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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagacttcggctaccacttttaccgatcttgatttctatgtgctagtatcattattcctgtttgatgagtctttgccacaaaaatgtatgtactgtgcgatctcatcgtgccaagaatttactagtctaattactctgtgtcgctgcaatagGCTCTGATCAACATCATCAGCAACCCCGTGAACTCCACGGTTCCAATTGCTGCCGAGGTTCTCAAGGCCAAAGGTGTCTACGACCCCAAGAAGGTCTTCG

Basic information

species Physcomitrella patens
transcript PP1S79_110V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S79_110V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ07757 (Selaginella moellendorffii), 3'ss of exon 2
gtgagacttcggctaccacttttaccgatcttgatttctatgtgctagtatcattattcctgtttgatgagtctttgccacaaaaatgtatgtactgtgcgatctcatcgtgccaagaatttactagtctaattactctgtgtcgctgcaatagGCTCTGATCAACATCATCAGCAACCCCGTGAACTCCACGGTTCCAATTGCTGCCGAGGTTCTCAAGGCCAAAGGTGTCTACGACCCCAAGAAGGTCTTCG
                                                                                               |   |  | |  ||  |  ||| ||  | |   || | |||  ||||          |||||  ||||||||| |||||||| ||||||||||| || || || || ||||| |||||||| ||    || || || | ||| || |||||| |||| |
---------------------------------------------------------------------------------------------gttcgtcttttttctctagaaaaggatggaatgtactgaataccttgtg--------gcagGCTTGGATCAACATTATCAGCAATCCCGTGAACTCGACCGTGCCCATAGCTGCTGAGGTTCTTAAAAAGAAGGGAGTGTTCGATCCAAAGAAGCTCTTTG

upper sequence: PP1S79_110V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ07703 (Selaginella moellendorffii), 3'ss of exon 2
gtgagacttcggctaccacttttaccgatcttgatttctatgtgctagtatcattattcctgtttgatgagtctttgccacaaaaatgtatgtactgtgcgatctcatcgtgccaagaatttactagtctaattactctgtgtcgctgcaatagGCTCTGATCAACATCATCAGCAACCCCGTGAACTCCACGGTTCCAATTGCTGCCGAGGTTCTCAAGGCCAAAGGTGTCTACGACCCCAAGAAGGTCTTCG
                                                                                               |   |  | |  ||  |  ||| ||  | |   || | |||  ||||          |||||  ||||||||| |||||||| ||||||||||| || || || || ||||| |||||||| ||    || || || | ||| || |||||| |||| |
---------------------------------------------------------------------------------------------gttcgtcttttttctctagaaaaggatgaaatgtactgaataccttgtg--------gcagGCTTGGATCAACATTATCAGCAATCCCGTGAACTCGACCGTGCCCATAGCTGCTGAGGTTCTTAAAAAGAAGGGAGTGTTCGATCCAAAGAAGCTCTTTG
















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|67709714|gb|BJ965530.1|BJ965530
EST:     CCGGCATCGTCAGGAGTCTCGTTGAAGCAGTTGCGGAAAATTGCCCCAAC                         GCTCTGATCAACATCATCAGCAACCCCGTGAACTCCACGG
genomic: CCGGCATCGTCAGGAGTCTCGTTGAAGCAGTTGCGGAAAATTGCCCCAACgtgagacttc ... gctgcaatagGCTCTGATCAACATCATCAGCAACCCCGTGAACTCCACGG
EST: gi|67718039|gb|BJ968298.1|BJ968298
EST:     CCGGCATCGTCAGGAGTCTCGTTGAAGCAGTTGCGGAAAATTGCCCCAAC                         GCTCTGATCAACATCATCAGCAACCCCGTGAACTCCACGGTTCCAATTGCT
genomic: CCGGCATCGTCAGGAGTCTCGTTGAAGCAGTTGCGGAAAATTGCCCCAACgtgagacttc ... gctgcaatagGCTCTGATCAACATCATCAGCAACCCCGTGAACTCCACGGTTCCAATTGCT
EST: gi|208360119|gb|DC939158.1|DC939158
EST:     CCGGCATCGTCAGGAGTCTCGTTGAAGCAGTTGCGGAAAATTGCCCCAAC                         GCTCTGATCAACATCATCAGCAACCCCGTGAACTCCACGGTTCCA-TTGCT
genomic: CCGGCATCGTCAGGAGTCTCGTTGAAGCAGTTGCGGAAAATTGCCCCAACgtgagacttc ... gctgcaatagGCTCTGATCAACATCATCAGCAACCCCGTGAACTCCACGGTTCCAATTGCT
EST: gi|162170324|gb|FC346521.1|FC346521
EST:     CCGGCATCGTCAGGAGTCTCGTTGAAGCAGTTGCGGAAAATTGCCCCAAC                         GCTCTGATCAACATCATCAGCAACCCCGTGAACTCCACGGTTCCAATTGCT
genomic: CCGGCATCGTCAGGAGTCTCGTTGAAGCAGTTGCGGAAAATTGCCCCAACgtgagacttc ... gctgcaatagGCTCTGATCAACATCATCAGCAACCCCGTGAACTCCACGGTTCCAATTGCT
EST: gi|208400655|gb|DC908966.1|DC908966
EST:     CCGGCATCGTCAGGAGTCTCGTTGAAGCAGTTGCGGAAAATTGCCCCAAC                         GCTCTGATCAACATCATCAGCAACCCCGTGAACTCCACGGTTCNA-TTGCT
genomic: CCGGCATCGTCAGGAGTCTCGTTGAAGCAGTTGCGGAAAATTGCCCCAACgtgagacttc ... gctgcaatagGCTCTGATCAACATCATCAGCAACCCCGTGAACTCCACGGTTCCAATTGCT
EST: gi|100387527|gb|BY988398.1|BY988398
EST:     CGGCATCGTCAGGAGTCTCGTTGAAACAGTTGCGGGAAAAT-GCCCCAAC                         GCTCTGATCAA
genomic: CGGCATCGTCAGGAGTCTCGTTGAAGCAGTTGCGG-AAAATTGCCCCAACgtgagacttc ... gctgcaatagGCTCTGATCAA
EST: gi|162268356|gb|FC444125.1|FC444125
EST:     CCGGCATCGTCAGGAGTCTCGTTGAAGCAGTTGCGGAAAATTGCCCCAAC                         GCTCTGATCAACATCATCAGCAACCCCGTGAACTCCACGGTTCCAATTGCT
genomic: CCGGCATCGTCAGGAGTCTCGTTGAAGCAGTTGCGGAAAATTGCCCCAACgtgagacttc ... gctgcaatagGCTCTGATCAACATCATCAGCAACCCCGTGAACTCCACGGTTCCAATTGCT
EST: gi|100400057|gb|BY990757.1|BY990757
EST:     CCGGCATCGTCAGGAGTCTCGTTGAAGCAGTTGCGGAAAATTGCCCCAAC                         GCTCTGATCAACATCATCAGCAACCCCGTGAACTCCACGGTTCCAATTGCT
genomic: CCGGCATCGTCAGGAGTCTCGTTGAAGCAGTTGCGGAAAATTGCCCCAACgtgagacttc ... gctgcaatagGCTCTGATCAACATCATCAGCAACCCCGTGAACTCCACGGTTCCAATTGCT
EST: gi|162153053|gb|FC330083.1|FC330083
EST:     CCGGCATCGTCAGGAGTCTCGTTGAAGCAGTTGCGGAAAATTGCCCCAAC                         GCTCTGATCAACATCATCAGCAACCCCGTGAACTCCACGGTTCCAATTGCT
genomic: CCGGCATCGTCAGGAGTCTCGTTGAAGCAGTTGCGGAAAATTGCCCCAACgtgagacttc ... gctgcaatagGCTCTGATCAACATCATCAGCAACCCCGTGAACTCCACGGTTCCAATTGCT
EST: gi|162195925|gb|FC375658.1|FC375658
EST:     CCGGCATCGTCAGGAGTCTCGTTGAAGCAGTTGCGGAAAATTGCCCCAAC                         GCTCTGATCAACATCATCAGCAACCCCGTGAACTCCACGGTTCCAATTGCT
genomic: CCGGCATCGTCAGGAGTCTCGTTGAAGCAGTTGCGGAAAATTGCCCCAACgtgagacttc ... gctgcaatagGCTCTGATCAACATCATCAGCAACCCCGTGAACTCCACGGTTCCAATTGCT
EST: gi|208390508|gb|DC933765.1|DC933765
EST:     CCGGCATCGTCAGGAGTCTCGTTGAAGCAGTTGCGGAAAATTGCCCCAAC                         GCTCTGATCAACATCATCAGCAACCCCGTGAACTCCACGGTTCNA-TTGCT
genomic: CCGGCATCGTCAGGAGTCTCGTTGAAGCAGTTGCGGAAAATTGCCCCAACgtgagacttc ... gctgcaatagGCTCTGATCAACATCATCAGCAACCCCGTGAACTCCACGGTTCCAATTGCT
EST: gi|162168311|gb|FC344625.1|FC344625
EST:     CCGGCATCGTCAGGAGTCTCGTTGAAGCAGTTGCGGAAAATTGCCCCAAC                         GCTCTGATCAACATCATCAGCAACCCCGTGAACTCCACGGTTCCAATTGCT
genomic: CCGGCATCGTCAGGAGTCTCGTTGAAGCAGTTGCGGAAAATTGCCCCAACgtgagacttc ... gctgcaatagGCTCTGATCAACATCATCAGCAACCCCGTGAACTCCACGGTTCCAATTGCT
EST: gi|208370698|gb|DC936158.1|DC936158
EST:     CCGGCATCGTCAGGAGTCTCGTTGAAGCAGTTGCGGAAA-TTGCCCCAAC                         GCTCTGATCAACATCATCAGCAACCCCGTGAACTCCACGGTNCCA-TTGCT
genomic: CCGGCATCGTCAGGAGTCTCGTTGAAGCAGTTGCGGAAAATTGCCCCAACgtgagacttc ... gctgcaatagGCTCTGATCAACATCATCAGCAACCCCGTGAACTCCACGGTTCCAATTGCT
EST: gi|100384137|gb|BY950523.1|BY950523
EST:     CCGGCATCGTCAGGAGTCTCGTTGAAGCAGTTGCGGAAAATTGCCCCAAC                         GCTCTGATCAACATCATCAGCAACCCCGTGAACTCCACGGTTCCAATTGCT
genomic: CCGGCATCGTCAGGAGTCTCGTTGAAGCAGTTGCGGAAAATTGCCCCAACgtgagacttc ... gctgcaatagGCTCTGATCAACATCATCAGCAACCCCGTGAACTCCACGGTTCCAATTGCT
EST: gi|67508508|gb|BJ941373.1|BJ941373
EST:     CCGGCATCGTCAGGAGTCTCGTTGAAGCAGTTGCGGAAAATTGCCCCAAC                         GCTCTGATCAACATCATCAGCAACCCCGTGAACTCCACGGTTCCAATTGCT
genomic: CCGGCATCGTCAGGAGTCTCGTTGAAGCAGTTGCGGAAAATTGCCCCAACgtgagacttc ... gctgcaatagGCTCTGATCAACATCATCAGCAACCCCGTGAACTCCACGGTTCCAATTGCT
EST: gi|100410309|gb|BY992042.1|BY992042
EST:     CCGGCATCGTCAGGAGTCTCGTTGAAGCAGTTGCGGAAAATTGCCCCAAC                         GCTCTGATCAACATCATCAGCAACCCCGTGAACTCCACGGTTCCAATTGCT
genomic: CCGGCATCGTCAGGAGTCTCGTTGAAGCAGTTGCGGAAAATTGCCCCAACgtgagacttc ... gctgcaatagGCTCTGATCAACATCATCAGCAACCCCGTGAACTCCACGGTTCCAATTGCT
EST: gi|67712620|gb|BJ966069.1|BJ966069
EST:     CCGGCATCGTCAGGAGTCTCGTTGAAGCAGTTGCGGAAAATTGCCCCAAC                         GCTCTGATCAACATCATCAGCAACC
genomic: CCGGCATCGTCAGGAGTCTCGTTGAAGCAGTTGCGGAAAATTGCCCCAACgtgagacttc ... gctgcaatagGCTCTGATCAACATCATCAGCAACC
EST: gi|100405442|gb|BY955527.1|BY955527
EST:     CCGGCATCGTCAGGAGTCTCGTTGAAGCAGTTGCGGAAAATTGCCCCAAC                         GCTCTGATCAACATCATCAGCAACCCCGTGAACTCCACGGTTCCA
genomic: CCGGCATCGTCAGGAGTCTCGTTGAAGCAGTTGCGGAAAATTGCCCCAACgtgagacttc ... gctgcaatagGCTCTGATCAACATCATCAGCAACCCCGTGAACTCCACGGTTCCA
EST: gi|18371317|gb|BJ202919.1|BJ202919
EST:     CCGGCATCGTCAGGAGTCTCGTTGAAGCAGTTGCGGAAAATTGCCCCAAC                         GCTCTGATCAACATCATCAGCAACCCCGTGAACTCCAAGGTTCCAATTGCT
genomic: CCGGCATCGTCAGGAGTCTCGTTGAAGCAGTTGCGGAAAATTGCCCCAACgtgagacttc ... gctgcaatagGCTCTGATCAACATCATCAGCAACCCCGTGAACTCCACGGTTCCAATTGCT
EST: gi|208358903|gb|DC942985.1|DC942985
EST:     CCGGCATCGTCAGGAGTCTCGTTGAAGCAGTTGCGGAAAATTGCCCCAAC                         GCTCTGATCAACATCATCAGCAACCCCGTGAACTCCACGGTTCCAAT-GCT
genomic: CCGGCATCGTCAGGAGTCTCGTTGAAGCAGTTGCGGAAAATTGCCCCAACgtgagacttc ... gctgcaatagGCTCTGATCAACATCATCAGCAACCCCGTGAACTCCACGGTTCCAATTGCT
EST: gi|100406294|gb|BY955560.1|BY955560
EST:     CCGGCATCGTCAGGAGTCTCGTTGAAGCAGTTGCGGAAAATTGCCCCAAC                         GCTCTGATCAACATCATCAGCAACCCCGTGAACTCCACGGTTCCAATTGCT
genomic: CCGGCATCGTCAGGAGTCTCGTTGAAGCAGTTGCGGAAAATTGCCCCAACgtgagacttc ... gctgcaatagGCTCTGATCAACATCATCAGCAACCCCGTGAACTCCACGGTTCCAATTGCT

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: 16

AGTACCCCGCAAACCCGGCATGACCAGAGATGATTTGTTCAACATCAACGCCGGCATCGTCAGGAGTCTCGTTGAAGCAGTTGCGGAAAATTGCCCCAACgtgagacttc ... gctgcaatagGCTCTGATCAACATCATCAGCAACCCCGTGAACTCCACGGTTCCAATTGCTGCCGAGGTTCTCAAGGCCAAAGGTGTCTACGACCCCAAGAAGGTCTTCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgatctcatcgtgccaagaatttactagtctaattactctgtgtcgctgcaatagGCTCTGATCAACATCATCAGCAACCCCGTGAACTCCACGGTTCCAATTGCTGCCGAGGTTCTCAAGGCCAAAGGTGTCTACGACCCCAAGAAGGTCTTCG
                           gtctaat  putative branch site (score: 16)
               aagaattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagacttcggctaccacttttaccgatcttgatttctatgtgctagtatcattattcctgtttgatgagtctttgccacaaaaatgtatgtactgtgcgatctcatcgtgccaagaatttactagtctaattactctgtgtcgctgcaatagGCTCTGATCAACATCATCAGCAACCCCGTGAACTCCACGGTTCCAATTGCTGCCGAGGTTCTCAAGGCCAAAGGTGTCTACGACCCCAAGAAGGTCTTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG