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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATCAGTCAGGCCCTTATCTTCGTCACTCGTTCCCGGAGCTGGTCATTCGTTGAGAGACCGGGAGCACTGCTTATGATTGCATTTCTTGCTGCTCAGCTGgtaagatttcagtttgttatcggttcagctgaagcatttgctgaagaactgagtgacattgcagtgagtgttttcctttactattttcagactaattaagaagggaatttctacgttcaagaagttaggcgaagttgacactaataacaatgtgttgctccttcccacag

Basic information

species Physcomitrella patens
transcript PP1S6_11V6.1
intron # 15
splice site 5'
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|162252827|gb|FC428858.1|FC428858
EST:     TTGAGAGACCGGGAGCACTGCTTATGATTGCATTTCTTGCTGCTCAGCTG                         ATAGCTACATTCATTGCCGTGTACGCT
genomic: TTGAGAGACCGGGAGCACTGCTTATGATTGCATTTCTTGCTGCTCAGCTGgtaagatttc ... cttcccacagATAGCTACATTCATTGCCGTGTACGCT
EST: gi|162267612|gb|FC444675.1|FC444675
EST:     TTGAGAGACCGGGAGCACTGCTTATGATTGCATTTCTTGCTGCTCAGCTG                         ATAGCTACATTCATTGCCGTGTACGCTAATTGGGGATTCGCGCACATTCGT
genomic: TTGAGAGACCGGGAGCACTGCTTATGATTGCATTTCTTGCTGCTCAGCTGgtaagatttc ... cttcccacagATAGCTACATTCATTGCCGTGTACGCTAATTGGGGATTCGCGCACATTCGT
EST: gi|162185478|gb|FC362560.1|FC362560
EST:     TTGAGAGACCGGGAGCACTGCTTATGATTGCATTTCTTGCTGCTCAGCTG                         ATAGCTACATTCATTGCCGTGTACGCTAATTGGGGGATTCGCGCACATTCG
genomic: TTGAGAGACCGGGAGCACTGCTTATGATTGCATTTCTTGCTGCTCAGCTGgtaagatttc ... cttcccacagATAGCTACATTCATTGCCGTGTACGCTAATTGGGG-ATTCGCGCACATTCG
EST: gi|162198374|gb|FC375547.1|FC375547
EST:     TTGAGAGACCGGGAGCACTGCTTATGATTGCATTTCTTGCTGCTCAGCTG                         ATAGCTACATTCATTGCCGTGTACGCTAATTGGGGATTCGCGCACATT
genomic: TTGAGAGACCGGGAGCACTGCTTATGATTGCATTTCTTGCTGCTCAGCTGgtaagatttc ... cttcccacagATAGCTACATTCATTGCCGTGTACGCTAATTGGGGATTCGCGCACATT
EST: gi|162183362|gb|FC359277.1|FC359277
EST:     TTGAGAGACCGGGAGCACTGCTTATGATTGCATTTCTTGCTGCTCAGCTG                         ATAGCTACATTCATTGCCGTGTACGCTAATTGGGGATTCGCGCACATT
genomic: TTGAGAGACCGGGAGCACTGCTTATGATTGCATTTCTTGCTGCTCAGCTGgtaagatttc ... cttcccacagATAGCTACATTCATTGCCGTGTACGCTAATTGGGGATTCGCGCACATT
EST: gi|162164471|gb|FC341584.1|FC341584
EST:     TTGAGAGACCGGGAGCACTGCTTATGATTGCATTTCTTGCTGCTCAGCTG                         ATAGCTACATTCATTGCCGTGTACGCTAATTGGGGATTCGCGCACATTCGT
genomic: TTGAGAGACCGGGAGCACTGCTTATGATTGCATTTCTTGCTGCTCAGCTGgtaagatttc ... cttcccacagATAGCTACATTCATTGCCGTGTACGCTAATTGGGGATTCGCGCACATTCGT
EST: gi|162179356|gb|FC356305.1|FC356305
EST:     TTGAGAGACCGGGAGCACTGCTTATGATTGCATTTCTTGCTGCTCAGCTG                         ATAGCTACATTCATTGCCGTGTACGCTAA
genomic: TTGAGAGACCGGGAGCACTGCTTATGATTGCATTTCTTGCTGCTCAGCTGgtaagatttc ... cttcccacagATAGCTACATTCATTGCCGTGTACGCTAA
EST: gi|162157211|gb|FC332845.1|FC332845
EST:     TTGAGAGACCGGGAGCACTGCTTATGATTGCATTTCTTGCTGCTCAGCTG                         ATAGCTACATTCATTGCCGTGTACGCTAATTGGGGATTCGCGCACATTCGT
genomic: TTGAGAGACCGGGAGCACTGCTTATGATTGCATTTCTTGCTGCTCAGCTGgtaagatttc ... cttcccacagATAGCTACATTCATTGCCGTGTACGCTAATTGGGGATTCGCGCACATTCGT
EST: gi|162176072|gb|FC351866.1|FC351866
EST:     TTGAGAGACCGGGAGCACTGCTTATGATTGCATTTCTTGCTGCTCAGCTG                         ATAGCTACATTCATTGCCGTGTACGCTAATTGGGGATTCGCGCACATTCGT
genomic: TTGAGAGACCGGGAGCACTGCTTATGATTGCATTTCTTGCTGCTCAGCTGgtaagatttc ... cttcccacagATAGCTACATTCATTGCCGTGTACGCTAATTGGGGATTCGCGCACATTCGT
EST: gi|162168958|gb|FC345640.1|FC345640
EST:     TTGAGAGACCGGGAGCACTGCTTATGATTGCATTTCTTGCTGCTCAGCTG                         ATAGCTACATTCATTGCCGTGTACGCTAATTGGGGATTCG
genomic: TTGAGAGACCGGGAGCACTGCTTATGATTGCATTTCTTGCTGCTCAGCTGgtaagatttc ... cttcccacagATAGCTACATTCATTGCCGTGTACGCTAATTGGGGATTCG
EST: gi|162185798|gb|FC362354.1|FC362354
EST:     TTGAGAGACCGGGAGCACTGCTTATGATTGCATTTCTTGCTGCTCAGCTG                         ATAGCTACATTCATTGCCGTGTACGCTAATTGGGGATTCG
genomic: TTGAGAGACCGGGAGCACTGCTTATGATTGCATTTCTTGCTGCTCAGCTGgtaagatttc ... cttcccacagATAGCTACATTCATTGCCGTGTACGCTAATTGGGGATTCG

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), 26 (downstream exon)
Score: 25

CATCAGTCAGGCCCTTATCTTCGTCACTCGTTCCCGGAGCTGGTCATTCGTTGAGAGACCGGGAGCACTGCTTATGATTGCATTTCTTGCTGCTCAGCTGgtaagatttc ... cttcccacagATAGCTACATTCATTGCCGTGTACGCTAATTGGGGATTCGCGCACATTCGTGGTTGTGGATGGGGCTGGGCTGGGATTATCTGGCTGTACAGCACCGTCA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATCAGTCAGGCCCTTATCTTCGTCACTCGTTCCCGGAGCTGGTCATTCGTTGAGAGACCGGGAGCACTGCTTATGATTGCATTTCTTGCTGCTCAGCTGgtaagatttcagtttgttatcggttcagctgaagcatttgctgaagaactgagtgacattgcagtgagtgttttcctttactattttcagactaattaagaagggaatttctacgttcaagaagttaggcgaagttgacactaataacaatgtgttgctccttcccacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG