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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atttattgtgctatgttcgaagaggtacgccaatgttggagatggtgctggtttgatcatcagaactgaccatcttttggcctgtatgtgagatatacagGAATCTGGTGAGCAGTTGGCCATGGGAGTTGCATTTGGCGAAAACCCACCAAAGAAGGAG

Basic information

species Physcomitrella patens
transcript PP1S99_201V6.1
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|162221878|gb|FC398445.1|FC398445
EST:     TGGAAGCCATTCGCCTTACCATCATAAACAACCTGCTTCAGTACCATCCT                         GAATCTGGTGAGCAGTTGGCCATGGGAGTTGCATTTGGCGAAAACCCACCA
genomic: TGGAAGCCATTCGCCTTACCATCATAAACAACCTGCTTCAGTACCATCCTgtacgaacct ... agatatacagGAATCTGGTGAGCAGTTGGCCATGGGAGTTGCATTTGGCGAAAACCCACCA
EST: gi|162167067|gb|FC342529.1|FC342529
EST:     TGGAAGCCATTCGCCTTACCATCATAAACAACCTGCTTCAGTACCATCCT                         GAATCTGGTGAGCAGTTGGCCATGGGAGTTGCATTTGGCGAAAACCCACCA
genomic: TGGAAGCCATTCGCCTTACCATCATAAACAACCTGCTTCAGTACCATCCTgtacgaacct ... agatatacagGAATCTGGTGAGCAGTTGGCCATGGGAGTTGCATTTGGCGAAAACCCACCA
EST: gi|162226649|gb|FC402733.1|FC402733
EST:     TGGAAGCCATTCGCCTTACCATCATAAACAACCTGCTTCAGTACCATCCT                         GAATCTGGTGAGCAGTTGGCCATGGGAGTTGCATTTGGCGAAAACCCACCA
genomic: TGGAAGCCATTCGCCTTACCATCATAAACAACCTGCTTCAGTACCATCCTgtacgaacct ... agatatacagGAATCTGGTGAGCAGTTGGCCATGGGAGTTGCATTTGGCGAAAACCCACCA
EST: gi|208386153|gb|DC949064.1|DC949064
EST:     TGGAAGCCATTCGCCTTACCATCATAAACAACCTGCTTCAGTACCATCCT                         GAATCTGGTGAGCAGTTGGCCATGGGAGTTGCATTTGGCGAAAACCCACCA
genomic: TGGAAGCCATTCGCCTTACCATCATAAACAACCTGCTTCAGTACCATCCTgtacgaacct ... agatatacagGAATCTGGTGAGCAGTTGGCCATGGGAGTTGCATTTGGCGAAAACCCACCA
EST: gi|162190768|gb|FC367030.1|FC367030
EST:     TGGAAGCCATTCGCCTTACCATCATAAACAACCTGCTTCAGTACCATCCT                         GAATCTGGTGAGCAGTTGGCCATGGGAGTTGCATTTGGCGAAAACCCACCA
genomic: TGGAAGCCATTCGCCTTACCATCATAAACAACCTGCTTCAGTACCATCCTgtacgaacct ... agatatacagGAATCTGGTGAGCAGTTGGCCATGGGAGTTGCATTTGGCGAAAACCCACCA
EST: gi|208361835|gb|DC950107.1|DC950107
EST:     TGGAAGCCATTCGCCTTACCATCATAAACAACCTGCTTCAGTACCATCCT                         GAATCTGGTGAGCAGTTGGCCATGGGAGTTGCATTTGGCGAAAACCCACCA
genomic: TGGAAGCCATTCGCCTTACCATCATAAACAACCTGCTTCAGTACCATCCTgtacgaacct ... agatatacagGAATCTGGTGAGCAGTTGGCCATGGGAGTTGCATTTGGCGAAAACCCACCA
EST: gi|162229328|gb|FC405519.1|FC405519
EST:     TGGAAGCCATTCGCCTTACCATCATAAACAACCTGCTTCAGTACCATCCT                         GAATCTGGTGAGCAGTTGGCCATGGGAGTTGCATTTGGCGAAAACCCACCA
genomic: TGGAAGCCATTCGCCTTACCATCATAAACAACCTGCTTCAGTACCATCCTgtacgaacct ... agatatacagGAATCTGGTGAGCAGTTGGCCATGGGAGTTGCATTTGGCGAAAACCCACCA
EST: gi|67695217|gb|BJ955450.1|BJ955450
EST:     TGGAAGCCATTCGCCTTACCATCATAAACAACCTGCTTCAGTACCATCCT                         GAATCTGGTGAGCAGTTGGCCATGGGAGTTGCATTTGGCGAAAACCCACCA
genomic: TGGAAGCCATTCGCCTTACCATCATAAACAACCTGCTTCAGTACCATCCTgtacgaacct ... agatatacagGAATCTGGTGAGCAGTTGGCCATGGGAGTTGCATTTGGCGAAAACCCACCA
EST: gi|162190767|gb|FC367029.1|FC367029
EST:     TGGAAGCCATTCGCCTTACCATCATAAACAACCTGCTTCAGTACCATCCT                         GAATCTGGTGAGCAGTTGGCCATGGGAGTTGCATTTGGCGAAAACCCACCA
genomic: TGGAAGCCATTCGCCTTACCATCATAAACAACCTGCTTCAGTACCATCCTgtacgaacct ... agatatacagGAATCTGGTGAGCAGTTGGCCATGGGAGTTGCATTTGGCGAAAACCCACCA
EST: gi|67571853|gb|BJ944677.1|BJ944677
EST:     TGGAAGCCATTCGCCTTACCATCATAAACAACCTGCTTCAGTACCATCCT                         GAATCTGGTGAGCAGTTGGCCATGGGAGTTGCATTTGGCGAA
genomic: TGGAAGCCATTCGCCTTACCATCATAAACAACCTGCTTCAGTACCATCCTgtacgaacct ... agatatacagGAATCTGGTGAGCAGTTGGCCATGGGAGTTGCATTTGGCGAA
EST: gi|162226648|gb|FC402732.1|FC402732
EST:     TGGAAGCCATTCGCCTTACCATCATAAACAACCTGCTTCAGTACCATCCT                         GAATCTGGTGAGCAGTTGGCCATGGGAGTTGCATTTGGCGAAAACCCACCA
genomic: TGGAAGCCATTCGCCTTACCATCATAAACAACCTGCTTCAGTACCATCCTgtacgaacct ... agatatacagGAATCTGGTGAGCAGTTGGCCATGGGAGTTGCATTTGGCGAAAACCCACCA
EST: gi|162202685|gb|FC379004.1|FC379004
EST:     TGGAAGCCATTCGCCTTACCATCATAAACAACCTGCTTCAGTACCATCCT                         GAATCTGGTGAGCAGTTGGCCATGGGAGTTGCATTTGGCGAAAACCCACCA
genomic: TGGAAGCCATTCGCCTTACCATCATAAACAACCTGCTTCAGTACCATCCTgtacgaacct ... agatatacagGAATCTGGTGAGCAGTTGGCCATGGGAGTTGCATTTGGCGAAAACCCACCA
EST: gi|162202684|gb|FC379003.1|FC379003
EST:     TGGAAGCCATTCGCCTTACCATCATAAACAACCTGCTTCAGTACCATCCT                         GAATCTGGTGAGCAGTTGGCCATGGGAGTTGCATTTGGCGAAAACCCACCA
genomic: TGGAAGCCATTCGCCTTACCATCATAAACAACCTGCTTCAGTACCATCCTgtacgaacct ... agatatacagGAATCTGGTGAGCAGTTGGCCATGGGAGTTGCATTTGGCGAAAACCCACCA
EST: gi|162229329|gb|FC405520.1|FC405520
EST:     TGGAAGCCATTCGCCTTACCATCATAAACAACCTGCTTCAGTACCATCCT                         GAATCTGGTGAGCAGTTGGCCATGGGAGTTGCATTTGGCGAAAACCCACCA
genomic: TGGAAGCCATTCGCCTTACCATCATAAACAACCTGCTTCAGTACCATCCTgtacgaacct ... agatatacagGAATCTGGTGAGCAGTTGGCCATGGGAGTTGCATTTGGCGAAAACCCACCA

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: 35 (upstream exon), 35 (downstream exon)
Score: 67

GGATAACAACAAAAAAGTGGAGGATCCTGAGCTGCTGGAAGCCATTCGCCTTACCATCATAAACAACCTGCTTCAGTACCATCCTgtacgaacct ... agatatacagGAATCTGGTGAGCAGTTGGCCATGGGAGTTGCATTTGGCGAAAACCCACCAAAGAAGGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctggtttgatcatcagaactgaccatcttttggcctgtatgtgagatatacagGAATCTGGTGAGCAGTTGGCCATGGGAGTTGCATTTGGCGAAAACCCACCAAAGAAGGAG
                  aactgac  putative branch site (score: 67)
                          atctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atttattgtgctatgttcgaagaggtacgccaatgttggagatggtgctggtttgatcatcagaactgaccatcttttggcctgtatgtgagatatacagGAATCTGGTGAGCAGTTGGCCATGGGAGTTGCATTTGGCGAAAACCCACCAAAGAAGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG