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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttctttttgttttgttcttttttgttctttttcttgctgatccttgcatgagtttcaacttgtagcatgctgtcttaatttcgcaccatgtatgaaacagTGGCCGAAGCAGCTCAATGCCGACATCTCCGAGGTTGATCCCGAGATCACTGACATCATTGAACACGAGAAGAATCGTCAATGGAAG

Basic information

species Physcomitrella patens
transcript PP1S79_54V6.1
intron # 2
splice site 3'
intron type U2

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|162179835|gb|FC355906.1|FC355906
EST:     ACTGCGGTTGCTTCAGAGTACTCAAGTTCGGCTAAGTCGAATGTAACG                         TGGCCGAAGCAGCTCAATGCCGACATCTCCGAGGTTGATCCCGAGATCACT
genomic: ACTGCGGTTGCTTCAGAGTACTCAAGTTCGGCTAAGTCGAATGTAACGgtgagattta ... tatgaaacagTGGCCGAAGCAGCTCAATGCCGACATCTCCGAGGTTGATCCCGAGATCACT
EST: gi|162182305|gb|FC357176.1|FC357176
EST:     ACTGCGGTTGCTTCAGAGTACTCAAGTTCGGCTAAGTCGAATGTAACG                         TGGCCGAAGCAGCTCAATGCCGACATCTCCGAGGTTGATCCCGAGATCACT
genomic: ACTGCGGTTGCTTCAGAGTACTCAAGTTCGGCTAAGTCGAATGTAACGgtgagattta ... tatgaaacagTGGCCGAAGCAGCTCAATGCCGACATCTCCGAGGTTGATCCCGAGATCACT
EST: gi|18369273|gb|BJ201358.1|BJ201358
EST:     ACTGCGGTTGCTTCAGAGTACTCAAGTTCGGCTAAGTCGAATGTAACG                         TGGCCGAAGCAGCTCAATGCCGACATCTCCGAGGTTGATCCCGAGATCACT
genomic: ACTGCGGTTGCTTCAGAGTACTCAAGTTCGGCTAAGTCGAATGTAACGgtgagattta ... tatgaaacagTGGCCGAAGCAGCTCAATGCCGACATCTCCGAGGTTGATCCCGAGATCACT
EST: gi|100385980|gb|BY951174.1|BY951174
EST:     ACTGCGGTTGCTTCAGAGTACTCAAGTTCGGCTAAGTCGAATGTAACG                         TGGCCGAAGCAGCTCAATGCCGACATCTCCGAGGTTGATCCCGAGATCACT
genomic: ACTGCGGTTGCTTCAGAGTACTCAAGTTCGGCTAAGTCGAATGTAACGgtgagattta ... tatgaaacagTGGCCGAAGCAGCTCAATGCCGACATCTCCGAGGTTGATCCCGAGATCACT
EST: gi|18365567|gb|BJ197644.1|BJ197644
EST:     ACTGCGGTTGCTTCAGAGTACTCAAGTTCGGCTAAGTCGAATGTAACG                         TGGCCGAAGCAGCTCAATGCCGACATCTCCGAGGTTGATCCCGAGATCACT
genomic: ACTGCGGTTGCTTCAGAGTACTCAAGTTCGGCTAAGTCGAATGTAACGgtgagattta ... tatgaaacagTGGCCGAAGCAGCTCAATGCCGACATCTCCGAGGTTGATCCCGAGATCACT
EST: gi|18362808|gb|BJ194880.1|BJ194880
EST:     ACTGCGGTTGCTTCAGAGTACTCAAGTTCGGCTAAGTCGAATGTAACG                         TGGCCGAAGCAGCTCAATGCCGACATCTCCGAGGTTGATCCCGAGATCACT
genomic: ACTGCGGTTGCTTCAGAGTACTCAAGTTCGGCTAAGTCGAATGTAACGgtgagattta ... tatgaaacagTGGCCGAAGCAGCTCAATGCCGACATCTCCGAGGTTGATCCCGAGATCACT
EST: gi|208358811|gb|DC935197.1|DC935197
EST:     ACTGCGGTTGCTTCAGAGTACTCAAGTTCGGCTAAGTCGAATGTAACG                         TGGCCGAAGCAGCTCAATGCCGACATCTCCGAGGTTGATCCCGAGATCACT
genomic: ACTGCGGTTGCTTCAGAGTACTCAAGTTCGGCTAAGTCGAATGTAACGgtgagattta ... tatgaaacagTGGCCGAAGCAGCTCAATGCCGACATCTCCGAGGTTGATCCCGAGATCACT
EST: gi|100428360|gb|BY977766.1|BY977766
EST:     ACTGCGGTTGCTTCAGAGTACTCAAGTTCGGCTAAGTCGAATGTAACG                         TGGCCGAAGCAGCTCAATGCCGACATCTCCGAGGTTGATCCCGAGATCACT
genomic: ACTGCGGTTGCTTCAGAGTACTCAAGTTCGGCTAAGTCGAATGTAACGgtgagattta ... tatgaaacagTGGCCGAAGCAGCTCAATGCCGACATCTCCGAGGTTGATCCCGAGATCACT
EST: gi|18361307|gb|BJ193373.1|BJ193373
EST:     ACTGCGGTTGCTTCAGAGTACTCAAGTTCGGCTAAGTCGAATGTAACG                         TGGCCGAAGCAGCTCAATGCCGACATCTCCGAGGTTGATCCCGAGATCACT
genomic: ACTGCGGTTGCTTCAGAGTACTCAAGTTCGGCTAAGTCGAATGTAACGgtgagattta ... tatgaaacagTGGCCGAAGCAGCTCAATGCCGACATCTCCGAGGTTGATCCCGAGATCACT
EST: gi|18374142|gb|BJ205720.1|BJ205720
EST:     ACTGCGGTTGCTTCAGAGTACTCAAGTTCGGCTAAGTCGAATGTAACG                         TGGCCGAAGCAGCTCAATGCCGACATCTCCGAGGTTGATCCCGAGATCACT
genomic: ACTGCGGTTGCTTCAGAGTACTCAAGTTCGGCTAAGTCGAATGTAACGgtgagattta ... tatgaaacagTGGCCGAAGCAGCTCAATGCCGACATCTCCGAGGTTGATCCCGAGATCACT
EST: gi|18360348|gb|BJ192410.1|BJ192410
EST:     ACTGCGGTTGCTTCAGAGTACTCAAGTTCGGCTAAGTCGAATGTAACG                         TGGCCGAAGCAGCTCAATGCCGACATCTCCGAGGTTGATCCCGAGATCACT
genomic: ACTGCGGTTGCTTCAGAGTACTCAAGTTCGGCTAAGTCGAATGTAACGgtgagattta ... tatgaaacagTGGCCGAAGCAGCTCAATGCCGACATCTCCGAGGTTGATCCCGAGATCACT
EST: gi|18369196|gb|BJ201281.1|BJ201281
EST:     ACTGCGGTTGCTTCAGANTACTCAAGTTCGGCTAAGTCGAATGTAACG                         TGGCCGAAGCAGCTCAATGCCGACATCTCCGAGGTTGATCCCGAGATCACT
genomic: ACTGCGGTTGCTTCAGAGTACTCAAGTTCGGCTAAGTCGAATGTAACGgtgagattta ... tatgaaacagTGGCCGAAGCAGCTCAATGCCGACATCTCCGAGGTTGATCCCGAGATCACT
EST: gi|208379665|gb|DC903720.1|DC903720
EST:     ACTGCGGTTGCTTCAGAGTACTCAAGTTCGGCTAAGTCNAATGTAACG                         TGGCCGAAGCANCTCAATGCCGACATCTCCGAGGTTGATCCCGAGATCACT
genomic: ACTGCGGTTGCTTCAGAGTACTCAAGTTCGGCTAAGTCGAATGTAACGgtgagattta ... tatgaaacagTGGCCGAAGCAGCTCAATGCCGACATCTCCGAGGTTGATCCCGAGATCACT
EST: gi|162155361|gb|FC331767.1|FC331767
EST:     ACTGCGGTTGCTTCAGAGTACTCAAGTTCGGCTAAGTCGAATGTAACG                         TGGCCGAAGCAGCTCAATGCCGACATCTCCGAGGTTGATCCCGAGATCACT
genomic: ACTGCGGTTGCTTCAGAGTACTCAAGTTCGGCTAAGTCGAATGTAACGgtgagattta ... tatgaaacagTGGCCGAAGCAGCTCAATGCCGACATCTCCGAGGTTGATCCCGAGATCACT
EST: gi|18356126|gb|BJ188185.1|BJ188185
EST:     ACTGCGGTTGCTTCAGAGTACTCAAGTTCGGCTAANTCGAATGTAACG                         TGGCCGAAGCAGCTCAATGCCGACATCTCCGAGGTTGATCCCGAGATCACT
genomic: ACTGCGGTTGCTTCAGAGTACTCAAGTTCGGCTAAGTCGAATGTAACGgtgagattta ... tatgaaacagTGGCCGAAGCAGCTCAATGCCGACATCTCCGAGGTTGATCCCGAGATCACT
EST: gi|18366816|gb|BJ198896.1|BJ198896
EST:     ACTGCGGTTGCTTCAGAGTACTCAAGTTCGGCTAAGTCGAATGTAACG                         TGGCCGAAGCAGCTCAATGCCGACATCTCCGAGGTTGATCCCGAGATCACT
genomic: ACTGCGGTTGCTTCAGAGTACTCAAGTTCGGCTAAGTCGAATGTAACGgtgagattta ... tatgaaacagTGGCCGAAGCAGCTCAATGCCGACATCTCCGAGGTTGATCCCGAGATCACT
EST: gi|100392460|gb|BY953374.1|BY953374
EST:     ACTGCGGTTGCTTCAGAGTACTCAAGTTCGGCTAAGTCGAATGTAACG                         TGGCCGAAGCAGCTCAATGCCGACATCTCCGAGGTTGATCCCGAGATCACT
genomic: ACTGCGGTTGCTTCAGAGTACTCAAGTTCGGCTAAGTCGAATGTAACGgtgagattta ... tatgaaacagTGGCCGAAGCAGCTCAATGCCGACATCTCCGAGGTTGATCCCGAGATCACT
EST: gi|18370401|gb|BJ202003.1|BJ202003
EST:     ACTGCGGTTGCTTCAGAGTACTCAAGTTCGGCTAAGTCGAATGTAACG                         TGGCCGAAGCAGCTCAATGCCGACATCTCCGAGGTTGATCCCGAGATCACT
genomic: ACTGCGGTTGCTTCAGAGTACTCAAGTTCGGCTAAGTCGAATGTAACGgtgagattta ... tatgaaacagTGGCCGAAGCAGCTCAATGCCGACATCTCCGAGGTTGATCCCGAGATCACT

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: 8 (upstream exon), 28 (downstream exon)
Score: 1

ACTGCGGTTGCTTCAGAGTACTCAAGTTCGGCTAAGTCGAATGTAACGgtgagattta ... tatgaaacagTGGCCGAAGCAGCTCAATGCCGACATCTCCGAGGTTGATCCCGAGATCACTGACATCATTGAACACGAGAAGAATCGTCAATGGAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcatgagtttcaacttgtagcatgctgtcttaatttcgcaccatgtatgaaacagTGGCCGAAGCAGCTCAATGCCGACATCTCCGAGGTTGATCCCGAGATCACTGACATCATTGAACACGAGAAGAATCGTCAATGGAAG
                           tcttaat  putative branch site (score: 1)
                           tcttaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttctttttgttttgttcttttttgttctttttcttgctgatccttgcatgagtttcaacttgtagcatgctgtcttaatttcgcaccatgtatgaaacagTGGCCGAAGCAGCTCAATGCCGACATCTCCGAGGTTGATCCCGAGATCACTGACATCATTGAACACGAGAAGAATCGTCAATGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG