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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtttctttgacgagaatttcctagttcctgcagatgtagttgcacaatctttaaattgtctcaccataacatgtaagtcgtttactggtttgtgtggcagGATGCAAACGTCAAGGATATTTACCTGGTTTTTAGTCACTAGTAATAGTGTCATCATGCTCTGCTGCAGCCAACAGTTGTTTAATGAGAAGCAGGTCTTG

Basic information

species Physcomitrella patens
transcript PP1S101_10V6.1
intron # 1
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|67720934|gb|BJ971193.1|BJ971193
EST:     GGAGCTTGGAAAGTTGAGGAGGGGAAAGGCTTAAGTCGACTGAAAATCTG                         GATGCAAACGTCAAGGATATTTACCTGGTTTTTAGTCACTAGTAATAGTGT
genomic: GGAGCTTGGAAAGTTGAGGAGGGGAAAGGCTTAAGTCGACTGAAAATCTGgtaaaaggac ... tgtgtggcagGATGCAAACGTCAAGGATATTTACCTGGTTTTTAGTCACTAGTAATAGTGT
EST: gi|208360802|gb|DC930543.1|DC930543
EST:     GGAGCTTGGAAAGTTGANNNNNNNAAAGGCTTAAGTCGACTGAAAATCTG                         GATGCAAACGTCAAGGATATTTACCTGGTTTTTAGTCACTAGTAATAGTGT
genomic: GGAGCTTGGAAAGTTGAGGAGGGGAAAGGCTTAAGTCGACTGAAAATCTGgtaaaaggac ... tgtgtggcagGATGCAAACGTCAAGGATATTTACCTGGTTTTTAGTCACTAGTAATAGTGT
EST: gi|162217343|gb|FC392811.1|FC392811
EST:     GGAGCTTGGAAAGTTGAGGAGGGGAAAGGCTTAAGTCGACTGAAAATCTG                         GATGCAAACGTCAAGGATATTTACCTGGTTTTTAGTCACTAGTAATAGTGT
genomic: GGAGCTTGGAAAGTTGAGGAGGGGAAAGGCTTAAGTCGACTGAAAATCTGgtaaaaggac ... tgtgtggcagGATGCAAACGTCAAGGATATTTACCTGGTTTTTAGTCACTAGTAATAGTGT
EST: gi|162278882|gb|FC454933.1|FC454933
EST:     GGAGCTTGGAAAGTTGAGGAGGGGAAAGGCTTAAGTCGACTGAAAATCTG                         GATGCAAACGTCAAGGATATTTACCTGGTTTTTAGTCACTAGTAATAGTGT
genomic: GGAGCTTGGAAAGTTGAGGAGGGGAAAGGCTTAAGTCGACTGAAAATCTGgtaaaaggac ... tgtgtggcagGATGCAAACGTCAAGGATATTTACCTGGTTTTTAGTCACTAGTAATAGTGT
EST: gi|37838284|gb|BJ596292.1|BJ596292
EST:     GGAGCTTGGAAAGTTGAGGAGGGGAAAGGCTTAAGTCGACTGAAAATCTG                         GATGCAAACGTCAAGGATATTTACCTGGTTTTTAGTCACTAGTAATAGTGT
genomic: GGAGCTTGGAAAGTTGAGGAGGGGAAAGGCTTAAGTCGACTGAAAATCTGgtaaaaggac ... tgtgtggcagGATGCAAACGTCAAGGATATTTACCTGGTTTTTAGTCACTAGTAATAGTGT
EST: gi|37839426|gb|BJ597434.1|BJ597434
EST:     GGAGCTTGGAAAGTTGAGGAGGGGAAAGACTTAAGTCGACTGAAAATCTG                         GATGCAAACGTCAAGGATATTTACCTGGTTTTTAGTCACTAGTAATAGTGT
genomic: GGAGCTTGGAAAGTTGAGGAGGGGAAAGGCTTAAGTCGACTGAAAATCTGgtaaaaggac ... tgtgtggcagGATGCAAACGTCAAGGATATTTACCTGGTTTTTAGTCACTAGTAATAGTGT
EST: gi|162228730|gb|FC405758.1|FC405758
EST:     GGAGCTTGGAAAGTTGAGGAGGGGAAAGGCTTAAGTCGACTGAAAATCTG                         GATGCAAACGTCAAGGATATTTACCTGGTTTTTAGTCACTAGTAATAGTGT
genomic: GGAGCTTGGAAAGTTGAGGAGGGGAAAGGCTTAAGTCGACTGAAAATCTGgtaaaaggac ... tgtgtggcagGATGCAAACGTCAAGGATATTTACCTGGTTTTTAGTCACTAGTAATAGTGT
EST: gi|37821050|gb|BJ579116.1|BJ579116
EST:     GGAGCTTGGAAAGTTGAGGAGGGGAAAGGCTTAAGTCGACTGAAAATCTG                         GATGCAAACGTCAAGGATATTTACCTGGTTTTTAGTCACTAGTAATAGTGT
genomic: GGAGCTTGGAAAGTTGAGGAGGGGAAAGGCTTAAGTCGACTGAAAATCTGgtaaaaggac ... tgtgtggcagGATGCAAACGTCAAGGATATTTACCTGGTTTTTAGTCACTAGTAATAGTGT
EST: gi|162217237|gb|FC391977.1|FC391977
EST:     GGAGCTTGGAAAGTTGAGGAGGGGAAAGGCTTAAGTCGACTGAAAATCTG                         GATGCAAACGTCAAGGATATTTACCTGGTTTTTAGTCACTAGTAATAGTGT
genomic: GGAGCTTGGAAAGTTGAGGAGGGGAAAGGCTTAAGTCGACTGAAAATCTGgtaaaaggac ... tgtgtggcagGATGCAAACGTCAAGGATATTTACCTGGTTTTTAGTCACTAGTAATAGTGT
EST: gi|37832690|gb|BJ590702.1|BJ590702
EST:     GGAGCTTGGAAAGTTGAGGAGGGGAAAGGCTTAAGTCGACTGAAAATCTG                         GATGCAAACGTCAAGGATATTTACCTGGTTTTTAGTCACTAGTAATAGTGT
genomic: GGAGCTTGGAAAGTTGAGGAGGGGAAAGGCTTAAGTCGACTGAAAATCTGgtaaaaggac ... tgtgtggcagGATGCAAACGTCAAGGATATTTACCTGGTTTTTAGTCACTAGTAATAGTGT
EST: gi|67719660|gb|BJ969919.1|BJ969919
EST:     GGAGCTTGGAAAGTTGAGGAGGGGAAAGGCTTAAGTCGACTGAAAATCTG                         GATGCAAACGTCAAGGATATTTACCTGGTTTTTAGTCACTAGTAATAGTGT
genomic: GGAGCTTGGAAAGTTGAGGAGGGGAAAGGCTTAAGTCGACTGAAAATCTGgtaaaaggac ... tgtgtggcagGATGCAAACGTCAAGGATATTTACCTGGTTTTTAGTCACTAGTAATAGTGT
EST: gi|67718995|gb|BJ969254.1|BJ969254
EST:     GGAGCTTGGAAAGTTGAGGAGGGGAAAGGCTTAAGTCGACTGAAAATCTG                         GATGCAAACGTCAAGGATATTTACCTGGTTTTTAGTCACTAGTAATAGTGT
genomic: GGAGCTTGGAAAGTTGAGGAGGGGAAAGGCTTAAGTCGACTGAAAATCTGgtaaaaggac ... tgtgtggcagGATGCAAACGTCAAGGATATTTACCTGGTTTTTAGTCACTAGTAATAGTGT
EST: gi|67573272|gb|BJ946096.1|BJ946096
EST:     GGAGCTTGGAAAGTTGAGGAGGGGAAAGGCTTAAGTCGACTGAAAATCTG                         GATGCAAACGTCAAGGATATTTACCTGGTTTTTAGTCACTAGTAATAGTGT
genomic: GGAGCTTGGAAAGTTGAGGAGGGGAAAGGCTTAAGTCGACTGAAAATCTGgtaaaaggac ... tgtgtggcagGATGCAAACGTCAAGGATATTTACCTGGTTTTTAGTCACTAGTAATAGTGT
EST: gi|67727924|gb|BJ978183.1|BJ978183
EST:     GGAGCTTGGAAAGTTGAGGAGGGGAAAGGCTTAAGTCGACTGAAAATCTG                         GATGCAAACGTCAAGGATATTTACCTGGTTTTTAGTCACTAGTAATAGTGT
genomic: GGAGCTTGGAAAGTTGAGGAGGGGAAAGGCTTAAGTCGACTGAAAATCTGgtaaaaggac ... tgtgtggcagGATGCAAACGTCAAGGATATTTACCTGGTTTTTAGTCACTAGTAATAGTGT
EST: gi|162200268|gb|FC376608.1|FC376608
EST:     GGAGCTTGGAAAGTTGAGGAGGGGAAAGGCTTAAGTCGACTGAAAATCTG                         GATGCAAACGTCAAGGATATTTACCTGGTTTTTAGTCACTAGTAATAGTGT
genomic: GGAGCTTGGAAAGTTGAGGAGGGGAAAGGCTTAAGTCGACTGAAAATCTGgtaaaaggac ... tgtgtggcagGATGCAAACGTCAAGGATATTTACCTGGTTTTTAGTCACTAGTAATAGTGT
EST: gi|100359592|gb|BY947060.1|BY947060
EST:     GGAGCTTGGAAAGTTGAGGAGGGGAAAGGCTTAAGTCGACTGANAATCTG                         GATGCAAACGTCAAGGATATTTACCTGGTTTTTAGTCACTAGTAATAGTGT
genomic: GGAGCTTGGAAAGTTGAGGAGGGGAAAGGCTTAAGTCGACTGAAAATCTGgtaaaaggac ... tgtgtggcagGATGCAAACGTCAAGGATATTTACCTGGTTTTTAGTCACTAGTAATAGTGT
EST: gi|67696658|gb|BJ956891.1|BJ956891
EST:     GGAGCTTGGAAAGTTGAGGAGGGGAAAGGCTTAAGTCGACTGAAAATCTG                         GATGCAAACGTCAAGGATATTTACCTGGTTTTTAGTCACTAGTAATAGTGT
genomic: GGAGCTTGGAAAGTTGAGGAGGGGAAAGGCTTAAGTCGACTGAAAATCTGgtaaaaggac ... tgtgtggcagGATGCAAACGTCAAGGATATTTACCTGGTTTTTAGTCACTAGTAATAGTGT
EST: gi|18362083|gb|BJ194150.1|BJ194150
EST:     GGAGCTTGGAAAGTTGAGGAGGGGAAAGACTTAAGTCGACTGAAAATCTG                         GATGCAAACGTCAAGGATATTTACCTGGTTTTTAGTCACTAGTAATAGTGT
genomic: GGAGCTTGGAAAGTTGAGGAGGGGAAAGGCTTAAGTCGACTGAAAATCTGgtaaaaggac ... tgtgtggcagGATGCAAACGTCAAGGATATTTACCTGGTTTTTAGTCACTAGTAATAGTGT
EST: gi|162217342|gb|FC392810.1|FC392810
EST:     GGAGCTTGGAAAGTTGAGGAGGGGAAAGGCTTAAGTCGACTGAAAATCTG                         GATGCAAACGTCAAGGATATTTACCTGGTTTTTAGTCACTAGTAATAGTGT
genomic: GGAGCTTGGAAAGTTGAGGAGGGGAAAGGCTTAAGTCGACTGAAAATCTGgtaaaaggac ... tgtgtggcagGATGCAAACGTCAAGGATATTTACCTGGTTTTTAGTCACTAGTAATAGTGT
EST: gi|208375425|gb|DC945068.1|DC945068
EST:     GGAGCTTGGAAAGTTGANNNNNNNAAAGGCTTAAGTCGACTGAAAATCTG                         GATGCAAACGTCAAGGATATTTACCTGGTTTTTAGTCACTAGTAATAGTGT
genomic: GGAGCTTGGAAAGTTGAGGAGGGGAAAGGCTTAAGTCGACTGAAAATCTGgtaaaaggac ... tgtgtggcagGATGCAAACGTCAAGGATATTTACCTGGTTTTTAGTCACTAGTAATAGTGT
EST: gi|67698677|gb|BJ958910.1|BJ958910
EST:     GGAGCTTGGAAAGTTGAGGAGGGGAAAGGCTTAAGTCGACTGAAAATCTG                         GATGCAAACGTCAAGGATATTTACCTGGTTTTTAGTCACTAGTAATAGTGT
genomic: GGAGCTTGGAAAGTTGAGGAGGGGAAAGGCTTAAGTCGACTGAAAATCTGgtaaaaggac ... tgtgtggcagGATGCAAACGTCAAGGATATTTACCTGGTTTTTAGTCACTAGTAATAGTGT
EST: gi|162259754|gb|FC436747.1|FC436747
EST:     GGAGCTTGGAAAGTTGAGGAGGGGAAAGGCTTAAGTCGACTGAAAATCTG                         GATGCAAACGTCAAGGATATTTACCTGGTTTTTAGTCACTAGTAATAGTGT
genomic: GGAGCTTGGAAAGTTGAGGAGGGGAAAGGCTTAAGTCGACTGAAAATCTGgtaaaaggac ... tgtgtggcagGATGCAAACGTCAAGGATATTTACCTGGTTTTTAGTCACTAGTAATAGTGT
EST: gi|162278881|gb|FC454932.1|FC454932
EST:     GGAGCTTGGAAAGTTGAGGAGGGGAAAGGCTTAAGTCGACTGAAAATCTG                         GATGCAAACGTCAAGGATATTTACCTGGTTTTTAGTCACTAGTAATAGTGT
genomic: GGAGCTTGGAAAGTTGAGGAGGGGAAAGGCTTAAGTCGACTGAAAATCTGgtaaaaggac ... tgtgtggcagGATGCAAACGTCAAGGATATTTACCTGGTTTTTAGTCACTAGTAATAGTGT
EST: gi|67575218|gb|BJ948042.1|BJ948042
EST:     GGAGCTTGGAAAGTTGAGGAGGGGAAAGGCTTAAGTCGACTGAAAATCTG                         GATGCAAACGTCAAGGATATTTACCTGGTTTTTAGTCACTAGTAATAGTGT
genomic: GGAGCTTGGAAAGTTGAGGAGGGGAAAGGCTTAAGTCGACTGAAAATCTGgtaaaaggac ... tgtgtggcagGATGCAAACGTCAAGGATATTTACCTGGTTTTTAGTCACTAGTAATAGTGT
EST: gi|162224849|gb|FC401057.1|FC401057
EST:     GGAGCTTGGAAAGTTGAGGAGGGGAAAGGCTTAAGTCGACTGAAAATCTG                         GATGCAAACGTCAAGGATATTTACCTGGTTTTTAGTCACTAGTAATAGTGT
genomic: GGAGCTTGGAAAGTTGAGGAGGGGAAAGGCTTAAGTCGACTGAAAATCTGgtaaaaggac ... tgtgtggcagGATGCAAACGTCAAGGATATTTACCTGGTTTTTAGTCACTAGTAATAGTGT

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: 92

CGTTTCAAGGTCATGGTGGCGCGAGTCAAGAAGAGTTCCATTGTCCGCCGGGAGCTTGGAAAGTTGAGGAGGGGAAAGGCTTAAGTCGACTGAAAATCTGgtaaaaggac ... tgtgtggcagGATGCAAACGTCAAGGATATTTACCTGGTTTTTAGTCACTAGTAATAGTGTCATCATGCTCTGCTGCAGCCAACAGTTGTTTAATGAGAAGCAGGTCTTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatctttaaattgtctcaccataacatgtaagtcgtttactggtttgtgtggcagGATGCAAACGTCAAGGATATTTACCTGGTTTTTAGTCACTAGTAATAGTGTCATCATGCTCTGCTGCAGCCAACAGTTGTTTAATGAGAAGCAGGTCTTG
                  ccataac  putative branch site (score: 92)
     ttaaattgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttctttgacgagaatttcctagttcctgcagatgtagttgcacaatctttaaattgtctcaccataacatgtaagtcgtttactggtttgtgtggcagGATGCAAACGTCAAGGATATTTACCTGGTTTTTAGTCACTAGTAATAGTGTCATCATGCTCTGCTGCAGCCAACAGTTGTTTAATGAGAAGCAGGTCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - -tcctgca
- - - - - - - - - - - - - - - - - - - -ttgcaca