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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgttctcgtcctgtgtttcccctcttcactcaggggagaaggtttaagcacaatattgttcgaatggttgaatttacctaacgttgtcgaattcctcttgttggcagGGTACACAAATTCAAGCCACAATGTTTAAGGAGGCTGCTGACAAATTCTATGACGTTCTGCAACTGGACAAG

Basic information

species Physcomitrella patens
transcript PP1S257_1V6.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S257_1V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: Vv17s0000g07440.t01 (Vitis vinifera), 3'ss of exon 4
----------------------------gtacgttct-cgtcctgtgtttcccctcttcactcaggggagaaggtttaag-cacaatattgttcgaatggttgaatttacctaacgttgtcgaattcctcttgttggcagGGTACACAAATTCAAGCCACAATGTTTAAGGAGGCTGCTGACAAATTCTATGACGTTCTGCAACTGGACAAG----------------------------
                            | | | |        |||| |  |    ||  |        |   ||||  | || |    |      |   |   | ||   | |     | |  || |||||| || |||||||||||||| ||||| ||||||||||| || |||||    || ||||||||     | |||||||  |||                            
gtaagcagaaaaagaatccattttctgagaatgctagatactttgtgctgactaaatttgcaatattttgtgtgtttgggtcatatctctacaattaacatcataattgtttcagcaaattgg-tttctcttggtg-cagGGTACACAAATCCAAGCAACAATGTTTAACGAAGCTGCAAGGAAGTTCTATGAAAAGTTCCAACTGGGGAAGGTCTATTACATATCAAAAGGAGCTCTAA
















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|100378584|gb|BY968675.1|BY968675
EST:     ACGCACGTGGAGATGGGAATGTCTTCAACGTTGAGCTCACCGATGAAGAT                         GGTACACAAATTCAAGCCACAATGTTTAAGGAGGCTGCTGACAAATTCTAT
genomic: ACGCACGTGGAGATGGGAATGTCTTCAACGTTGAGCTCACCGATGAAGATgtacgttctc ... ttgttggcagGGTACACAAATTCAAGCCACAATGTTTAAGGAGGCTGCTGACAAATTCTAT
EST: gi|100359872|gb|BY947164.1|BY947164
EST:     ACGCACGTGGAGATGGGAATGTCTTCAACGTTGAGCTCACCGATGAAGAT                         GGTACACAAATTCAAGCCACAATGTTTAAGGAGGCTGCTGACAAATTCTAT
genomic: ACGCACGTGGAGATGGGAATGTCTTCAACGTTGAGCTCACCGATGAAGATgtacgttctc ... ttgttggcagGGTACACAAATTCAAGCCACAATGTTTAAGGAGGCTGCTGACAAATTCTAT

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: 33 (upstream exon), 17 (downstream exon)
Score: 2

GACAATTAAAGTGAGGGTCACGAGCAAGAGCCCTCTCAGGACTTTCAAGAACGCACGTGGAGATGGGAATGTCTTCAACGTTGAGCTCACCGATGAAGATgtacgttctc ... ttgttggcagGGTACACAAATTCAAGCCACAATGTTTAAGGAGGCTGCTGACAAATTCTATGACGTTCTGCAACTGGACAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atattgttcgaatggttgaatttacctaacgttgtcgaattcctcttgttggcagGGTACACAAATTCAAGCCACAATGTTTAAGGAGGCTGCTGACAAATTCTATGACGTTCTGCAACTGGACAAG
                       acctaac  putative branch site (score: 2)
                                       ttcctcttgtt  putative PPT
               ttgaattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgttctcgtcctgtgtttcccctcttcactcaggggagaaggtttaagcacaatattgttcgaatggttgaatttacctaacgttgtcgaattcctcttgttggcagGGTACACAAATTCAAGCCACAATGTTTAAGGAGGCTGCTGACAAATTCTATGACGTTCTGCAACTGGACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT