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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcttttacatctgatgttttttgagttcatgcgagtactgtccagtttctgaaaaagggcgtatggataattgcccatgatgttttattcgaaattgtgtacgggccgaagtctcttcttccagcttaccgtgtcattgcctcgagggacagGCATTCAAGTTGATTGTTACCGACCCAGATTCTGTTCTCAGCGGACTTACCAAGGAAGTAAAAGAAGTGGAAGGTGAAGAAGAG

Basic information

species Physcomitrella patens
transcript PP1S55_319V6.1
intron # 3
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|208370384|gb|DC931796.1|DC931796
EST:     ATCAAAACGTAGCCTGGCCGCTCTACAAAAAGTACGGGCATGCGTTTGAG                         GCATTCAAGTTGATTGTTACCGACCCAGATTCTGTTCTCAGCGGACTTACC
genomic: ATCAAAACGTAGCCTGGCCGCTCTACAAAAAGTACGGGCATGCGTTTGAGgtgagctttt ... cgagggacagGCATTCAAGTTGATTGTTACCGACCCAGATTCTGTTCTCAGCGGACTTACC
EST: gi|162189159|gb|FC365979.1|FC365979
EST:     ATCAAAACGTAGCCTGGCCGCTCTACAAAAAGTACGGGCATGCGTTTGAG                         GCATTCAAGTTGATTGTTACCGACCCAGATTCTGTTCTCAGCGGACTTACC
genomic: ATCAAAACGTAGCCTGGCCGCTCTACAAAAAGTACGGGCATGCGTTTGAGgtgagctttt ... cgagggacagGCATTCAAGTTGATTGTTACCGACCCAGATTCTGTTCTCAGCGGACTTACC
EST: gi|208379758|gb|DC907643.1|DC907643
EST:     ATCAAAACGTAGCCTGGCCGCTCTACAAAAAGTACGGGCATGCGTTTGAG                         GCATTCAAGTTGATTGTTACCGACCCAGATTCTGTTCTCAGCGGACTTACC
genomic: ATCAAAACGTAGCCTGGCCGCTCTACAAAAAGTACGGGCATGCGTTTGAGgtgagctttt ... cgagggacagGCATTCAAGTTGATTGTTACCGACCCAGATTCTGTTCTCAGCGGACTTACC
EST: gi|100359035|gb|BY946813.1|BY946813
EST:     ATCANAACGTAGCCTGGCCGCTCTACAAAAAGTACGGGCATGCGTTTGAG                         GCATTCAAGTTGATTGTTACCGACCCAGATTCTGTTCTCAGCGGACTTACC
genomic: ATCAAAACGTAGCCTGGCCGCTCTACAAAAAGTACGGGCATGCGTTTGAGgtgagctttt ... cgagggacagGCATTCAAGTTGATTGTTACCGACCCAGATTCTGTTCTCAGCGGACTTACC
EST: gi|100413715|gb|BY974954.1|BY974954
EST:     ATCAAAACGTAGCCTGGCCGCTCTACAAAAAGTACGGGCATGCGTTTGAG                         GCATTCAAGTTGATTGTTACCGACCCAGATTCTGTTCTCAGCGGACTTA
genomic: ATCAAAACGTAGCCTGGCCGCTCTACAAAAAGTACGGGCATGCGTTTGAGgtgagctttt ... cgagggacagGCATTCAAGTTGATTGTTACCGACCCAGATTCTGTTCTCAGCGGACTTA
EST: gi|208394236|gb|DC933904.1|DC933904
EST:     ATCAAAACGTAGCCTGGCCGCTCTACAAAAAGTACGGGCATGCGTTTGAG                         GCATTCAAGTTGATTGTTACCGACCCAGATTCTGTTCTCAGCGGACTTACC
genomic: ATCAAAACGTAGCCTGGCCGCTCTACAAAAAGTACGGGCATGCGTTTGAGgtgagctttt ... cgagggacagGCATTCAAGTTGATTGTTACCGACCCAGATTCTGTTCTCAGCGGACTTACC
EST: gi|208363800|gb|DC943257.1|DC943257
EST:     ATCAAAACGTAGCCTGGCCGCTCTACAAAAAGTACGGGCATGCGTTTGAG                         GCATTCAAGTTGATTGTTACCGACCCAGATTCTGTTCTCAGCGGACTTACC
genomic: ATCAAAACGTAGCCTGGCCGCTCTACAAAAAGTACGGGCATGCGTTTGAGgtgagctttt ... cgagggacagGCATTCAAGTTGATTGTTACCGACCCAGATTCTGTTCTCAGCGGACTTACC
EST: gi|162202525|gb|FC380040.1|FC380040
EST:     ATCAAAACGTAGCCTGGCCGCTCTACAAAAAGTACGGGCATGCGTTTGAG                         GCATTCAAGTTGATTGTTACCGACCCAGATTCTGTTCTCAGCGGACTTACC
genomic: ATCAAAACGTAGCCTGGCCGCTCTACAAAAAGTACGGGCATGCGTTTGAGgtgagctttt ... cgagggacagGCATTCAAGTTGATTGTTACCGACCCAGATTCTGTTCTCAGCGGACTTACC
EST: gi|100445417|gb|CJ975566.1|CJ975566
EST:     ATCAAAACGTAGCCTGGCCGCTCTACAAAAAGTACGGGCATGCGTTTGAG                         GCATTCANGTTGATNGTTACCGACCNAGATTCTGTTCTCAGC
genomic: ATCAAAACGTAGCCTGGCCGCTCTACAAAAAGTACGGGCATGCGTTTGAGgtgagctttt ... cgagggacagGCATTCAAGTTGATTGTTACCGACCCAGATTCTGTTCTCAGC
EST: gi|100400200|gb|BY990829.1|BY990829
EST:     ATCANAACGTAGCCTGGCCGCTCTACAAAAAGTACGGGCATGCGTTTGAG                         GCATTCAAGTTGATTGTTACCGACCCAGATTCTGTTCTCAGCGGACTTACC
genomic: ATCAAAACGTAGCCTGGCCGCTCTACAAAAAGTACGGGCATGCGTTTGAGgtgagctttt ... cgagggacagGCATTCAAGTTGATTGTTACCGACCCAGATTCTGTTCTCAGCGGACTTACC
EST: gi|100445091|gb|BY964390.1|BY964390
EST:     ATCAAAACGTAGCCTGGCCGCTCTACAAAAAGTACGGGCATGCGTTTGAG                         GCATTTCA-GTTGATTGTTACCCCGACC-AGATTCTGT-CTCAGCGGACTT
genomic: ATCAAAACGTAGCCTGGCCGCTCTACAAAAAGTACGGGCATGCGTTTGAGgtgagctttt ... cgagggacagGCATT-CAAGTTGATTGTTACC--GACCCAGATTCTGTTCTCAGCGGACTT
EST: gi|208365324|gb|DC931206.1|DC931206
EST:     ATCAAAACGTAGCCTGGCCGCTCTACAAAAAGTACGGGCATGCGTTTGAG                         GCATTCAAGTTGATTGTTACCGACCCAGATTCTGTTCTCAGCGGACTTACC
genomic: ATCAAAACGTAGCCTGGCCGCTCTACAAAAAGTACGGGCATGCGTTTGAGgtgagctttt ... cgagggacagGCATTCAAGTTGATTGTTACCGACCCAGATTCTGTTCTCAGCGGACTTACC
EST: gi|67694015|gb|BJ954248.1|BJ954248
EST:     TACGGGCATGCGTTTGAG                         GCATTCAAGNTGANTGTTACCGACCCAGATTCTGTTCTCAGCGGACTTACC
genomic: TACGGGCATGCGTTTGAGgtgagctttt ... cgagggacagGCATTCAAGTTGATTGTTACCGACCCAGATTCTGTTCTCAGCGGACTTACC
EST: gi|162149682|gb|FC326733.1|FC326733
EST:     ATCAAAACGTAGTCTGGCCGCTCTACAAAAAGTACGGGCATGCGTTTGAG                         GCATTCAAGTTGATTGTTACCGACCCAGATTCTGTTCTCAGCGGACTTACC
genomic: ATCAAAACGTAGCCTGGCCGCTCTACAAAAAGTACGGGCATGCGTTTGAGgtgagctttt ... cgagggacagGCATTCAAGTTGATTGTTACCGACCCAGATTCTGTTCTCAGCGGACTTACC
EST: gi|100395820|gb|BY972151.1|BY972151
EST:     ATCAAAACGTAGCCTGGCCGCTCTACAAAAAGTACGGGCATGCGTTTGAG                         GCATTCAAGTTGATTGTTACCGACCCAGATTCTGTTCTCAGCGGACTTACC
genomic: ATCAAAACGTAGCCTGGCCGCTCTACAAAAAGTACGGGCATGCGTTTGAGgtgagctttt ... cgagggacagGCATTCAAGTTGATTGTTACCGACCCAGATTCTGTTCTCAGCGGACTTACC
EST: gi|162163621|gb|FC339531.1|FC339531
EST:     ACGGGCATGCG-TTGAGG                         GCATTCAAGTTGATTGTTACCGACCCAGATTCTGTTCTCAGCGGACTTCC
genomic: ACGGGCATGCGTTTGA-Ggtgagctttt ... cgagggacagGCATTCAAGTTGATTGTTACCGACCCAGATTCTGTTCTCAGCGGACTTAC
EST: gi|22491982|gb|BU051905.1|BU051905
EST:     ATCAAAACGTAGCCTGGCCGCTCTACAAAAAGTACGGGCATGCGTTTGAG                         GCATTCAAGTTGATTGTTACCGACCCAGATTCTGTTCTCAGCGGACTTACC
genomic: ATCAAAACGTAGCCTGGCCGCTCTACAAAAAGTACGGGCATGCGTTTGAGgtgagctttt ... cgagggacagGCATTCAAGTTGATTGTTACCGACCCAGATTCTGTTCTCAGCGGACTTACC
EST: gi|162238556|gb|FC417411.1|FC417411
EST:     ATCAAAACGTAGCCTGGCCGCTCTACAAAAAGTACGGGCATGCGTTTGAG                         GCATTCAAGTTGATTGTTACCGACCCAGATTCTGTTCTCAGCGGACTTACC
genomic: ATCAAAACGTAGCCTGGCCGCTCTACAAAAAGTACGGGCATGCGTTTGAGgtgagctttt ... cgagggacagGCATTCAAGTTGATTGTTACCGACCCAGATTCTGTTCTCAGCGGACTTACC
EST: gi|100446960|gb|CJ971259.1|CJ971259
EST:     ATCAAAACGTANCCTGGCCGCTCTACAAAAAGTACGGGCATGCGTTTGAN                         GCATTCAAGTTGATTGTTACCGACCCANATTCNGTTCTCANCGNACT-ACC
genomic: ATCAAAACGTAGCCTGGCCGCTCTACAAAAAGTACGGGCATGCGTTTGAGgtgagctttt ... cgagggacagGCATTCAAGTTGATTGTTACCGACCCAGATTCTGTTCTCAGCGGACTTACC
EST: gi|162237619|gb|FC413052.1|FC413052
EST:     ATCAAAACGTAGCCTGGCCGCTCTACAAAAAGTACGGGCATGCGTTTGAG                         GCATTCAAGTTGATTGTTACCGACCCAGATTCTGTTCTCAGCGGACTTACC
genomic: ATCAAAACGTAGCCTGGCCGCTCTACAAAAAGTACGGGCATGCGTTTGAGgtgagctttt ... cgagggacagGCATTCAAGTTGATTGTTACCGACCCAGATTCTGTTCTCAGCGGACTTACC
EST: gi|100399885|gb|BY990670.1|BY990670
EST:     ATCANAACGTAGCCTGGCCGCTCTACAAAAAGTACGGGCATGCGTTTGAG                         GCNATTCA-GTTGATTGTTACCGACCCAGATTCTGTTCTCAGCGGACTTAC
genomic: ATCAAAACGTAGCCTGGCCGCTCTACAAAAAGTACGGGCATGCGTTTGAGgtgagctttt ... cgagggacagGC-ATTCAAGTTGATTGTTACCGACCCAGATTCTGTTCTCAGCGGACTTAC
EST: gi|208384915|gb|DC903422.1|DC903422
EST:     ATCAAAACGTAGCCTGGCCGCTCTACAAAAAGTACGGGCATGCGTTTGAG                         GCATTCAAGTTGATTGTTACCGACCCAGATTCTGTTCTCAGCGGACTTACC
genomic: ATCAAAACGTAGCCTGGCCGCTCTACAAAAAGTACGGGCATGCGTTTGAGgtgagctttt ... cgagggacagGCATTCAAGTTGATTGTTACCGACCCAGATTCTGTTCTCAGCGGACTTACC

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), 35 (downstream exon)
Score: 39

GATTTATATCAAAACGTAGCCTGGCCGCTCTACAAAAAGTACGGGCATGCGTTTGAGgtgagctttt ... cgagggacagGCATTCAAGTTGATTGTTACCGACCCAGATTCTGTTCTCAGCGGACTTACCAAGGAAGTAAAAGAAGTGGAAGGTGAAGAAGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtacgggccgaagtctcttcttccagcttaccgtgtcattgcctcgagggacagGCATTCAAGTTGATTGTTACCGACCCAGATTCTGTTCTCAGCGGACTTACCAAGGAAGTAAAAGAAGTGGAAGGTGAAGAAGAG
                         agcttac  putative branch site (score: 39)
                                       ttgcctc  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagcttttacatctgatgttttttgagttcatgcgagtactgtccagtttctgaaaaagggcgtatggataattgcccatgatgttttattcgaaattgtgtacgggccgaagtctcttcttccagcttaccgtgtcattgcctcgagggacagGCATTCAAGTTGATTGTTACCGACCCAGATTCTGTTCTCAGCGGACTTACCAAGGAAGTAAAAGAAGTGGAAGGTGAAGAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
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