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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattttctgtacttaaactgctgttgtttgttcttgattcttaactgcgtgcacatatttcctgaactgcatgaaaaaacacacgacttgatttgcgtaaacatcctgcttcatcttctgaatgatctcattatgaactactcgttttttagtagttctgacaaatgtcgtgattctttcagTTGCTGCGGATAGAGGAGGAGCTCGGCAATGTCCGTTACGCAGGACAGAGCTTCAGACAACCTCTCTAAAGGAAGGATAGAACTCTTAGTGACCACGAGT

Basic information

species Physcomitrella patens
transcript PP1S76_97V6.1
intron # 5
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|208371720|gb|DC951622.1|DC951622
EST:     TCAAAACTGGAGCTCCTTGCCGAAGTGAGCGTCTCGCCAAATACAACCAG                         TTGCTGCGGATAGAGGAGGAGCTCGGCAATGTCCGTTACGCAGGACAGAGC
genomic: TCAAAACTGGAGCTCCTTGCCGAAGTGAGCGTCTCGCCAAATACAACCAGgtattttctg ... attctttcagTTGCTGCGGATAGAGGAGGAGCTCGGCAATGTCCGTTACGCAGGACAGAGC
EST: gi|67693606|gb|BJ953839.1|BJ953839
EST:     TCAAAACTGGAGCTCCTTGCCGAAGTGAGCGTCTCGCCAAATACAACCAG                         TTGCTGCGGATAGAGGAGGAGCTCGGCAATGTCCGTTACGCAGGACAGAGC
genomic: TCAAAACTGGAGCTCCTTGCCGAAGTGAGCGTCTCGCCAAATACAACCAGgtattttctg ... attctttcagTTGCTGCGGATAGAGGAGGAGCTCGGCAATGTCCGTTACGCAGGACAGAGC
EST: gi|162219389|gb|FC396412.1|FC396412
EST:     TCAAAACTGGAGCTCCTTGCCGAAGTGAGCGTCTCGCCAAATACAACCAG                         TTGCTGCGGATAGAGGAGGAGCTCGGCAATGTCCGTTACGCAGGACAGAGC
genomic: TCAAAACTGGAGCTCCTTGCCGAAGTGAGCGTCTCGCCAAATACAACCAGgtattttctg ... attctttcagTTGCTGCGGATAGAGGAGGAGCTCGGCAATGTCCGTTACGCAGGACAGAGC
EST: gi|208367450|gb|DC943909.1|DC943909
EST:     TCAAAACTGGAGCTCCTTGCCGAAGTGAGCGTCTCGCCAAATACAACCAG                         TTGCTGCGGATAGAGGAGGAGCTCGGCAATGTCCGTTACGCAGGACAGAGC
genomic: TCAAAACTGGAGCTCCTTGCCGAAGTGAGCGTCTCGCCAAATACAACCAGgtattttctg ... attctttcagTTGCTGCGGATAGAGGAGGAGCTCGGCAATGTCCGTTACGCAGGACAGAGC
EST: gi|18332690|gb|BJ164703.1|BJ164703
EST:     TCAAAACTGGAGCTCCTTGCCGAAGTGAGCGTCTCGCCAAATACAACCAG                         TTGCTGCGGATAGAGGAGGAGCTCGGCAATGTCCGTTACGCAGGACAGAGC
genomic: TCAAAACTGGAGCTCCTTGCCGAAGTGAGCGTCTCGCCAAATACAACCAGgtattttctg ... attctttcagTTGCTGCGGATAGAGGAGGAGCTCGGCAATGTCCGTTACGCAGGACAGAGC
EST: gi|67570333|gb|BJ943157.1|BJ943157
EST:     TCAAAACTGGAGCTCCTTGCCGAAGTGAGCGTCTCGCCAAATACAACCAG                         TTGCTGCGGATAGAGGAGGAGCTCGGCAATGTCCGTTACGCAGGACAGAGC
genomic: TCAAAACTGGAGCTCCTTGCCGAAGTGAGCGTCTCGCCAAATACAACCAGgtattttctg ... attctttcagTTGCTGCGGATAGAGGAGGAGCTCGGCAATGTCCGTTACGCAGGACAGAGC
EST: gi|208364752|gb|DC943626.1|DC943626
EST:     TCAAAACTGGAGCTCCTTGCCGAAGTGAGCGTCTCGCCAAATACAACCAG                         TTGCTGCGGATAGAGGAGGAGCTCGGCAATGTCCGTTACGCAGGACAGAGC
genomic: TCAAAACTGGAGCTCCTTGCCGAAGTGAGCGTCTCGCCAAATACAACCAGgtattttctg ... attctttcagTTGCTGCGGATAGAGGAGGAGCTCGGCAATGTCCGTTACGCAGGACAGAGC
EST: gi|67725691|gb|BJ975950.1|BJ975950
EST:     TCAAAACTGGAGCTCCTTGCCGAAGTGAGCGTCTCGCCAAATACAACCAG                         TTGCTGCGGATAGAGGAGGAGCTCGGCGATGTCCGTTACGCAGGACAGAGC
genomic: TCAAAACTGGAGCTCCTTGCCGAAGTGAGCGTCTCGCCAAATACAACCAGgtattttctg ... attctttcagTTGCTGCGGATAGAGGAGGAGCTCGGCAATGTCCGTTACGCAGGACAGAGC
EST: gi|67727971|gb|BJ978230.1|BJ978230
EST:     TCAAAACTGGAGCTCCTTGCCGAAGTGAGCGTCTCGCCAAATACAACCAG                         TTGCTGCGGATAGAGGAGGAGCTCGGCAATGTCCGTTACGCAGGACAGAGC
genomic: TCAAAACTGGAGCTCCTTGCCGAAGTGAGCGTCTCGCCAAATACAACCAGgtattttctg ... attctttcagTTGCTGCGGATAGAGGAGGAGCTCGGCAATGTCCGTTACGCAGGACAGAGC
EST: gi|208374157|gb|DC945203.1|DC945203
EST:     TCAAAACTGGAGCTCCTTGCCGAAGTGAGCGTCTCGCCAAATACAACCAG                         TTGCTGCGGATAGAGGAGGAGCTCGGCAATGTCCGTTACGCAGGACAGAGC
genomic: TCAAAACTGGAGCTCCTTGCCGAAGTGAGCGTCTCGCCAAATACAACCAGgtattttctg ... attctttcagTTGCTGCGGATAGAGGAGGAGCTCGGCAATGTCCGTTACGCAGGACAGAGC
EST: gi|37839773|gb|BJ597781.1|BJ597781
EST:     TCAAAACTGGAGCTCCTTGCCGAAGTGAGCGTCTCGCCAAATACAACCAG                         TTGCTGCGGATAGAGGAGGAGCTCGGCAATGTCCGTTACGCAGGACAGAGC
genomic: TCAAAACTGGAGCTCCTTGCCGAAGTGAGCGTCTCGCCAAATACAACCAGgtattttctg ... attctttcagTTGCTGCGGATAGAGGAGGAGCTCGGCAATGTCCGTTACGCAGGACAGAGC
EST: gi|67698210|gb|BJ958443.1|BJ958443
EST:     TCAAAACTGGAGCTCCTTGCCGAAGTGAGCGTCTCGCCAAATACAACCAG                         TTGCTGCGGATAGAGGAGGAGCTCGGCAATGTCCGTTACGCAGGACAGAGC
genomic: TCAAAACTGGAGCTCCTTGCCGAAGTGAGCGTCTCGCCAAATACAACCAGgtattttctg ... attctttcagTTGCTGCGGATAGAGGAGGAGCTCGGCAATGTCCGTTACGCAGGACAGAGC
EST: gi|208371256|gb|DC944420.1|DC944420
EST:     TCAAAACTGGAGCTCCTTGCCGAAGTGAGCGTCTCGCCAAATACAACCAG                         TTGCTGCGGATAGAGGAGGAGCTCGGCAATGTCCGTTACGCAGGACAGAGC
genomic: TCAAAACTGGAGCTCCTTGCCGAAGTGAGCGTCTCGCCAAATACAACCAGgtattttctg ... attctttcagTTGCTGCGGATAGAGGAGGAGCTCGGCAATGTCCGTTACGCAGGACAGAGC
EST: gi|208386286|gb|DC952999.1|DC952999
EST:     TCAAAACTGGAGCTCCTTGCCGAAGTGAGCGTCTCGCCAAATACAACCAG                         TTGCTGCGGATAGAGGAGGAGCTCGGCAATGTCCGTTACGCAGGACAGAGC
genomic: TCAAAACTGGAGCTCCTTGCCGAAGTGAGCGTCTCGCCAAATACAACCAGgtattttctg ... attctttcagTTGCTGCGGATAGAGGAGGAGCTCGGCAATGTCCGTTACGCAGGACAGAGC
EST: gi|208366457|gb|DC955570.1|DC955570
EST:     TCAAAACTGGAGCTCCTTGCCGAAGTGAGCGTCTCGCCAAATACAACCAG                         TTGCTGCGGATAGAGGAGGAGCTCGGCAATGTCCGTTACGCAGGACAGAGC
genomic: TCAAAACTGGAGCTCCTTGCCGAAGTGAGCGTCTCGCCAAATACAACCAGgtattttctg ... attctttcagTTGCTGCGGATAGAGGAGGAGCTCGGCAATGTCCGTTACGCAGGACAGAGC
EST: gi|208347383|gb|DC925351.1|DC925351
EST:     TCAAAACTGGAGCTCCTTGCCGAAGTGAGCGTCTCGCCAAATACAACCAG                         TTGCTGCGGATAGAGGAGGAGCTCGGCAATGTCCGTTACGCAGGACAGAGC
genomic: TCAAAACTGGAGCTCCTTGCCGAAGTGAGCGTCTCGCCAAATACAACCAGgtattttctg ... attctttcagTTGCTGCGGATAGAGGAGGAGCTCGGCAATGTCCGTTACGCAGGACAGAGC
EST: gi|162214125|gb|FC389963.1|FC389963
EST:     TCAAAACTGGAGCTCCTTGCCGAAGTGAGCGTCTCGCCAAATACAACCAG                         TTGCTGCGGATAGAGGAGGAGCTCGGCAATGTCCGTTACGCAGGACAGAGC
genomic: TCAAAACTGGAGCTCCTTGCCGAAGTGAGCGTCTCGCCAAATACAACCAGgtattttctg ... attctttcagTTGCTGCGGATAGAGGAGGAGCTCGGCAATGTCCGTTACGCAGGACAGAGC
EST: gi|208361853|gb|DC950125.1|DC950125
EST:     TCAAAACTGGAGCTCCTTGCCGAAGTGAGCGTCTCGCCAAATACAACCAG                         TTGCTGCGGATAGAGGAGGAGCTCGGCAATGTCCGTTACGCAGGACAGAGC
genomic: TCAAAACTGGAGCTCCTTGCCGAAGTGAGCGTCTCGCCAAATACAACCAGgtattttctg ... attctttcagTTGCTGCGGATAGAGGAGGAGCTCGGCAATGTCCGTTACGCAGGACAGAGC
EST: gi|162185551|gb|FC361483.1|FC361483
EST:     TCAAAACTGGAGCTCCTTGCCGAAGTGAGCGTCTCGCCAAATACAACCAG                         TTGCTGCGGATAGAGGAGGAGCTCGGCAATGTCCGTTACGCAGGACAGAGC
genomic: TCAAAACTGGAGCTCCTTGCCGAAGTGAGCGTCTCGCCAAATACAACCAGgtattttctg ... attctttcagTTGCTGCGGATAGAGGAGGAGCTCGGCAATGTCCGTTACGCAGGACAGAGC
EST: gi|162167351|gb|FC342339.1|FC342339
EST:     TCAAAACTGGAGCTCCTTGCCGAAGTGAGCGTCTCGCCAAATACAACCAG                         TTGCTGCGGATAGAGGAGGAGCTCGGCAATGTCCGTTACGCAGGACAGAGC
genomic: TCAAAACTGGAGCTCCTTGCCGAAGTGAGCGTCTCGCCAAATACAACCAGgtattttctg ... attctttcagTTGCTGCGGATAGAGGAGGAGCTCGGCAATGTCCGTTACGCAGGACAGAGC
EST: gi|67697196|gb|BJ957429.1|BJ957429
EST:     TCAAAACTGGAGCTCCTTGCCGAAGTGAGCGTCTCGCCAAATACAACCAG                         TTGCTGCGGATAGAGGAGGAGCTCGGCAATGTCCGTTACGCAGGACAGAGC
genomic: TCAAAACTGGAGCTCCTTGCCGAAGTGAGCGTCTCGCCAAATACAACCAGgtattttctg ... attctttcagTTGCTGCGGATAGAGGAGGAGCTCGGCAATGTCCGTTACGCAGGACAGAGC
EST: gi|208368997|gb|DC955082.1|DC955082
EST:     TCAAAACTGGAGCTCCTTGCCGAAGTGAGCGTCTCGCCAAATACAACCAG                         TTGCTGCGGATAGAGGAGGAGCTCGGCAATGTCCGTTACGCAGGACAGAGC
genomic: TCAAAACTGGAGCTCCTTGCCGAAGTGAGCGTCTCGCCAAATACAACCAGgtattttctg ... attctttcagTTGCTGCGGATAGAGGAGGAGCTCGGCAATGTCCGTTACGCAGGACAGAGC
EST: gi|67698367|gb|BJ958600.1|BJ958600
EST:     TCAAAACTGGAGCTCCTTGCCGAAGTGAGCGTCTCGCCAAATACAACCAG                         TTGCTGCGGATAGAGGAGGAGCTCGGCAATGTCCGTTACGCAGGACAGAGC
genomic: TCAAAACTGGAGCTCCTTGCCGAAGTGAGCGTCTCGCCAAATACAACCAGgtattttctg ... attctttcagTTGCTGCGGATAGAGGAGGAGCTCGGCAATGTCCGTTACGCAGGACAGAGC

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: 18

ATCAAAACTGGAGCTCCTTGCCGAAGTGAGCGTCTCGCCAAATACAACCAGgtattttctg ... attctttcagTTGCTGCGGATAGAGGAGGAGCTCGGCAATGTCCGTTACGCAGGACAGAGCTTCAGACAACCTCTCTAAAGGAAGGATAGAACTCTTAGTGACCACGAGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcattatgaactactcgttttttagtagttctgacaaatgtcgtgattctttcagTTGCTGCGGATAGAGGAGGAGCTCGGCAATGTCCGTTACGCAGGACAGAGCTTCAGACAACCTCTCTAAAGGAAGGATAGAACTCTTAGTGACCACGAGT
                            ttctgac  putative branch site (score: 18)
                                              ttctttc  putative PPT
                 ttttttagta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattttctgtacttaaactgctgttgtttgttcttgattcttaactgcgtgcacatatttcctgaactgcatgaaaaaacacacgacttgatttgcgtaaacatcctgcttcatcttctgaatgatctcattatgaactactcgttttttagtagttctgacaaatgtcgtgattctttcagTTGCTGCGGATAGAGGAGGAGCTCGGCAATGTCCGTTACGCAGGACAGAGCTTCAGACAACCTCTCTAAAGGAAGGATAGAACTCTTAGTGACCACGAGT

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