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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattttcttatttacattaactctttggctcgtcgggttaacgaatctcttttgatatgttatacacgaactatatattcaccttgtcgattctattttaagcatacctaaatgtgattaggctcttctttcgttgaccgtggtaaaatgatgtggaagataaatcttcggtaagtcgtaactgttatttgcagGTTGGAGCTCAAACTGAGACCGAGTTGAAAGAGAAGAAACTTCGTGTTGAAGATGCGCTGAATGCAACCAAGGCTGCTGTGGAGGAAGGCATTGTTGTTG

Basic information

species Physcomitrella patens
transcript PP1S14_298V6.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S14_298V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: EFJ32217 (Selaginella moellendorffii), 3'ss of exon 8
gtattttcttatttacattaactctttggctcgtcgggttaacgaatctcttttgatatgttatacacgaactatatattcaccttgtcgattctattttaagcatacctaaatgtgattaggctcttctttcgttgaccgtggtaaaatgatgtggaagataaatcttcggtaagtcgtaactgttatttgcagGTTGGAGCTCAAACTGAGACCGAGTTGAAAGAGAAGAAACTTCGTGTTGAAGATGCGCTGAATGCAACCAAGGCTGCTGTGGAGGAAGGCATTGTTGTTG
                                                                                                                      | || |    ||||  ||| ||||          |   | | | || |||||        |  | || |    |||||| ||||||||||| || |||||| ||||||||||||| ||| | || || || || || |||||||| |||                            
---------------------------------------------------------------------------------------------------------------------gtaagacatcgctttttttg-ccgt----------ttccggaaaaaattcttc-------tgacattgattcgcgcagGTGGGAGCTCAAACGGAAACCGAGCTGAAAGAGAAGAAGCTTAGAGTGGAGGACGCTCTAAATGCAACAAAG----------------------------
















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|162162748|gb|FC337802.1|FC337802
EST:     AGCTGAATGAGAGGATTGCGAAGCTGTCTGGGGGAGTAGCCATTATTCAG                         GTTGGAGCTCAAACTGAGACCGAGTTGAAAGAGAAGAAACTTCGTGTTGAA
genomic: AGCTGAATGAGAGGATTGCGAAGCTGTCTGGGGGAGTAGCCATTATTCAGgtattttctt ... ttatttgcagGTTGGAGCTCAAACTGAGACCGAGTTGAAAGAGAAGAAACTTCGTGTTGAA
EST: gi|162248294|gb|FC422548.1|FC422548
EST:     AGCTGAATGAGAGGATTGCGAAGCTGTCTGGGGGAGTAGCCATTATTCAG                         GTTGGAGCTCAAACTGAGACCGAGTTGAAAGAGAAGAAACTTCGTGTTGAA
genomic: AGCTGAATGAGAGGATTGCGAAGCTGTCTGGGGGAGTAGCCATTATTCAGgtattttctt ... ttatttgcagGTTGGAGCTCAAACTGAGACCGAGTTGAAAGAGAAGAAACTTCGTGTTGAA
EST: gi|162153950|gb|FC329457.1|FC329457
EST:     AGCTGAATGAGAGGATTGCGAAGCTGTCTGGGGGAGTAGCCATTATTCAG                         GTTGGAGCTCAAACTGAGACCGAGTTGAAAGAGAAGAAACTTCGTGTTGAA
genomic: AGCTGAATGAGAGGATTGCGAAGCTGTCTGGGGGAGTAGCCATTATTCAGgtattttctt ... ttatttgcagGTTGGAGCTCAAACTGAGACCGAGTTGAAAGAGAAGAAACTTCGTGTTGAA
EST: gi|162181645|gb|FC357947.1|FC357947
EST:     AGCTGAATGAGAGGATTGCGAAGCTGTCTGGGGGAGTAGCCATTATTCAG                         GTTGGAGCTCAAACTGAGACCGAGTTGAAAGAGAAGAAACTTCGTGTTGAA
genomic: AGCTGAATGAGAGGATTGCGAAGCTGTCTGGGGGAGTAGCCATTATTCAGgtattttctt ... ttatttgcagGTTGGAGCTCAAACTGAGACCGAGTTGAAAGAGAAGAAACTTCGTGTTGAA
EST: gi|67723761|gb|BJ974020.1|BJ974020
EST:     GGGGAGTAGCC-NTATTCAG                         GTTGGAGCTCAAACTGAGACCGAG-TGAAAGAGAAGAAACTTCGTGTTGAA
genomic: GGGGAGTAGCCATTATTCAGgtattttctt ... ttatttgcagGTTGGAGCTCAAACTGAGACCGAGTTGAAAGAGAAGAAACTTCGTGTTGAA
EST: gi|208379255|gb|DC927266.1|DC927266
EST:     AGCTGAATGAGAGGATTGCGAAGCTGTCT-GGGGAGTAGCCATTATTCAG                         GTTGGAGCTCAAACTGAGACCGAGTTGAAAGAGAAGAAACTTCGTGTTGAA
genomic: AGCTGAATGAGAGGATTGCGAAGCTGTCTGGGGGAGTAGCCATTATTCAGgtattttctt ... ttatttgcagGTTGGAGCTCAAACTGAGACCGAGTTGAAAGAGAAGAAACTTCGTGTTGAA
EST: gi|162248295|gb|FC422549.1|FC422549
EST:     AGCTGAATGAGAGGATTGCGAAGCTGTCTGGGGGAGTAGCCATTATTCAG                         GTTGGAGCTCAAACTGAGACCGAGTTGAAAGAGAAGAAACTTCGTGTTGAA
genomic: AGCTGAATGAGAGGATTGCGAAGCTGTCTGGGGGAGTAGCCATTATTCAGgtattttctt ... ttatttgcagGTTGGAGCTCAAACTGAGACCGAGTTGAAAGAGAAGAAACTTCGTGTTGAA
EST: gi|162164012|gb|FC339300.1|FC339300
EST:     AGCTGAATGAGAGGATTGCGAAGCTGTCTGGGGGAGTAGCCATTATTCAG                         GTTGGAGCTCAAACTGAGACCGAGTTGAAAGAGAAGAAACTTCGTGTTGAA
genomic: AGCTGAATGAGAGGATTGCGAAGCTGTCTGGGGGAGTAGCCATTATTCAGgtattttctt ... ttatttgcagGTTGGAGCTCAAACTGAGACCGAGTTGAAAGAGAAGAAACTTCGTGTTGAA
EST: gi|162158909|gb|FC334795.1|FC334795
EST:     AGCTGAATGAGAGGATTGCGAAGCTGTCTGGGGGAGTAGCCATTATTCAG                         GTTGGAGCTCAAACTGAGACCGAGTTGAAAGAGAAGAAACTTCGTGTTGAA
genomic: AGCTGAATGAGAGGATTGCGAAGCTGTCTGGGGGAGTAGCCATTATTCAGgtattttctt ... ttatttgcagGTTGGAGCTCAAACTGAGACCGAGTTGAAAGAGAAGAAACTTCGTGTTGAA
EST: gi|162156889|gb|FC333043.1|FC333043
EST:     AGCTGAATGAGAGGATTGCGAAGCTGTCTGGGGGAGTAGCCATTATTCAG                         GTTGGAGCTCAAACTGAGACCGAGTTGAAAGAGAAGAAACTTCGTGTTGAA
genomic: AGCTGAATGAGAGGATTGCGAAGCTGTCTGGGGGAGTAGCCATTATTCAGgtattttctt ... ttatttgcagGTTGGAGCTCAAACTGAGACCGAGTTGAAAGAGAAGAAACTTCGTGTTGAA
EST: gi|162192859|gb|FC370178.1|FC370178
EST:     GCGAAGCTGTCTGGGGGAGTAGCCATTATTCAG                         GTTGGAGCTCAAACTGAGACCGAGTTGAAAGAGAAGAAACTTCGTGTTGAA
genomic: GCGAAGCTGTCTGGGGGAGTAGCCATTATTCAGgtattttctt ... ttatttgcagGTTGGAGCTCAAACTGAGACCGAGTTGAAAGAGAAGAAACTTCGTGTTGAA

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), 34 (downstream exon)
Score: 51

CCAAATCCGCAACCTAATCGAAGTCGCCGAGCAAGAGTATGAGAAGGAGAAGCTGAATGAGAGGATTGCGAAGCTGTCTGGGGGAGTAGCCATTATTCAGgtattttctt ... ttatttgcagGTTGGAGCTCAAACTGAGACCGAGTTGAAAGAGAAGAAACTTCGTGTTGAAGATGCGCTGAATGCAACCAAGGCTGCTGTGGAGGAAGGCATTGTTGTTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtggtaaaatgatgtggaagataaatcttcggtaagtcgtaactgttatttgcagGTTGGAGCTCAAACTGAGACCGAGTTGAAAGAGAAGAAACTTCGTGTTGAAGATGCGCTGAATGCAACCAAGGCTGCTGTGGAGGAAGGCATTGTTGTTG
                                    tcgtaac  putative branch site (score: 51)
                 aagataaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattttcttatttacattaactctttggctcgtcgggttaacgaatctcttttgatatgttatacacgaactatatattcaccttgtcgattctattttaagcatacctaaatgtgattaggctcttctttcgttgaccgtggtaaaatgatgtggaagataaatcttcggtaagtcgtaactgttatttgcagGTTGGAGCTCAAACTGAGACCGAGTTGAAAGAGAAGAAACTTCGTGTTGAAGATGCGCTGAATGCAACCAAGGCTGCTGTGGAGGAAGGCATTGTTGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA