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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGCTGATGAGATTGGAATTCCCTTCTTGGAAACTAGCGCCAAGAATGCGACTAACGTGGAGCAGGCTTTTATGACAATGGCTGCCGAGATTAAAAATAGgtgagaatcaattgaagttctttgaccttatcattgcttcagatcgggaaccaaaaacaaattcttaacattcttcgtctgtgagagttattgcattgcg...

Basic information

species Physcomitrella patens
transcript PP1S95_20V6.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S95_20V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: EFJ14515 (Selaginella moellendorffii), 5'ss of exon 7
TTGCTGATGAGATTGGAATTCCCTTCTTGGAAACTAGCGCCAAGAATGCGACTAACGTGGAGCAGGCTTTTATGACAATGGCTGCCGAGATTAAAAATAGgtgagaatcaattgaagttctttgaccttatcattgcttcagatcgggaaccaaaaacaaattcttaacattcttcgtctgtgagagttattgcattgcg
| || || ||||| ||||| || ||| | ||||| || |||||||||||||| ||||| |||||||| || ||||| |||||||| ||||| || || ||||    ||  |   ||| ||   |     ||||     | ||     |||      |    |||                                    
TCGCAGACGAGATAGGAATCCCGTTCCTAGAAACCAGTGCCAAGAATGCGACCAACGTAGAGCAGGCATTCATGACCATGGCTGCGGAGATCAAGAACAGgt----atgtagaaaagatcaaagg---gatcacgatctaagcggaagaattcgtgattgtttccag---------------------------------

upper sequence: PP1S95_20V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: EFJ26216 (Selaginella moellendorffii), 5'ss of exon 7
TTGCTGATGAGATTGGAATTCCCTTCTTGGAAACTAGCGCCAAGAATGCGACTAACGTGGAGCAGGCTTTTATGACAATGGCTGCCGAGATTAAAAATAGgtgagaatcaattgaagttctttgaccttatcattgcttcagatcgggaaccaaaaacaaattcttaacattcttcgtctgtgagagttattgcattgcg
|||| || ||||| ||||| || ||| | ||||| || |||||||||||||| ||||| |||||||| || ||||| |||||||| ||||| || || ||||    ||  |   ||| ||   |     ||||     | ||     |||      |    |||                                    
TTGCAGACGAGATAGGAATCCCGTTCCTAGAAACCAGTGCCAAGAATGCGACCAACGTAGAGCAGGCATTCATGACCATGGCTGCGGAGATCAAGAACAGgt----atgtagaaaagatcaaagg---gatcacgatctaagcggaagaattcgtgattgtttccag---------------------------------

upper sequence: PP1S95_20V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: EFJ20286 (Selaginella moellendorffii), 5'ss of exon 7
TTGCTGATGAGATTGGAATTCCCTTCTTGGAAACTAGCGCCAAGAATGCGACTAACGTGGAGCAGGCTTTTATGACAATGGCTGCCGAGATTAAAAATAGgtgagaatcaattgaagttctttgac-cttatcattgcttcagatcgggaaccaaaaacaaattcttaacattcttcgtctgtgagagttattgcattgcg
|||| |||||||||||||| || ||  | || || |||||||||||||| || ||||| ||||| ||||| ||||| |||||||||||||| ||||| ||||  |      ||||  |||| |    ||| |  | | ||    |      |     |                                           
TTGCGGATGAGATTGGAATCCCGTTTCTAGAGACCAGCGCCAAGAATGCTACCAACGTTGAGCAAGCTTTCATGACCATGGCTGCCGAGATCAAAAACAGgtacgttggtgttgatcttctctctttctttttctcgttttctcttctttcctgtgtag------------------------------------------

upper sequence: PP1S95_20V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: EFJ23285 (Selaginella moellendorffii), 5'ss of exon 7
TTGCTGATGAGATTGGAATTCCCTTCTTGGAAACTAGCGCCAAGAATGCGACTAACGTGGAGCAGGCTTTTATGACAATGGCTGCCGAGATTAAAAATAGgtgagaatcaattgaagttctttgaccttatca-ttgcttcagatcgggaaccaaaaacaaattcttaacattcttcgtctgtgagagttattgcattgcg
|||| |||||||||||||| || ||  | ||||| |||||||||||||| || ||||| ||||| ||||| ||||| |||||||||||||| ||||| ||||  |      |||  ||   |||| ||| ||  || |||    |||                | ||  | |  ||||  |||                  
TTGCGGATGAGATTGGAATCCCGTTTCTAGAAACCAGCGCCAAGAATGCTACCAACGTTGAGCAAGCTTTCATGACCATGGCTGCCGAGATCAAAAACAGgtacg------ttggtgt---ttgatcttctctctttctttttctcg----------------ttttctcttctttcgcgtgtag----------------

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|37843982|gb|BJ601990.1|BJ601990
EST:     ACTAACGTGGAGCAGGCTTTTATGACAATGGCTGCCGAGATTAAAAATAG                         GATGGCAAGTCAACCTGCATTAAGCAGTACGAGCAGGCCAAACAATGTGCA
genomic: ACTAACGTGGAGCAGGCTTTTATGACAATGGCTGCCGAGATTAAAAATAGgtgagaatca ... gtttttgcagGATGGCAAGTCAACCTGCATTAAGCAGTACGAGCAGGCCAAACAATGTGCA
EST: gi|208352608|gb|DC918317.1|DC918317
EST:     ACTAACGTGGAGCAGGCTTTTATGACAATGGCTGCCGAGATTAAAAATAG                         GATGGCAAGTCAACCTGCATTAAGCAGTACGAGCAGGCCAAACAATGTGCA
genomic: ACTAACGTGGAGCAGGCTTTTATGACAATGGCTGCCGAGATTAAAAATAGgtgagaatca ... gtttttgcagGATGGCAAGTCAACCTGCATTAAGCAGTACGAGCAGGCCAAACAATGTGCA
EST: gi|208349735|gb|DC917913.1|DC917913
EST:     ACTAACGTGGAGCAGGCTTTTATGACAATGGCTGCCGAGATTAAAAATAG                         GATGGCAAGTCAACCTGCATTAAGCAGTACGAGCAGGCCAAACAATGTGCA
genomic: ACTAACGTGGAGCAGGCTTTTATGACAATGGCTGCCGAGATTAAAAATAGgtgagaatca ... gtttttgcagGATGGCAAGTCAACCTGCATTAAGCAGTACGAGCAGGCCAAACAATGTGCA
EST: gi|208393356|gb|DC904016.1|DC904016
EST:     ACTAACGTGGAGCAGGCTTTTATGACAATGGCTGCCGAGATTAAAAATAG                         GATGGCAAGTCAACCTGCATTAAGCAGTACGAGCAGGCCAAACAATGTGCA
genomic: ACTAACGTGGAGCAGGCTTTTATGACAATGGCTGCCGAGATTAAAAATAGgtgagaatca ... gtttttgcagGATGGCAAGTCAACCTGCATTAAGCAGTACGAGCAGGCCAAACAATGTGCA
EST: gi|37846790|gb|BJ604798.1|BJ604798
EST:     ACTAACGTGGAGCAGGCTTTTATGACAATGGCTGCCGAGATTAAAAATAG                         GATGGCAAGTCAACCTGCATTAAGCAGTACGAGCAGGCCAAACAATGTGCA
genomic: ACTAACGTGGAGCAGGCTTTTATGACAATGGCTGCCGAGATTAAAAATAGgtgagaatca ... gtttttgcagGATGGCAAGTCAACCTGCATTAAGCAGTACGAGCAGGCCAAACAATGTGCA
EST: gi|18333435|gb|BJ165450.1|BJ165450
EST:     ACTAACGTGGAGCAGGCTTTTATGACAATGGCTGCCGAGATTAAAAATAG                         GATGGCAAGTCAACCTGCATTAAGCAGTACGAGCAGGCCAAACAATGTGCA
genomic: ACTAACGTGGAGCAGGCTTTTATGACAATGGCTGCCGAGATTAAAAATAGgtgagaatca ... gtttttgcagGATGGCAAGTCAACCTGCATTAAGCAGTACGAGCAGGCCAAACAATGTGCA
EST: gi|18333444|gb|BJ165459.1|BJ165459
EST:     ACTAACGTGGAGCAGGCTTTTATGGCAATGGCTGCCGAGATTAAAAATAG                         GATGGCAAGTCAACCTGCATTAAGCAGTACGAGCAGGCCAAACAATGTGCA
genomic: ACTAACGTGGAGCAGGCTTTTATGACAATGGCTGCCGAGATTAAAAATAGgtgagaatca ... gtttttgcagGATGGCAAGTCAACCTGCATTAAGCAGTACGAGCAGGCCAAACAATGTGCA
EST: gi|208365886|gb|DC955461.1|DC955461
EST:     ACTAACGTGGAGCAGGCTTTTATGACAATGGCTGCCGAGATTAAAAATAG                         GATGGCAAGTCAACCTGCATTAAGCAGTACGAGCAGGCCAAACAATGTGCA
genomic: ACTAACGTGGAGCAGGCTTTTATGACAATGGCTGCCGAGATTAAAAATAGgtgagaatca ... gtttttgcagGATGGCAAGTCAACCTGCATTAAGCAGTACGAGCAGGCCAAACAATGTGCA
EST: gi|37845387|gb|BJ603395.1|BJ603395
EST:     ACTAACGTGGAGCAGGCTTTTATGACAATGGCTGCCGAGATTAAAAATAG                         GATGGCAAGTCAACCTGCATTAAGCAGTACGAGCAGGCCAAACAATGTGCA
genomic: ACTAACGTGGAGCAGGCTTTTATGACAATGGCTGCCGAGATTAAAAATAGgtgagaatca ... gtttttgcagGATGGCAAGTCAACCTGCATTAAGCAGTACGAGCAGGCCAAACAATGTGCA
EST: gi|37835693|gb|BJ593705.1|BJ593705
EST:     ACTAACGTGGAGCAGGCTTTTATGACAATGGCTGCCGAGATTAAAAATAG                         GATGGCAAGTCAACCTGCATTAAGCAGTACGAGCAGGCCAAACAATGTGCA
genomic: ACTAACGTGGAGCAGGCTTTTATGACAATGGCTGCCGAGATTAAAAATAGgtgagaatca ... gtttttgcagGATGGCAAGTCAACCTGCATTAAGCAGTACGAGCAGGCCAAACAATGTGCA
EST: gi|37851673|gb|BJ609681.1|BJ609681
EST:     ACTAACGTGGAGCAGGCTTTTATGACAATGGCTGCCGAGATTAAAAATAG                         GATGGCAAGTCAACCTGCATTAAGCAGTACGAGCAGGCCAAACAATGTGCA
genomic: ACTAACGTGGAGCAGGCTTTTATGACAATGGCTGCCGAGATTAAAAATAGgtgagaatca ... gtttttgcagGATGGCAAGTCAACCTGCATTAAGCAGTACGAGCAGGCCAAACAATGTGCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGCTGATGAGATTGGAATTCCCTTCTTGGAAACTAGCGCCAAGAATGCGACTAACGTGGAGCAGGCTTTTATGACAATGGCTGCCGAGATTAAAAATAGgtgagaatcaattgaagttctttgaccttatcattgcttcagatcgggaaccaaaaacaaattcttaacattcttcgtctgtgagagttattgcattgcg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caaaaaca