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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggcctctcactcattttcttgaactttaaaaataataataataagccttctctgtatagcacatattattattgtacacactcttgctgaatgttttcgctttcatgtgaccgactttctcaatctgacaatttccacgcgtcttgcagGCTGGCTGGAAGCTGTGGCCCTTTGCGCATCTTATCACGTATGGTTTGGTTCCCGTCGAACAGCGTCTGCTGTGGGTAGACTGTGTGGAGATTCTTTGGG

Basic information

species Physcomitrella patens
transcript PP1S79_119V6.1
intron # 3
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|162187828|gb|FC364402.1|FC364402
EST:     CCGTTAGGATACTCAAGGATTTAAGAGAAACATTCTTCCCTCTTTTGACG                         GCTGGCTGGAAGCTGTGGCCCTTTGCGCATCTTATCACGTATGGTTTGGTT
genomic: CCGTTAGGATACTCAAGGATTTAAGAGAAACATTCTTCCCTCTTTTGACGgtaaggcctc ... cgtcttgcagGCTGGCTGGAAGCTGTGGCCCTTTGCGCATCTTATCACGTATGGTTTGGTT
EST: gi|162183031|gb|FC360597.1|FC360597
EST:     CGTTAGGATACTCAAGGATTTAAGAGAAACATTCTTCCCCTCTTT-GACG                         GCTGGCTGGAAGCTGTGGCCCTTTGCGCATCTTATCAC
genomic: CGTTAGGATACTCAAGGATTTAAGAGAAACATTCTTCCC-TCTTTTGACGgtaaggcctc ... cgtcttgcagGCTGGCTGGAAGCTGTGGCCCTTTGCGCATCTTATCAC
EST: gi|162264786|gb|FC440353.1|FC440353
EST:     CCGTTAGGATACTCAAGGATTTAAGAGAAACATTCTTCCCTCTTTTGACG                         GCTGGCTGGAAGCTGTGGCCCTTTGCGCATCTTATCACGTATGGTTTGGTT
genomic: CCGTTAGGATACTCAAGGATTTAAGAGAAACATTCTTCCCTCTTTTGACGgtaaggcctc ... cgtcttgcagGCTGGCTGGAAGCTGTGGCCCTTTGCGCATCTTATCACGTATGGTTTGGTT
EST: gi|162192850|gb|FC369662.1|FC369662
EST:     CCGTTAGGATACTCAAGGATTTAAGAGAAACATTCTTCCCTCTTTTGACG                         GCTGGCTGGAAGCTGTGGCCCTTTGCGCATCTTATCACGTATGGTTTGGTT
genomic: CCGTTAGGATACTCAAGGATTTAAGAGAAACATTCTTCCCTCTTTTGACGgtaaggcctc ... cgtcttgcagGCTGGCTGGAAGCTGTGGCCCTTTGCGCATCTTATCACGTATGGTTTGGTT
EST: gi|162183030|gb|FC360596.1|FC360596
EST:     CCGTTAGGATACTCAAGGATTTAAGAGAAACATTCTTCCCTCTTTTGACG                         GCTGGCTGGAAGCTGTGGCCCTTTGCGCATCTTATCACGTATGGTTTGGTT
genomic: CCGTTAGGATACTCAAGGATTTAAGAGAAACATTCTTCCCTCTTTTGACGgtaaggcctc ... cgtcttgcagGCTGGCTGGAAGCTGTGGCCCTTTGCGCATCTTATCACGTATGGTTTGGTT
EST: gi|162246112|gb|FC421923.1|FC421923
EST:     CCGTTAGGATACTCAAGGATTTAAGAGAAACATTCTTCCCTCTTTTGACG                         GCTGGCTGGAAGCTGTGGCCCTTTGCGCATCTTATCACGTATGGTTTGGTT
genomic: CCGTTAGGATACTCAAGGATTTAAGAGAAACATTCTTCCCTCTTTTGACGgtaaggcctc ... cgtcttgcagGCTGGCTGGAAGCTGTGGCCCTTTGCGCATCTTATCACGTATGGTTTGGTT
EST: gi|162196348|gb|FC373026.1|FC373026
EST:     CCGTTAGGATACTCAAGGATTTAAGAGAAACATTCTTCCCTCTTTTGACG                         GCTGGCTGGAAGCTGTGGCCCTTTGCGCATCTTATCACGTATGGTTTGGTT
genomic: CCGTTAGGATACTCAAGGATTTAAGAGAAACATTCTTCCCTCTTTTGACGgtaaggcctc ... cgtcttgcagGCTGGCTGGAAGCTGTGGCCCTTTGCGCATCTTATCACGTATGGTTTGGTT
EST: gi|162246113|gb|FC421924.1|FC421924
EST:     CCGTTAGGATACTCAAGGATTTAAGAGAAACATTCTTCCCTCTTTTGACG                         GCTGGCTGGAAGCTGTGGCCCTTTGCGCATCTTATCACGTATGGTTTGGTT
genomic: CCGTTAGGATACTCAAGGATTTAAGAGAAACATTCTTCCCTCTTTTGACGgtaaggcctc ... cgtcttgcagGCTGGCTGGAAGCTGTGGCCCTTTGCGCATCTTATCACGTATGGTTTGGTT
EST: gi|162182268|gb|FC357139.1|FC357139
EST:     CCGTTAGGATACTCAAGGATTTAAGAGAAACATTCTTCCCTCTTTTGACG                         GCTGGCTGGAAGCTGTGGCCCTTTGCGCATCTTATCACGTATGGTTTGGTT
genomic: CCGTTAGGATACTCAAGGATTTAAGAGAAACATTCTTCCCTCTTTTGACGgtaaggcctc ... cgtcttgcagGCTGGCTGGAAGCTGTGGCCCTTTGCGCATCTTATCACGTATGGTTTGGTT
EST: gi|162192851|gb|FC369663.1|FC369663
EST:     CCGTTAGGATACTCAAGGATTTAAGAGAAACATTCTTCCCTCTTTTGACG                         GCTGGCTGGAAGCTGTGGCCCTTTGCGCATCTTATCACGTATGGTTTGGTT
genomic: CCGTTAGGATACTCAAGGATTTAAGAGAAACATTCTTCCCTCTTTTGACGgtaaggcctc ... cgtcttgcagGCTGGCTGGAAGCTGTGGCCCTTTGCGCATCTTATCACGTATGGTTTGGTT
EST: gi|162273185|gb|FC449205.1|FC449205
EST:     CCGTTAGGATACTCAAGGATTTAAGAGAAACATTCTTCCCTCTTTTGACG                         GCTGGCTGGAAGCTGTGGCCCTTTGCGCATCTTATCACGTATGGTTTGGTT
genomic: CCGTTAGGATACTCAAGGATTTAAGAGAAACATTCTTCCCTCTTTTGACGgtaaggcctc ... cgtcttgcagGCTGGCTGGAAGCTGTGGCCCTTTGCGCATCTTATCACGTATGGTTTGGTT
EST: gi|162273186|gb|FC449206.1|FC449206
EST:     CCGTTAGGATACTCAAGGATTTAAGAGAAACATTCTTCCCTCTTTTGACG                         GCTGGCTGGAAGCTGTGGCCCTTTGCGCATCTTATCACGTATGGTTTGGTT
genomic: CCGTTAGGATACTCAAGGATTTAAGAGAAACATTCTTCCCTCTTTTGACGgtaaggcctc ... cgtcttgcagGCTGGCTGGAAGCTGTGGCCCTTTGCGCATCTTATCACGTATGGTTTGGTT
EST: gi|162150582|gb|FC326438.1|FC326438
EST:     CCGTTAGGATACTCAAGGATTTAAGAGAAACATTCTTCCCTCTTTTGACG                         GCTGGCTGGAAGCTGTGGCCCTTTGCGCATCTTATCACGTATGGTTTGGTT
genomic: CCGTTAGGATACTCAAGGATTTAAGAGAAACATTCTTCCCTCTTTTGACGgtaaggcctc ... cgtcttgcagGCTGGCTGGAAGCTGTGGCCCTTTGCGCATCTTATCACGTATGGTTTGGTT
EST: gi|162251432|gb|FC425552.1|FC425552
EST:     CCGTTAGGATACTCAAGGATTTAAGAGAAACATTCTTCCCTCTTTTGACG                         GCTGGCTGGAAGCTGTGGCCCTTTGCGCATCTTATCACGTATGGTTTGGTT
genomic: CCGTTAGGATACTCAAGGATTTAAGAGAAACATTCTTCCCTCTTTTGACGgtaaggcctc ... cgtcttgcagGCTGGCTGGAAGCTGTGGCCCTTTGCGCATCTTATCACGTATGGTTTGGTT
EST: gi|162196349|gb|FC373027.1|FC373027
EST:     CCGTTAGGATACTCAAGGATTTAAGAGAAACATTCTTCCCTCTTTTGACG                         GCTGGCTGGAAGCTGTGGCCCTTTGCGCATCTTATCACGTATGGTTTGGTT
genomic: CCGTTAGGATACTCAAGGATTTAAGAGAAACATTCTTCCCTCTTTTGACGgtaaggcctc ... cgtcttgcagGCTGGCTGGAAGCTGTGGCCCTTTGCGCATCTTATCACGTATGGTTTGGTT
EST: gi|162256233|gb|FC432289.1|FC432289
EST:     CCGTTAGGATACTCAAGGATTTAAGAGAAACATTCTTCCCTCTTTTGACG                         GCTGGCTGGAAGCTGTGGCCCTTTGCGCATCTTATCACGTATGGTTTGGTT
genomic: CCGTTAGGATACTCAAGGATTTAAGAGAAACATTCTTCCCTCTTTTGACGgtaaggcctc ... cgtcttgcagGCTGGCTGGAAGCTGTGGCCCTTTGCGCATCTTATCACGTATGGTTTGGTT
EST: gi|208365934|gb|DC955481.1|DC955481
EST:     CCGTTAGGATACTCAAGGATTTAAGAGAAACATTCTTCCCTCTTTTGACG                         GCTGGCTGGAAGCTGTGGCCCTTTGCGCATCTTATCACGTATGGTTTGGTT
genomic: CCGTTAGGATACTCAAGGATTTAAGAGAAACATTCTTCCCTCTTTTGACGgtaaggcctc ... cgtcttgcagGCTGGCTGGAAGCTGTGGCCCTTTGCGCATCTTATCACGTATGGTTTGGTT

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: 35 (upstream exon), 35 (downstream exon)
Score: 185

TTGGAATAGTATCTACTTCATAACTCTAGGATTGCTTCGATTTGAGTCTCCCGTTAGGATACTCAAGGATTTAAGAGAAACATTCTTCCCTCTTTTGACGgtaaggcctc ... cgtcttgcagGCTGGCTGGAAGCTGTGGCCCTTTGCGCATCTTATCACGTATGGTTTGGTTCCCGTCGAACAGCGTCTGCTGTGGGTAGACTGTGTGGAGATTCTTTGGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcgctttcatgtgaccgactttctcaatctgacaatttccacgcgtcttgcagGCTGGCTGGAAGCTGTGGCCCTTTGCGCATCTTATCACGTATGGTTTGGTTCCCGTCGAACAGCGTCTGCTGTGGGTAGACTGTGTGGAGATTCTTTGGG
                            atctgac  putative branch site (score: 185)
                                 acaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggcctctcactcattttcttgaactttaaaaataataataataagccttctctgtatagcacatattattattgtacacactcttgctgaatgttttcgctttcatgtgaccgactttctcaatctgacaatttccacgcgtcttgcagGCTGGCTGGAAGCTGTGGCCCTTTGCGCATCTTATCACGTATGGTTTGGTTCCCGTCGAACAGCGTCTGCTGTGGGTAGACTGTGTGGAGATTCTTTGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT