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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTAGCTGCAGCAGTCATTGCCGCCATCAGAGACGAAGGTTTCAGCATGGGCAAGACGTTTGAGCTAGGAGGACCAGATGTTTTCACAGTCAATGAACTTgtaaggaaattgacttgattccctgtgaagtctgttttttttttttttttctacttgcaacgaaatggcatatgtagttgatatatttgcgttgcaatccatcttacaactcccgtgctcattaactacag

Basic information

species Physcomitrella patens
transcript PP1S79_105V6.1
intron # 8
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|67573788|gb|BJ946612.1|BJ946612
EST:     GCAAGACGTTTGAGCTAGGAGGACCAGATGTTTTCACAGTCAATGAACTT                         GTTGCGCTGATGTTTGAGGCAATTCGTGAGTATCCGCGTGTCGTACATATT
genomic: GCAAGACGTTTGAGCTAGGAGGACCAGATGTTTTCACAGTCAATGAACTTgtaaggaaat ... ttaactacagGTTGCGCTGATGTTTGAGGCAATTCGTGAGTATCCGCGTGTCGTACATATT
EST: gi|37842479|gb|BJ600487.1|BJ600487
EST:     GCGAGACGTTTGAGCTAGGAGGACCAGATGTTTTCACAGTCAATGAACTT                         GTTGCGCTGATGTTTGAGGCAATTCGTGAGTATCCGCGTGTCGTACATATT
genomic: GCAAGACGTTTGAGCTAGGAGGACCAGATGTTTTCACAGTCAATGAACTTgtaaggaaat ... ttaactacagGTTGCGCTGATGTTTGAGGCAATTCGTGAGTATCCGCGTGTCGTACATATT
EST: gi|208367986|gb|DC955393.1|DC955393
EST:     GCAAGACGTTTGAGCTAGGAGGACCAGATGTTTTCACAGTCAATGAACTT                         GTTGCGCTGATGTTTGAGGCAATTCGTGAGTATCCGCGTGTCGTACATATT
genomic: GCAAGACGTTTGAGCTAGGAGGACCAGATGTTTTCACAGTCAATGAACTTgtaaggaaat ... ttaactacagGTTGCGCTGATGTTTGAGGCAATTCGTGAGTATCCGCGTGTCGTACATATT
EST: gi|67700799|gb|BJ961032.1|BJ961032
EST:     CCAGATGTTTTTCACAGTCAATGAACTT                         GTTGCGCTGATGTTTGAGGCAATTCGTGAGTATCCGCGTGTCGTACATATT
genomic: CCAGATG-TTTTCACAGTCAATGAACTTgtaaggaaat ... ttaactacagGTTGCGCTGATGTTTGAGGCAATTCGTGAGTATCCGCGTGTCGTACATATT
EST: gi|208352691|gb|DC921425.1|DC921425
EST:     GCAAGACGTTTGAGCTAGGAGGACCAGATGTTTTCACAGTCAATGAACTT                         GTTGCGCTGATGTTTGAGGCAATTCGTGAGTATCCGCGTGTCGTACATATT
genomic: GCAAGACGTTTGAGCTAGGAGGACCAGATGTTTTCACAGTCAATGAACTTgtaaggaaat ... ttaactacagGTTGCGCTGATGTTTGAGGCAATTCGTGAGTATCCGCGTGTCGTACATATT
EST: gi|162256291|gb|FC432197.1|FC432197
EST:     GCAAGACGTTTGAGCTAGGAGGACCAGATGTTTTCACAGTCAATGAACTT                         GTTGCGCTGATGTTTGAGGCAATTCGTGAGTATCCGCGTGTCGTACATATT
genomic: GCAAGACGTTTGAGCTAGGAGGACCAGATGTTTTCACAGTCAATGAACTTgtaaggaaat ... ttaactacagGTTGCGCTGATGTTTGAGGCAATTCGTGAGTATCCGCGTGTCGTACATATT
EST: gi|208377554|gb|DC922657.1|DC922657
EST:     GCAAGACGTTTGAGCTAGGAGGACCAGATGTTTTCACAGTCAATGAACTT                         GTTGCGCTGATGTTTGAGGCAATTCGTGAGTATCCGCGTGTCGTACATATT
genomic: GCAAGACGTTTGAGCTAGGAGGACCAGATGTTTTCACAGTCAATGAACTTgtaaggaaat ... ttaactacagGTTGCGCTGATGTTTGAGGCAATTCGTGAGTATCCGCGTGTCGTACATATT
EST: gi|162259818|gb|FC435953.1|FC435953
EST:     GCAAGACGTTTGAGCTAGGAGGACCAGATGTTTTCACAGTCAATGAACTT                         GTTGCGCTGATGTTTGAGGCAATTCGTGAGTATCCGCGTGTCGTACATATT
genomic: GCAAGACGTTTGAGCTAGGAGGACCAGATGTTTTCACAGTCAATGAACTTgtaaggaaat ... ttaactacagGTTGCGCTGATGTTTGAGGCAATTCGTGAGTATCCGCGTGTCGTACATATT
EST: gi|208367694|gb|DC955025.1|DC955025
EST:     GCAAGACGTTTGAGCTAGGAGGACCAGATGTTTTCACAGTCAATGAACTT                         GTTGCGCTGATGTTTGAGGCAATTCGTGAGTATCCGCGTGTCGTACATATT
genomic: GCAAGACGTTTGAGCTAGGAGGACCAGATGTTTTCACAGTCAATGAACTTgtaaggaaat ... ttaactacagGTTGCGCTGATGTTTGAGGCAATTCGTGAGTATCCGCGTGTCGTACATATT
EST: gi|162220174|gb|FC396569.1|FC396569
EST:     GCAAGACGTTTGAGCTAGGAGGACCAGATGTTTTCACAGTCAATGAACTT                         GTTGCGCTGATGTTTGAGGCAATTCGTGAGTATCCGCGTGTCGTACATATT
genomic: GCAAGACGTTTGAGCTAGGAGGACCAGATGTTTTCACAGTCAATGAACTTgtaaggaaat ... ttaactacagGTTGCGCTGATGTTTGAGGCAATTCGTGAGTATCCGCGTGTCGTACATATT
EST: gi|67700542|gb|BJ960775.1|BJ960775
EST:     GCAAGACGTTTGAGCTAGGAGGACCAGATGTTTTCACAGTCAATGAACTT                         GTTGCGCTGATGTTTGAGGCAATTCGTGAGTATCCGCGTGTCGTACATATT
genomic: GCAAGACGTTTGAGCTAGGAGGACCAGATGTTTTCACAGTCAATGAACTTgtaaggaaat ... ttaactacagGTTGCGCTGATGTTTGAGGCAATTCGTGAGTATCCGCGTGTCGTACATATT
EST: gi|67697174|gb|BJ957407.1|BJ957407
EST:     GCAAGACGTTTGAGCTAGGAGGACCAGATGTTTTCACAGTCAATGAACTT                         GTTGCGCTGATGTTTGAGGCAATTCGTGAGTATCCGCGTGTCGTACATATT
genomic: GCAAGACGTTTGAGCTAGGAGGACCAGATGTTTTCACAGTCAATGAACTTgtaaggaaat ... ttaactacagGTTGCGCTGATGTTTGAGGCAATTCGTGAGTATCCGCGTGTCGTACATATT
EST: gi|37846724|gb|BJ604732.1|BJ604732
EST:     GCAAGACGTTTGAGCTAGGAGGACCAGATGTTTTCACAGTCAATGAACTT                         GTTGCGCTGATGTTTGAGGCAATTCGTGAGTATCCGCGTGTCGTACATATT
genomic: GCAAGACGTTTGAGCTAGGAGGACCAGATGTTTTCACAGTCAATGAACTTgtaaggaaat ... ttaactacagGTTGCGCTGATGTTTGAGGCAATTCGTGAGTATCCGCGTGTCGTACATATT
EST: gi|67578914|gb|BJ951081.1|BJ951081
EST:     GCAAGACGTTTGAGCTAGGAGGACCAGATGTTTTCACAGTCAATGAACTT                         GTTGCGCTGATGTTTGAGGCAATTCGTGAGTATCCGCGTGTCGTACATATT
genomic: GCAAGACGTTTGAGCTAGGAGGACCAGATGTTTTCACAGTCAATGAACTTgtaaggaaat ... ttaactacagGTTGCGCTGATGTTTGAGGCAATTCGTGAGTATCCGCGTGTCGTACATATT
EST: gi|162276086|gb|FC452362.1|FC452362
EST:     GCAAGACGTTTGAGCTAGGAGGACCAGATGTTTTCACAGTCAATGAACTT                         GTTGCGCTGATGTTTGAGGCAATTCGTGAGTATCCGCGTGTCGTACATATT
genomic: GCAAGACGTTTGAGCTAGGAGGACCAGATGTTTTCACAGTCAATGAACTTgtaaggaaat ... ttaactacagGTTGCGCTGATGTTTGAGGCAATTCGTGAGTATCCGCGTGTCGTACATATT
EST: gi|67577666|gb|BJ949833.1|BJ949833
EST:     GCAAGACGTTTGAGCTAGGAGGACCAGATGTTTTCACAGTCAATGAACTT                         GTTGCGCTGATGTTTGAGGCAATTCGTGAGTATCCGCGTGTCGTACATATT
genomic: GCAAGACGTTTGAGCTAGGAGGACCAGATGTTTTCACAGTCAATGAACTTgtaaggaaat ... ttaactacagGTTGCGCTGATGTTTGAGGCAATTCGTGAGTATCCGCGTGTCGTACATATT

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: 27 (upstream exon), 22 (downstream exon)
Score: 6

TGTAGCTGCAGCAGTCATTGCCGCCATCAGAGACGAAGGTTTCAGCATGGGCAAGACGTTTGAGCTAGGAGGACCAGATGTTTTCACAGTCAATGAACTTgtaaggaaat ... ttaactacagGTTGCGCTGATGTTTGAGGCAATTCGTGAGTATCCGCGTGTCGTACATATTCCTATGCCCCTTTGTCAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTAGCTGCAGCAGTCATTGCCGCCATCAGAGACGAAGGTTTCAGCATGGGCAAGACGTTTGAGCTAGGAGGACCAGATGTTTTCACAGTCAATGAACTTgtaaggaaattgacttgattccctgtgaagtctgttttttttttttttttctacttgcaacgaaatggcatatgtagttgatatatttgcgttgcaatccatcttacaactcccgtgctcattaactacag

- - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG