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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgtggagcatacccttgttcattcagctcttttcagtcctgttactatgtgattactttcatgtctaattctctctgaatgggcgtatgcagGAGTCGGTAGGAATTGCTAAAGCTTTGGCAGCTAAAAATGGTTATGAGATTGATTCTAACCAAGAG

Basic information

species Physcomitrella patens
transcript PP1S53_215V6.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S53_215V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GRMZM2G068212_T01 (Zea mays), 3'ss of exon 7
gttcgtggagcatacccttgttcattcagctcttttcagtcctgttactatgtgattactttcatgtctaattctctctgaatgggcgtatgcagGAGTCGGTAGGAATTGCTAAAGCTTTGGCAGCTAAAAATGGTTATGAGATTGATTCTAACCAAGAG
    |||    ||    ||| |  ||  |   |    | | |    |   | |    |  |||     ||| | | |    ||   |   | ||||| || || || |||||||||||||||||||| || ||||| |||||| | || |||||| |||||
----gtgagaaat-ttgttgctattttgg---tgagaaataccac-agggtcttcccaggttctccattaagtattttaccata--ccattccagGAATCTGTTGGTATTGCTAAAGCTTTGGCAGCGAAGAATGGGTATGAGTTGGACTCTAACAAAGAG
















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|162174226|gb|FC350609.1|FC350609
EST:     CTGTTCAACTAATGCCTACAGCAGCTCTTATATGTGGTGTTGCTATCCTG                         GAGTCGGTAGGAATTGCTAAAGCTTTGGCAGCTAANAATGGTTATGAGATT
genomic: CTGTTCAACTAATGCCTACAGCAGCTCTTATATGTGGTGTTGCTATCCTGgttcgtggag ... gcgtatgcagGAGTCGGTAGGAATTGCTAAAGCTTTGGCAGCTAAAAATGGTTATGAGATT
EST: gi|162191853|gb|FC368002.1|FC368002
EST:     CTGTTCAACTAATGCCTACAGCAGCTCTTATATGTGGTGTTGCTATCCTG                         GAGTCGGTAGGAATTGCTAAAGCTTTGGCAGCTAAAAATGGTTATGAGATT
genomic: CTGTTCAACTAATGCCTACAGCAGCTCTTATATGTGGTGTTGCTATCCTGgttcgtggag ... gcgtatgcagGAGTCGGTAGGAATTGCTAAAGCTTTGGCAGCTAAAAATGGTTATGAGATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctgttactatgtgattactttcatgtctaattctctctgaatgggcgtatgcagGAGTCGGTAGGAATTGCTAAAGCTTTGGCAGCTAAAAATGGTTATGAGATTGATTCTAACCAAGAG
                         gtctaat  putative branch site (score: 3)
              attacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcgtggagcatacccttgttcattcagctcttttcagtcctgttactatgtgattactttcatgtctaattctctctgaatgggcgtatgcagGAGTCGGTAGGAATTGCTAAAGCTTTGGCAGCTAAAAATGGTTATGAGATTGATTCTAACCAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT