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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agggatgctagtgcaggtgtaaagctgttttattgcaatatatggttggatagaaatgacgagaagaaatattctcatggttctctggttttcttcgcagGCCTTTGTGCGGAAGGTCATTGAGTTACATGACAAGTATCTGCAGTATGTGAGCGAGTGCTTCGTCAACCACTCCCTTTTTCACAAA

Basic information

species Physcomitrella patens
transcript PP1S144_158V6.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S144_158V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: EFJ25647 (Selaginella moellendorffii), 3'ss of exon 9
agggatgctagtgcaggtgtaaagctgttttattgcaatatatggttggatagaaatgacgagaagaaatattctcatggttctctggttttcttcgcagGCCTTTGTGCGGAAGGTCATTGAGTTACATGACAAGTATCTGCAGTATGTGAGCGAGTGCTTCGTCAACCACTCCCTTTTTCACAAA
                                      |||   || |  |   |||   |   | | ||  | |      |||    | |||| | ||||| ||||| ||||| || |||||| | |||||||| ||| |||| ||||| ||||||||||| || || || |||||||| ||||| 
-------------------------------------gtattgtgtcgccttttaattttgtccatagatgctata-----tcttaaatgttctccccagGCTTTTGTTCGGAAAGTGATTGAGCTGCATGACAAATATTTGCAATATGTCAGCGAGTGCTTTGTTAATCATTCCCTTTTCCACAAG

upper sequence: PP1S144_158V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: EFJ12300 (Selaginella moellendorffii), 3'ss of exon 9
agggatgctagtgcaggtgtaaagctgttttattgcaatatatggttggatagaaatgacgagaagaaatattctcatggttctctggttttcttcgcagGCCTTTGTGCGGAAGGTCATTGAGTTACATGACAAGTATCTGCAGTATGTGAGCGAGTGCTTCGTCAACCACTCCCTTTTTCACAAA
                                      |||   || |  |   |||   |   | | ||  | |      |||    | |||| | ||||| ||||| ||||| || |||||| | |||||||| ||| |||| ||||| ||||||||||| || || ||||||||||| ||||| 
-------------------------------------gtattgtgtcgccttttaattttgtccatagatgctata-----tcttaaatgttctccccagGCTTTTGTTCGGAAAGTGATTGAGCTGCATGACAAATATTTGCAATATGTCAGCGAGTGCTTTGTTAATCACTCCCTTTTCCACAAG
















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|162153374|gb|FC329884.1|FC329884
EST:     GCTGAAAAGAAAGATACTGTTGGAGTTCAAGAACAG                         GCCTTTGTGCGGAAGGTCATTGAGTTACATGACAAGTATCTGCAGTATGTG
genomic: GCTGAAAAGAAAGATACTGTTGGAGTTCAAGAACAGgtaataacca ... ttcttcgcagGCCTTTGTGCGGAAGGTCATTGAGTTACATGACAAGTATCTGCAGTATGTG
EST: gi|162236074|gb|FC412233.1|FC412233
EST:     GCTGAAAAGAAAGATACTGTTGGAGTTCAAGAACAG                         GCCTTTGTGCGGAAGGTCATTGAGTTACATGACAAGTATCTGCAGTATGTG
genomic: GCTGAAAAGAAAGATACTGTTGGAGTTCAAGAACAGgtaataacca ... ttcttcgcagGCCTTTGTGCGGAAGGTCATTGAGTTACATGACAAGTATCTGCAGTATGTG
EST: gi|100388565|gb|BY952167.1|BY952167
EST:     GAAAGATACTGTTGGAGTTCAAGAACAG                         GCCTTTGTGCGGAAGGTCATTGAGTTACATGACAAGTATCTGCAGTATGTG
genomic: GAAAGATACTGTTGGAGTTCAAGAACAGgtaataacca ... ttcttcgcagGCCTTTGTGCGGAAGGTCATTGAGTTACATGACAAGTATCTGCAGTATGTG
EST: gi|162191204|gb|FC367882.1|FC367882
EST:     GCTGAAAAGAAAGATACTGTTGGAGTTCAAGAACAG                         GCCTTTGTGCGGAAGGTCATTGAGTTACATGACAAGTATCTGCAGTATGTG
genomic: GCTGAAAAGAAAGATACTGTTGGAGTTCAAGAACAGgtaataacca ... ttcttcgcagGCCTTTGTGCGGAAGGTCATTGAGTTACATGACAAGTATCTGCAGTATGTG
EST: gi|162191670|gb|FC367715.1|FC367715
EST:     GCTGAAAAGAAAGATACTGTTGGAGTTCAAGAACAG                         GCCTTTGTGCGGAAGGTCATTGAGTTACATGACAAGTATCTGCAGTATGTG
genomic: GCTGAAAAGAAAGATACTGTTGGAGTTCAAGAACAGgtaataacca ... ttcttcgcagGCCTTTGTGCGGAAGGTCATTGAGTTACATGACAAGTATCTGCAGTATGTG
EST: gi|162155930|gb|FC332479.1|FC332479
EST:     GCTGAAAAGAAAGATACTGTTGGAGTTCAAGAACAG                         GCCTTTGTGCGGAAGGTCATTGAGTTACATGACAAGTATCTGCAGTATGTG
genomic: GCTGAAAAGAAAGATACTGTTGGAGTTCAAGAACAGgtaataacca ... ttcttcgcagGCCTTTGTGCGGAAGGTCATTGAGTTACATGACAAGTATCTGCAGTATGTG
EST: gi|162168333|gb|FC344647.1|FC344647
EST:     GCTGAAAAGAAAGATACTGTTGGAGTTCAAGAACAG                         GCCTTTGTGCGGAAGGTCATTGAGTTACATGACAAGTATCTGCAGTATGTG
genomic: GCTGAAAAGAAAGATACTGTTGGAGTTCAAGAACAGgtaataacca ... ttcttcgcagGCCTTTGTGCGGAAGGTCATTGAGTTACATGACAAGTATCTGCAGTATGTG
EST: gi|162197659|gb|FC374493.1|FC374493
EST:     GCTGAAAAGAAAGATACTGTTGGAGTTCAAGAACAG                         GCCTTTGTGCGGAAGGTCATTGAGTTACATGACAAGTATCTGCAGTATGTG
genomic: GCTGAAAAGAAAGATACTGTTGGAGTTCAAGAACAGgtaataacca ... ttcttcgcagGCCTTTGTGCGGAAGGTCATTGAGTTACATGACAAGTATCTGCAGTATGTG

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), 28 (downstream exon)
Score: 6

GCTGAAAAGAAAGATACTGTTGGAGTTCAAGAACAGgtaataacca ... ttcttcgcagGCCTTTGTGCGGAAGGTCATTGAGTTACATGACAAGTATCTGCAGTATGTGAGCGAGTGCTTCGTCAACCACTCCCTTTTTCACAAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggatagaaatgacgagaagaaatattctcatggttctctggttttcttcgcagGCCTTTGTGCGGAAGGTCATTGAGTTACATGACAAGTATCTGCAGTATGTGAGCGAGTGCTTCGTCAACCACTCCCTTTTTCACAAA
                                   ttctctggttttcttc  CT-rich tract
                  aagaaatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agggatgctagtgcaggtgtaaagctgttttattgcaatatatggttggatagaaatgacgagaagaaatattctcatggttctctggttttcttcgcagGCCTTTGTGCGGAAGGTCATTGAGTTACATGACAAGTATCTGCAGTATGTGAGCGAGTGCTTCGTCAACCACTCCCTTTTTCACAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG