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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTGTTTTTAAGGAGGACTTTGGAACTCAAGGACGAGGTGGTTATTTTGATGAGTATGGgtaagtgatctaaaaggagttcagttcttgatttgctagatttacgcgtactggttgcacaaattggaaatgagtcagcagaaacaccatcatttaattt...

Basic information

species Physcomitrella patens
transcript PP1S222_130V6.2
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S222_130V6.2 (Physcomitrella patens), 5'ss of exon 8
lower sequence: GRMZM2G031107_T01 (Zea mays), 5'ss of exon 8
ATTGTTTTTAAGGAGGACTTTGGAACTCAAGGACGAGGTGGTTATTTTGATGAGTATGGgtaagtgatctaaaaggagttcagttcttgatttgctagattt---acgcgtactggttgcacaaattgga-aatgagtcagcagaaacaccatcatttaattt-
|| || ||||||||||||||||||||| ||||||| || || ||||||||| | |||||||| ||    |  |||  | |   ||||||  | | |    ||   |     | | |||| |   |    |   | ||     | ||| | || |  |  | || 
ATCGTATTTAAGGAGGACTTTGGAACTGAAGGACGTGGAGGATATTTTGATCAATATGGgtacgt----tggaagcggctacattcttgcatggttgtcctttgcataaaaaattgttgtaagcaccatatggtcaggttata-aaatatcagctctatacttc

upper sequence: PP1S222_130V6.2 (Physcomitrella patens), 5'ss of exon 8
lower sequence: Vv14s0171g00490.t01 (Vitis vinifera), 5'ss of exon 8
ATTGTTTTTAAGGAGGACTTTGGAACTCAAGGACGAGGTGGTTATTTTGATGAGTATGGgtaagtgatctaaaaggagttcagttcttgatttgctagatttacgcgtactggttgcacaaattggaaatgagtcagcagaaacaccatcatttaattt-
||||| || | |||||| ||||||||| |||| || ||||| ||||||||||| |||||||| |  ||  || |  ||    |   |   |    ||    |     |  |  | |||    ||    || | | |    | |    |  | ||| | | 
ATTGTGTTCAGGGAGGATTTTGGAACTGAAGGTCGTGGTGGATATTTTGATGAATATGGgtatgccattgaacactagcaagggaatcagtaatataaggctttattttttattagcatctctttttcattattgaatgtatat-ttaaaacttattatg
















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|162153066|gb|FC330096.1|FC330096
EST:     AAGGAGGACTTTGGAACTCAAGGACGAGGTGGTTATTTTGATGAGTATGG                         GATCATTCGGGACATCATCCAAAATCATCTCGTGCAG
genomic: AAGGAGGACTTTGGAACTCAAGGACGAGGTGGTTATTTTGATGAGTATGGgtaagtgatc ... cttattgtagGATCATTCGGGACATCATCCAAAATCATCTCGTGCAG
EST: gi|162165174|gb|FC341676.1|FC341676
EST:     AAGGAGGACTTTGGAACTCAAGGACGAGGTGGTTATTTTGATGAGTATGG                         GATCATTCGGGACATCATCCAAAATCATCTCGTGCAG
genomic: AAGGAGGACTTTGGAACTCAAGGACGAGGTGGTTATTTTGATGAGTATGGgtaagtgatc ... cttattgtagGATCATTCGGGACATCATCCAAAATCATCTCGTGCAG
EST: gi|162263641|gb|FC440125.1|FC440125
EST:     AAGGAGGACTTTGGAACTCAAGGACGAGGTGGTTATTTTGATGAGTATGG                         GATCATTCGGGACATCATCCAAAATCATCTCGTGCAG
genomic: AAGGAGGACTTTGGAACTCAAGGACGAGGTGGTTATTTTGATGAGTATGGgtaagtgatc ... cttattgtagGATCATTCGGGACATCATCCAAAATCATCTCGTGCAG
EST: gi|162276852|gb|FC452534.1|FC452534
EST:     AAGGAGGACTTTGGAACTCAAGGACGAGGTGGTTATTTTGATGAGTATGG                         GATCATTCGGGACATCATCCAAAATCATCTCGTGCAG
genomic: AAGGAGGACTTTGGAACTCAAGGACGAGGTGGTTATTTTGATGAGTATGGgtaagtgatc ... cttattgtagGATCATTCGGGACATCATCCAAAATCATCTCGTGCAG
EST: gi|162149665|gb|FC326716.1|FC326716
EST:     AAGGAGGACTTTGGAACTCAAGGACGAGGTGGTTATTTTGATGAGTATGG                         GATCATTCGGGGACATCATCCAAAATCATCTCGTGCAGGTTCTGTGTC
genomic: AAGGAGGACTTTGGAACTCAAGGACGAGGTGGTTATTTTGATGAGTATGGgtaagtgatc ... cttattgtagGATCATTCGGG-ACATCATCCAAAATCATCTCGTGCAGGTTCTGTGTC
EST: gi|162162513|gb|FC338607.1|FC338607
EST:     -GGAGGACTTTGGAAACTCA-GGACGAGGTGGTTATTTTGATGAGTATGG                         GATCATTCGGGACATCATCCANAATCATCTC
genomic: AGGAGGACTTTGGAA-CTCAAGGACGAGGTGGTTATTTTGATGAGTATGGgtaagtgatc ... cttattgtagGATCATTCGGGACATCATCCAAAATCATCTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTGTTTTTAAGGAGGACTTTGGAACTCAAGGACGAGGTGGTTATTTTGATGAGTATGGgtaagtgatctaaaaggagttcagttcttgatttgctagatttacgcgtactggttgcacaaattggaaatgagtcagcagaaacaccatcatttaattt

- - - -  AAGGAG
- - - - -  GGAGGA