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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgttttttttattccaaatgtttatttcactaaaggttctagttcgttgacacgcggcgatttattactctcaaataaaatcattttaagacgaacgtggatgaagtttctactgttctctacagttatgttggatagttatgtcataacagttctttgtcttggccttgttgaagGTGGATGAAAGGGACACGCGATGGTTCTACACAGGCGACATTGGACAGTTTCACGAGGATGGTTGTGTTGAGATCATTGACCGCAAGAAAGACATCGTAA

Basic information

species Physcomitrella patens
transcript PP1S186_65V6.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S186_65V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GRMZM2G117064_T01 (Zea mays), 3'ss of exon 7
gtgttttttttattccaaatgtttatttcactaaaggttctagttcgttgacacgcggcgatttattactctcaaataaaatcattttaagacgaacgtggatgaagtttctactgttctctacagt-tatgttggatagttatgtcataacagttctttgtcttggccttgttgaagGTGGATGAAAGGGACACGCGATGGTTCTACACAGGCGACATTGGACAGTTTCACGAGGATGGTTGTGTTGAGATCATTGACCGCAAGAAAGACATCGTAA
                                                                                             |    || |  || |  | | ||  |   | ||| | | |||  | | ||  | |    |   || ||  |      | |||||||| |||||||| | || ||||||||||||| | ||||||||||| |  || |||   ||||| ||| |||| || || ||||||||||| || || || |
-------------------------------------------------------------------------------------------gtgtgtttgcaacaaatacccagtgcccaggaaagtgtttattg--tggctactttacctgaacactatgcata-----ttttgaagGTTGATGAAAGAGGCATGCGATGGTTCTACTCTGGCGACATTGGGCGCTTGCACCCAGATGGATGTCTTGAAATTATCGACCGCAAGAAGGATATAGTCA
















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|208354168|gb|DC957402.1|DC957402
EST:     TAACATTGGGGTACTTCAAGAATCAAGAAAAGACAGACCAAGACTTTAAG                         GTGGATGAAAGGGACACGCGATGGTTCTACACAGGCGACATTGGACAGTTT
genomic: TAACATTGGGGTACTTCAAGAATCAAGAAAAGACAGACCAAGACTTTAAGgtgttttttt ... cttgttgaagGTGGATGAAAGGGACACGCGATGGTTCTACACAGGCGACATTGGACAGTTT
EST: gi|162174770|gb|FC352186.1|FC352186
EST:     TAACATTGGGGTACTTCAAGAATCAAGAAAAGACAGACCAAGACTTTAAG                         GTGGATGAAAGGGACACGCGATGGTTCTACACAGGCGACATTGGACAGTTT
genomic: TAACATTGGGGTACTTCAAGAATCAAGAAAAGACAGACCAAGACTTTAAGgtgttttttt ... cttgttgaagGTGGATGAAAGGGACACGCGATGGTTCTACACAGGCGACATTGGACAGTTT
EST: gi|162213167|gb|FC389052.1|FC389052
EST:     TAACATTGGGGTACTTCAAGAATCAAGAAAAGACAGACCAAGACTTTAAG                         GTGGATGAAAGGGACACGCGATGGTTCTACACAGGCGACATTGGACAGTTT
genomic: TAACATTGGGGTACTTCAAGAATCAAGAAAAGACAGACCAAGACTTTAAGgtgttttttt ... cttgttgaagGTGGATGAAAGGGACACGCGATGGTTCTACACAGGCGACATTGGACAGTTT
EST: gi|162196325|gb|FC374368.1|FC374368
EST:     TAACATTGGGGTACTTCAAGAATCAAGAAAAGACAGACCAAGACTTTAAG                         GTGGATGAAAGGGACACGCGATGGTTCTACACAGGCGACATTGGACAGTTT
genomic: TAACATTGGGGTACTTCAAGAATCAAGAAAAGACAGACCAAGACTTTAAGgtgttttttt ... cttgttgaagGTGGATGAAAGGGACACGCGATGGTTCTACACAGGCGACATTGGACAGTTT
EST: gi|162273457|gb|FC449906.1|FC449906
EST:     TAACATTGGGGTACTTCAAGAATCAAGAAAAGACAGACCAAGACTTTAAG                         GTGGATGAAAGGGACACGCGATGGTTCTACACAGGCGACATTGGACAGTTT
genomic: TAACATTGGGGTACTTCAAGAATCAAGAAAAGACAGACCAAGACTTTAAGgtgttttttt ... cttgttgaagGTGGATGAAAGGGACACGCGATGGTTCTACACAGGCGACATTGGACAGTTT
EST: gi|162188839|gb|FC364853.1|FC364853
EST:     TAACATTGGGGTACTTCAAGAATCAAGAAAAGACAGACCAAGACTTTAAG                         GTGGATGAAAGGGACACGCGATGGTTCTACACAGGCGACATTGGACAGTTT
genomic: TAACATTGGGGTACTTCAAGAATCAAGAAAAGACAGACCAAGACTTTAAGgtgttttttt ... cttgttgaagGTGGATGAAAGGGACACGCGATGGTTCTACACAGGCGACATTGGACAGTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acagttatgttggatagttatgtcataacagttctttgtcttggccttgttgaagGTGGATGAAAGGGACACGCGATGGTTCTACACAGGCGACATTGGACAGTTTCACGAGGATGGTTGTGTTGAGATCATTGACCGCAAGAAAGACATCGTAA
                      tcataac  putative branch site (score: 2)
                                            ccttgtt  putative PPT
             atagttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgttttttttattccaaatgtttatttcactaaaggttctagttcgttgacacgcggcgatttattactctcaaataaaatcattttaagacgaacgtggatgaagtttctactgttctctacagttatgttggatagttatgtcataacagttctttgtcttggccttgttgaagGTGGATGAAAGGGACACGCGATGGTTCTACACAGGCGACATTGGACAGTTTCACGAGGATGGTTGTGTTGAGATCATTGACCGCAAGAAAGACATCGTAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA