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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagactattgtttctcgcagagttctgttgttctgatatcacctaagtacctggctttgtgtcggcgaagctctgttcagctagatcctgatttaatgattcacttgtcgcagATTCCTGGTGTTCCAATAATGTACATCTCACAGCATCAATATTCTATAGAGAGATTACCTGAAGCTACAATTGGGGGAG

Basic information

species Physcomitrella patens
transcript PP1S153_101V6.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S153_101V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA13G38690.2 (Glycine max), 3'ss of exon 8
gttagactattgtttctcgcagagttctgttgttctgatatcacctaagtacctggctttgtgtcggcgaagctctgttcagctagatcc-tgatttaatgattcacttgtcgcagATTCCTGGTGTTCCAATAATGTACATCTCACAGCATCAATATTCTATAGAGAGATTACCTGAAGCTACAATTGGGGGAG
                  | | |||    || |||   | || | |   |   ||  ||  | | ||     | ||| |  || ||| || |||| |   | ||    | |  |||||||| ||||||||||||||||||||| |  | |   | || || || ||| |||| |||||||| |||||||| ||||
------------------gtaaagtc--attattcacttttc-catctttgattgttttaatattgg----accctgat--gccagacccatgatctg--ggtttctgtattacagATTCCCGGTGTTCCAATAATGTACATCACCAAACGCAAGTACTCGATTGAGCGATTGCCTGAAGCAACAATTGGTGGAG

upper sequence: PP1S153_101V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA12G31740.1 (Glycine max), 3'ss of exon 8
gttagactattgtttctcgcagagttctgttgttctgatatcacctaagtacctggctttgtgtcggcgaagctctgttcagctagatc-ctgatttaatgattcact-tgtcgcagATTCCTGGTGTTCCAATAATGTACATCTCACAGCATCAATATTCTATAGAGAGATTACCTGAAGCTACAATTGGGGGAG
                               ||   |  || |   |  |  |   |||||  |     |   |     | | |  ||  |  |||   || ||  || | |  |||||||| ||||||||||||||||||||| |  | |   | || || || ||| |||| |||||||| |||||||| ||||
-------------------------------gtaaagtcattattcacttttccatctttggtttttaaatattggaccctgatgcatgacccattatgtggttttctgtattacagATTCCCGGTGTTCCAATAATGTACATCACCAAACGCAAGTACTCAATTGAGCGATTGCCTGAAGCAACAATTGGTGGAG
















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|208359401|gb|DC939140.1|DC939140
EST:     GCTATATTGTTGCTACATGTGATCGGGATTTGAAACGTCGCATTCGTAAG                         ATTCCTGGTGTTCCAATAATGTACATCTCACAGCATCAATATTCTATAGAG
genomic: GCTATATTGTTGCTACATGTGATCGGGATTTGAAACGTCGCATTCGTAAGgttagactat ... cttgtcgcagATTCCTGGTGTTCCAATAATGTACATCTCACAGCATCAATATTCTATAGAG
EST: gi|37822267|gb|BJ580333.1|BJ580333
EST:     GCTATATTGTTGCTACATGTGATCGGGATTTGAAACGTCGCATTCGTAAG                         ATTCCTGGTGTTCCAATAATGTACATCTCACAGCATCAATATTCTATAGAG
genomic: GCTATATTGTTGCTACATGTGATCGGGATTTGAAACGTCGCATTCGTAAGgttagactat ... cttgtcgcagATTCCTGGTGTTCCAATAATGTACATCTCACAGCATCAATATTCTATAGAG
EST: gi|100365650|gb|BY948205.1|BY948205
EST:     GCTATATTGTTGCTACATGTGATCGGGATTTGAAACGTCGCATTCGTAAG                         ATTCCTGGTGTTCCAATAATGTACATCTCACAGCATCAATATTCTATAGAG
genomic: GCTATATTGTTGCTACATGTGATCGGGATTTGAAACGTCGCATTCGTAAGgttagactat ... cttgtcgcagATTCCTGGTGTTCCAATAATGTACATCTCACAGCATCAATATTCTATAGAG
EST: gi|208383700|gb|DC928031.1|DC928031
EST:     GCTATATTGTTGCTACATGTGATCGGGATTTGAAACGTCGCATTCGTAAG                         ATTCCTGGTGTTCCAATAATGTACATCTCACAGCATCAATATTCTATAGAG
genomic: GCTATATTGTTGCTACATGTGATCGGGATTTGAAACGTCGCATTCGTAAGgttagactat ... cttgtcgcagATTCCTGGTGTTCCAATAATGTACATCTCACAGCATCAATATTCTATAGAG
EST: gi|37827579|gb|BJ585591.1|BJ585591
EST:     GCTATATTGTTGCTACATGTGATCGGGATTTGAAACGTCGCATTCGTAAG                         ATTCCTGGTGTTCCAATAATGTACATCTCACAGCATCAATATTCTATAGAG
genomic: GCTATATTGTTGCTACATGTGATCGGGATTTGAAACGTCGCATTCGTAAGgttagactat ... cttgtcgcagATTCCTGGTGTTCCAATAATGTACATCTCACAGCATCAATATTCTATAGAG
EST: gi|208400155|gb|DC904803.1|DC904803
EST:     GCTATATTGTTGCTACATGTGATCGGGATTTGAAACGTCGCATTCGTAAG                         ATTCCTGGTGTTCCAATAATGTACATCTCACAGCATCAATATTCTATAGAG
genomic: GCTATATTGTTGCTACATGTGATCGGGATTTGAAACGTCGCATTCGTAAGgttagactat ... cttgtcgcagATTCCTGGTGTTCCAATAATGTACATCTCACAGCATCAATATTCTATAGAG
EST: gi|162206440|gb|FC383433.1|FC383433
EST:     GCTATATTGTTGCTACATGTGATCGGGATTTGAAACGTCGCATTCGTAAG                         ATTCCTGGTGTTCCAATAATGTACATCTCACAGCATCAATATTCTATAGAG
genomic: GCTATATTGTTGCTACATGTGATCGGGATTTGAAACGTCGCATTCGTAAGgttagactat ... cttgtcgcagATTCCTGGTGTTCCAATAATGTACATCTCACAGCATCAATATTCTATAGAG
EST: gi|162253618|gb|FC430356.1|FC430356
EST:     GTTGCTACATGTGATCGGGATTTGAAACGTCGCATTCGTAAG                         ATTCCTGGTGTTCCAATAATGTACATCTCACAGCATCAATATTCTATAGAG
genomic: GTTGCTACATGTGATCGGGATTTGAAACGTCGCATTCGTAAGgttagactat ... cttgtcgcagATTCCTGGTGTTCCAATAATGTACATCTCACAGCATCAATATTCTATAGAG
EST: gi|208370447|gb|DC952150.1|DC952150
EST:     GCTATATTGTTGCTACATGTGATCGGGATTTGAAACGTCGCATTCGTAAG                         ATTCCTGGTGTTCCAATAATGTACATCTCACAGCATCAATATTCTATAGAG
genomic: GCTATATTGTTGCTACATGTGATCGGGATTTGAAACGTCGCATTCGTAAGgttagactat ... cttgtcgcagATTCCTGGTGTTCCAATAATGTACATCTCACAGCATCAATATTCTATAGAG
EST: gi|208354670|gb|DC918696.1|DC918696
EST:     GCTATATTGTTGCTACATGTGATCGGGATTTGAAACGTCGCATTCGTAAG                         ATTCCTGGTGTTCCAATAATGTACATCTCACAGCATCAATATTCTATAGAG
genomic: GCTATATTGTTGCTACATGTGATCGGGATTTGAAACGTCGCATTCGTAAGgttagactat ... cttgtcgcagATTCCTGGTGTTCCAATAATGTACATCTCACAGCATCAATATTCTATAGAG
EST: gi|37823705|gb|BJ581771.1|BJ581771
EST:     GCTATATTGTTGCTACATGTGATCGGGATTTGAAACGTCGCATTCGTAAG                         ATTCCTGGTGTTCCAATAATGTACATCTCACAGCATCAATATTCTATAGAG
genomic: GCTATATTGTTGCTACATGTGATCGGGATTTGAAACGTCGCATTCGTAAGgttagactat ... cttgtcgcagATTCCTGGTGTTCCAATAATGTACATCTCACAGCATCAATATTCTATAGAG

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: 21 (upstream exon), 32 (downstream exon)
Score: 7

AATAAGTGCTATATTGTTGCTACATGTGATCGGGATTTGAAACGTCGCATTCGTAAGgttagactat ... cttgtcgcagATTCCTGGTGTTCCAATAATGTACATCTCACAGCATCAATATTCTATAGAGAGATTACCTGAAGCTACAATTGGGGGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgtcggcgaagctctgttcagctagatcctgatttaatgattcacttgtcgcagATTCCTGGTGTTCCAATAATGTACATCTCACAGCATCAATATTCTATAGAGAGATTACCTGAAGCTACAATTGGGGGAG
                                         ttcactt  CT-rich tract
                                atttaatgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagactattgtttctcgcagagttctgttgttctgatatcacctaagtacctggctttgtgtcggcgaagctctgttcagctagatcctgatttaatgattcacttgtcgcagATTCCTGGTGTTCCAATAATGTACATCTCACAGCATCAATATTCTATAGAGAGATTACCTGAAGCTACAATTGGGGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC