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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCTAAGAAGGATAACTTGTACAAGGATGCCATGGAAACCGCCTCACAATCAGGCGATCGTGATCTTGCTGAGGAATTGCTTACCTTCTTTGTGGACAAGgtagctaattgatttatgttatcattatttggctaaggcttatgcatattaaaataaattaattgattctaattctgcgtattgggatgtatgacacag

Basic information

species Physcomitrella patens
transcript PP1S452_30V6.1
intron # 27
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S452_30V6.1 (Physcomitrella patens), 5'ss of exon 27
lower sequence: GLYMA02G42560.1 (Glycine max), 5'ss of exon 27
TTCTAAGAAGGATAACTTGTACAAGGATGCCATGGAAACCGCCTCACAATCAGGCGATCGTGATCTTGCTGAGGAATTGCTTACCTTCTTTGTGGACAAGgtagctaattgatttatgttatcattatttggctaaggcttatgca-tattaaaataaattaa--ttgattctaattctgcgtattgggatgtatgacacag
 || |||||||||||| | ||||| ||||||||||| || ||||||||||| ||||| ||||| ||||||||||| ||||||   |  ||  | ||  ||||    |||| | ||      |   ||| |   | |   |  |||| |||     |  ||||   ||     || |  ||  || || | | | |   |   
GTCAAAGAAGGATAACCTTTACAAAGATGCCATGGAGACAGCCTCACAATCTGGCGAGCGTGAACTTGCTGAGGAGTTGCTTGTTTATTTCATTGATCAGgtgctaaattcagtttcaaacttcatatataattcattttcttgcaatatcttgtttgattaggtttaccattattcttggataatgtgttttgtttaat--

upper sequence: PP1S452_30V6.1 (Physcomitrella patens), 5'ss of exon 27
lower sequence: GLYMA18G02960.1 (Glycine max), 5'ss of exon 26
TTCTAAGAAGGATAACTTGTACAAGGATGCCATGGAAACCGCCTCACAATCAGGCGATCGTGATCTTGCTGAGGAATTGCTTACCTTCTTTGTGGACAAGgtagctaatt-gatttatgt----tatcattatttggctaaggcttatgcatattaaaataaattaattgattctaattctgcgtattgggatgtatgacacag
 || |||||||||||| | ||||| ||||||||||| || ||||| ||||| || || ||||| ||||||||||| ||||||   |  ||  | ||  ||||  | ||||  ||||   |    ||| |||  ||   ||       |||  |  | |  |   | || ||||    ||   |  |||   || ||  |     
-TCAAAGAAGGATAACCTTTACAAAGATGCCATGGAGACAGCCTCGCAATCTGGTGACCGTGAACTTGCTGAGGAGTTGCTTGTTTATTTCATTGATCAGGtgccaaattcaatttcaatggcatataattcattttttagcaacattgcccagcagaccagcattat-gatttgggttg-actcattctcatttaacatttt-

upper sequence: PP1S452_30V6.1 (Physcomitrella patens), 5'ss of exon 27
lower sequence: GLYMA14G06340.1 (Glycine max), 5'ss of exon 27
TTCTAAGAAGGATAACTTGTACAAGGATGCCATGGAAACCGCCTCACAATCAGGCGATCGTGATCTTGCTGAGGAATTGCTTACCTTCTTTGTGGACAAGgtagctaattgattta--tgttat-cattatttggctaaggcttatgc-atattaaaataaattaattgattctaattctgcgtattgggatgtatgacacag
 || |||||||||||| | ||||| ||||||||||| || ||||| ||||| || || ||||| ||||||||||| ||||||   |  ||  | ||  ||||    |||| ||||   ||  ||   |||||||  || |  |  ||  ||  |   ||||  |  ||  || ||||| |   || ||  ||   |    || 
GTCAAAGAAGGATAACCTTTACAAAGATGCCATGGAGACAGCCTCCCAATCCGGGGAGCGTGAACTTGCTGAGGAGTTGCTTGTTTATTTCATTGATCAGgtgctaaattcattttcttgcaatatcttatttgattaggtttactgttattcttggataatgtgttttgtt-taattgt-tataatgtcatactttgtgca-

upper sequence: PP1S452_30V6.1 (Physcomitrella patens), 5'ss of exon 27
lower sequence: GLYMA11G35460.1 (Glycine max), 5'ss of exon 26
TTCTAAGAAGGATAACTTGTACAAGGATGCCATGGAAACCGCCTCACAATCAGGCGATCGTGATCTTGCTGAGGAATTGCTTACCTTCTTTGTGGACAAGgtagctaattgatttatgt-----tatcattatttggctaaggcttatgcatattaaaataaattaattgattctaattctgcgtattgggatg-tatgacacag
 || ||||| |||||| | ||||| ||||||||||| || ||||||||||| || || ||||| ||||||||||| ||||||   |  ||  | ||  ||||| | |||| | ||         ||| |||  ||   ||       |||  |  |   | | ||||    || ||  | ||   | |  |||| || |  |   
GTCAAAGAAAGATAACCTTTACAAAGATGCCATGGAGACAGCCTCACAATCTGGTGACCGTGAACTTGCTGAGGAGTTGCTTGTTTATTTCATTGATCAGgtaccaaattcaatttcaacggcatataattcattttttagcaacattgcccagcattctcatttaacatgtttta--tttgaagactaagatgctaagcta---

upper sequence: PP1S452_30V6.1 (Physcomitrella patens), 5'ss of exon 27
lower sequence: GLYMA14G06340.2 (Glycine max), 5'ss of exon 27
TTCTAAGAAGGATAACTTGTACAAGGATGCCATGGAAACCGCCTCACAATCAGGCGATCGTGATCTTGCTGAG--GAATTGC-TTACCTTCTTTGTGGACAAGgtagctaattgatttatgttatc-attatttggctaaggcttatgcatattaaaataaattaattgattctaattctgcgtattgggatgtatgacacag---
                                                ||      | | ||| |||  ||||  ||   |  || |    | | |  |||||   ||   | | |  | |   || |||  || |  || |       |  || | | | ||    ||     |      |     |||  |  |||    |   
------------------------------------------------ATTGAA-AAGCATGAGCTTCTTGAGATGAGACGTGTTGCTGCTTATATTTACAAGAAGgcaggtaggtggaagcagtctattgctttgtcaaagaaggataacctttacaaagatgccatggagacagcctcccaatccggggagcgtgaacttgctg

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|162243866|gb|FC423183.1|FC423183
EST:     CAGGCGATCGTGATCTTGCTGAGGAATTGCTTACCTTCTTTGTGGACAAG                         GGCAAGAAAGAATGCTTTGCTGCATGCCTATACACCTGTTACGATCTCATT
genomic: CAGGCGATCGTGATCTTGCTGAGGAATTGCTTACCTTCTTTGTGGACAAGgtagctaatt ... tatgacacagGGCAAGAAAGAATGCTTTGCTGCATGCCTATACACCTGTTACGATCTCATT
EST: gi|162195289|gb|FC369276.1|FC369276
EST:     CAGGCGATCGTGATCTTGCTGAGGAATTGCTTACCTTCTTTGTGGACAAG                         GGCAAGAAAGAATGCTTTGCTGCATGCCTATACACCTGTTACGATCTCATT
genomic: CAGGCGATCGTGATCTTGCTGAGGAATTGCTTACCTTCTTTGTGGACAAGgtagctaatt ... tatgacacagGGCAAGAAAGAATGCTTTGCTGCATGCCTATACACCTGTTACGATCTCATT
EST: gi|162150854|gb|FC327334.1|FC327334
EST:     CAGGCGATCGTGATCTTGCTGAGGAATTGCTTACCTTCTTTGTGGACAAG                         GGCAAGAAAGAATGCTTTGCTGCATGCCTATACACCTGTTACGATCTCATT
genomic: CAGGCGATCGTGATCTTGCTGAGGAATTGCTTACCTTCTTTGTGGACAAGgtagctaatt ... tatgacacagGGCAAGAAAGAATGCTTTGCTGCATGCCTATACACCTGTTACGATCTCATT
EST: gi|162227861|gb|FC403669.1|FC403669
EST:     CAGGCGATCGTGATCTTGCTGAGGAATTGCTTACCTTCTTTGTGGACAAG                         GGCAAGAAAGAATGCTTTGCTGCATGCCTATACACCTGTTACGATCTCATT
genomic: CAGGCGATCGTGATCTTGCTGAGGAATTGCTTACCTTCTTTGTGGACAAGgtagctaatt ... tatgacacagGGCAAGAAAGAATGCTTTGCTGCATGCCTATACACCTGTTACGATCTCATT
EST: gi|162243367|gb|FC417068.1|FC417068
EST:     CAGGCGATCGTGATCTTGCTGAGGAATTGCTTACCTTCTTTGTGGACAAG                         GGCAAGAAAGAATGCTTTGCTGCATGCCTATACACCTGTTACGATCTCATT
genomic: CAGGCGATCGTGATCTTGCTGAGGAATTGCTTACCTTCTTTGTGGACAAGgtagctaatt ... tatgacacagGGCAAGAAAGAATGCTTTGCTGCATGCCTATACACCTGTTACGATCTCATT
EST: gi|162172579|gb|FC348624.1|FC348624
EST:     CAGGCGATCGTGATCTTGCTGAGGAATTGCTTACCTTCTTTGTGGACAAG                         GGCAAGAAAGAATGCTTTGCTGCATGCCTATACACCTGTTACGATCTCATT
genomic: CAGGCGATCGTGATCTTGCTGAGGAATTGCTTACCTTCTTTGTGGACAAGgtagctaatt ... tatgacacagGGCAAGAAAGAATGCTTTGCTGCATGCCTATACACCTGTTACGATCTCATT
EST: gi|162271744|gb|FC448877.1|FC448877
EST:     CAGGCGATCGTGATCTTGCTGAGGAATTGCTTACCTTCTTTGTGGACAAG                         GGCAAGAAAGAATGCTTTGCTGCATGCCTATACACCTGTTACGATCTCATT
genomic: CAGGCGATCGTGATCTTGCTGAGGAATTGCTTACCTTCTTTGTGGACAAGgtagctaatt ... tatgacacagGGCAAGAAAGAATGCTTTGCTGCATGCCTATACACCTGTTACGATCTCATT
EST: gi|162211494|gb|FC387366.1|FC387366
EST:     CAGGCGATCGTGATCTTGCTGAGGAATTGCTTACCTTCTTTGTGGACAAG                         GGCAAGAAAGAATGCTTTGCTGCATGCCTATACACCTGTTACGATCTCATT
genomic: CAGGCGATCGTGATCTTGCTGAGGAATTGCTTACCTTCTTTGTGGACAAGgtagctaatt ... tatgacacagGGCAAGAAAGAATGCTTTGCTGCATGCCTATACACCTGTTACGATCTCATT

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: 24

TTCTAAGAAGGATAACTTGTACAAGGATGCCATGGAAACCGCCTCACAATCAGGCGATCGTGATCTTGCTGAGGAATTGCTTACCTTCTTTGTGGACAAGgtagctaatt ... tatgacacagGGCAAGAAAGAATGCTTTGCTGCATGCCTATACACCTGTTACGATCTCATTCGTGCTGATGTTGCGGTGGAGCTCGCCTGGATGCATGGCATGATGGATT




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