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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcgtttttcctaaaagttatatttccacaatggttataggttgtgttttctgaatattggtttcatattgaaacttgtattgtctttttgtgggtgcagGTTTGAGGAGACTGAGCATGCTGGATCAAGATCCTTTTTTACAGAAATCATAGCTTCTATTTCTGATATTAAGTTTGCGAGAGGCGGTCGGTACATTCTG

Basic information

species Physcomitrella patens
transcript PP1S167_51V6.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S167_51V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GRMZM2G165418_T02 (Zea mays), 3'ss of exon 9
-----tgcgtttttcctaaaagttatatttccacaatggttataggttgtgttttctgaatattggtttcatattgaaacttgtattgtctttttgtgggtgcagGTTTGAGGAGACTGAGCATGCTGGATCAAGATCCTTTTTTACAGAAATCATAGCTTCTATTTCTGATATTAAGTTTGCGAGAGGCGGTCGGTACATTCTG
          |    ||  |   ||| | |     ||| | |||  || | ||     | |  |  | |  | |   |  |   |  | | |          ||| ||||||||   |||     |||||||||||||||| ||||||||||| || || || ||||||||||| |||||| | ||    ||    || ||||| 
cctagacaactaaggctgtagcctatgtataacatatgctaataatttatattgcagaagttattatatgttttatgagttaacaaaggcct-----aaaaacagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAAATTATTGCATCAATTTCTGATATAAAGTTTTCAAGGAATGGCAAATATATTCTT

upper sequence: PP1S167_51V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GRMZM2G069631_T01 (Zea mays), 3'ss of exon 8
--------------------------------------------tgcgtttttcctaaaagttatatttccacaatggttataggttgtgttttctgaatattggtttcatattgaaacttgtattgtctttttgtgg------gtgcagGTTTGAGGAGACTGAGCATGCTGGATCAAGATCCTTTTTTACAGAAATCATAGCTTCTATTTCTGATATTAAGTTTGCGAGAGGCGGTCGGTACATTCTG
                                               |   | | || |  ||||  || |  ||||| || |       ||||  |  ||||  ||    || |   ||| | | || |   || ||      || ||| |||||||||  |||     ||||||||||||||||||||||||| || ||||| ||  |||| ||||| || ||||| || |  ||  |  ||||||| 
gttagtaaccccccttgaacttcagtaacattattgttgattagaaggcaatgcttagattttatcatttc-taatggctacaaac---attttaagtttatttattggtcatggt--cttatctggtttaactggggcatcttgttcagATTTGAGGAGCATGAAGCACCTGGATCAAGATCCTTTTTTACAGAGATAATAGCATCAGTTTCAGATATAAAATTTGCAAGGGATGGAAGACACATTCTT
















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|162181126|gb|FC357285.1|FC357285
EST:     CGACTCATTGATATGCGTCAATCAGCCTTGTGTGATCGACATTCAAAGCT                         GTTTGAGGAGACTGAGCATGCTGGATCAAGATCCTTTTTTACAGAAATCAT
genomic: CGACTCATTGATATGCGTCAATCAGCCTTGTGTGATCGACATTCAAAGCTgtatgttatt ... gtgggtgcagGTTTGAGGAGACTGAGCATGCTGGATCAAGATCCTTTTTTACAGAAATCAT
EST: gi|100366505|gb|BY985168.1|BY985168
EST:     CGACTCATTGATATGCGTCAATCAGCCTTGTGTGATCGACATTCAAAGCT                         GTTTGAGGAGACTGAGCATGCTGGATCAAGATCCTTTTTTACAGAAATCAT
genomic: CGACTCATTGATATGCGTCAATCAGCCTTGTGTGATCGACATTCAAAGCTgtatgttatt ... gtgggtgcagGTTTGAGGAGACTGAGCATGCTGGATCAAGATCCTTTTTTACAGAAATCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttttctgaatattggtttcatattgaaacttgtattgtctttttgtgggtgcagGTTTGAGGAGACTGAGCATGCTGGATCAAGATCCTTTTTTACAGAAATCATAGCTTCTATTTCTGATATTAAGTTTGCGAGAGGCGGTCGGTACATTCTG
                                      tctttttgt  CT-rich tract
                tttcatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcgtttttcctaaaagttatatttccacaatggttataggttgtgttttctgaatattggtttcatattgaaacttgtattgtctttttgtgggtgcagGTTTGAGGAGACTGAGCATGCTGGATCAAGATCCTTTTTTACAGAAATCATAGCTTCTATTTCTGATATTAAGTTTGCGAGAGGCGGTCGGTACATTCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG