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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttttctctatcttgatcatcttgtatcatgactgatggactgttgtttgatgtcttcatgctaattctgaccatacattttaaaataacgattgtacagGTATCTTATTTAGGCTTGTTGGGCAAGCTACGAATCAACCGCTGCTAGGAGCAAAGGCTGTGGCTGGCATGCTCATGTTTGCCACGGTCTCTGGCATTTT

Basic information

species Physcomitrella patens
transcript PP1S28_200V6.1
intron # 14
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|37838818|gb|BJ596826.1|BJ596826
EST:     TGAGATGATAAANCCAGGAGCTTTGGCGGTCATCTCTCCTATTGCTATTG                         GTATCTTATTTAGGCTTGTTGGGCAAGCTACGAATCAACCGCTGCTAGGAG
genomic: TGAGATGATAAAACCAGGAGCTTTGGCGGTCATCTCTCCTATTGCTATTGgtaatagact ... gattgtacagGTATCTTATTTAGGCTTGTTGGGCAAGCTACGAATCAACCGCTGCTAGGAG
EST: gi|162252044|gb|FC428283.1|FC428283
EST:     TGAGATGATAAAACCAGGAGCTTTGGCGGTCATCTCTCCTATTGCTATTG                         GTATCTTATTTAGGCTTGTTGGGCAAGCTACGAATCAACCGCTGCTAGGAG
genomic: TGAGATGATAAAACCAGGAGCTTTGGCGGTCATCTCTCCTATTGCTATTGgtaatagact ... gattgtacagGTATCTTATTTAGGCTTGTTGGGCAAGCTACGAATCAACCGCTGCTAGGAG
EST: gi|37836235|gb|BJ594243.1|BJ594243
EST:     TGAGATGATAAAACCAGGAGCTTTGGCGGTCATCTCTCCTATTGCTATTG                         GTATCTTATTTAGGCTTGTTGGGCAAGCTACGAATCAACCGCTGCTAGGAG
genomic: TGAGATGATAAAACCAGGAGCTTTGGCGGTCATCTCTCCTATTGCTATTGgtaatagact ... gattgtacagGTATCTTATTTAGGCTTGTTGGGCAAGCTACGAATCAACCGCTGCTAGGAG
EST: gi|37852045|gb|BJ610053.1|BJ610053
EST:     TGAGATGATAAAACCAGGAGCTTTGGCGGTCATCTCTCCTATTGCTATTG                         GTATCTTATTTAGGCTTGTTGGGCAAGCTACGAATCAACCGCTGCTAGGAG
genomic: TGAGATGATAAAACCAGGAGCTTTGGCGGTCATCTCTCCTATTGCTATTGgtaatagact ... gattgtacagGTATCTTATTTAGGCTTGTTGGGCAAGCTACGAATCAACCGCTGCTAGGAG
EST: gi|37848728|gb|BJ606736.1|BJ606736
EST:     TGAGATGATAAAACCAGGAGCTTTGGCGGTCATCTCTCCTATTGCTATTG                         GTATCTTATTTAGGCTTGTTGGGCAAGCTACGAATCAACCGCTGCTAGGAG
genomic: TGAGATGATAAAACCAGGAGCTTTGGCGGTCATCTCTCCTATTGCTATTGgtaatagact ... gattgtacagGTATCTTATTTAGGCTTGTTGGGCAAGCTACGAATCAACCGCTGCTAGGAG
EST: gi|37833703|gb|BJ591715.1|BJ591715
EST:     TGAGATGATAAAACCAGGAGCTTTGGCGGTCATCTCTCCTATTGCTATTG                         GTATCTTATTTAGGCTTGTTGGGCAAGCTACGAATCANCCGCTGCTAGGAG
genomic: TGAGATGATAAAACCAGGAGCTTTGGCGGTCATCTCTCCTATTGCTATTGgtaatagact ... gattgtacagGTATCTTATTTAGGCTTGTTGGGCAAGCTACGAATCAACCGCTGCTAGGAG
EST: gi|37838853|gb|BJ596861.1|BJ596861
EST:     TGAGATGATAAAACCAGGAGCTTTGGCGGTCATCTCTCCTATTGCTATTG                         GTATCTTATTTAGGCTTGTTGGGCAAGCTACGAATCAACCGCTGCTAGGAG
genomic: TGAGATGATAAAACCAGGAGCTTTGGCGGTCATCTCTCCTATTGCTATTGgtaatagact ... gattgtacagGTATCTTATTTAGGCTTGTTGGGCAAGCTACGAATCAACCGCTGCTAGGAG
EST: gi|37852556|gb|BJ610564.1|BJ610564
EST:     GAGATGATAAAACCAGGAGCTTTGGCGGTCATCTCTCCCTATTGCTATTG                         GTATCTTATTTAGGCTTGTTGGGCAAGCTACGAATCAACCGCTGCTAGGAG
genomic: GAGATGATAAAACCAGGAGCTTTGGCGGTCATCTCT-CCTATTGCTATTGgtaatagact ... gattgtacagGTATCTTATTTAGGCTTGTTGGGCAAGCTACGAATCAACCGCTGCTAGGAG
EST: gi|162255698|gb|FC432112.1|FC432112
EST:     TGAGATGATAAAACCAGGAGCTTTGGCGGTCATCTCTCCTATTGCTATTG                         GTATCTTATTTAGGCTTGTTGGGCAAGCTACGAATCAACCGCTGCTAGGAG
genomic: TGAGATGATAAAACCAGGAGCTTTGGCGGTCATCTCTCCTATTGCTATTGgtaatagact ... gattgtacagGTATCTTATTTAGGCTTGTTGGGCAAGCTACGAATCAACCGCTGCTAGGAG
EST: gi|162164624|gb|FC341919.1|FC341919
EST:     TGAGATGATAAAACCAGGAGCTTTGGCGGTCATCTCTCCTATTGCTATTG                         GTATCTTATTTAGGCTTGTTGGGCAAGCTACGAATCAACCGCTGCTAGGAG
genomic: TGAGATGATAAAACCAGGAGCTTTGGCGGTCATCTCTCCTATTGCTATTGgtaatagact ... gattgtacagGTATCTTATTTAGGCTTGTTGGGCAAGCTACGAATCAACCGCTGCTAGGAG
EST: gi|37853223|gb|BJ611231.1|BJ611231
EST:     TGAGATGATAAAACCAGGAGCTTTGGCGGTCATCTCTCCTATTGCTATTG                         GTATCTTATTTAGGCTTGTTGGGCAAGCTACGAATCAACCGCTGCTAGGAG
genomic: TGAGATGATAAAACCAGGAGCTTTGGCGGTCATCTCTCCTATTGCTATTGgtaatagact ... gattgtacagGTATCTTATTTAGGCTTGTTGGGCAAGCTACGAATCAACCGCTGCTAGGAG
EST: gi|37844974|gb|BJ602982.1|BJ602982
EST:     TGAGATGATAAAACCAGGAGCTTTGGCGGTCATCTCTCCTATTGCTATTG                         GTATCTTATTTAGGCTTGTTGGGCAAGCTACGAATCAACCGCTGCTAGGAG
genomic: TGAGATGATAAAACCAGGAGCTTTGGCGGTCATCTCTCCTATTGCTATTGgtaatagact ... gattgtacagGTATCTTATTTAGGCTTGTTGGGCAAGCTACGAATCAACCGCTGCTAGGAG

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: 22 (upstream exon), 14 (downstream exon)
Score: 1

AAACCCGATTATGCTCGATGTGTGTCCATCGTTGCAGCTGCATCTCTTCGTGAGATGATAAAACCAGGAGCTTTGGCGGTCATCTCTCCTATTGCTATTGgtaatagact ... gattgtacagGTATCTTATTTAGGCTTGTTGGGCAAGCTACGAATCAACCGCTGCTAGGAGCAAAGGCTGTGGCTGGCATGCTCATGTTTGCCACGGTCTCTGGCATTTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttgatgtcttcatgctaattctgaccatacattttaaaataacgattgtacagGTATCTTATTTAGGCTTGTTGGGCAAGCTACGAATCAACCGCTGCTAGGAGCAAAGGCTGTGGCTGGCATGCTCATGTTTGCCACGGTCTCTGGCATTTT
                                      aaataac  putative branch site (score: 1)
                            atacattttaaaataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttttctctatcttgatcatcttgtatcatgactgatggactgttgtttgatgtcttcatgctaattctgaccatacattttaaaataacgattgtacagGTATCTTATTTAGGCTTGTTGGGCAAGCTACGAATCAACCGCTGCTAGGAGCAAAGGCTGTGGCTGGCATGCTCATGTTTGCCACGGTCTCTGGCATTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG