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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgaatgtttcagcattgctcagtccttacacatggagtgaattattcgtagaaatggttgcgctatcactgtgatcccttgccagtattgattgatactacgtgacgtaaatgcaatgcatgtgatttttctcacagcctgagaatattctcctaacttgcagGATCCACTTCGATCATTTAAAGGGCGGGACAAGTACAAAGGCGCAAACTGGATCAAGACTGCCTTGGAGAAGCCCACAGTG

Basic information

species Physcomitrella patens
transcript PP1S99_109V6.1
intron # 2
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|100362720|gb|BY947494.1|BY947494
EST:     GAGAGGGCGAGAGATCATTGTCAAATTTCGGAGTTAATGTTGAATATAAG                         GATCCACTTCGATCATTTAAAGGGCGGGACAAGTACAAAGGCGCAAACTGG
genomic: GAGAGGGCGAGAGATCATTGTCAAATTTCGGAGTTAATGTTGAATATAAGgttcgaatgt ... taacttgcagGATCCACTTCGATCATTTAAAGGGCGGGACAAGTACAAAGGCGCAAACTGG
EST: gi|162224373|gb|FC399567.1|FC399567
EST:     GAGAGGGCGAGAGATCATTGTCAAATTTCGGAGTTAATGTTGAATATAAG                         GATCCACTTCGATCATTTAAAGGGCGGGACAAGTACAAAGGCGCAAACTGG
genomic: GAGAGGGCGAGAGATCATTGTCAAATTTCGGAGTTAATGTTGAATATAAGgttcgaatgt ... taacttgcagGATCCACTTCGATCATTTAAAGGGCGGGACAAGTACAAAGGCGCAAACTGG
EST: gi|208381777|gb|DC928440.1|DC928440
EST:     GAGAGGGCGAGAGATCANTGTCAAATTTCGGAGTTAATGGTGNATATAAG                         GATCCACTTCGATCATTT-AAGGGCGGGACAAGTACNAAGGCGCAANCTGG
genomic: GAGAGGGCGAGAGATCATTGTCAAATTTCGGAGTTAATGTTGAATATAAGgttcgaatgt ... taacttgcagGATCCACTTCGATCATTTAAAGGGCGGGACAAGTACAAAGGCGCAAACTGG
EST: gi|100396934|gb|BY953901.1|BY953901
EST:     GAGAGGGCGAGAGATCATTGTCAAATTTCGGAGTTAATGTTGAATATAAG                         GATCCACTTCGATCATTTAAAGGGCGGGACAAGTACAAAGGCGCAAACTGG
genomic: GAGAGGGCGAGAGATCATTGTCAAATTTCGGAGTTAATGTTGAATATAAGgttcgaatgt ... taacttgcagGATCCACTTCGATCATTTAAAGGGCGGGACAAGTACAAAGGCGCAAACTGG
EST: gi|100380070|gb|BY968831.1|BY968831
EST:     GAGAGGGCGAGAGATCATTGTCAAATTTCGGAGTTAATGTTGAATATAAG                         GATCCACTTCGATCATTTAAAGGGCGGGACAAGTA
genomic: GAGAGGGCGAGAGATCATTGTCAAATTTCGGAGTTAATGTTGAATATAAGgttcgaatgt ... taacttgcagGATCCACTTCGATCATTTAAAGGGCGGGACAAGTA
EST: gi|100399137|gb|BY954218.1|BY954218
EST:     GAGAGGGCGAGAGATCATTGTCAAATTTCGGAGTTAATGGTGAATATAAG                         GATCCACTTCGATCATTTAAAGGGCGGGACAAGTACAAAGGCGCAAACTGG
genomic: GAGAGGGCGAGAGATCATTGTCAAATTTCGGAGTTAATGTTGAATATAAGgttcgaatgt ... taacttgcagGATCCACTTCGATCATTTAAAGGGCGGGACAAGTACAAAGGCGCAAACTGG
EST: gi|100446520|gb|CJ970819.1|CJ970819
EST:     GAGAGGGCGAGAGATCATTGTCAAATTTCGGAGTTAATGTTGAATATAAG                         GATCCACTTCGATCATTTAAAGGGCGGGACAAGTACAAAGGCGCAAACTGG
genomic: GAGAGGGCGAGAGATCATTGTCAAATTTCGGAGTTAATGTTGAATATAAGgttcgaatgt ... taacttgcagGATCCACTTCGATCATTTAAAGGGCGGGACAAGTACAAAGGCGCAAACTGG
EST: gi|162224372|gb|FC399566.1|FC399566
EST:     GAGTTAATG-TGNAATATAAG                         GATCCACTTCGATCA-TTAAAGGGCGGGACAAGTACAAAGGCGCAAACTG
genomic: GAGTTAATGTTG-AATATAAGgttcgaatgt ... taacttgcagGATCCACTTCGATCATTTAAAGGGCGGGACAAGTACAAAGGCGCAAACTG
EST: gi|162251558|gb|FC427745.1|FC427745
EST:     GAGAGGGCGAGAGATCATTGTCAAATTTCGGAGTTAATGTTGAATATAAG                         GATCCACTTCGATCATTTAAAGGGCGGGACAAGTACAAAGGCGCAAACTGG
genomic: GAGAGGGCGAGAGATCATTGTCAAATTTCGGAGTTAATGTTGAATATAAGgttcgaatgt ... taacttgcagGATCCACTTCGATCATTTAAAGGGCGGGACAAGTACAAAGGCGCAAACTGG
EST: gi|162180016|gb|FC356087.1|FC356087
EST:     GAGAGGGCGAGAGATCATTGTCAAATTTCGGAGTTAATGTTGAATATAAG                         GATCCACTTCGATCATTTAAAGGGCGGGACAAGTACAAAGGCGCAAACTGG
genomic: GAGAGGGCGAGAGATCATTGTCAAATTTCGGAGTTAATGTTGAATATAAGgttcgaatgt ... taacttgcagGATCCACTTCGATCATTTAAAGGGCGGGACAAGTACAAAGGCGCAAACTGG
EST: gi|100353692|gb|BY983262.1|BY983262
EST:     GAGAGGGCGAGAGATCATTGTCAAATTTCGGAGTTAATGTTGAATATAAG                         GATCCACTTCGATCATTTAAAGGGCGGGACAAGTACAAAGGCGCAAACTGG
genomic: GAGAGGGCGAGAGATCATTGTCAAATTTCGGAGTTAATGTTGAATATAAGgttcgaatgt ... taacttgcagGATCCACTTCGATCATTTAAAGGGCGGGACAAGTACAAAGGCGCAAACTGG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 34 (upstream exon), 35 (downstream exon)
Score: 15

GGCTGTAGAAAGAACGGCACGGCAGCTTGTGAAGGACATCATAGACCTTCGAGAGGGCGAGAGATCATTGTCAAATTTCGGAGTTAATGTTGAATATAAGgttcgaatgt ... taacttgcagGATCCACTTCGATCATTTAAAGGGCGGGACAAGTACAAAGGCGCAAACTGGATCAAGACTGCCTTGGAGAAGCCCACAGTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatgcaatgcatgtgatttttctcacagcctgagaatattctcctaacttgcagGATCCACTTCGATCATTTAAAGGGCGGGACAAGTACAAAGGCGCAAACTGGATCAAGACTGCCTTGGAGAAGCCCACAGTG
                                          tcctaac  putative branch site (score: 15)
                                     tattctcct  CT-rich tract
              tgattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcgaatgtttcagcattgctcagtccttacacatggagtgaattattcgtagaaatggttgcgctatcactgtgatcccttgccagtattgattgatactacgtgacgtaaatgcaatgcatgtgatttttctcacagcctgagaatattctcctaacttgcagGATCCACTTCGATCATTTAAAGGGCGGGACAAGTACAAAGGCGCAAACTGGATCAAGACTGCCTTGGAGAAGCCCACAGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC