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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaaggtcattttccaagatgagcaggaacttcaatcctttcagatcacatagcagccatttcagggtgtgcactgctcgagctagcaatccatattgcgtgcaagactaatcgttgcttgtctcccatgtagGATTTCGCTCGAGAAAGCCATATCAGCAGGATACGATGACTCGACTTGGCCATTGAAGTCTCATAGTGGGAAGTATGCAGGAGAGTTAAGGTTGATCCTG

Basic information

species Physcomitrella patens
transcript PP1S78_70V6.1
intron # 4
splice site 3'
intron type U2

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|100418032|gb|BY993303.1|BY993303
EST:     GTCTGGAATAGCAATACACTTTCCACCGACGATTTCATTGGCAGTACAAG                         GATTTCGCTCGAGAAAGCCATACCAGCAGGATACGATGACTCGACTTGGCC
genomic: GTCTGGAATAGCAATACACTTTCCACCGACGATTTCATTGGCAGTACAAGgtaaaaggtc ... tcccatgtagGATTTCGCTCGAGAAAGCCATATCAGCAGGATACGATGACTCGACTTGGCC
EST: gi|67571633|gb|BJ944457.1|BJ944457
EST:     GTCTGGAATAGCAATACACTTTCCACCGACGATTTCATTGGCAGTACAAG                         GATTTCGCTCGAGAAAGCCATATCAGCAGGATACGATGACTCGACTTGGCC
genomic: GTCTGGAATAGCAATACACTTTCCACCGACGATTTCATTGGCAGTACAAGgtaaaaggtc ... tcccatgtagGATTTCGCTCGAGAAAGCCATATCAGCAGGATACGATGACTCGACTTGGCC
EST: gi|162235840|gb|FC412391.1|FC412391
EST:     GTCTGGAATAGCAATACACTTTCCACCGACGATTTCATTGGCAGTACAAG                         GATTTCGCTCGAGAAAGCCATATCAGCAGGATACGATGACTCGACTTGGCC
genomic: GTCTGGAATAGCAATACACTTTCCACCGACGATTTCATTGGCAGTACAAGgtaaaaggtc ... tcccatgtagGATTTCGCTCGAGAAAGCCATATCAGCAGGATACGATGACTCGACTTGGCC
EST: gi|67577778|gb|BJ949945.1|BJ949945
EST:     GTCTGGAATAGCAATACACTTTCCACCGACGATTTCATTGGCAGTACAAG                         GATTTCGCTCGAGAAAGCCATATCAGCAGGATACGATGACTCGACTTGGCC
genomic: GTCTGGAATAGCAATACACTTTCCACCGACGATTTCATTGGCAGTACAAGgtaaaaggtc ... tcccatgtagGATTTCGCTCGAGAAAGCCATATCAGCAGGATACGATGACTCGACTTGGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgagctagcaatccatattgcgtgcaagactaatcgttgcttgtctcccatgtagGATTTCGCTCGAGAAAGCCATATCAGCAGGATACGATGACTCGACTTGGCCATTGAAGTCTCATAGTGGGAAGTATGCAGGAGAGTTAAGGTTGATCCTG
                           gactaat  putative branch site (score: 2)
                                       cttgtctccc  putative PPT
              atatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaaggtcattttccaagatgagcaggaacttcaatcctttcagatcacatagcagccatttcagggtgtgcactgctcgagctagcaatccatattgcgtgcaagactaatcgttgcttgtctcccatgtagGATTTCGCTCGAGAAAGCCATATCAGCAGGATACGATGACTCGACTTGGCCATTGAAGTCTCATAGTGGGAAGTATGCAGGAGAGTTAAGGTTGATCCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA