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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaccggcacgattgcttgtgacggagattgcccgttggtgttattggaaatgaagctgctcctcatatgtaattgatcaacacgtgttttataattgatgaccagtttaaatacaggttcatatagtcttctgtttcctctcgtttctttaagttcgtcgttatgttccaacggagtttttgttctttgactttgcagGATGTCACAGCTAAGTATGAGGTTCTTGCCATGCCAACTTTCTTGTTTATCAAGGATGGTAAACAAGTTGAGAGGCTTGTTGGGGCTAACGACGAACTCG

Basic information

species Physcomitrella patens
transcript PP1S98_9V6.1
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|162203546|gb|FC380462.1|FC380462
EST:     AAGAGTACTCCGACATGGTTTTCCTCGAGGTTGATGTCGACAAAGTTCAG                         GATGTCACAGCTAAGTATGAGGTTCTTGCCATGCCAACTTTCTTGTTTATC
genomic: AAGAGTACTCCGACATGGTTTTCCTCGAGGTTGATGTCGACAAAGTTCAGgtaccggcac ... gactttgcagGATGTCACAGCTAAGTATGAGGTTCTTGCCATGCCAACTTTCTTGTTTATC
EST: gi|37849696|gb|BJ607704.1|BJ607704
EST:     ATGTCGACAAAGTTCAG                         GATGTCACAGCTAAGTATGAGGTTCTTGCCATGCCAACTTTCTTGTTTATC
genomic: ATGTCGACAAAGTTCAGgtaccggcac ... gactttgcagGATGTCACAGCTAAGTATGAGGTTCTTGCCATGCCAACTTTCTTGTTTATC
EST: gi|162201227|gb|FC378462.1|FC378462
EST:     AAGAGTACTCCGACATGGTTTTCCTCGAGGTTGATGTCGACAAAGTTCAG                         GATGTCACAGCTAAGTATGAGGTTCTTGCCATGCCAACTTTCTTGTTTATC
genomic: AAGAGTACTCCGACATGGTTTTCCTCGAGGTTGATGTCGACAAAGTTCAGgtaccggcac ... gactttgcagGATGTCACAGCTAAGTATGAGGTTCTTGCCATGCCAACTTTCTTGTTTATC
EST: gi|162203547|gb|FC380463.1|FC380463
EST:     AAGAGTACTCCGACATGGTTTTCCTCGAGGTTGATGTCGACAAAGTTCAG                         GATGTCACAGCTAAGTATGAGGTTCTTGCCATGCCAACTTTCTTGTTTATC
genomic: AAGAGTACTCCGACATGGTTTTCCTCGAGGTTGATGTCGACAAAGTTCAGgtaccggcac ... gactttgcagGATGTCACAGCTAAGTATGAGGTTCTTGCCATGCCAACTTTCTTGTTTATC
EST: gi|162165368|gb|FC340843.1|FC340843
EST:     AAGAGTACTCCGACATGGTTTTCCTCGAGGTTGATGTCGACAAAGTTCAG                         GATGTCACAGCTAAGTATGAGGTTCTTGCCATGCCAACTTTCTTGTTTATC
genomic: AAGAGTACTCCGACATGGTTTTCCTCGAGGTTGATGTCGACAAAGTTCAGgtaccggcac ... gactttgcagGATGTCACAGCTAAGTATGAGGTTCTTGCCATGCCAACTTTCTTGTTTATC
EST: gi|37849499|gb|BJ607507.1|BJ607507
EST:     AAGAGTACTCCGACATGGTTTTCCTCGAGGTTGATGTCGACAAAGTTCAG                         GATGTCACAGCTAAGTATGAGGTTCTTGCCATGCCAACTTTCTTGTTTATC
genomic: AAGAGTACTCCGACATGGTTTTCCTCGAGGTTGATGTCGACAAAGTTCAGgtaccggcac ... gactttgcagGATGTCACAGCTAAGTATGAGGTTCTTGCCATGCCAACTTTCTTGTTTATC
EST: gi|162201228|gb|FC378463.1|FC378463
EST:     CTCGAGGTTGATGTCGACAAAGTTCAG                         GATGTCACAGCTAAGTATGAGGTTCTTGCCATGCCAACTGTCTTGTTTATC
genomic: CTCGAGGTTGATGTCGACAAAGTTCAGgtaccggcac ... gactttgcagGATGTCACAGCTAAGTATGAGGTTCTTGCCATGCCAACTTTCTTGTTTATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttctttaagttcgtcgttatgttccaacggagtttttgttctttgactttgcagGATGTCACAGCTAAGTATGAGGTTCTTGCCATGCCAACTTTCTTGTTTATCAAGGATGGTAAACAAGTTGAGAGGCTTGTTGGGGCTAACGACGAACTCG
                                         ctttgac  putative branch site (score: 4)
                                       ttctttg  CT-rich tract
                                 tttttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaccggcacgattgcttgtgacggagattgcccgttggtgttattggaaatgaagctgctcctcatatgtaattgatcaacacgtgttttataattgatgaccagtttaaatacaggttcatatagtcttctgtttcctctcgtttctttaagttcgtcgttatgttccaacggagtttttgttctttgactttgcagGATGTCACAGCTAAGTATGAGGTTCTTGCCATGCCAACTTTCTTGTTTATCAAGGATGGTAAACAAGTTGAGAGGCTTGTTGGGGCTAACGACGAACTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG