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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtacaaagcactccactaatccttgccaagtgggaccaatttctgaatcggaattgatttctaacgcagtatagatgttaagagacaacacatacttaatgtactgtttgcaatacatgcagGTATACAAGGATCAAACAAATGTTGATGAGTATTTGGTGAATTCCATTGTTCAACCCACAGCAGATCCGAACGCAGCAGAGGTTTATTACAG

Basic information

species Physcomitrella patens
transcript PP1S55_317V6.1
intron # 5
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|162266519|gb|FC442555.1|FC442555
EST:     CATTTTGGCAAGCCAAGCAGCCTAAACGTATAGAATCAGTTCTACGAAAT                         GTATACAAGGATCAAACAAATGTTGATGAGTATTTGGTGAATTCCATTGTT
genomic: CATTTTGGCAAGCCAAGCAGCCTAAACGTATAGAATCAGTTCTACGAAATgtaagtacaa ... atacatgcagGTATACAAGGATCAAACAAATGTTGATGAGTATTTGGTGAATTCCATTGTT
EST: gi|162270099|gb|FC446799.1|FC446799
EST:     CATTTTGGCAAGCCAAGCAGCCTAAACGTATAGAATCAGTTCTACGAAAT                         GTATACAAGGATCAAACAAATGTTGATGAGTATTTGGTGAATTCCATTGTT
genomic: CATTTTGGCAAGCCAAGCAGCCTAAACGTATAGAATCAGTTCTACGAAATgtaagtacaa ... atacatgcagGTATACAAGGATCAAACAAATGTTGATGAGTATTTGGTGAATTCCATTGTT
EST: gi|162156079|gb|FC332246.1|FC332246
EST:     CATTTTGGCAAGCCAAGCAGCCTAAACGTATAGAATCAGTTCTACGAAAT                         GTATACAAGGATCAAACAAATGTTGATGAGTATTTGGTGAATTCCATTGTT
genomic: CATTTTGGCAAGCCAAGCAGCCTAAACGTATAGAATCAGTTCTACGAAATgtaagtacaa ... atacatgcagGTATACAAGGATCAAACAAATGTTGATGAGTATTTGGTGAATTCCATTGTT
EST: gi|22492515|gb|BU052438.1|BU052438
EST:     CATTTTGGCAAGCCAAGCAGCCTAAACGTATAGAATCAGTTCTACGAAAT                         GTATACAAGGATCAAACAAATGTTGATGAGTATTTGGTGAATTCCATTGTT
genomic: CATTTTGGCAAGCCAAGCAGCCTAAACGTATAGAATCAGTTCTACGAAATgtaagtacaa ... atacatgcagGTATACAAGGATCAAACAAATGTTGATGAGTATTTGGTGAATTCCATTGTT
EST: gi|37842094|gb|BJ600102.1|BJ600102
EST:     CATTTTGGCAAGCCAAGCAGCCTAAACGTATAGAATCAGTTCTACGAAAT                         GTATACAAGGATCAAACAAATGTTGATGAGTATTTGGTGAATTCCATTGTT
genomic: CATTTTGGCAAGCCAAGCAGCCTAAACGTATAGAATCAGTTCTACGAAATgtaagtacaa ... atacatgcagGTATACAAGGATCAAACAAATGTTGATGAGTATTTGGTGAATTCCATTGTT
EST: gi|22491929|gb|BU051852.1|BU051852
EST:     CATTTTGGCAAGCCAAGCAGCCTAAACGTATAGAATCAGTTCTACGAAAT                         GTATACAAGGATCAAACAAATGTTGATGAGTATTTGGTGAATTCCATTGTT
genomic: CATTTTGGCAAGCCAAGCAGCCTAAACGTATAGAATCAGTTCTACGAAATgtaagtacaa ... atacatgcagGTATACAAGGATCAAACAAATGTTGATGAGTATTTGGTGAATTCCATTGTT
EST: gi|22131375|gb|BQ826583.1|BQ826583
EST:     CATTTTGGCAAGCCAAGCAGCCTAAACGTATAGAATCAGTTCTACGAAAT                         GTATACAAGGATCAAACAAATGTTGATGAGTATTTGGTGAATTCCATTGTT
genomic: CATTTTGGCAAGCCAAGCAGCCTAAACGTATAGAATCAGTTCTACGAAATgtaagtacaa ... atacatgcagGTATACAAGGATCAAACAAATGTTGATGAGTATTTGGTGAATTCCATTGTT
EST: gi|162266520|gb|FC442556.1|FC442556
EST:     CATTTTGGCAAGCCAAGCAGCCTAAACGTATAGAATCAGTTCTACGAAAT                         GTATACAAGGATCAAACAAATGTTGATGAGTATTTGGTGAATTCCATTGTT
genomic: CATTTTGGCAAGCCAAGCAGCCTAAACGTATAGAATCAGTTCTACGAAATgtaagtacaa ... atacatgcagGTATACAAGGATCAAACAAATGTTGATGAGTATTTGGTGAATTCCATTGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtatagatgttaagagacaacacatacttaatgtactgtttgcaatacatgcagGTATACAAGGATCAAACAAATGTTGATGAGTATTTGGTGAATTCCATTGTTCAACCCACAGCAGATCCGAACGCAGCAGAGGTTTATTACAG
                          acttaat  putative branch site (score: 4)
                        atacttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtacaaagcactccactaatccttgccaagtgggaccaatttctgaatcggaattgatttctaacgcagtatagatgttaagagacaacacatacttaatgtactgtttgcaatacatgcagGTATACAAGGATCAAACAAATGTTGATGAGTATTTGGTGAATTCCATTGTTCAACCCACAGCAGATCCGAACGCAGCAGAGGTTTATTACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT