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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaatgtgaactgtagattgcaaaccaattctatatctgaacagagcgacatattaacaccacgtgattattgctccttgctttgcgtcgttatcacccagGTCTCTTGACGAAGAAGTTCATTGACCTTATAAAGCAAGCAGATGATGGAGTATTGGATCTCAACAAGGCTGCAGATACTTTACAT

Basic information

species Physcomitrella patens
transcript PP1S38_356V6.1
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|162176994|gb|FC353671.1|FC353671
EST:     AAGCAGTGCACCGACTCCTACCAGCACCTGTCGCTACGACAGCTCTCTTG                         GTCTCTTGACGAAGAAGTTCATTGACCTTATAAAGCAAGCAGATGATGGAG
genomic: AAGCAGTGCACCGACTCCTACCAGCACCTGTCGCTACGACAGCTCTCTTGgtaacaccaa ... tatcacccagGTCTCTTGACGAAGAAGTTCATTGACCTTATAAAGCAAGCAGATGATGGAG
EST: gi|18372653|gb|BJ204255.1|BJ204255
EST:     AAGCAGTGCACCGACTCCTACCAGCACCTGTCGCTACGACAGCTCTCTTG                         GTCTCTTGACGAAGAAGTTCATTGACCTTATAAAGCAAGCAGATGATGGAG
genomic: AAGCAGTGCACCGACTCCTACCAGCACCTGTCGCTACGACAGCTCTCTTGgtaacaccaa ... tatcacccagGTCTCTTGACGAAGAAGTTCATTGACCTTATAAAGCAAGCAGATGATGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgacatattaacaccacgtgattattgctccttgctttgcgtcgttatcacccagGTCTCTTGACGAAGAAGTTCATTGACCTTATAAAGCAAGCAGATGATGGAGTATTGGATCTCAACAAGGCTGCAGATACTTTACAT
     tattaac  putative branch site (score: 1)
     tattaaca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaatgtgaactgtagattgcaaaccaattctatatctgaacagagcgacatattaacaccacgtgattattgctccttgctttgcgtcgttatcacccagGTCTCTTGACGAAGAAGTTCATTGACCTTATAAAGCAAGCAGATGATGGAGTATTGGATCTCAACAAGGCTGCAGATACTTTACAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - -ctgaaca