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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAGGAGGACGTTGCCAGCTGTGAGGAACGTTATAACAAAAGCAAGTTGGTGCACTCTATCATGCGCCATGTCGCCGACACAATGGATGCTGATTTGGAGgtaaaattctactaagtgaatgtgatcattattgaaacgattgagcaatcaagtgatcgacgtcgccgtctgcagaccctttgagtctagctcgaaatct...

Basic information

species Physcomitrella patens
transcript PP1S55_319V6.1
intron # 2
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|208370384|gb|DC931796.1|DC931796
EST:     TGCACTCTATCATGCGCCATGTCGCCGACACAATGGATGCTGATTTGGAG                         GATTTATATCAAAACGTAGCCTGGCCGCTCTACAAAAAGTACGGGCATGCG
genomic: TGCACTCTATCATGCGCCATGTCGCCGACACAATGGATGCTGATTTGGAGgtaaaattct ... cctcttgcagGATTTATATCAAAACGTAGCCTGGCCGCTCTACAAAAAGTACGGGCATGCG
EST: gi|162189159|gb|FC365979.1|FC365979
EST:     TGCACTCTATCATGCGCCATGTCGCCGACACAATGGATGCTGATTTGGAG                         GATTTATATCAAAACGTAGCCTGGCCGCTCTACAAAAAGTACGGGCATGCG
genomic: TGCACTCTATCATGCGCCATGTCGCCGACACAATGGATGCTGATTTGGAGgtaaaattct ... cctcttgcagGATTTATATCAAAACGTAGCCTGGCCGCTCTACAAAAAGTACGGGCATGCG
EST: gi|208379758|gb|DC907643.1|DC907643
EST:     TGCACTCTATCATGCGCCATGTCGCCGACACAATGGATGCTGATTTGGAG                         GATTTATATCAAAACGTAGCCTGGCCGCTCTACAAAAAGTACGGGCATGCG
genomic: TGCACTCTATCATGCGCCATGTCGCCGACACAATGGATGCTGATTTGGAGgtaaaattct ... cctcttgcagGATTTATATCAAAACGTAGCCTGGCCGCTCTACAAAAAGTACGGGCATGCG
EST: gi|100359035|gb|BY946813.1|BY946813
EST:     TGCACTCTATCATGCGCCATGTCGCCGACACAATGGATGCTGATTTGGAG                         GATTTATATCANAACGTAGCCTGGCCGCTCTACAAAAAGTACGGGCATGCG
genomic: TGCACTCTATCATGCGCCATGTCGCCGACACAATGGATGCTGATTTGGAGgtaaaattct ... cctcttgcagGATTTATATCAAAACGTAGCCTGGCCGCTCTACAAAAAGTACGGGCATGCG
EST: gi|18357069|gb|BJ189128.1|BJ189128
EST:     TGCACTCTATCATGCGCCATGTCGCCGACACAATGGATGCTGATTTGGAG                         GATTTATATCAAAACGTAGCCTGGCCGCTCTACAAAAAGTACGGGCATGCG
genomic: TGCACTCTATCATGCGCCATGTCGCCGACACAATGGATGCTGATTTGGAGgtaaaattct ... cctcttgcagGATTTATATCAAAACGTAGCCTGGCCGCTCTACAAAAAGTACGGGCATGCG
EST: gi|100413715|gb|BY974954.1|BY974954
EST:     TGCACTCTATCATGCGCCATGTCGCCGACACAATGGATGCTGATTTGGAG                         GATTTATATCAAAACGTAGCCTGGCCGCTCTACAAAAAGTACGGGCATGCG
genomic: TGCACTCTATCATGCGCCATGTCGCCGACACAATGGATGCTGATTTGGAGgtaaaattct ... cctcttgcagGATTTATATCAAAACGTAGCCTGGCCGCTCTACAAAAAGTACGGGCATGCG
EST: gi|208394236|gb|DC933904.1|DC933904
EST:     TGCACTCTATCATGCGCCATGTCGCCGACACAATGGATGCTGATTTGGAG                         GATTTATATCAAAACGTAGCCTGGCCGCTCTACAAAAAGTACGGGCATGCG
genomic: TGCACTCTATCATGCGCCATGTCGCCGACACAATGGATGCTGATTTGGAGgtaaaattct ... cctcttgcagGATTTATATCAAAACGTAGCCTGGCCGCTCTACAAAAAGTACGGGCATGCG
EST: gi|208363800|gb|DC943257.1|DC943257
EST:     TGCACTCTATCATGCGCCATGTCGCCGACACAATGGATGCTGATTTGGAG                         GATTTATATCAAAACGTAGCCTGGCCGCTCTACAAAAAGTACGGGCATGCG
genomic: TGCACTCTATCATGCGCCATGTCGCCGACACAATGGATGCTGATTTGGAGgtaaaattct ... cctcttgcagGATTTATATCAAAACGTAGCCTGGCCGCTCTACAAAAAGTACGGGCATGCG
EST: gi|162202525|gb|FC380040.1|FC380040
EST:     TGCACTCTATCATGCGCCATGTCGCCGACACAATGGATGCTGATTTGGAG                         GATTTATATCAAAACGTAGCCTGGCCGCTCTACAAAAAGTACGGGCATGCG
genomic: TGCACTCTATCATGCGCCATGTCGCCGACACAATGGATGCTGATTTGGAGgtaaaattct ... cctcttgcagGATTTATATCAAAACGTAGCCTGGCCGCTCTACAAAAAGTACGGGCATGCG
EST: gi|100445417|gb|CJ975566.1|CJ975566
EST:     TGCACTCTATCATGCGCCATGTCGCCGACACAATGGATGCTGATTTGGAG                         GATTTATATCAAAACGTAGCCTGGCCGCTCTACAAAAAGTACGGGCATGCG
genomic: TGCACTCTATCATGCGCCATGTCGCCGACACAATGGATGCTGATTTGGAGgtaaaattct ... cctcttgcagGATTTATATCAAAACGTAGCCTGGCCGCTCTACAAAAAGTACGGGCATGCG
EST: gi|100400200|gb|BY990829.1|BY990829
EST:     TGCACTCTATCATGCGCCATGTCGCCGACACAATGGATGCTGATTTGGAG                         GATTTATATCANAACGTAGCCTGGCCGCTCTACAAAAAGTACGGGCATGCG
genomic: TGCACTCTATCATGCGCCATGTCGCCGACACAATGGATGCTGATTTGGAGgtaaaattct ... cctcttgcagGATTTATATCAAAACGTAGCCTGGCCGCTCTACAAAAAGTACGGGCATGCG
EST: gi|100445091|gb|BY964390.1|BY964390
EST:     TGCACTCTATCATGCGCCATGTCGCCGACACAATGGATGCTGATTTGGAG                         GATTTATATCAAAACGTAGCCTGGCCGCTCTACAAAAAGTACGGGCATGCG
genomic: TGCACTCTATCATGCGCCATGTCGCCGACACAATGGATGCTGATTTGGAGgtaaaattct ... cctcttgcagGATTTATATCAAAACGTAGCCTGGCCGCTCTACAAAAAGTACGGGCATGCG
EST: gi|208365324|gb|DC931206.1|DC931206
EST:     TGCGCTCTATCATGCGCCATGTCGCCGACACAATGGATGCTGATTTGGAG                         GATTTATATCAAAACGTAGCCTGGCCGCTCTACAAAAAGTACGGGCATGCG
genomic: TGCACTCTATCATGCGCCATGTCGCCGACACAATGGATGCTGATTTGGAGgtaaaattct ... cctcttgcagGATTTATATCAAAACGTAGCCTGGCCGCTCTACAAAAAGTACGGGCATGCG
EST: gi|162149682|gb|FC326733.1|FC326733
EST:     TGCACTCTATCATGCGCCATGTCGCCGACACAATGGATGCTGATTTGGAG                         GATTTATATCAAAACGTAGTCTGGCCGCTCTACAAAAAGTACGGGCATGCG
genomic: TGCACTCTATCATGCGCCATGTCGCCGACACAATGGATGCTGATTTGGAGgtaaaattct ... cctcttgcagGATTTATATCAAAACGTAGCCTGGCCGCTCTACAAAAAGTACGGGCATGCG
EST: gi|100395820|gb|BY972151.1|BY972151
EST:     TGCACTCTATCATGCGCCATGTCGCCGACACAATGGATGCTGATTTGGAG                         GATTTATATCAAAACGTAGCCTGGCCGCTCTACAAAAAGTACGGGCATGCG
genomic: TGCACTCTATCATGCGCCATGTCGCCGACACAATGGATGCTGATTTGGAGgtaaaattct ... cctcttgcagGATTTATATCAAAACGTAGCCTGGCCGCTCTACAAAAAGTACGGGCATGCG
EST: gi|22491982|gb|BU051905.1|BU051905
EST:     GCGCCATGTCGCCGACACAATGGATGCTGATTTGGAG                         GATTTATATCAAAACGTAGCCTGGCCGCTCTACAAAAAGTACGGGCATGCG
genomic: GCGCCATGTCGCCGACACAATGGATGCTGATTTGGAGgtaaaattct ... cctcttgcagGATTTATATCAAAACGTAGCCTGGCCGCTCTACAAAAAGTACGGGCATGCG
EST: gi|162238556|gb|FC417411.1|FC417411
EST:     TGCACTCTATCATGCGCCATGTCGCCGACACAATGGATGCTGATTTGGAG                         GATTTATATCAAAACGTAGCCTGGCCGCTCTACAAAAAGTACGGGCATGCG
genomic: TGCACTCTATCATGCGCCATGTCGCCGACACAATGGATGCTGATTTGGAGgtaaaattct ... cctcttgcagGATTTATATCAAAACGTAGCCTGGCCGCTCTACAAAAAGTACGGGCATGCG
EST: gi|100446960|gb|CJ971259.1|CJ971259
EST:     TGCACTCTATCATGCGCCATGTCGCCGACACAATGGATGCTGATTTGGAG                         GATTTATATCAAAACGTANCCTGGCCGCTCTACAAAAAGTACGGGCATGCG
genomic: TGCACTCTATCATGCGCCATGTCGCCGACACAATGGATGCTGATTTGGAGgtaaaattct ... cctcttgcagGATTTATATCAAAACGTAGCCTGGCCGCTCTACAAAAAGTACGGGCATGCG
EST: gi|162237619|gb|FC413052.1|FC413052
EST:     TGCACTCTATCATGCGCCATGTCGCCGACACAATGGATGCTGATTTGGAG                         GATTTATATCAAAACGTAGCCTGGCCGCTCTACAAAAAGTACGGGCATGCG
genomic: TGCACTCTATCATGCGCCATGTCGCCGACACAATGGATGCTGATTTGGAGgtaaaattct ... cctcttgcagGATTTATATCAAAACGTAGCCTGGCCGCTCTACAAAAAGTACGGGCATGCG
EST: gi|100399885|gb|BY990670.1|BY990670
EST:     TGCACTCTATCATGCGCCATGTCGCCGACACAATGGATGCTGATTTGGAG                         GATTTATATCANAACGTAGCCTGGCCGCTCTACAAAAAGTACGGGCATGCG
genomic: TGCACTCTATCATGCGCCATGTCGCCGACACAATGGATGCTGATTTGGAGgtaaaattct ... cctcttgcagGATTTATATCAAAACGTAGCCTGGCCGCTCTACAAAAAGTACGGGCATGCG
EST: gi|208384915|gb|DC903422.1|DC903422
EST:     TGCACTCTATCATGCGCCATGTCGCCGACACAATGGATGCTGATTTGGAG                         GATTTATATCAAAACGTAGCCTGGCCGCTCTACAAAAAGTACGGGCATGCG
genomic: TGCACTCTATCATGCGCCATGTCGCCGACACAATGGATGCTGATTTGGAGgtaaaattct ... cctcttgcagGATTTATATCAAAACGTAGCCTGGCCGCTCTACAAAAAGTACGGGCATGCG

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: 32 (upstream exon), 34 (downstream exon)
Score: 20

TGAGGAGGACGTTGCCAGCTGTGAGGAACGTTATAACAAAAGCAAGTTGGTGCACTCTATCATGCGCCATGTCGCCGACACAATGGATGCTGATTTGGAGgtaaaattct ... cctcttgcagGATTTATATCAAAACGTAGCCTGGCCGCTCTACAAAAAGTACGGGCATGCGTTTGAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAGGAGGACGTTGCCAGCTGTGAGGAACGTTATAACAAAAGCAAGTTGGTGCACTCTATCATGCGCCATGTCGCCGACACAATGGATGCTGATTTGGAGgtaaaattctactaagtgaatgtgatcattattgaaacgattgagcaatcaagtgatcgacgtcgccgtctgcagaccctttgagtctagctcgaaatct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG