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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatctgtaaaattttgttcgactgaaggaatgctatgtggcgctggtaattttatcgcacaagcatggatgaaaatgctaatttgtggtacttcctacagGTTCCACCAACGTTGAGGTTTGTGCTCGATGGAGAAATGCCAAAGTACCTGTTAGCCAAGGATCTCATATTGCAG

Basic information

species Physcomitrella patens
transcript PP1S227_66V6.1
intron # 6
splice site 3'
intron type U2

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|162179912|gb|FC355983.1|FC355983
EST:     GTAACACTGATGCAGGCTTTATTATGGGCACCGGCAAGCTCCTGATTAAG                         GTTCCACCAACGTTGAGGTTTGTGCTCGATGGAGAAATGCCAAAGTACCTG
genomic: GTAACACTGATGCAGGCTTTATTATGGGCACCGGCAAGCTCCTGATTAAGgtacagttga ... cttcctacagGTTCCACCAACGTTGAGGTTTGTGCTCGATGGAGAAATGCCAAAGTACCTG
EST: gi|19790555|gb|BQ041934.1|BQ041934
EST:     GTAACACTGATGCAGGCTTTATTATGGGCACCGGCAAGCTCCTGATTAAG                         GTTCCACCAACGTTGAGGTTTGTGCTCGATGGAGAAATGCCAAAGTACCTG
genomic: GTAACACTGATGCAGGCTTTATTATGGGCACCGGCAAGCTCCTGATTAAGgtacagttga ... cttcctacagGTTCCACCAACGTTGAGGTTTGTGCTCGATGGAGAAATGCCAAAGTACCTG
EST: gi|100388195|gb|BY951797.1|BY951797
EST:     GTAACACTGATGCAGGCTTTATTATGGGCACCGGCAAGCTCCTGATTAAG                         GTTCCACCAACGTTGAGGTTTGTGCTCGATGGAGAAATGCCAAAGTACCTG
genomic: GTAACACTGATGCAGGCTTTATTATGGGCACCGGCAAGCTCCTGATTAAGgtacagttga ... cttcctacagGTTCCACCAACGTTGAGGTTTGTGCTCGATGGAGAAATGCCAAAGTACCTG
EST: gi|162213332|gb|FC389620.1|FC389620
EST:     GCACCGGCAAGCTCCTGATTAAG                         GTTCCACCAACGTTGAGGTTTGTGCTCGATGGAGAAATGCCAAAGTACCTG
genomic: GCACCGGCAAGCTCCTGATTAAGgtacagttga ... cttcctacagGTTCCACCAACGTTGAGGTTTGTGCTCGATGGAGAAATGCCAAAGTACCTG
EST: gi|7286764|gb|AW599251.1|AW599251
EST:     GTAACACTGATGCAGGCTTTATTATGGGCACCGGCAAGCTCCTGATTAAG                         GTTCCACCAACGTTGAGGTTTGTGCTCGATGGAGAAATGCCAAAGTACCTG
genomic: GTAACACTGATGCAGGCTTTATTATGGGCACCGGCAAGCTCCTGATTAAGgtacagttga ... cttcctacagGTTCCACCAACGTTGAGGTTTGTGCTCGATGGAGAAATGCCAAAGTACCTG
EST: gi|100413212|gb|BY956563.1|BY956563
EST:     GTAACACTGATGCAGGCTTTATTATGGGCACCGGCAAGCTCCTGATTAAG                         GTTCCACCAACGTTGAGGTTTGTGCTCGATGGAGAAATGCCAAAGTACCTG
genomic: GTAACACTGATGCAGGCTTTATTATGGGCACCGGCAAGCTCCTGATTAAGgtacagttga ... cttcctacagGTTCCACCAACGTTGAGGTTTGTGCTCGATGGAGAAATGCCAAAGTACCTG
EST: gi|162243293|gb|FC415642.1|FC415642
EST:     AGGCTTTATTATGGGCACCGGCAAGCTCCTGATTAAG                         GTTCCACCAACGTTGAGGTTTGTGCTCGATGGAGAAATGCCAAAGTACCTG
genomic: AGGCTTTATTATGGGCACCGGCAAGCTCCTGATTAAGgtacagttga ... cttcctacagGTTCCACCAACGTTGAGGTTTGTGCTCGATGGAGAAATGCCAAAGTACCTG
EST: gi|162261369|gb|FC437802.1|FC437802
EST:     GTAACACTGATGCAGGCTTTATTATGGGCACCGGCAAGCTCCTGATTAAG                         GTTCCACCAACGTTGAGGTTTGTGCTCGATGGAGAAATGCCAAAGTACCTG
genomic: GTAACACTGATGCAGGCTTTATTATGGGCACCGGCAAGCTCCTGATTAAGgtacagttga ... cttcctacagGTTCCACCAACGTTGAGGTTTGTGCTCGATGGAGAAATGCCAAAGTACCTG
EST: gi|100364743|gb|BY947886.1|BY947886
EST:     TAACACTGATGCAGGCTTTATTATGGGCACCGGCAAGCTCCCTGATTAAG                         GTCCCACCA-CGTTGAGGTTTGTGCTCGATGG
genomic: TAACACTGATGCAGGCTTTATTATGGGCACCGGCAAGCTCC-TGATTAAGgtacagttga ... cttcctacagGTTCCACCAACGTTGAGGTTTGTGCTCGATGG
EST: gi|162172982|gb|FC347892.1|FC347892
EST:     GTAACACTGATGCAGGCTTTATTATGGGCACCGGCAAGCTCCTGATTAAG                         GTTCCACCAACGTTGAGGTTTGTGCTCGATGGAGAAATGCCAAAGTACCTG
genomic: GTAACACTGATGCAGGCTTTATTATGGGCACCGGCAAGCTCCTGATTAAGgtacagttga ... cttcctacagGTTCCACCAACGTTGAGGTTTGTGCTCGATGGAGAAATGCCAAAGTACCTG
EST: gi|162199219|gb|FC375055.1|FC375055
EST:     GTAACACTGATGCAGGCTTTATTATGGGCACCGGCAAGCTCCTGATTAAG                         GTTCCACCAACGTTGAGGTTTGTGCTCGATGGAGAAATGCCAAAGTACCTG
genomic: GTAACACTGATGCAGGCTTTATTATGGGCACCGGCAAGCTCCTGATTAAGgtacagttga ... cttcctacagGTTCCACCAACGTTGAGGTTTGTGCTCGATGGAGAAATGCCAAAGTACCTG
EST: gi|162258438|gb|FC434445.1|FC434445
EST:     GTAACACTGATGCAGGCTTTATTATGGGCACCGGCAAGCTCCTGATTAAG                         GTTCCACCAACGTTGAGGTTTGTGCTCGATGGAGAAATGCCAAAGTACCTG
genomic: GTAACACTGATGCAGGCTTTATTATGGGCACCGGCAAGCTCCTGATTAAGgtacagttga ... cttcctacagGTTCCACCAACGTTGAGGTTTGTGCTCGATGGAGAAATGCCAAAGTACCTG
EST: gi|100410814|gb|BY956200.1|BY956200
EST:     GTAACACTGATGCAGGCTTTATTATGGGCACCGGCAAGCTCCTGATTAAG                         GTTCCACCAACGTTGAGGTTTGTGCTCGATGGAGAAATGCCAAAGTACCTG
genomic: GTAACACTGATGCAGGCTTTATTATGGGCACCGGCAAGCTCCTGATTAAGgtacagttga ... cttcctacagGTTCCACCAACGTTGAGGTTTGTGCTCGATGGAGAAATGCCAAAGTACCTG
EST: gi|162198077|gb|FC372104.1|FC372104
EST:     GTAACACTGATGCAGGCTTTATTATGGGCACCGGCAAGCTCCTGATTAAG                         GTTCCACCAACGTTG
genomic: GTAACACTGATGCAGGCTTTATTATGGGCACCGGCAAGCTCCTGATTAAGgtacagttga ... cttcctacagGTTCCACCAACGTTG
EST: gi|100362852|gb|BY947561.1|BY947561
EST:     TAACACTGATGCAGGCTTTATTATGGGCACCGGCAAGCTCCTGATTAANG                         GT-CCACCNACGNTGAGGTTTGTGCTCGA
genomic: TAACACTGATGCAGGCTTTATTATGGGCACCGGCAAGCTCCTGATTAA-Ggtacagttga ... cttcctacagGTTCCACCAACGTTGAGGTTTGTGCTCGA
EST: gi|19778198|gb|BQ039280.1|BQ039280
EST:     GTAACACTGATGCAGGCTTTATTATGGGCACCGGCAAGCTCCTGATTAAG                         GTTCCACCAACGTTGAGGTTTGTGCTCGATGGAGAAATGCCAAAGTACCTG
genomic: GTAACACTGATGCAGGCTTTATTATGGGCACCGGCAAGCTCCTGATTAAGgtacagttga ... cttcctacagGTTCCACCAACGTTGAGGTTTGTGCTCGATGGAGAAATGCCAAAGTACCTG
EST: gi|162222838|gb|FC399300.1|FC399300
EST:     GTAACACTGATGCAGGCTTTATTATGGGCACCGGCAAGCTCCTGATTAAG                         GTTCCACCAACGTTGAGGTTTGTGCTCGATGGAGAAATGCCAAAGTACCTG
genomic: GTAACACTGATGCAGGCTTTATTATGGGCACCGGCAAGCTCCTGATTAAGgtacagttga ... cttcctacagGTTCCACCAACGTTGAGGTTTGTGCTCGATGGAGAAATGCCAAAGTACCTG
EST: gi|19780614|gb|BQ039583.1|BQ039583
EST:     GTAACACTGATGCAGGCTTTATTATGGGCACCGGCAAGCTCCTGATTAAG                         GTTCCACCAACGTTGAGGTTTGTGCTCGATGGAGAAATGCCAAAGTACCTG
genomic: GTAACACTGATGCAGGCTTTATTATGGGCACCGGCAAGCTCCTGATTAAGgtacagttga ... cttcctacagGTTCCACCAACGTTGAGGTTTGTGCTCGATGGAGAAATGCCAAAGTACCTG
EST: gi|22492336|gb|BU052259.1|BU052259
EST:     GTAACACTGATGCAGGCTTTATTATGGGCACCGGCAAGCTCCTGATTAAG                         GTTCCACCAACGTTGAGGTTTGTGCTCGATGGAGAAATGCCAAAGTACCTG
genomic: GTAACACTGATGCAGGCTTTATTATGGGCACCGGCAAGCTCCTGATTAAGgtacagttga ... cttcctacagGTTCCACCAACGTTGAGGTTTGTGCTCGATGGAGAAATGCCAAAGTACCTG

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: 30 (upstream exon), 29 (downstream exon)
Score: 14

TTCCCACACTTGCAATGCTGGAGCGTTTGGTCAGTTTGCAACAGGGATCGGTAACACTGATGCAGGCTTTATTATGGGCACCGGCAAGCTCCTGATTAAGgtacagttga ... cttcctacagGTTCCACCAACGTTGAGGTTTGTGCTCGATGGAGAAATGCCAAAGTACCTGTTAGCCAAGGATCTCATATTGCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaattttatcgcacaagcatggatgaaaatgctaatttgtggtacttcctacagGTTCCACCAACGTTGAGGTTTGTGCTCGATGGAGAAATGCCAAAGTACCTGTTAGCCAAGGATCTCATATTGCAG
                              tgctaat  putative branch site (score: 14)
                                           tacttcct  putative PPT
                       atgaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatctgtaaaattttgttcgactgaaggaatgctatgtggcgctggtaattttatcgcacaagcatggatgaaaatgctaatttgtggtacttcctacagGTTCCACCAACGTTGAGGTTTGTGCTCGATGGAGAAATGCCAAAGTACCTGTTAGCCAAGGATCTCATATTGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -cacaagc