  |                                                     
GAGGTTGATAGATCCTCAAGGAAAACCAACAGGAGTAGTGGGATGGTGGCCTTCACGCGCTGTCACATTTTTGGAAAACCATGATACTGGGTCAACACAGgttctctctctctctctctctctctctatcacgcacatgcacatacacacacacacactcactttatctagggtatgtat-tgataaattagaatgattct-----------------------------------------------------

upper sequence: PP1S342_20V6.1 (Physcomitrella patens), 5'ss of exon 15
lower sequence: EFJ10742 (Selaginella moellendorffii), 5'ss of exon 8

GAGATTGATAGATCCTCAAGGGAAACCACCCGGAGTGATGGGCTGGTGGCCTTCTCGTGCAGTCACGTTCCTTGAGAACCATGACACCGGATCAACGCAGgtttgcactctatctaccattctagacttgatctatttggtaaccgtaagtatctagttagataattttagtcctgtatgctacaaaccactacaatcgtcgtccttgagtacttgacatgaccctgatagtgccatacgttactgttttcag
|||| | || ||||| | |  |||||| || || || |||||||||||||||||  | || || || |||||||||||||| ||||| |||||||| |||||  ||  |||  |     |||  ||             || || | |||| | || |  |  |                                                                                         
GAGACTCATTGATCCACGACAGAAACCCCCTGGTGTTATGGGCTGGTGGCCTTCGAGAGCGGTAACATTCCTTGAGAACCACGACACAGGATCAACTCAGgtacgccgtcttgcatgagttcctga------------agtgactgaaagtttttattctggcacag--------------------------------------------------------------------------------------

upper sequence: PP1S342_20V6.1 (Physcomitrella patens), 5'ss of exon 15
lower sequence: EFJ07538 (Selaginella moellendorffii), 5'ss of exon 8

GAGATTGATAGATCCTCAAGGGAAACCACCCGGAGTGATGGGCTGGTGGCCTTCTCGTGCAGTCACGTTCCTTGAGAACCATGACACCGGATCAACGCAGgtttgcactctatctaccattctagacttgatctatttggtaaccgtaagtatctagttagataattttagtcctgtatgctacaaaccactacaatcgtcgtccttgagtacttgacatgaccctgatagtgccatacgttactgttttcag
|||| | || ||||| | |  |||||| || || || |||||||||||||||||  | || || || |||||||||||||| ||||| |||||||| |||||    || |  |||  |||    || ||  || |    || || | |||| | || |  |  |                                                                                         
GAGACTCATTGATCCACGACAGAAACCCCCTGGTGTTATGGGCTGGTGGCCTTCGAGAGCGGTAACATTCCTTGAGAACCACGACACAGGATCAACTCAGgt----acgccgtcttgcat----gagttcctcaa----gtgactgaaagtttttattccggcacag--------------------------------------------------------------------------------------

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|37832216|gb|BJ590228.1|BJ590228

EST:     CTTCTCGTGCAGTCACGTTCCTTGAGAACCATGACACCGGATCAACGCAG                         GGTCATTGGCCATTCCCTCGCGACAAGCTAATGATGGGTTATGCGTACATC
genomic: CTTCTCGTGCAGTCACGTTCCTTGAGAACCATGACACCGGATCAACGCAGgtttgcactc ... ctgttttcagGGTCATTGGCCATTCCCTCGCGACAAGCTAATGATGGGTTATGCGTACATC

EST: gi|162150178|gb|FC326055.1|FC326055

EST:     CTTCTCGTGCAGTCACGTTCCTTGAGAACCATGACACCGGATCAACGCAG                         GGTCATTGGCCATTCCCTCGCGACAAGCTAATGATGGGTTATGCGTACATC
genomic: CTTCTCGTGCAGTCACGTTCCTTGAGAACCATGACACCGGATCAACGCAGgtttgcactc ... ctgttttcagGGTCATTGGCCATTCCCTCGCGACAAGCTAATGATGGGTTATGCGTACATC

EST: gi|162163444|gb|FC339978.1|FC339978

EST:     CTTCTCGTGCAGTCACGTTCCTTGAGAACCATGACACCGGATCAACGCAG                         GGTCATTGGCCATTCCCTCGCGACAAGCTAATGATGGGTTATGCGTACATC
genomic: CTTCTCGTGCAGTCACGTTCCTTGAGAACCATGACACCGGATCAACGCAGgtttgcactc ... ctgttttcagGGTCATTGGCCATTCCCTCGCGACAAGCTAATGATGGGTTATGCGTACATC

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), 31 (downstream exon)
Score: 4

GAGATTGATAGATCCTCAAGGGAAACCACCCGGAGTGATGGGCTGGTGGCCTTCTCGTGCAGTCACGTTCCTTGAGAACCATGACACCGGATCAACGCAGgtttgcactc ... ctgttttcagGGTCATTGGCCATTCCCTCGCGACAAGCTAATGATGGGTTATGCGTACATCTTAACACACCCTGGCACA