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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aataaatatatgtatttttgtctaacttttgagcatttttaggttttggtttgattatgttttcttttttcttttttcaattcttgatgttggattacagATGCTTGTGGATGATATCGGCGACGTTACTATAACAAATGATGGAGCTACCATTTTAAAAATGCTTGAGGTGGAGCACCCCGCTGCTAAG

Basic information

species Physcomitrella patens
transcript PP1S39_248V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S39_248V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os04g46620.1 (Oryza sativa), 3'ss of exon 2
aataaatatatgtatttttgtctaacttttgagcatttttaggttttggtttgattatgttttcttttttcttttttcaattcttgatgttgga-ttacagATGCTTGTGGATGATATCGGCGACGTTACTATAACAAATGATGGAGCTACCATTTTAAAAATGCTTGAGGTGGAGCACCCCGCTGCTAAG
 || |||  |  ||   ||   | | || ||  |      |     || |      |     |    |    |     ||||    || |     ||  ||||||||||||||||||| || || ||||| ||||||||||||||||| |||||||| |  ||| | || || ||||| || || || |||
-attaatgaagttagacttagatcagttctgcaccacaccaatccctgataattccaaaaggttggctggaatgagctaattgagcatatccttcttgtagATGCTTGTGGATGATATTGGTGATGTTACCATAACAAATGATGGAGCAACCATTTTGAGGATGTTGGAAGTCGAGCATCCAGCAGCCAAG

upper sequence: PP1S39_248V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT3G20050.1 (Arabidopsis thaliana), 3'ss of exon 2
aataaatatatgtatttttgtctaacttttgagcatttttaggttttgg---tttgattatgttttcttttttcttttttcaattcttgatg--ttggattacagATGCTTGTGGATGATATCGGCGACGTTACTATAACAAATGATGGAGCTACCATTTTAAAAATGCTTGAGGTGGAGCACCCCGCTGCTAAG
       || | || |||| |   |  | ||  |  | ||    ||||    || | |  |  || ||    || | |||||  |  || ||  |||  || |||||| | ||||||||||| || || || ||||| ||||||||||| ||||| ||| | |  ||| | ||||| |||||||| |||||||||
-----ccatttctagttttattctaaatctgctcgatattgtcctttgtattttcgttcctagttcctccaatcgtgtttcatgttatgttggcttgtgtttcagATGTTGGTGGATGATATTGGTGATGTGACTATTACAAATGATGGTGCTACTATTCTTAGGATGTTGGAGGTCGAGCACCCTGCTGCTAAG
















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|100450985|gb|CJ974539.1|CJ974539
EST:     CCATCGCCAACATTGTGAAAACTTCGTTAGGGCCAGTTGGTCTCGACAAG                         ATGCTTGTGGATGATATCGGCGACGTTACTATAACAAATGATGGAGCTACC
genomic: CCATCGCCAACATTGTGAAAACTTCGTTAGGGCCAGTTGGTCTCGACAAGgttcgtgttt ... tggattacagATGCTTGTGGATGATATCGGCGACGTTACTATAACAAATGATGGAGCTACC
EST: gi|100441417|gb|BY962706.1|BY962706
EST:     CCATCGCCAACATTGTGAAAACTTCGTTAGGGCCAGTTGGTCTCGACAAG                         ATGCTTGTGGATGATATCGGCGACGTTACTATAACAAATGATGGAGCTACC
genomic: CCATCGCCAACATTGTGAAAACTTCGTTAGGGCCAGTTGGTCTCGACAAGgttcgtgttt ... tggattacagATGCTTGTGGATGATATCGGCGACGTTACTATAACAAATGATGGAGCTACC
EST: gi|100360990|gb|BY946858.1|BY946858
EST:     CCATCGCCAACATTGTGAAAACTTCGTTAGGGCCAGTTGGTCTCGACAAG                         ATGCTTGTGGATGATATCGGCGACGTTACTATAACAAATGATGGAGCTACC
genomic: CCATCGCCAACATTGTGAAAACTTCGTTAGGGCCAGTTGGTCTCGACAAGgttcgtgttt ... tggattacagATGCTTGTGGATGATATCGGCGACGTTACTATAACAAATGATGGAGCTACC
EST: gi|208347324|gb|DC909715.1|DC909715
EST:     CCATCGCCAACATTGTGAAAACTTCGTTAGGGCCAGTTGGTCTCGACAAG                         ATGCTTGTGGATGATATCGGCGACGTTACTATAACAAATGATGGAGCTACC
genomic: CCATCGCCAACATTGTGAAAACTTCGTTAGGGCCAGTTGGTCTCGACAAGgttcgtgttt ... tggattacagATGCTTGTGGATGATATCGGCGACGTTACTATAACAAATGATGGAGCTACC
EST: gi|100417876|gb|BY993228.1|BY993228
EST:     CCATCGCCAACATTGTGAAAACTTCGTTAGGGCCAGTTGGTCTCGACAAG                         ATGCTTGTGGATGATATCGGCGACGTTACTATAACAAATGATGGAGCTACC
genomic: CCATCGCCAACATTGTGAAAACTTCGTTAGGGCCAGTTGGTCTCGACAAGgttcgtgttt ... tggattacagATGCTTGTGGATGATATCGGCGACGTTACTATAACAAATGATGGAGCTACC
EST: gi|18358450|gb|BJ190509.1|BJ190509
EST:     CCATCGCCAACATTGTGAAAACTTCGNTAGGGC-AGNTGGTCTCGACAAG                         ATGCTTGTGGATGATATCGGCGACGTTACTATAACAAATGATGGAGCTACC
genomic: CCATCGCCAACATTGTGAAAACTTCGTTAGGGCCAGTTGGTCTCGACAAGgttcgtgttt ... tggattacagATGCTTGTGGATGATATCGGCGACGTTACTATAACAAATGATGGAGCTACC
EST: gi|208360034|gb|DC934923.1|DC934923
EST:     CCATCGCCAACATTGTGAAAACTTCGTTAGGGCCAGTTGGTCTCGACAAG                         ATGCTTGTGGATGATATCGGCGACGTTACTATAACAAATGATGGAGCTACC
genomic: CCATCGCCAACATTGTGAAAACTTCGTTAGGGCCAGTTGGTCTCGACAAGgttcgtgttt ... tggattacagATGCTTGTGGATGATATCGGCGACGTTACTATAACAAATGATGGAGCTACC
EST: gi|100449912|gb|CJ973999.1|CJ973999
EST:     CCATCGCCAACATTGTGAAAACTTCGTTAGGGCCAGTTGGTCTCGACAAG                         ATGCTTGTGGATGATATCGGCGACGTTACTATAACAAATGATGGAGCTACC
genomic: CCATCGCCAACATTGTGAAAACTTCGTTAGGGCCAGTTGGTCTCGACAAGgttcgtgttt ... tggattacagATGCTTGTGGATGATATCGGCGACGTTACTATAACAAATGATGGAGCTACC
EST: gi|18373059|gb|BJ204661.1|BJ204661
EST:     CCATCGCCAACATTGTGAAAACTTCGTTAGGG-CAGTTGGTCTCGACAAG                         ATGCTTGTGGATGATATCGGCGACGTTACTATAACAAATGATGGAGCTACC
genomic: CCATCGCCAACATTGTGAAAACTTCGTTAGGGCCAGTTGGTCTCGACAAGgttcgtgttt ... tggattacagATGCTTGTGGATGATATCGGCGACGTTACTATAACAAATGATGGAGCTACC
EST: gi|67719559|gb|BJ969818.1|BJ969818
EST:     CCATCGCCAACATTGTGAAAACTTCGTTAGGGCCAGTTGGTCTCGACAAG                         ATGCTTGTGGATGATATCGGCGACGTTACTATAACAAATGATGGAGCTACC
genomic: CCATCGCCAACATTGTGAAAACTTCGTTAGGGCCAGTTGGTCTCGACAAGgttcgtgttt ... tggattacagATGCTTGTGGATGATATCGGCGACGTTACTATAACAAATGATGGAGCTACC

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: 9 (upstream exon), 27 (downstream exon)
Score: 1

TTATGGCTTGTCAAGCCATCGCCAACATTGTGAAAACTTCGTTAGGGCCAGTTGGTCTCGACAAGgttcgtgttt ... tggattacagATGCTTGTGGATGATATCGGCGACGTTACTATAACAAATGATGGAGCTACCATTTTAAAAATGCTTGAGGTGGAGCACCCCGCTGCTAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggtttgattatgttttcttttttcttttttcaattcttgatgttggattacagATGCTTGTGGATGATATCGGCGACGTTACTATAACAAATGATGGAGCTACCATTTTAAAAATGCTTGAGGTGGAGCACCCCGCTGCTAAG
                                    tcttgat  putative branch site (score: 1)
        attatgttttcttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aataaatatatgtatttttgtctaacttttgagcatttttaggttttggtttgattatgttttcttttttcttttttcaattcttgatgttggattacagATGCTTGTGGATGATATCGGCGACGTTACTATAACAAATGATGGAGCTACCATTTTAAAAATGCTTGAGGTGGAGCACCCCGCTGCTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT