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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggcattggcgacgatcgtttttactgccttaaagttgtgagctccgcccttgtttgtgactgtgttgaggtcttcagtaaagtagttattcttcataaagtctggcaattgaagtggtgggataatgttttgcagTCGCTGATGGAAAACTTGGCTGGGAAGAGTGTGGACCCTACGATGCCATTCATGTCGGAGCTGCCGCAGCGG

Basic information

species Physcomitrella patens
transcript PP1S55_159V6.3
intron # 6
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|208365688|gb|DC944144.1|DC944144
EST:     AATGACTCCTGCTTCGTCCCTCATGGAAATGGGCCGTCTTGTAGTTCATG                         TCGCTGATGGAAAACTTGGCTGGGAAGAGTGTGGACCCTACGATGCCATTC
genomic: AATGACTCCTGCTTCGTCCCTCATGGAAATGGGCCGTCTTGTAGTTCATGgtaaggcatt ... tgttttgcagTCGCTGATGGAAAACTTGGCTGGGAAGAGTGTGGACCCTACGATGCCATTC
EST: gi|162171977|gb|FC349257.1|FC349257
EST:     AATGACTCCTGCTTCGTCCCTCATGGAAATGGGCCGTCTTGTAGTTCATG                         TCGCTGATGGAAAACTTGGCTGGGAAGAGTGTGGACCCTACGATGCCATTC
genomic: AATGACTCCTGCTTCGTCCCTCATGGAAATGGGCCGTCTTGTAGTTCATGgtaaggcatt ... tgttttgcagTCGCTGATGGAAAACTTGGCTGGGAAGAGTGTGGACCCTACGATGCCATTC
EST: gi|37841565|gb|BJ599573.1|BJ599573
EST:     AATGACTCCTGCTTCGTCCCTCATGGAAATGGGCCGTCTTGTAGTTCATG                         TCGCTGATGGAAAACTTGGCTGGGAAGAGTGTGGACCCTACGATGCCATTC
genomic: AATGACTCCTGCTTCGTCCCTCATGGAAATGGGCCGTCTTGTAGTTCATGgtaaggcatt ... tgttttgcagTCGCTGATGGAAAACTTGGCTGGGAAGAGTGTGGACCCTACGATGCCATTC
EST: gi|162179521|gb|FC356561.1|FC356561
EST:     AATGACTCCTGCTTCGTCCCTCATGGAAATGGGCCGTCTTGTAGTTCATG                         TCGCTGATGGAAAACTTGGCTGGGAAGAGTGTGGACCCTACGATGCCATTC
genomic: AATGACTCCTGCTTCGTCCCTCATGGAAATGGGCCGTCTTGTAGTTCATGgtaaggcatt ... tgttttgcagTCGCTGATGGAAAACTTGGCTGGGAAGAGTGTGGACCCTACGATGCCATTC
EST: gi|162158828|gb|FC335351.1|FC335351
EST:     AATGACTCCTGCTTCGTCCCTCATGGAAATGGGCCGTCTTGTAGTTCATG                         TCGCTGATGGAAAACTTGGCTGGGAAGAGTGTGGACCTTACGATGCCATTC
genomic: AATGACTCCTGCTTCGTCCCTCATGGAAATGGGCCGTCTTGTAGTTCATGgtaaggcatt ... tgttttgcagTCGCTGATGGAAAACTTGGCTGGGAAGAGTGTGGACCCTACGATGCCATTC
EST: gi|162174063|gb|FC350578.1|FC350578
EST:     AATGACTCCTGCTTCGTCCCTCATGGAAATGGGCCGTCTTGTAGTTCATG                         TCGCTGATGGAAAACTTGGCTGGGAAGAGTGTGGACCCTACGATGCCATTC
genomic: AATGACTCCTGCTTCGTCCCTCATGGAAATGGGCCGTCTTGTAGTTCATGgtaaggcatt ... tgttttgcagTCGCTGATGGAAAACTTGGCTGGGAAGAGTGTGGACCCTACGATGCCATTC
EST: gi|162266763|gb|FC442279.1|FC442279
EST:     AATGACTCCTGCTTCGTCCCTCATGGAAATGGGCCGTCTTGTAGTTCATG                         TCGCTGATGGAAAACTTGGCTGGGAAGAGTGTGGACCCTACGATGCCATTC
genomic: AATGACTCCTGCTTCGTCCCTCATGGAAATGGGCCGTCTTGTAGTTCATGgtaaggcatt ... tgttttgcagTCGCTGATGGAAAACTTGGCTGGGAAGAGTGTGGACCCTACGATGCCATTC
EST: gi|37852089|gb|BJ610097.1|BJ610097
EST:     AATGACTCCTGCTTCGTCCCTCATGGAAATGGGCCGTCTTGTAGTTCATG                         TCGCTGATGGAAAACTTGGCTGGGAAGAGTGTGGACCCTACGATGCCATTC
genomic: AATGACTCCTGCTTCGTCCCTCATGGAAATGGGCCGTCTTGTAGTTCATGgtaaggcatt ... tgttttgcagTCGCTGATGGAAAACTTGGCTGGGAAGAGTGTGGACCCTACGATGCCATTC
EST: gi|37842080|gb|BJ600088.1|BJ600088
EST:     AATGACTCCTGCTTCGTCCCTCATGGAAATGGGCCGTCTTGTAGTTCATG                         TCGCTGATGGAAAACTTGGCTGGGAAGAGTGTGGACCCTACGATGCCATTC
genomic: AATGACTCCTGCTTCGTCCCTCATGGAAATGGGCCGTCTTGTAGTTCATGgtaaggcatt ... tgttttgcagTCGCTGATGGAAAACTTGGCTGGGAAGAGTGTGGACCCTACGATGCCATTC
EST: gi|162179520|gb|FC356560.1|FC356560
EST:     AATGACTCCTGCTTCGTCCCTCATGGAAATGGGCCGTCTTGTAGTTCATG                         TCGCTGATGGAAAACTTGGCTGGGAAGAGTGTGGACCCTACGATGCCATTC
genomic: AATGACTCCTGCTTCGTCCCTCATGGAAATGGGCCGTCTTGTAGTTCATGgtaaggcatt ... tgttttgcagTCGCTGATGGAAAACTTGGCTGGGAAGAGTGTGGACCCTACGATGCCATTC
EST: gi|37846074|gb|BJ604082.1|BJ604082
EST:     AATGACTCCTGCTTCGTCCCTCATGGAAATGGGCCGTCTTGTAGTTCATG                         TCGCTGATGGAAAACTTGGCTGGGAAGAGTGTGGACCCTACGATGCCATTC
genomic: AATGACTCCTGCTTCGTCCCTCATGGAAATGGGCCGTCTTGTAGTTCATGgtaaggcatt ... tgttttgcagTCGCTGATGGAAAACTTGGCTGGGAAGAGTGTGGACCCTACGATGCCATTC
EST: gi|162197969|gb|FC373984.1|FC373984
EST:     AATGACTCCTGCTTCGTCCCTCATGGAAATGGGCCGTCTTGTAGTTCATG                         TCGCTGATGGAAAACTTGGCTGGGAAGAGTGTGGACCCTACGATGCCATTC
genomic: AATGACTCCTGCTTCGTCCCTCATGGAAATGGGCCGTCTTGTAGTTCATGgtaaggcatt ... tgttttgcagTCGCTGATGGAAAACTTGGCTGGGAAGAGTGTGGACCCTACGATGCCATTC
EST: gi|37841159|gb|BJ599167.1|BJ599167
EST:     AATGACTCCTGCTTCGTCCCTCATGGAAATGGGCCGTCTTGTAGTTCATG                         TCGCTGATGGAAAACTTGGCTGGGAAGAGTGTGGACCCTACGATGCCATTC
genomic: AATGACTCCTGCTTCGTCCCTCATGGAAATGGGCCGTCTTGTAGTTCATGgtaaggcatt ... tgttttgcagTCGCTGATGGAAAACTTGGCTGGGAAGAGTGTGGACCCTACGATGCCATTC
EST: gi|162162076|gb|FC338867.1|FC338867
EST:     AATGACTCCTGCTTCGTCCCTCATGGAAATGGGCCGTCTTGTAGTTCATG                         TCGCTGATGGAAAACTTGGCTGGGAAGAGTGTGGACCCTACGATGCCATTC
genomic: AATGACTCCTGCTTCGTCCCTCATGGAAATGGGCCGTCTTGTAGTTCATGgtaaggcatt ... tgttttgcagTCGCTGATGGAAAACTTGGCTGGGAAGAGTGTGGACCCTACGATGCCATTC
EST: gi|37852017|gb|BJ610025.1|BJ610025
EST:     AATGACTCCTGCTTCGTCCCTCATGGAAATGGGCCGTCTTGTAGTTCATG                         TCGCTGATGGAAAACTTGGCTGGGAAGAGTGTGGACCCTACGATGCCATTC
genomic: AATGACTCCTGCTTCGTCCCTCATGGAAATGGGCCGTCTTGTAGTTCATGgtaaggcatt ... tgttttgcagTCGCTGATGGAAAACTTGGCTGGGAAGAGTGTGGACCCTACGATGCCATTC
EST: gi|37853578|gb|BJ611586.1|BJ611586
EST:     CCCTCATGGAAATGGGCCGTCTTGTAGTTCATG                         TCGCTGATGGAAAACTTGGCTGGGAAGAGTGTGGACCCTACGATGCCATTC
genomic: CCCTCATGGAAATGGGCCGTCTTGTAGTTCATGgtaaggcatt ... tgttttgcagTCGCTGATGGAAAACTTGGCTGGGAAGAGTGTGGACCCTACGATGCCATTC
EST: gi|18341709|gb|BJ173744.1|BJ173744
EST:     TCTTGTAGTTCATG                         TCGCTGATGGAAAACTTGGCTGGGAAGAGTGTGGACCCTACGATGCCATTC
genomic: TCTTGTAGTTCATGgtaaggcatt ... tgttttgcagTCGCTGATGGAAAACTTGGCTGGGAAGAGTGTGGACCCTACGATGCCATTC

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: 25 (upstream exon), 20 (downstream exon)
Score: 3

GGAGTAGAGCATATTCCTCAACTTGTTGAGAGGTCGATCGACGCCATAAAAATGACTCCTGCTTCGTCCCTCATGGAAATGGGCCGTCTTGTAGTTCATGgtaaggcatt ... tgttttgcagTCGCTGATGGAAAACTTGGCTGGGAAGAGTGTGGACCCTACGATGCCATTCATGTCGGAGCTGCCGCAGCGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtagttattcttcataaagtctggcaattgaagtggtgggataatgttttgcagTCGCTGATGGAAAACTTGGCTGGGAAGAGTGTGGACCCTACGATGCCATTCATGTCGGAGCTGCCGCAGCGG
     ttattcttcataaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggcattggcgacgatcgtttttactgccttaaagttgtgagctccgcccttgtttgtgactgtgttgaggtcttcagtaaagtagttattcttcataaagtctggcaattgaagtggtgggataatgttttgcagTCGCTGATGGAAAACTTGGCTGGGAAGAGTGTGGACCCTACGATGCCATTCATGTCGGAGCTGCCGCAGCGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC