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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagccaggtcaagaaacttatctgctagtgtcgttttctgctagttcttcgttctagagtaaatacatgaaaattgtcaatggaaaaatacataaacaaacaaaattgctttgggttatcatttctggattaatgttcatagtagaatgtttctgatgagcttgtggtcaaatttcacagGTGATTTACACAGATGTGGCGCTAGATCCTTACTCTTCAGATGGTCACGATGGCATAGTTCGGGAAGACG

Basic information

species Physcomitrella patens
transcript PP1S450_21V6.2
intron # 5
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|208362694|gb|DC931059.1|DC931059
EST:     GGCTGGTTCCACGGTGCATTCGGTTACTCAAAGACAAATTCCCTGATTTG                         GTGATTTACACAGATGTGGCGCTAGATCCTNACTCTTCAAATGGTCACGAT
genomic: GGCTGGTTCCACGGTGCATTCGGTTACTCAAAGACAAATTCCCTGATTTGgtaagccagg ... aatttcacagGTGATTTACACAGATGTGGCGCTAGATCCTTACTCTTCAGATGGTCACGAT
EST: gi|208354190|gb|DC902446.1|DC902446
EST:     GGCTGGTTCCACGGTGCATTCGGTTACTCAAAGACAAATTCCCTGATTTG                         GTGATTTACACAGATGTGGCGCTAGATCCTNACTCTTCA
genomic: GGCTGGTTCCACGGTGCATTCGGTTACTCAAAGACAAATTCCCTGATTTGgtaagccagg ... aatttcacagGTGATTTACACAGATGTGGCGCTAGATCCTTACTCTTCA
EST: gi|162234870|gb|FC410643.1|FC410643
EST:     GGCTGGTTCCACGGTGCATTCGGTTACTCAAAGACAAATTCCCTGATTTG                         GTGATTTACACAGATGTGGCGCTAGATCCTTACTCTTCAGATGGTCACGAT
genomic: GGCTGGTTCCACGGTGCATTCGGTTACTCAAAGACAAATTCCCTGATTTGgtaagccagg ... aatttcacagGTGATTTACACAGATGTGGCGCTAGATCCTTACTCTTCAGATGGTCACGAT
EST: gi|100379688|gb|BY949894.1|BY949894
EST:     GGCTGGTTCCACGGTGCATTCGGTTACTCAAAGACAAATTCCCTGATTTG                         GTGATTTACACAGATGTGGCGCTAGATCCTTACTCTTCAGATGGTCACGAT
genomic: GGCTGGTTCCACGGTGCATTCGGTTACTCAAAGACAAATTCCCTGATTTGgtaagccagg ... aatttcacagGTGATTTACACAGATGTGGCGCTAGATCCTTACTCTTCAGATGGTCACGAT
EST: gi|162163264|gb|FC339382.1|FC339382
EST:     GGCTGGTTCCACGGTGCATTCGGTTACTCANAGACAAATTCCCTGATTTG                         GTGATTTACACAGATGTG
genomic: GGCTGGTTCCACGGTGCATTCGGTTACTCAAAGACAAATTCCCTGATTTGgtaagccagg ... aatttcacagGTGATTTACACAGATGTG
EST: gi|162218488|gb|FC395065.1|FC395065
EST:     GGCTGGTTCCACGGTGCATTCGGTTACTCANAGACAAATTCCCTGATTTG                         GTGATTTACACAGATGTGGCGCTAGATCCTTACTCTTCAGATGGTCACGAT
genomic: GGCTGGTTCCACGGTGCATTCGGTTACTCAAAGACAAATTCCCTGATTTGgtaagccagg ... aatttcacagGTGATTTACACAGATGTGGCGCTAGATCCTTACTCTTCAGATGGTCACGAT
EST: gi|208400620|gb|DC904596.1|DC904596
EST:     GGCTGGTCCCACGGTGCATTCGGTTACTCAAAGACAAATTCCCTGATTTG                         GTGATTTACACAGATGTGGCGCTAGATCCTTACTCTTCAGATGGTCACGAT
genomic: GGCTGGTTCCACGGTGCATTCGGTTACTCAAAGACAAATTCCCTGATTTGgtaagccagg ... aatttcacagGTGATTTACACAGATGTGGCGCTAGATCCTTACTCTTCAGATGGTCACGAT
EST: gi|100370598|gb|BY948423.1|BY948423
EST:     GCTGGTTCCACGGTGCATTCGGTTACTCAAAGACAA-TTNNCCTGATTNG                         GTGATTTACACAGATGTGGCGCTAGATCCTTACTCTTCAGATGGTCACGA
genomic: GCTGGTTCCACGGTGCATTCGGTTACTCAAAGACAAATTC-CCTGATTTGgtaagccagg ... aatttcacagGTGATTTACACAGATGTGGCGCTAGATCCTTACTCTTCAGATGGTCACGA
EST: gi|208344405|gb|DC912764.1|DC912764
EST:     GGCTGGTTCCACGGTGCATTCGGTTACTCAAAGACAA-TTCCCTGATTTG                         GTGATT-ACACAGATGTGGCGCTAGATCCTTACTCTTC
genomic: GGCTGGTTCCACGGTGCATTCGGTTACTCAAAGACAAATTCCCTGATTTGgtaagccagg ... aatttcacagGTGATTTACACAGATGTGGCGCTAGATCCTTACTCTTC
EST: gi|162268623|gb|FC443677.1|FC443677
EST:     GGCTGGTTCCACGGTGCATTCGGTTACTCAAAGACAAATTCCCTGATTTG                         GTGATTTACACAGATGTGGCGCTAGATCCTTACTCTTCAGATGGTCACGAT
genomic: GGCTGGTTCCACGGTGCATTCGGTTACTCAAAGACAAATTCCCTGATTTGgtaagccagg ... aatttcacagGTGATTTACACAGATGTGGCGCTAGATCCTTACTCTTCAGATGGTCACGAT
EST: gi|162227018|gb|FC403362.1|FC403362
EST:     GGCTGGTTCCACGGTGCATTCGGTTACTCAAAGACAAATTCCCTGATTTG                         GTGATTTACACAGATGTGGCGCTAGATCCTTACTCTTCAGATGGTCACGAT
genomic: GGCTGGTTCCACGGTGCATTCGGTTACTCAAAGACAAATTCCCTGATTTGgtaagccagg ... aatttcacagGTGATTTACACAGATGTGGCGCTAGATCCTTACTCTTCAGATGGTCACGAT
EST: gi|67727441|gb|BJ977700.1|BJ977700
EST:     GGCTGGTTCCACGGTGCATTCGGTTACTCAAAGACAAATTCCCTGATTTG                         GTGATTTACACAGATGTGGCGCTAGATCCTTACTCTTCAGATGGTCACGAT
genomic: GGCTGGTTCCACGGTGCATTCGGTTACTCAAAGACAAATTCCCTGATTTGgtaagccagg ... aatttcacagGTGATTTACACAGATGTGGCGCTAGATCCTTACTCTTCAGATGGTCACGAT
EST: gi|100357521|gb|BY946437.1|BY946437
EST:     GGCTGGTTCCACGGTGCATTCGGTTACTCAAAGACAAATTCCCTGATTTG                         GTGATTTACACAGATGTGGCGCTAGATCCTTACTCTTCAGATGGTCACGAT
genomic: GGCTGGTTCCACGGTGCATTCGGTTACTCAAAGACAAATTCCCTGATTTGgtaagccagg ... aatttcacagGTGATTTACACAGATGTGGCGCTAGATCCTTACTCTTCAGATGGTCACGAT
EST: gi|162176323|gb|FC353508.1|FC353508
EST:     GGCTGGTTCCACGGTGCATTCGGTTACTCAAAGACAAATTCCCTGATTTG                         GTGATTTACACAGATGTGGCGCTAGATCCTTACTCTTCAGATGGTCACGAT
genomic: GGCTGGTTCCACGGTGCATTCGGTTACTCAAAGACAAATTCCCTGATTTGgtaagccagg ... aatttcacagGTGATTTACACAGATGTGGCGCTAGATCCTTACTCTTCAGATGGTCACGAT

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: 4

TCCTCAACTGGAGATGAGGCTTACAACCCCGATGGGCTGGTTCCACGGTGCATTCGGTTACTCAAAGACAAATTCCCTGATTTGgtaagccagg ... aatttcacagGTGATTTACACAGATGTGGCGCTAGATCCTTACTCTTCAGATGGTCACGATGGCATAGTTCGGGAAGACG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggattaatgttcatagtagaatgtttctgatgagcttgtggtcaaatttcacagGTGATTTACACAGATGTGGCGCTAGATCCTTACTCTTCAGATGGTCACGATGGCATAGTTCGGGAAGACG
                         ttctgat  putative branch site (score: 4)
                                          tcaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagccaggtcaagaaacttatctgctagtgtcgttttctgctagttcttcgttctagagtaaatacatgaaaattgtcaatggaaaaatacataaacaaacaaaattgctttgggttatcatttctggattaatgttcatagtagaatgtttctgatgagcttgtggtcaaatttcacagGTGATTTACACAGATGTGGCGCTAGATCCTTACTCTTCAGATGGTCACGATGGCATAGTTCGGGAAGACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA