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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCCGAACCGGACTGGTAGTGTTACCATTGTTGGAGCTGTTTCACCTCCTGGTGGAGACTTCTCAGACCCTGTAACTGCAGCTACTCTTGGTATCGTTCAGgttggtatttacttcagaatgttgtgttcttctctagttaataattatatgggaaagcaagttatctttttaattatacttcaacagtaaggactaaaatacgtggggattcag

Basic information

species Physcomitrella patens
transcript PP1S44_102V6.1
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S44_102V6.1 (Physcomitrella patens), 5'ss of exon 14
lower sequence: GRMZM2G421857_T02 (Zea mays), 5'ss of exon 13
CCCGAACCGGACTGGTAGTGTTACCATTGTTGGAGCTGTTTCACCTCCTGGTGGAGACTTCTCAGACCCTGTAACTGCAGCTACTCTTGGTATCGTTCAGgttggtatttacttcagaatgttgtgttcttctctagttaa-taattatatgggaaagc-aagttatctttttaattatacttcaacagtaaggactaaaatacgtggggattcag---
 ||  || ||| ||| ||||| || |||||||||||||| || ||||||||||| || || ||||||||||| ||  | || || ||  |||| ||||||||  | |       || | |  |    | | ||  |||    | || ||  |   |  |  | |||     ||  || |      | | |||    ||   | |       ||  |   
TCCAGACAGGAATGGCAGTGTCACAATTGTTGGAGCTGTCTCTCCTCCTGGTGGTGATTTTTCAGACCCTGTTACCTCCGCAACCCTCAGTATTGTTCAGgtaagaaggc-tgccaaattacttcaatatacttcagtcctctgatcattagtccagcctgatttacagcgtttgttgtttcaatatattaaatcatatgctgctctttttttttgcag

upper sequence: PP1S44_102V6.1 (Physcomitrella patens), 5'ss of exon 14
lower sequence: GLYMA07G00430.1 (Glycine max), 5'ss of exon 14
CCCGAACCGGACTGGTAGTGTTACCATTGTTGGAGCTGTTTCACCTCCTGGTGGAGACTTCTCAGACCCTGTAACTGCAGCTACTCTTGGTATCGTTCAGgttggtatttacttcagaatgttgtgttcttctctagttaataattatatgggaaagcaagttatctttttaattatacttcaacagtaaggactaaaatacgtggggattcag
|||  | || || |||||||| || |||||||| |||||||| || ||||| ||||| |||||||||||||| ||  | || || ||  | || ||||||||     | | |||   ||| | ||     |   ||  |       |  |  |  |||      |  | || | || | | |  ||  ||    |||||  |            
CCCTGAACGTACAGGTAGTGTAACAATTGTTGGTGCTGTTTCGCCACCTGGAGGAGATTTCTCAGACCCTGTGACATCTGCAACCCTCAGCATAGTTCAGgtaaaactattctttcaaatatggttaaaatgggtaactgcctgcaaagtaagtcagcctaaggttgtcttgacta-attcccgca--aattgttaaaaccct-----------

upper sequence: PP1S44_102V6.1 (Physcomitrella patens), 5'ss of exon 14
lower sequence: EFJ33015 (Selaginella moellendorffii), 5'ss of exon 13
CCCGAACCGGACTGGTAGTGTTACCATTGTTGGAGCTGTTTCACCTCCTGGTGGAGACTTCTCAGACCCTGTAACTGCAGCTACTCTTGGTATCGTTCAGgttggtatttacttcagaatgttgtgttcttctctagttaataattatatgggaaagcaagttatctttttaattatacttcaacagtaaggactaaaatacgtggggattcag
      | | ||||| |||||| | ||||| || || || || ||||||||||| || |||||||||||||| || ||||| ||||||  ||| || ||||   |  | |         ||    ||| || |  |||      ||   ||||| |    ||| | | ||  |                                         
------CAGAACTGGAAGTGTTTCTATTGTCGGTGCCGTGTCTCCTCCTGGTGGCGATTTCTCAGACCCTGTTACGGCAGCGACTCTTAATATTGTCCAGGCAAGCgtcttt------gtgcca-gttgtttttcagt-----gttgactgggacact--gttgtttgttgcag----------------------------------------

upper sequence: PP1S44_102V6.1 (Physcomitrella patens), 5'ss of exon 14
lower sequence: EFJ30330 (Selaginella moellendorffii), 5'ss of exon 14
CCCGAACCGGACTGGTAGTGTTACCATTGTTGGAGCTGTTTCACCTCCTGGTGGAGACTTCTCAGACCCTGTAACTGCAGCTACTCTTGGTATCGTTCAGgttggtatttacttcagaatgttgtgttcttctctagttaataattatatgggaaagcaagttatctttttaattatacttcaacagtaaggactaaaatacgtggggattcag
        | ||||| |||||| | ||||| || || || || ||||||||||| || |||||||||||||| ||  |||| ||||||||||| || ||||   |  | |           |||||    | | |  | | |  ||   ||||| |    ||| | | ||  |                                         
------TAGAACTGGAAGTGTTTCTATTGTCGGTGCCGTGTCTCCTCCTGGTGGCGATTTCTCAGACCCTGTTACGACAGCGACTCTTGGTATTGTCCAGGCAAGCgtct-----------ttgtgccagttttttttcagtg-ttgactgggacact--gttgtttgttgcag----------------------------------------

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|37836831|gb|BJ594839.1|BJ594839
EST:     GTGGAGACTTCTCAGACCCTGTAACTGCAGCTACTCTTGGTATCGTTCAG                         GTGTTTTGGGGACTTGACAAGAAACTTGCACAACGTAAACATTTTCCAGCT
genomic: GTGGAGACTTCTCAGACCCTGTAACTGCAGCTACTCTTGGTATCGTTCAGgttggtattt ... ggggattcagGTGTTTTGGGGACTTGACAAGAAACTTGCACAACGTAAACATTTTCCAGCT
EST: gi|22133115|gb|BQ827551.1|BQ827551
EST:     GTGGAGACTTCTCAGACCCTGTAACTGCAGCTACTCTTGGTATCGTTCAG                         GTGTTTTGGGGACTTGACAAGAAACTTGCACAACGTAAACATTTTCCAGCT
genomic: GTGGAGACTTCTCAGACCCTGTAACTGCAGCTACTCTTGGTATCGTTCAGgttggtattt ... ggggattcagGTGTTTTGGGGACTTGACAAGAAACTTGCACAACGTAAACATTTTCCAGCT
EST: gi|37838710|gb|BJ596718.1|BJ596718
EST:     CTGTAACTGCAGCTACTCTTGGTATCGTTCAG                         GTGTTTTGGGGACTTGACAAGAAACTTGCACAACGTAAACATTTTCCAGCT
genomic: CTGTAACTGCAGCTACTCTTGGTATCGTTCAGgttggtattt ... ggggattcagGTGTTTTGGGGACTTGACAAGAAACTTGCACAACGTAAACATTTTCCAGCT
EST: gi|162276207|gb|FC452899.1|FC452899
EST:     GTGGAGACTTCTCAGACCCTGTAACTGCAGCTACTCTTGGTATCGTTCAG                         GTGTTTTGGGGACTTGACAAGAAACTTGCACAACGTAAACATTTTCCAGCT
genomic: GTGGAGACTTCTCAGACCCTGTAACTGCAGCTACTCTTGGTATCGTTCAGgttggtattt ... ggggattcagGTGTTTTGGGGACTTGACAAGAAACTTGCACAACGTAAACATTTTCCAGCT
EST: gi|37845049|gb|BJ603057.1|BJ603057
EST:     GTAACTGCAGCTACTCTTGGTATCGTTCAG                         GTGTTTTGGGGACTTGACAAGAAACTTGCACAACGTAAACATTTTCCAGCT
genomic: GTAACTGCAGCTACTCTTGGTATCGTTCAGgttggtattt ... ggggattcagGTGTTTTGGGGACTTGACAAGAAACTTGCACAACGTAAACATTTTCCAGCT
EST: gi|37838267|gb|BJ596275.1|BJ596275
EST:     GTAACTGCAGCTACTCTTGGTATCGTTCAG                         GTGTTTTGGGGACTTGACAAGAAACTTGCACAACGTAAACATTTTCCAGCT
genomic: GTAACTGCAGCTACTCTTGGTATCGTTCAGgttggtattt ... ggggattcagGTGTTTTGGGGACTTGACAAGAAACTTGCACAACGTAAACATTTTCCAGCT
EST: gi|22492681|gb|BU052604.1|BU052604
EST:     GTGGAGACTTCTCAGACCCTGTAACTGCAGCTACTCTTGGTATCGTTCAG                         GTGTTTTGGGGACTTGACAAGAAACTTGCACAACGTAAACATTTTCCAGCT
genomic: GTGGAGACTTCTCAGACCCTGTAACTGCAGCTACTCTTGGTATCGTTCAGgttggtattt ... ggggattcagGTGTTTTGGGGACTTGACAAGAAACTTGCACAACGTAAACATTTTCCAGCT
EST: gi|22492244|gb|BU052167.1|BU052167
EST:     GTGGAGACTTCTCAGACCCTGTAACTGCAGCTACTCTTGGTATCGTTCAG                         GTGTTTTGGGGACTTGACAAGAAACTTGCACAACGTAAACATTTTCCAGCT
genomic: GTGGAGACTTCTCAGACCCTGTAACTGCAGCTACTCTTGGTATCGTTCAGgttggtattt ... ggggattcagGTGTTTTGGGGACTTGACAAGAAACTTGCACAACGTAAACATTTTCCAGCT
EST: gi|37852823|gb|BJ610831.1|BJ610831
EST:     GTGGAGACTTCTCAGACCCTGTAACTGCAGCTACTCTTGGTATCGTTCAG                         GTGTTTTGGGGACTTGACAAGAAACTTGCACAACGTAAACATTTTCCAGCT
genomic: GTGGAGACTTCTCAGACCCTGTAACTGCAGCTACTCTTGGTATCGTTCAGgttggtattt ... ggggattcagGTGTTTTGGGGACTTGACAAGAAACTTGCACAACGTAAACATTTTCCAGCT
EST: gi|162276206|gb|FC452898.1|FC452898
EST:     CAGACCCTGTAACTGCAGCTACTCTTGGTATCGTTCAG                         GTGTTTTGGGGACTTGACAAGAAACTTGCACAACGTAAACATTTTCCAGCT
genomic: CAGACCCTGTAACTGCAGCTACTCTTGGTATCGTTCAGgttggtattt ... ggggattcagGTGTTTTGGGGACTTGACAAGAAACTTGCACAACGTAAACATTTTCCAGCT
EST: gi|37834888|gb|BJ592900.1|BJ592900
EST:     TGTAACTGCAGCTACTCTTGGTATCGTTCAG                         GTGTTTTGGGGACTTGACAAGAAACTTGCACAACGTAAACATTTTCCAGCT
genomic: TGTAACTGCAGCTACTCTTGGTATCGTTCAGgttggtattt ... ggggattcagGTGTTTTGGGGACTTGACAAGAAACTTGCACAACGTAAACATTTTCCAGCT
EST: gi|37846602|gb|BJ604610.1|BJ604610
EST:     CCTGTAACTGCAGCTACTCTTGGTATCGTTCAG                         GTGTTTTGGGGACTNGACAAGAAACTNGCACAACGTAAACATTTTCCAGCT
genomic: CCTGTAACTGCAGCTACTCTTGGTATCGTTCAGgttggtattt ... ggggattcagGTGTTTTGGGGACTTGACAAGAAACTTGCACAACGTAAACATTTTCCAGCT
EST: gi|37834988|gb|BJ593000.1|BJ593000
EST:     CTCAGACCCCTGTAACTGCAGCTACTCTTGGTATCGTTCAG                         GTGTTTTGGGGACTTGACAAGAAACTTGCACAACGTAAACATTTTCCAGCT
genomic: CTCAGA-CCCTGTAACTGCAGCTACTCTTGGTATCGTTCAGgttggtattt ... ggggattcagGTGTTTTGGGGACTTGACAAGAAACTTGCACAACGTAAACATTTTCCAGCT
EST: gi|162239653|gb|FC418014.1|FC418014
EST:     CAGACCCTGTAACTGCAGCTACTCTTGGTATCGTTCAG                         GTGTTTTGGGGACTTGACAAGAAACTTGCACAACGTAAACATTTTCCAGCT
genomic: CAGACCCTGTAACTGCAGCTACTCTTGGTATCGTTCAGgttggtattt ... ggggattcagGTGTTTTGGGGACTTGACAAGAAACTTGCACAACGTAAACATTTTCCAGCT
EST: gi|37850336|gb|BJ608344.1|BJ608344
EST:     TGGAGACTTCTCAGACCCCTGTAACTGCAGCTACTCTTGGTATCGTTCAG                         GTGTTTTGGGGACTTGACAAGAAACTTGCACAACGTAAACATTTTCCAGCT
genomic: TGGAGACTTCTCAGA-CCCTGTAACTGCAGCTACTCTTGGTATCGTTCAGgttggtattt ... ggggattcagGTGTTTTGGGGACTTGACAAGAAACTTGCACAACGTAAACATTTTCCAGCT
EST: gi|162179502|gb|FC356542.1|FC356542
EST:     GTGGAGACTTCTCAGACCCTGTAACTGCAGCTACTCTTGGTATCGTTCAG                         GTGTTTTGGGGACTTGACAAGAAACTTGCACAACGTAAACATTTTCCAGCT
genomic: GTGGAGACTTCTCAGACCCTGTAACTGCAGCTACTCTTGGTATCGTTCAGgttggtattt ... ggggattcagGTGTTTTGGGGACTTGACAAGAAACTTGCACAACGTAAACATTTTCCAGCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCCGAACCGGACTGGTAGTGTTACCATTGTTGGAGCTGTTTCACCTCCTGGTGGAGACTTCTCAGACCCTGTAACTGCAGCTACTCTTGGTATCGTTCAGgttggtatttacttcagaatgttgtgttcttctctagttaataattatatgggaaagcaagttatctttttaattatacttcaacagtaaggactaaaatacgtggggattcag

- - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT