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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagatctcgctcttttgacttgaaatcagttgctgactcttgtgtatgtcacaagcttgttttgaatacttgtttttgtgaatgcgacctctttttcctgcatttgagaagctgatggcatttcatgctggtgttgctgcagTTGAATCCCCGGAGTCCAGCCCTGTGGAGTCTCCTGTCGATGCTCCCGCTTCTTCCGAGGGTCCCGTTGCCTCCTCCCCCGGACCCAGCCCAGCTGAGTC

Basic information

species Physcomitrella patens
transcript PP1S495_1V6.1
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|162203447|gb|FC378842.1|FC378842
EST:     CATGGCTCCTGAGATGGCACCTTCCTCGTCGACTCCCATGTCACCACCAG                         TTGAATCCCCGGAGTCCAGCCCTGTGGAGTCTCCTGTCGATGCTCCCGCTT
genomic: CATGGCTCCTGAGATGGCACCTTCCTCGTCGACTCCCATGTCACCACCAGgttagatctc ... gttgctgcagTTGAATCCCCGGAGTCCAGCCCTGTGGAGTCTCCTGTCGATGCTCCCGCTT
EST: gi|162209934|gb|FC385764.1|FC385764
EST:     CATGGCTCCTGAGATGGCACCTTCCTCGTCGACTCCCATGTCACCACCAG                         TTGAATCCCCGGAGTCCAGCCCTGTGGAGTCTCCTGTCGATGCTCCCGCTT
genomic: CATGGCTCCTGAGATGGCACCTTCCTCGTCGACTCCCATGTCACCACCAGgttagatctc ... gttgctgcagTTGAATCCCCGGAGTCCAGCCCTGTGGAGTCTCCTGTCGATGCTCCCGCTT
EST: gi|162241492|gb|FC414666.1|FC414666
EST:     CATGGCTCCTGAGATGGCACCTTCCTCGTCGACTCCCATGTCACCACCAG                         TTGAATCCCCGGAGTCCAGCCCTGTGGAGTCTCCTGTCGATGCTCCCGCTT
genomic: CATGGCTCCTGAGATGGCACCTTCCTCGTCGACTCCCATGTCACCACCAGgttagatctc ... gttgctgcagTTGAATCCCCGGAGTCCAGCCCTGTGGAGTCTCCTGTCGATGCTCCCGCTT
EST: gi|162209933|gb|FC385763.1|FC385763
EST:     CATGGCTCCTGAGATGGCACCTTCCTCGTCGACTCCCATGTCACCACCAG                         TTGAATCCCCGGAGTCCAGCCCTGTGGAGTCTCCTGTCGATGCTCCCGCTT
genomic: CATGGCTCCTGAGATGGCACCTTCCTCGTCGACTCCCATGTCACCACCAGgttagatctc ... gttgctgcagTTGAATCCCCGGAGTCCAGCCCTGTGGAGTCTCCTGTCGATGCTCCCGCTT
EST: gi|162229498|gb|FC404818.1|FC404818
EST:     CATGGCTCCTGAGATGGCACCTTCCTCGTCGACTCCCATGTCACCACCAG                         TTGAATCCCCGGAGTCCAGCCCTGTGGAGTCTCCTGTCGATGCTCCCGCTT
genomic: CATGGCTCCTGAGATGGCACCTTCCTCGTCGACTCCCATGTCACCACCAGgttagatctc ... gttgctgcagTTGAATCCCCGGAGTCCAGCCCTGTGGAGTCTCCTGTCGATGCTCCCGCTT
EST: gi|162215262|gb|FC391030.1|FC391030
EST:     CATGGCTCCTGAGATGGCACCTTCCTCGTCGACTCCCATGTCACCACCAG                         TTGAATCCCCGGAGTCCAGCCCTGTGGAGTCTCCTGTCGATGCTCCCGCTT
genomic: CATGGCTCCTGAGATGGCACCTTCCTCGTCGACTCCCATGTCACCACCAGgttagatctc ... gttgctgcagTTGAATCCCCGGAGTCCAGCCCTGTGGAGTCTCCTGTCGATGCTCCCGCTT
EST: gi|162201928|gb|FC376926.1|FC376926
EST:     CATGGCTCCTGAGATGGCACCTTCCTCGTCGACTCCCATGTCACCACCAG                         TTGAATCCCCGGAGTCCAGCCCTGTGGAGTCTCCTGTCGATGCTCCCGCTT
genomic: CATGGCTCCTGAGATGGCACCTTCCTCGTCGACTCCCATGTCACCACCAGgttagatctc ... gttgctgcagTTGAATCCCCGGAGTCCAGCCCTGTGGAGTCTCCTGTCGATGCTCCCGCTT
EST: gi|162241493|gb|FC414667.1|FC414667
EST:     CATGGCTCCTGAGATGGCACCTTCCTCGTCGACTCCCATGTCACCACCAG                         TTGAATCCCCGGAGTCCAGCCCTGTGGAGTCTCCTGTCGATGCTCCCGCTT
genomic: CATGGCTCCTGAGATGGCACCTTCCTCGTCGACTCCCATGTCACCACCAGgttagatctc ... gttgctgcagTTGAATCCCCGGAGTCCAGCCCTGTGGAGTCTCCTGTCGATGCTCCCGCTT
EST: gi|162203448|gb|FC378843.1|FC378843
EST:     CATGGCTCCTGAGATGGCACCTTCCTCGTCGACTCCCATGTCACCACCAG                         TTGAATCCCCGGAGTCCAGCCCTGTGGAGTCTCCTGTCGATGCTCCCGCTT
genomic: CATGGCTCCTGAGATGGCACCTTCCTCGTCGACTCCCATGTCACCACCAGgttagatctc ... gttgctgcagTTGAATCCCCGGAGTCCAGCCCTGTGGAGTCTCCTGTCGATGCTCCCGCTT
EST: gi|162201927|gb|FC376925.1|FC376925
EST:     CATGGCTCCTGAGATGGCACCTTCCTCGTCGACTCCCATGTCACCACCAG                         TTGAATCCCCGGAGTCCAGCCCTGTGGAGTCTCCTGTCGATGCTCCCGCTT
genomic: CATGGCTCCTGAGATGGCACCTTCCTCGTCGACTCCCATGTCACCACCAGgttagatctc ... gttgctgcagTTGAATCCCCGGAGTCCAGCCCTGTGGAGTCTCCTGTCGATGCTCCCGCTT
EST: gi|162215261|gb|FC391029.1|FC391029
EST:     CATGGCTCCTGAGATGGCACCTTCCTCGTCGACTCCCATGTCACCACCAG                         TTGAATCCCCGGAGTCCAGCCCTGTGGAGTCTCCTGTCGATGCTCCCGCTT
genomic: CATGGCTCCTGAGATGGCACCTTCCTCGTCGACTCCCATGTCACCACCAGgttagatctc ... gttgctgcagTTGAATCCCCGGAGTCCAGCCCTGTGGAGTCTCCTGTCGATGCTCCCGCTT
EST: gi|162244622|gb|FC420130.1|FC420130
EST:     CATGGCTCCTGAGATGGCACCTTCCTCGTCGACTCCCATGTCACCACCAG                         TTGAATCCCCGGAGTCCAGCCCTGTGGAGTCTCCTGTCGATGCTCCCGCTT
genomic: CATGGCTCCTGAGATGGCACCTTCCTCGTCGACTCCCATGTCACCACCAGgttagatctc ... gttgctgcagTTGAATCCCCGGAGTCCAGCCCTGTGGAGTCTCCTGTCGATGCTCCCGCTT
EST: gi|162244623|gb|FC420131.1|FC420131
EST:     CATGGCTCCTGAGATGGCACCTTCCTCGTCGACTCCCATGTCACCACCAG                         TTGAATCCCCGGAGTCCAGCCCTGTGGAGTCTCCTGTCGATGCTCCCGCTT
genomic: CATGGCTCCTGAGATGGCACCTTCCTCGTCGACTCCCATGTCACCACCAGgttagatctc ... gttgctgcagTTGAATCCCCGGAGTCCAGCCCTGTGGAGTCTCCTGTCGATGCTCCCGCTT
EST: gi|162229484|gb|FC404817.1|FC404817
EST:     CATGGCTCCTGAGATGGCACCTTCCTCGTCGACTCCCATGTCACCACCAG                         TTGAATCCCCGGAGTCCAGCCCTGTGGAGTCTCCTGTCGATGCTCCCGCTT
genomic: CATGGCTCCTGAGATGGCACCTTCCTCGTCGACTCCCATGTCACCACCAGgttagatctc ... gttgctgcagTTGAATCCCCGGAGTCCAGCCCTGTGGAGTCTCCTGTCGATGCTCCCGCTT

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: 12 (upstream exon), 24 (downstream exon)
Score: 1

CCTCATTCTGCACCCATGTACTCTCCCGAATACTCCCCCGAAAGCTCGCCCATGGCTCCTGAGATGGCACCTTCCTCGTCGACTCCCATGTCACCACCAGgttagatctc ... gttgctgcagTTGAATCCCCGGAGTCCAGCCCTGTGGAGTCTCCTGTCGATGCTCCCGCTTCTTCCGAGGGTCCCGTTGCCTCCTCCCCCGGACCCAGCCCAGCTGAGTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctctttttcctgcatttgagaagctgatggcatttcatgctggtgttgctgcagTTGAATCCCCGGAGTCCAGCCCTGTGGAGTCTCCTGTCGATGCTCCCGCTTCTTCCGAGGGTCCCGTTGCCTCCTCCCCCGGACCCAGCCCAGCTGAGTC
                      agctgat  putative branch site (score: 1)
                                atttcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagatctcgctcttttgacttgaaatcagttgctgactcttgtgtatgtcacaagcttgttttgaatacttgtttttgtgaatgcgacctctttttcctgcatttgagaagctgatggcatttcatgctggtgttgctgcagTTGAATCCCCGGAGTCCAGCCCTGTGGAGTCTCCTGTCGATGCTCCCGCTTCTTCCGAGGGTCCCGTTGCCTCCTCCCCCGGACCCAGCCCAGCTGAGTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA