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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattcactaactcatctttgtgacgctgtggtgacttgagcaaccatttttttgggttctttagaaggagttccacctttatcacacgttagaatgcagccgccttgtaggctacagcgtgacgccttggtattgttatgtacacccagAAAATGGGGATGAAAAGGACAAGGGGAAGAGCAACTGGTTGATGACATATCACACACGACAGTCGGGTGGTCCGAATAATTTCGGATTCTTCTCAGCTGG

Basic information

species Physcomitrella patens
transcript PP1S61_112V6.1
intron # 4
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|67695150|gb|BJ955383.1|BJ955383
EST:     CNCCTNGGATGAGAATGGGGTGTCGTGGCCTAGAGTGTTGCCTCCTGAGG                         AAAATGGGGATGAAAAGGACAAGGGGAAGAGCAACTGGTTGATGACATATC
genomic: CGCCTGGGATGAGAATGGGGTGTCGTGGCCTAGAGTGTTGCCTCCTGAGGgtaattcact ... gtacacccagAAAATGGGGATGAAAAGGACAAGGGGAAGAGCAACTGGTTGATGACATATC
EST: gi|208397892|gb|DC916647.1|DC916647
EST:     CCTGGGATGAGAATGGGGTGTCGTGGCCTAGAGTGTTGCCTCCTGAGG                         AAAATGGGGATGAAAAGGACAAGGGGAAGAGCAACTGGTTGATGACATATC
genomic: CCTGGGATGAGAATGGGGTGTCGTGGCCTAGAGTGTTGCCTCCTGAGGgtaattcact ... gtacacccagAAAATGGGGATGAAAAGGACAAGGGGAAGAGCAACTGGTTGATGACATATC
EST: gi|162224737|gb|FC400737.1|FC400737
EST:     CGCCTGGGATGAGAATGGGGTGTCGTGGCCTAGAGTGTTGCCTCCTGAGG                         AAAATGGGGAT
genomic: CGCCTGGGATGAGAATGGGGTGTCGTGGCCTAGAGTGTTGCCTCCTGAGGgtaattcact ... gtacacccagAAAATGGGGAT
EST: gi|162151086|gb|FC326903.1|FC326903
EST:     CGCCTGGGATGAGAATGGGGTGTCGTGGCCTAGAGTGTTGCCTCCTGAGG                         AAAATGGGGATGAAAAGGACAAGGGGAAGAGCAACTGGTTGATGACATATC
genomic: CGCCTGGGATGAGAATGGGGTGTCGTGGCCTAGAGTGTTGCCTCCTGAGGgtaattcact ... gtacacccagAAAATGGGGATGAAAAGGACAAGGGGAAGAGCAACTGGTTGATGACATATC
EST: gi|208357889|gb|DC918637.1|DC918637
EST:     GGATGAGAATGGGGTGTCGTNGCCTAGAGTGTTGCCTCCTGAGA                         AAAATGGGGATGAAAAGGACAAGGGGAAGAGCAACTGGTTGATGACATATC
genomic: GGATGAGAATGGGGTGTCGTGGCCTAGAGTGTTGCCTCCTGAGGgtaattcact ... gtacacccagAAAATGGGGATGAAAAGGACAAGGGGAAGAGCAACTGGTTGATGACATATC
EST: gi|162240672|gb|FC416290.1|FC416290
EST:     GGTGTCGTGGCCTAGAGTGTTGCCTCCTGAGG                         AAAATGGGGATGAAAAGGACAAGGGGAAGAGCAACTGGTTGATGACATATC
genomic: GGTGTCGTGGCCTAGAGTGTTGCCTCCTGAGGgtaattcact ... gtacacccagAAAATGGGGATGAAAAGGACAAGGGGAAGAGCAACTGGTTGATGACATATC
EST: gi|162151085|gb|FC326902.1|FC326902
EST:     TAGAGTGTTGCCTCCTGAGG                         AAAATGGGGATGAAAAGGACAAGGGGAAGAGCAACTGGTTGATGACATATC
genomic: TAGAGTGTTGCCTCCTGAGGgtaattcact ... gtacacccagAAAATGGGGATGAAAAGGACAAGGGGAAGAGCAACTGGTTGATGACATATC

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: 34 (upstream exon), 29 (downstream exon)
Score: 5

CTTTCATTTGATGATAGGGAGGGTCCTATCCTTGAGCTGGGAGAGAAAGGCGCCTGGGATGAGAATGGGGTGTCGTGGCCTAGAGTGTTGCCTCCTGAGGgtaattcact ... gtacacccagAAAATGGGGATGAAAAGGACAAGGGGAAGAGCAACTGGTTGATGACATATCACACACGACAGTCGGGTGGTCCGAATAATTTCGGATTCTTCTCAGCTGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcagccgccttgtaggctacagcgtgacgccttggtattgttatgtacacccagAAAATGGGGATGAAAAGGACAAGGGGAAGAGCAACTGGTTGATGACATATCACACACGACAGTCGGGTGGTCCGAATAATTTCGGATTCTTCTCAGCTGG
                                    tattgttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattcactaactcatctttgtgacgctgtggtgacttgagcaaccatttttttgggttctttagaaggagttccacctttatcacacgttagaatgcagccgccttgtaggctacagcgtgacgccttggtattgttatgtacacccagAAAATGGGGATGAAAAGGACAAGGGGAAGAGCAACTGGTTGATGACATATCACACACGACAGTCGGGTGGTCCGAATAATTTCGGATTCTTCTCAGCTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG