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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttggggcttaatcttctgttaacattgctctgagaaagttttcagtttttcgcttgtcttcaagcattgtaagcgaactagtgtaactcatcatcatcatcatcataatccttattattattattattattattattattatcatcatttttaggtctcctcactttttggatgtgacatcgcacagAAGAGGTTTTGGAGCGTGATGCTGCTTCAAAGGCGTTGATGTCAGTGCTACGTCAGGATACAAAAG

Basic information

species Physcomitrella patens
transcript PP1S47_196V6.1
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|18355356|gb|BJ187415.1|BJ187415
EST:     ACTGCACTTGCCGAAAATTGCAGATGTGTTGGGACAATTACTTCTTGCAG                         AAGAGGTTTTGGAGCGTGATGCTGCTTCAAAGGCGTTGATGTCAGTGCTAC
genomic: ACTGCACTTGCCGAAAATTGCAGATGTGTTGGGACAATTACTTCTTGCAGgtttggggct ... catcgcacagAAGAGGTTTTGGAGCGTGATGCTGCTTCAAAGGCGTTGATGTCAGTGCTAC
EST: gi|100361575|gb|BY984075.1|BY984075
EST:     ACTGCACTTGCCGAAAATTGCAGATGTGTTGGGACAATTACTTCTTGCAG                         AAGAGGTTTTGGAGCGTGATGCTGCTTCAAAGGCGTTGATGCCAGTGCTAC
genomic: ACTGCACTTGCCGAAAATTGCAGATGTGTTGGGACAATTACTTCTTGCAGgtttggggct ... catcgcacagAAGAGGTTTTGGAGCGTGATGCTGCTTCAAAGGCGTTGATGTCAGTGCTAC
EST: gi|18345792|gb|BJ177835.1|BJ177835
EST:     ACTGCACTTGCCGAAAATTGCAGATGTGTTGGGACAATTACTTCTTGCAG                         AAGAGGTTTTGGAGCGTGATGCTGCTTCAA
genomic: ACTGCACTTGCCGAAAATTGCAGATGTGTTGGGACAATTACTTCTTGCAGgtttggggct ... catcgcacagAAGAGGTTTTGGAGCGTGATGCTGCTTCAA
EST: gi|208383270|gb|DC907244.1|DC907244
EST:     ACTGCACTTGCCGAAAATTGCAGATGTGTTGGGACAATTACTTCTTGCAC                         AAGAGGTTTTGGAGCGTGATGCTGCTTCAAAGGCGTTGATGTCAGTGCTAC
genomic: ACTGCACTTGCCGAAAATTGCAGATGTGTTGGGACAATTACTTCTTGCAGgtttggggct ... catcgcacagAAGAGGTTTTGGAGCGTGATGCTGCTTCAAAGGCGTTGATGTCAGTGCTAC
EST: gi|162177459|gb|FC353720.1|FC353720
EST:     ACTGCACTTGCCGAAAATTGCAGATGTGTTGGGACAATTACTTCTTGCAG                         AAGAGGTTTTGGAGCGTGATGCTGCTTCAAAGGCGTTGATGTCAGTGCTAC
genomic: ACTGCACTTGCCGAAAATTGCAGATGTGTTGGGACAATTACTTCTTGCAGgtttggggct ... catcgcacagAAGAGGTTTTGGAGCGTGATGCTGCTTCAAAGGCGTTGATGTCAGTGCTAC
EST: gi|18325198|gb|BJ157194.1|BJ157194
EST:     ACTGCACTTGCCGAAAATTGCAGATGTGTTGGGACAATTACTTCTTGCAG                         AAGAGGTTTTGGAGCGTGATGCTGCTTCAAAGGCGTTGATGTCAGTGCTAC
genomic: ACTGCACTTGCCGAAAATTGCAGATGTGTTGGGACAATTACTTCTTGCAGgtttggggct ... catcgcacagAAGAGGTTTTGGAGCGTGATGCTGCTTCAAAGGCGTTGATGTCAGTGCTAC
EST: gi|100363091|gb|BY984352.1|BY984352
EST:     ACTGCACTTGCCGAANATTGCAGATGTGTTGGGACAATTACTTCTTGCAG                         AAGAGGTTTTGGAGCGTGATGCTGCTTCAAAGGCGTTGATGTCAGTGCTAC
genomic: ACTGCACTTGCCGAAAATTGCAGATGTGTTGGGACAATTACTTCTTGCAGgtttggggct ... catcgcacagAAGAGGTTTTGGAGCGTGATGCTGCTTCAAAGGCGTTGATGTCAGTGCTAC
EST: gi|100386966|gb|BY988235.1|BY988235
EST:     ACTGCACTTGCCGAAAATTGCAGATGTGTTGGGACAATTACTTCTTGCAG                         AAGAGGTTTTGGAGCGTGATGCTGCTTCAAAGGCGTTGATGTCAGTGCTAC
genomic: ACTGCACTTGCCGAAAATTGCAGATGTGTTGGGACAATTACTTCTTGCAGgtttggggct ... catcgcacagAAGAGGTTTTGGAGCGTGATGCTGCTTCAAAGGCGTTGATGTCAGTGCTAC
EST: gi|18325679|gb|BJ157676.1|BJ157676
EST:     ACTGCACTTGCCGAAAATTGCAGATGTGTTGGGACAATTACTTCTTGCAG                         AAGAGGTTTTGGAGCGTGATGCTGC
genomic: ACTGCACTTGCCGAAAATTGCAGATGTGTTGGGACAATTACTTCTTGCAGgtttggggct ... catcgcacagAAGAGGTTTTGGAGCGTGATGCTGC
EST: gi|18352423|gb|BJ184477.1|BJ184477
EST:     ACTGCACTTGCCGAAAATTGCAGATGTGTTGGGACAATTACTTCTTGCAG                         AAGAGGTTTTGGAGCGTGATGCTGCTTCAAAGGCGTTGATGTCAGTGCTAC
genomic: ACTGCACTTGCCGAAAATTGCAGATGTGTTGGGACAATTACTTCTTGCAGgtttggggct ... catcgcacagAAGAGGTTTTGGAGCGTGATGCTGCTTCAAAGGCGTTGATGTCAGTGCTAC
EST: gi|162186312|gb|FC361620.1|FC361620
EST:     ACTGCACTTGCCGAAAATTGCAGATGTGTTGGGACAATTACTTCTTGCAG                         AAGAGGTTTTGGAGCGTGATGCTGCTTCAAAGGCGTTGATGTCAGTGCTAC
genomic: ACTGCACTTGCCGAAAATTGCAGATGTGTTGGGACAATTACTTCTTGCAGgtttggggct ... catcgcacagAAGAGGTTTTGGAGCGTGATGCTGCTTCAAAGGCGTTGATGTCAGTGCTAC
EST: gi|100359470|gb|BY984270.1|BY984270
EST:     ACTGCACTTGCCGAANATTGCAGATGTGTTGGGACAATTACTTCTTGCAG                         AAGAGGTTTTGGAGCGTGATGCTGCTTCAAAGGCGTTGATGCCAGTGCTAC
genomic: ACTGCACTTGCCGAAAATTGCAGATGTGTTGGGACAATTACTTCTTGCAGgtttggggct ... catcgcacagAAGAGGTTTTGGAGCGTGATGCTGCTTCAAAGGCGTTGATGTCAGTGCTAC

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: 34 (upstream exon), 14 (downstream exon)
Score: 2

ATTCGGGTGCAGGCGATTAGAGGATTGCCGCTTTTATGCAAAGACACACCACTGCACTTGCCGAAAATTGCAGATGTGTTGGGACAATTACTTCTTGCAGgtttggggct ... catcgcacagAAGAGGTTTTGGAGCGTGATGCTGCTTCAAAGGCGTTGATGTCAGTGCTACGTCAGGATACAAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttattattatcatcatttttaggtctcctcactttttggatgtgacatcgcacagAAGAGGTTTTGGAGCGTGATGCTGCTTCAAAGGCGTTGATGTCAGTGCTACGTCAGGATACAAAAG
                         tcctcac  putative branch site (score: 2)
     attatcatcattttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttggggcttaatcttctgttaacattgctctgagaaagttttcagtttttcgcttgtcttcaagcattgtaagcgaactagtgtaactcatcatcatcatcatcataatccttattattattattattattattattattatcatcatttttaggtctcctcactttttggatgtgacatcgcacagAAGAGGTTTTGGAGCGTGATGCTGCTTCAAAGGCGTTGATGTCAGTGCTACGTCAGGATACAAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT