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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgtattcttctccatttgttttatcatgacccgaatatgttgcctttgatagtataaccatcttccagttattttactcttggtctcaaatcacaaaggaacatttgcatttacaaataagttttctgtgtgcagGCATTTGCATCACAGTTCACATACTGTGCTCAAGAGCTGGGACTAGATGAAGAGAAGGTGAATGTGAATGGAGGTGCTATGGCTCTTGGTCATCCTCTTG

Basic information

species Physcomitrella patens
transcript PP1S55_275V6.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S55_275V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: Vv07s0005g05610.t01 (Vitis vinifera), 3'ss of exon 11
gttgtattcttctccatttgttttatcatgacccgaatatgttgcctttgatagtataaccatcttccagttattttactcttggtctcaaatcacaaaggaacatttgcatttacaaataagttttctgtgtgcagGCATTTGCATCACAGTTCACATACTGTGCTCAAGAGCTGGGACTAGATGAAGAGAAGGTGAATGTGAATGGAGGTGCTATGGCTCTTGGTCATCCTCTTG
                         |  |||   | ||   || |  |   || ||| || |      | ||| | |    ||    ||||    || | |||  |  ||| ||   |    | | | | | |||||||||||||||| || |    ||||||   | |  | ||||  || |||    | ||||| ||||| |||||||||||| |||||||||| ||||| || |
------------------------gtattgatttggatg-atttctataattattatgacaa------aattagtat----ttaaattcaag---catatgaaagtgggcaattctgat---gctctttatatgcagGCATTTGCATCCCAATATGTATACTGCTGTAAGAAACTGGATCTTGATCCTAAAAAGGTCAATGTTAATGGAGGTGCTTTGGCTCTTGGGCATCCCCTGG
















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|208361705|gb|DC954139.1|DC954139
EST:     AGGCAGCTGGCCTAGAGCTCAGCGACATCGACCTTTTTGAAATCAACGAG                         GCATTTGCATCACAGTTCACATACTGTGCTCAAGAGCTGGGGCTAGATGAA
genomic: AGGCAGCTGGCCTAGAGCTCAGCGACATCGACCTTTTTGAAATCAACGAGgttgtattct ... ctgtgtgcagGCATTTGCATCACAGTTCACATACTGTGCTCAAGAGCTGGGACTAGATGAA
EST: gi|18335020|gb|BJ167038.1|BJ167038
EST:     AGGCAGCTGGCCTAGAGCTCAGCGACATCGACCTTTTTGAAATCAACGAG                         GCATTTGCATCACAGTTCACATACTGTGCTCAAGAGCTGGGACTAGATGAA
genomic: AGGCAGCTGGCCTAGAGCTCAGCGACATCGACCTTTTTGAAATCAACGAGgttgtattct ... ctgtgtgcagGCATTTGCATCACAGTTCACATACTGTGCTCAAGAGCTGGGACTAGATGAA
EST: gi|67699972|gb|BJ960205.1|BJ960205
EST:     AGGCAGCTGGCCTAGAGCTCAGCGACATCGACCTTTTTGAAATCAACGAG                         GCATTTGCATCACAGTTCACATACTGTGCTCAAGAGCTGGGACTAGATGAA
genomic: AGGCAGCTGGCCTAGAGCTCAGCGACATCGACCTTTTTGAAATCAACGAGgttgtattct ... ctgtgtgcagGCATTTGCATCACAGTTCACATACTGTGCTCAAGAGCTGGGACTAGATGAA
EST: gi|162233183|gb|FC409006.1|FC409006
EST:     AGGCAGCTGGCCTAGAGCTCAGCGATATCGACCTTTTTGAAATCAACGAG                         GCATTTGCATCACAGTTCACATACTGTGCTCAAGAGCTGGGACTAGATGAA
genomic: AGGCAGCTGGCCTAGAGCTCAGCGACATCGACCTTTTTGAAATCAACGAGgttgtattct ... ctgtgtgcagGCATTTGCATCACAGTTCACATACTGTGCTCAAGAGCTGGGACTAGATGAA
EST: gi|18334159|gb|BJ166175.1|BJ166175
EST:     AGGCAGCTGGCCTAGAGCTCAGCGACATCGACCTTTTTGAAATCAACGAG                         GCATTTGCATCACAGTTCACATACTGTGCTCAAGAGCTGGGACTAGATGAA
genomic: AGGCAGCTGGCCTAGAGCTCAGCGACATCGACCTTTTTGAAATCAACGAGgttgtattct ... ctgtgtgcagGCATTTGCATCACAGTTCACATACTGTGCTCAAGAGCTGGGACTAGATGAA
EST: gi|162211009|gb|FC387315.1|FC387315
EST:     AGGCAGCTGGCCTAGAGCTCAGCGATATCGACCTTTTTGAAATCAACGAG                         GCATTTGCATCACAGTTCACATACTGTGCTCAAGAGCTGGGACTAGATGAA
genomic: AGGCAGCTGGCCTAGAGCTCAGCGACATCGACCTTTTTGAAATCAACGAGgttgtattct ... ctgtgtgcagGCATTTGCATCACAGTTCACATACTGTGCTCAAGAGCTGGGACTAGATGAA
EST: gi|162211010|gb|FC387316.1|FC387316
EST:     AGGCAGCTGGCCTAGAGCTCAGCGATATCGACCTTTTTGAAATCAACGAG                         GCATTTGCATCACAGTTCACATACTGTGCTCAAGAGCTGGGACTAGATGAA
genomic: AGGCAGCTGGCCTAGAGCTCAGCGACATCGACCTTTTTGAAATCAACGAGgttgtattct ... ctgtgtgcagGCATTTGCATCACAGTTCACATACTGTGCTCAAGAGCTGGGACTAGATGAA
EST: gi|208379163|gb|DC927306.1|DC927306
EST:     AGGCAGCTGGCCTAGAGCTCAGCGACATCGACCTTTTTGAAATCAACGAG                         GCATTTGCATCACAGTTCACATACTGTGCTCAAGAGCTGGGACTAGATGAA
genomic: AGGCAGCTGGCCTAGAGCTCAGCGACATCGACCTTTTTGAAATCAACGAGgttgtattct ... ctgtgtgcagGCATTTGCATCACAGTTCACATACTGTGCTCAAGAGCTGGGACTAGATGAA
EST: gi|37826209|gb|BJ584221.1|BJ584221
EST:     GGCAGCTGGCCTAGAGCTCAGCGACATCGACCTTTTTTGAAATCAACGAG                         GCATTTGCATCACAGTTCACATACTGTGCTCAAGAGCTGGGACTAGATGAA
genomic: GGCAGCTGGCCTAGAGCTCAGCGACATCGACC-TTTTTGAAATCAACGAGgttgtattct ... ctgtgtgcagGCATTTGCATCACAGTTCACATACTGTGCTCAAGAGCTGGGACTAGATGAA
EST: gi|67700189|gb|BJ960422.1|BJ960422
EST:     AGGCAGCTGGCCTAGAGCTCAGCGACATCGACCTTTTTGAAATCAACGAG                         GCATTTGCATCACAGTTCACATACTGTGCTCAAGAGCTGGGACTAGATGAA
genomic: AGGCAGCTGGCCTAGAGCTCAGCGACATCGACCTTTTTGAAATCAACGAGgttgtattct ... ctgtgtgcagGCATTTGCATCACAGTTCACATACTGTGCTCAAGAGCTGGGACTAGATGAA
EST: gi|37837486|gb|BJ595494.1|BJ595494
EST:     GGCAGCTGGCCTAGAGCTCAGCGACATCGACCTTTTTTGAAATCAACGAG                         GCATTTGCATCACAGTTCACATACTGTGCTCAAGAGCTGGGACTAGATGAA
genomic: GGCAGCTGGCCTAGAGCTCAGCGACATCGACC-TTTTTGAAATCAACGAGgttgtattct ... ctgtgtgcagGCATTTGCATCACAGTTCACATACTGTGCTCAAGAGCTGGGACTAGATGAA
EST: gi|67724200|gb|BJ974459.1|BJ974459
EST:     AGGCAGCTGGCCTAGAGCTCAGCGACATCGACCTTTTTGAAATCAACGAG                         GCATTTGCATCACAGTTCACATACTGTGCTCAAGAGCTGGGACTAGATGAA
genomic: AGGCAGCTGGCCTAGAGCTCAGCGACATCGACCTTTTTGAAATCAACGAGgttgtattct ... ctgtgtgcagGCATTTGCATCACAGTTCACATACTGTGCTCAAGAGCTGGGACTAGATGAA

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: 22 (upstream exon), 14 (downstream exon)
Score: 2

CCCATCTGTTATGGGTATCGGTCCTGCTGTTGCCATTCCCGCTGCTGTTAAGGCAGCTGGCCTAGAGCTCAGCGACATCGACCTTTTTGAAATCAACGAGgttgtattct ... ctgtgtgcagGCATTTGCATCACAGTTCACATACTGTGCTCAAGAGCTGGGACTAGATGAAGAGAAGGTGAATGTGAATGGAGGTGCTATGGCTCTTGGTCATCCTCTTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggtctcaaatcacaaaggaacatttgcatttacaaataagttttctgtgtgcagGCATTTGCATCACAGTTCACATACTGTGCTCAAGAGCTGGGACTAGATGAAGAGAAGGTGAATGTGAATGGAGGTGCTATGGCTCTTGGTCATCCTCTTG
                                         ttttctgt  CT-rich tract
                            atttacaaataagttt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgtattcttctccatttgttttatcatgacccgaatatgttgcctttgatagtataaccatcttccagttattttactcttggtctcaaatcacaaaggaacatttgcatttacaaataagttttctgtgtgcagGCATTTGCATCACAGTTCACATACTGTGCTCAAGAGCTGGGACTAGATGAAGAGAAGGTGAATGTGAATGGAGGTGCTATGGCTCTTGGTCATCCTCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG