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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcaattccggtctgactcgctgtttccgcgatctgagctctgacatgttaagcgttgtttaatttgaactttggccaaccgcatgtgaaacctgaaaggatccaattggaactcacctttcttgaatttatctttgactgttaatccgtgttggccctgcagGATGCATGCTCCAGTATGCTCTCCTCCACCTCGCCGGGTACGACAGCGTTAAG

Basic information

species Physcomitrella patens
transcript PP1S120_127V6.1
intron # 1
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|18359437|gb|BJ191498.1|BJ191498
EST:     GAACCCGTACTGGTTCAACAGGGACCGATTCGTATTGTCTGCTGGCCACG                         GATGCATGCTCCAGTATGCTCTCCTCCACCTCGCCGGGTACGACAGCGTTA
genomic: GAACCCGTACTGGTTCAACAGGGACCGATTCGTATTGTCTGCTGGCCACGgtaagcaatt ... ggccctgcagGATGCATGCTCCAGTATGCTCTCCTCCACCTCGCCGGGTACGACAGCGTTA
EST: gi|100384448|gb|BY987307.1|BY987307
EST:     GAACCCGTACTGGTTCAACAGGGACCGATTCGTATTGTCTGCTGGCCACG                         GATGCATGCTCCAGTATGCTCTCCTCCACCTCGCCGGGTACGACAGCGTTA
genomic: GAACCCGTACTGGTTCAACAGGGACCGATTCGTATTGTCTGCTGGCCACGgtaagcaatt ... ggccctgcagGATGCATGCTCCAGTATGCTCTCCTCCACCTCGCCGGGTACGACAGCGTTA
EST: gi|100392587|gb|BY971784.1|BY971784
EST:     GAACCCGTACTGGTTCAACAGGGACCGATTCGTATTGTCTGCTGGCCACG                         GATGCATGCTCCAGTATGCTCTCCTCCACCTCGCCGGGTACGACAGCGTTA
genomic: GAACCCGTACTGGTTCAACAGGGACCGATTCGTATTGTCTGCTGGCCACGgtaagcaatt ... ggccctgcagGATGCATGCTCCAGTATGCTCTCCTCCACCTCGCCGGGTACGACAGCGTTA
EST: gi|18359052|gb|BJ191112.1|BJ191112
EST:     GAACCCGTACTGGTTCAACAGGGACCGATTCGTATTGTCTGCTGGCCACG                         GATGCATGCTCCAGTATGCTCTCCTCCACCTCGCCGGGTACGACAGCGTTA
genomic: GAACCCGTACTGGTTCAACAGGGACCGATTCGTATTGTCTGCTGGCCACGgtaagcaatt ... ggccctgcagGATGCATGCTCCAGTATGCTCTCCTCCACCTCGCCGGGTACGACAGCGTTA
EST: gi|100443954|gb|BY982182.1|BY982182
EST:     GAACCCGTACTGGTTCAACAGGGACCGATTCGTATTGTCTGCTGGCCACG                         GATGCATGCTCCAGTATGCTCTCCTCCCAC-TCGCCGGGTACGACAGCGTT
genomic: GAACCCGTACTGGTTCAACAGGGACCGATTCGTATTGTCTGCTGGCCACGgtaagcaatt ... ggccctgcagGATGCATGCTCCAGTATGCTCTCCTCC-ACCTCGCCGGGTACGACAGCGTT
EST: gi|100391075|gb|BY953085.1|BY953085
EST:     GAACCCGTACTGGTTCAACAGGGACCGATTCGTATTGTCTGCTGGCCACG                         GATGCATGCTCCAGTATGCTCTCCTCCACCTCGCCGGGTACGACAGCGTTA
genomic: GAACCCGTACTGGTTCAACAGGGACCGATTCGTATTGTCTGCTGGCCACGgtaagcaatt ... ggccctgcagGATGCATGCTCCAGTATGCTCTCCTCCACCTCGCCGGGTACGACAGCGTTA
EST: gi|100377414|gb|BY968511.1|BY968511
EST:     GAACCCGTACTGGTTCAACAGGGACCGATTCGTATTGTCTGCTGGCCACG                         GATGCATGCTCCAGTATGCTCTCCTCCACCTCGNCGGGTACGACAGC
genomic: GAACCCGTACTGGTTCAACAGGGACCGATTCGTATTGTCTGCTGGCCACGgtaagcaatt ... ggccctgcagGATGCATGCTCCAGTATGCTCTCCTCCACCTCGCCGGGTACGACAGC
EST: gi|18367583|gb|BJ199666.1|BJ199666
EST:     GAACCCGTACTGGTTCAACAGGGACCGATTCGTATTGTCTGCTGGCCACG                         GATGCATGCTCCANTATGCTCTCCTCCACCTCGCCGGGTACGAC
genomic: GAACCCGTACTGGTTCAACAGGGACCGATTCGTATTGTCTGCTGGCCACGgtaagcaatt ... ggccctgcagGATGCATGCTCCAGTATGCTCTCCTCCACCTCGCCGGGTACGAC
EST: gi|18372214|gb|BJ203816.1|BJ203816
EST:     GAACCCGTACTGGTTCAACAGGGACCGATTCGTATTGTCTGCTGGCCACG                         GATGCATGCTCCAGTATGCTCTCCTCCACCTCGCCGGGTACGACAGCGTTA
genomic: GAACCCGTACTGGTTCAACAGGGACCGATTCGTATTGTCTGCTGGCCACGgtaagcaatt ... ggccctgcagGATGCATGCTCCAGTATGCTCTCCTCCACCTCGCCGGGTACGACAGCGTTA
EST: gi|100361725|gb|BY947791.1|BY947791
EST:     GAACCCGTACTGGTTCAACAGGGACCGATTCGTATTGTCTGCTGGCCACG                         GATGCATGCTCCAGTATGCTCTCCTCCACCTCGCCGGGTACGACAGCGTTA
genomic: GAACCCGTACTGGTTCAACAGGGACCGATTCGTATTGTCTGCTGGCCACGgtaagcaatt ... ggccctgcagGATGCATGCTCCAGTATGCTCTCCTCCACCTCGCCGGGTACGACAGCGTTA
EST: gi|18367248|gb|BJ199329.1|BJ199329
EST:     AACCCGTACTGGGTTCAACAGGGACCGATTCGTATTGTCTGCTGGCC-CG                         GGATGCATGCTCCANTATGCTCTCCTCCACCTCGCCGG
genomic: AACCCGTACTGG-TTCAACAGGGACCGATTCGTATTGTCTGCTGGCCACGgtaagcaatt ... ggccctgcagG-ATGCATGCTCCAGTATGCTCTCCTCCACCTCGCCGG
EST: gi|100397735|gb|BY990374.1|BY990374
EST:     GAACCCGTACTGGTTCAACAGGGACCGATTCGTATTGTCTGCTGGCCACG                         GATGCATGCTCCAGTATGCTCTCCTCCACCTCGCCGGGTACGACAGCGTTA
genomic: GAACCCGTACTGGTTCAACAGGGACCGATTCGTATTGTCTGCTGGCCACGgtaagcaatt ... ggccctgcagGATGCATGCTCCAGTATGCTCTCCTCCACCTCGCCGGGTACGACAGCGTTA
EST: gi|100363212|gb|BY984413.1|BY984413
EST:     GAACCCGTACTGGTTCAACAGGGACCGATTCGTATTGTCTGCTGGCCACG                         GATGCATGCTCCAGTATGCTCTCCTCCACCTCGCCGGGTACGACAGCGTTA
genomic: GAACCCGTACTGGTTCAACAGGGACCGATTCGTATTGTCTGCTGGCCACGgtaagcaatt ... ggccctgcagGATGCATGCTCCAGTATGCTCTCCTCCACCTCGCCGGGTACGACAGCGTTA

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: 65

GCCCCCATGGGACACATTTTGTACGATGAGGTGATGAAGTATAACCCGAAGAACCCGTACTGGTTCAACAGGGACCGATTCGTATTGTCTGCTGGCCACGgtaagcaatt ... ggccctgcagGATGCATGCTCCAGTATGCTCTCCTCCACCTCGCCGGGTACGACAGCGTTAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggaactcacctttcttgaatttatctttgactgttaatccgtgttggccctgcagGATGCATGCTCCAGTATGCTCTCCTCCACCTCGCCGGGTACGACAGCGTTAAG
          tttcttgaatttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcaattccggtctgactcgctgtttccgcgatctgagctctgacatgttaagcgttgtttaatttgaactttggccaaccgcatgtgaaacctgaaaggatccaattggaactcacctttcttgaatttatctttgactgttaatccgtgttggccctgcagGATGCATGCTCCAGTATGCTCTCCTCCACCTCGCCGGGTACGACAGCGTTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC