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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggagagtttgtaacttaggtcagtttctaggtgcgtacttatcatctgttgtcttcctctggattaagtgtcctcaccaatcccttccatttttaatcgctcataaattggtattgccccagGAGGAGCTTGTTCCTGCTGTTGCACAACATTTTGCTGCCCAG

Basic information

species Physcomitrella patens
transcript PP1S9_162V6.1
intron # 8
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|37822568|gb|BJ580634.1|BJ580634
EST:     ACGGTACAGACGCGTCTATAATCTCCGCGAAGTGGCGAGCAGCTGCAAG                         GAGGAGCTTGTTCCTGCTGTTGCACAACATTTTGCTGCCCAG
genomic: ACGGTACAGACGCGTCTATAATCTCCGCGAAGTGGCGAGCAGCTGCAAGgtatggagag ... attgccccagGAGGAGCTTGTTCCTGCTGTTGCACAACATTTTGCTGCCCAG
EST: gi|67725795|gb|BJ976054.1|BJ976054
EST:     AACGGTACAGACGCGTCTATAATCTCCGCGAAGTGGCGAGCAGCTGCAAG                         GAGGAGCTTGTTCCTGCTGTTGCACAACATTTTGCTGCCCAG
genomic: AACGGTACAGACGCGTCTATAATCTCCGCGAAGTGGCGAGCAGCTGCAAGgtatggagag ... attgccccagGAGGAGCTTGTTCCTGCTGTTGCACAACATTTTGCTGCCCAG
EST: gi|100447259|gb|CJ971558.1|CJ971558
EST:     AACGGTACAGACGCGTCTATNATCTCCGCGAANTGCC-ANCAGCTGCAAG                         GAAGANCTGGT-CCTGCTGTTGCACA-CATTT-GCTGCC
genomic: AACGGTACAGACGCGTCTATAATCTCCGCGAAGTGGCGAGCAGCTGCAAGgtatggagag ... attgccccagGAGGAGCTTGTTCCTGCTGTTGCACAACATTTTGCTGCC
EST: gi|67724351|gb|BJ974610.1|BJ974610
EST:     AACGGTACAGACGCGTCTATAATCTCCGCGAAGTGGCGAGCAGCTGCAAG                         GAGGAGCTTGTTCCTGCTGTTGCACAACATTTTGCTGCCCAG
genomic: AACGGTACAGACGCGTCTATAATCTCCGCGAAGTGGCGAGCAGCTGCAAGgtatggagag ... attgccccagGAGGAGCTTGTTCCTGCTGTTGCACAACATTTTGCTGCCCAG
EST: gi|208358608|gb|DC949943.1|DC949943
EST:     AACGGTACAGACGCGTCTATAATCTCCGCGAAGTGGCGAGCAGCTGCAAG                         GAGGAGCTTGTTCCTGCTGTTGCACAACATTTTGCTGCCCAG
genomic: AACGGTACAGACGCGTCTATAATCTCCGCGAAGTGGCGAGCAGCTGCAAGgtatggagag ... attgccccagGAGGAGCTTGTTCCTGCTGTTGCACAACATTTTGCTGCCCAG
EST: gi|208353685|gb|DC949761.1|DC949761
EST:     AACGGTACAGACGCGTCTATAATCTCCGCGAAGTGGCGAGCAGCTGCAAG                         GAGGAGCTTGTTCCTGCTGTTGCACAACATTTTGCTGCCCAG
genomic: AACGGTACAGACGCGTCTATAATCTCCGCGAAGTGGCGAGCAGCTGCAAGgtatggagag ... attgccccagGAGGAGCTTGTTCCTGCTGTTGCACAACATTTTGCTGCCCAG
EST: gi|208397201|gb|DC920581.1|DC920581
EST:     AACGGTACAGACGCGTCTATAATCTCCGCGAAGTGGCGAGCAGCTGCAAG                         GAGGAGCTTGTTCCTGCTGTTGCACAACATTTTGCTGCCCAG
genomic: AACGGTACAGACGCGTCTATAATCTCCGCGAAGTGGCGAGCAGCTGCAAGgtatggagag ... attgccccagGAGGAGCTTGTTCCTGCTGTTGCACAACATTTTGCTGCCCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgtcctcaccaatcccttccatttttaatcgctcataaattggtattgccccagGAGGAGCTTGTTCCTGCTGTTGCACAACATTTTGCTGCCCAG
                                              ttgcccc  CT-rich tract
                     atttttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggagagtttgtaacttaggtcagtttctaggtgcgtacttatcatctgttgtcttcctctggattaagtgtcctcaccaatcccttccatttttaatcgctcataaattggtattgccccagGAGGAGCTTGTTCCTGCTGTTGCACAACATTTTGCTGCCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC