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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccgtgatgattctgcctgtagaaggttgtttgatcctaaaatcccagtccagcgtaatatcctgtctatagtcttgacgtcgatttttctcttaatgcagGATTGGCTACTTGGACATCGTGAAAGTGATCGAGAAGACCTGCGAGAAGCACAGGGAGGAGTTGGTTGAATTGCCTTCCTTGGCAGAGATTCTTCACTAC

Basic information

species Physcomitrella patens
transcript PP1S62_157V6.1
intron # 11
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|162156415|gb|FC332647.1|FC332647
EST:     GTACTGAGTGCTGCAAATGAAAAGGCCGTTGAGCTTTTCCTTGAGGAGAG                         GATTGGCTACTTGGACATCGTGAAAGTGATCGAGAAGACCTGCGAGAAGCA
genomic: GTACTGAGTGCTGCAAATGAAAAGGCCGTTGAGCTTTTCCTTGAGGAGAGgtactcacga ... cttaatgcagGATTGGCTACTTGGACATCGTGAAAGTGATCGAGAAGACCTGCGAGAAGCA
EST: gi|37826113|gb|BJ584125.1|BJ584125
EST:     GTACTGAGTGCTGCAAATGAAAAGGCCGTTGAGCTTTTCCTTGAGGAGAG                         GATTGGCTACTTGGACATCGTGAAAGTGATCGAGAAGACCTGCGAGAAGCA
genomic: GTACTGAGTGCTGCAAATGAAAAGGCCGTTGAGCTTTTCCTTGAGGAGAGgtactcacga ... cttaatgcagGATTGGCTACTTGGACATCGTGAAAGTGATCGAGAAGACCTGCGAGAAGCA
EST: gi|18336329|gb|BJ168351.1|BJ168351
EST:     GTACTGAGTGCTGCAAATGAAAAGGCCGTTGAGCTTTTCCTTGAGGAGAG                         GATTGGCTACTTGGACATCGTGAAAGTGATCGAGAAGACCTGCGAGAAGCA
genomic: GTACTGAGTGCTGCAAATGAAAAGGCCGTTGAGCTTTTCCTTGAGGAGAGgtactcacga ... cttaatgcagGATTGGCTACTTGGACATCGTGAAAGTGATCGAGAAGACCTGCGAGAAGCA
EST: gi|37853648|gb|BJ611656.1|BJ611656
EST:     GTACTGAGTGCTGCAAATGAAAAGGCCGTTGAGCTTTTCCTTGAGGAGAG                         GATTGGCTACTTGGACATCGTGAAAGTGATCGAGAAGACCTGCGAGAAGCA
genomic: GTACTGAGTGCTGCAAATGAAAAGGCCGTTGAGCTTTTCCTTGAGGAGAGgtactcacga ... cttaatgcagGATTGGCTACTTGGACATCGTGAAAGTGATCGAGAAGACCTGCGAGAAGCA
EST: gi|162203496|gb|FC380412.1|FC380412
EST:     GTACTGAGTGCTGCAAATGAAAAGGCCGTTGAGCTTTTCCTTGAGGAGAG                         GATTGGCTACTTGGACATCGTGAAAGTGATCGAGAAGACCTGCGAGAAGCA
genomic: GTACTGAGTGCTGCAAATGAAAAGGCCGTTGAGCTTTTCCTTGAGGAGAGgtactcacga ... cttaatgcagGATTGGCTACTTGGACATCGTGAAAGTGATCGAGAAGACCTGCGAGAAGCA
EST: gi|37822960|gb|BJ581026.1|BJ581026
EST:     GTACTGAGTGCTGCAAATGAAAAGGCCGTTGAGCTTTTCCTTGAGGAGAG                         GATTGGCTACTTGGACATCGTGAAAGTGATCGAGAAGACCTGCGAGAAGCA
genomic: GTACTGAGTGCTGCAAATGAAAAGGCCGTTGAGCTTTTCCTTGAGGAGAGgtactcacga ... cttaatgcagGATTGGCTACTTGGACATCGTGAAAGTGATCGAGAAGACCTGCGAGAAGCA
EST: gi|162272850|gb|FC448006.1|FC448006
EST:     GTACTGAGTGCTGCAAATGAAAAGGCCGTTGAGCTTTTCCTTGAGGAGAG                         GATTGGCTACTTGGACATCGTGAAAGTGATCGAGAAGACCTGCGAGAAGCA
genomic: GTACTGAGTGCTGCAAATGAAAAGGCCGTTGAGCTTTTCCTTGAGGAGAGgtactcacga ... cttaatgcagGATTGGCTACTTGGACATCGTGAAAGTGATCGAGAAGACCTGCGAGAAGCA
EST: gi|162185513|gb|FC361237.1|FC361237
EST:     GTACTGAGTGCTGCAAATGAAAAGGCCGTTGAGCTTTTCCTTGAGGAGAG                         GATTGGCTACTTGGACATCGTGAAAGTGATCGAGAAGACCTGCGAGAAGCA
genomic: GTACTGAGTGCTGCAAATGAAAAGGCCGTTGAGCTTTTCCTTGAGGAGAGgtactcacga ... cttaatgcagGATTGGCTACTTGGACATCGTGAAAGTGATCGAGAAGACCTGCGAGAAGCA
EST: gi|162208297|gb|FC384401.1|FC384401
EST:     GTACTGAGTGCTGCAAATGAAAAGGCCGTTGAGCTTTTCCTTGAGGAGAG                         GATTGGCTACTTGGACATCGTGAAAGTGATCGAGAAGACCTGCGAGAAGCA
genomic: GTACTGAGTGCTGCAAATGAAAAGGCCGTTGAGCTTTTCCTTGAGGAGAGgtactcacga ... cttaatgcagGATTGGCTACTTGGACATCGTGAAAGTGATCGAGAAGACCTGCGAGAAGCA
EST: gi|18336552|gb|BJ168574.1|BJ168574
EST:     GTACTGAGTGCTGCAAATGAAAAGGCCGTTGAGCTTTTCCTTGAGGAGAG                         GATTGGCTACTTGGACATCGTGAAAGTGATCGAGAAGACCTGCGAGAAGCA
genomic: GTACTGAGTGCTGCAAATGAAAAGGCCGTTGAGCTTTTCCTTGAGGAGAGgtactcacga ... cttaatgcagGATTGGCTACTTGGACATCGTGAAAGTGATCGAGAAGACCTGCGAGAAGCA
EST: gi|37851472|gb|BJ609480.1|BJ609480
EST:     GTACTGAGTGCTGCAAATGAAAAGGCCGTTGAGCTTTTCCTTGAGGAGAG                         GATTGGCTACTTGGACATCGTGAAAGTGATCGAGAAGACCTGCGAGAAGCA
genomic: GTACTGAGTGCTGCAAATGAAAAGGCCGTTGAGCTTTTCCTTGAGGAGAGgtactcacga ... cttaatgcagGATTGGCTACTTGGACATCGTGAAAGTGATCGAGAAGACCTGCGAGAAGCA
EST: gi|37837974|gb|BJ595982.1|BJ595982
EST:     GTACTGAGTGCTGCAAATGAAAAGGCCGTTGAGCTTTTCCTTGAGGAGAG                         GATTGGCTACTTGGACATCGTGAAAGTGATCGAGAAGACCTGCGAGAAGCA
genomic: GTACTGAGTGCTGCAAATGAAAAGGCCGTTGAGCTTTTCCTTGAGGAGAGgtactcacga ... cttaatgcagGATTGGCTACTTGGACATCGTGAAAGTGATCGAGAAGACCTGCGAGAAGCA
EST: gi|18337266|gb|BJ169290.1|BJ169290
EST:     GTACTGAGTGCTGCAAATGAAAAGGCCGTTGAGCTTTTCCTTGAGGAGAG                         GATTGGCTACTTGGACATCGTGAAAGTGATCGAGAAGACCTGCGAGAAGCA
genomic: GTACTGAGTGCTGCAAATGAAAAGGCCGTTGAGCTTTTCCTTGAGGAGAGgtactcacga ... cttaatgcagGATTGGCTACTTGGACATCGTGAAAGTGATCGAGAAGACCTGCGAGAAGCA
EST: gi|162250937|gb|FC425759.1|FC425759
EST:     GTACTGAGTGCTGCAAATGAAAAGGCCGTTGAGCTTTTCCTTGAGGAGAG                         GATTGGCTACTTGGACATCGTGAAAGTGATCGAGAAGACCTGCGAGAAGCA
genomic: GTACTGAGTGCTGCAAATGAAAAGGCCGTTGAGCTTTTCCTTGAGGAGAGgtactcacga ... cttaatgcagGATTGGCTACTTGGACATCGTGAAAGTGATCGAGAAGACCTGCGAGAAGCA
EST: gi|162151596|gb|FC327309.1|FC327309
EST:     AATGAAAAGGCCGTTGAGCTTTTCCTTGAGGAGAG                         GATTGGCTACTTGGACATCGTGAAAGTGATCGAGAAGACCTGCGAGAAGCA
genomic: AATGAAAAGGCCGTTGAGCTTTTCCTTGAGGAGAGgtactcacga ... cttaatgcagGATTGGCTACTTGGACATCGTGAAAGTGATCGAGAAGACCTGCGAGAAGCA
EST: gi|37825047|gb|BJ583113.1|BJ583113
EST:     GTACTGAGTGCTGCAAATGAAAAGGCCGTTGAGCTTTTCCTTGAGGAGAG                         GATTGGCTACTTGGACATCGTGAAAGTGATCGAGAAGACCTGCGAGAAGCA
genomic: GTACTGAGTGCTGCAAATGAAAAGGCCGTTGAGCTTTTCCTTGAGGAGAGgtactcacga ... cttaatgcagGATTGGCTACTTGGACATCGTGAAAGTGATCGAGAAGACCTGCGAGAAGCA
EST: gi|37831588|gb|BJ589600.1|BJ589600
EST:     GTACTGAGTGCTGCAAATGAAAAGGCCGTTGAGCTTTTCCTTGAGGAGAG                         GATTGGCTACTTGGACATCGTGAAAGTGATCGAGAAGACCTGCGAGAAGCA
genomic: GTACTGAGTGCTGCAAATGAAAAGGCCGTTGAGCTTTTCCTTGAGGAGAGgtactcacga ... cttaatgcagGATTGGCTACTTGGACATCGTGAAAGTGATCGAGAAGACCTGCGAGAAGCA
EST: gi|37844707|gb|BJ602715.1|BJ602715
EST:     GTACTGAGTGCTGCAAATGAAAAGNCCGTTGAGCTTTTCCTTGAGGAGAG                         GATTGGCTACTTGGACATCGTGAAAGTGATCGAGAAGACCTGCGAGAAGCA
genomic: GTACTGAGTGCTGCAAATGAAAAGGCCGTTGAGCTTTTCCTTGAGGAGAGgtactcacga ... cttaatgcagGATTGGCTACTTGGACATCGTGAAAGTGATCGAGAAGACCTGCGAGAAGCA
EST: gi|162203495|gb|FC380411.1|FC380411
EST:     GTACTGAGTGCTGCAAATGAAAAGGCCGTTGAGCTTTTCCTTGAGGAGAG                         GATTGGCTACTTGGACATCGTGAAAGTGATCGAGAAGACCTGCGAGAAGCA
genomic: GTACTGAGTGCTGCAAATGAAAAGGCCGTTGAGCTTTTCCTTGAGGAGAGgtactcacga ... cttaatgcagGATTGGCTACTTGGACATCGTGAAAGTGATCGAGAAGACCTGCGAGAAGCA
EST: gi|208382561|gb|DC919771.1|DC919771
EST:     GTACTGAGTGCTGCAAATGAAAAGGCCGTTGAGCTTTTCCTTGAGGAGAG                         GATTGGCTACTTGGACATCGTGAAAGTGATCGAGAAGACCTGCGAGAAGCA
genomic: GTACTGAGTGCTGCAAATGAAAAGGCCGTTGAGCTTTTCCTTGAGGAGAGgtactcacga ... cttaatgcagGATTGGCTACTTGGACATCGTGAAAGTGATCGAGAAGACCTGCGAGAAGCA
EST: gi|162179791|gb|FC356382.1|FC356382
EST:     GTACTGAGTGCTGCAAATGAAAAGGCCGTTGAGCTTTTCCTTGAGGAGAG                         GATTGGCTACTTGGACATCGTGAAAGTGATCGAGAAGACCTGCGAGAAGCA
genomic: GTACTGAGTGCTGCAAATGAAAAGGCCGTTGAGCTTTTCCTTGAGGAGAGgtactcacga ... cttaatgcagGATTGGCTACTTGGACATCGTGAAAGTGATCGAGAAGACCTGCGAGAAGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtccagcgtaatatcctgtctatagtcttgacgtcgatttttctcttaatgcagGATTGGCTACTTGGACATCGTGAAAGTGATCGAGAAGACCTGCGAGAAGCACAGGGAGGAGTTGGTTGAATTGCCTTCCTTGGCAGAGATTCTTCACTAC
                                            tcttaat  putative branch site (score: 3)
                                  tcgatttttctctt  CT-rich tract
                                     atttttctcttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccgtgatgattctgcctgtagaaggttgtttgatcctaaaatcccagtccagcgtaatatcctgtctatagtcttgacgtcgatttttctcttaatgcagGATTGGCTACTTGGACATCGTGAAAGTGATCGAGAAGACCTGCGAGAAGCACAGGGAGGAGTTGGTTGAATTGCCTTCCTTGGCAGAGATTCTTCACTAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG