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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gactgcttccagttgtaagcttcagcggcgttgaggttctgatgtttaaaggtttctagctacgattatactgttcttactcaacttgtggtttctttagGCTGTTCGAAAGCTTACAGATGCAAAGAAGTTGGAATCAAGTGCTCATTATAGCACAGATTTTGGCAAGGAGTAGGATGTTCAAATCCTCTCGTCCCCAT

Basic information

species Physcomitrella patens
transcript PP1S47_46V6.3
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S47_46V6.3 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GRMZM2G171604_T01 (Zea mays), 3'ss of exon 9
---gactgcttccagttgtaagcttcagcggcgttgaggttctgatgtttaaaggtttctagctacgattatactgttcttactcaacttgtggtttctttagGCTGTTCGAAAGCTTACAGATGCAAAGAAGTTGGAATCAAGTGCTCATTATAGCACAGATTTTGGCAAGGAGTAGGATGTTCAAATCCTCTCGTCCCCAT--
    | ||  |     |  || |||   |    ||    |  ||  | |||||  ||   |   |  ||    |||        |||||   |     || ||||||| || ||||| |  ||||| || ||| ||||||||||||| ||||| ||| ||||||||||||| |||||  ||||   |  |    |     |||  
gtgcattgtcttgcactccaatcttatacc---tttgcatggtggcggttaaaaattgacactcaaaatcg--ctg--------caactcccg----tttcagGCTGTGCGGAAGCTAAATGATGCGAAAAAGCTGGAATCAAGTGCGCATTACAGCGCAGATTTTGGCAAAGAGTA--ATGTATGATGCTGGACAGATGCATAA

upper sequence: PP1S47_46V6.3 (Physcomitrella patens), 3'ss of exon 8
lower sequence: EFJ28962 (Selaginella moellendorffii), 3'ss of exon 9
gactgcttccagttgtaagcttcagcggcgttgaggttctgatgtttaaaggtttctagctacgattatactgttcttactcaact-tgtggtttctttagGCTGTTCGAAAGCTTACAGATGCAAAGAAGTTGGAATCAAGTGCTCATTATAGCACAGATTTTGGCAAGGAGTA-GGATGTTCAAATCCTCTCGTCCCCAT
                                              |||| |      | |   ||||| || ||| | ||||| | ||||  |||   |||| ||  | ||||| |  || || |||||| |||||||||| ||||| |||||| |||| ||||||||||| || |||  ||    || ||   |   |  
---------------------------------------------gtaaatgcc----gttcatattatccttttcattctcaaatgtgtgacttcc--agGCCGTGAGGAAGCTAAACGACGCCAAGAAGCTGGAATCAAGCGCTCACTATAGCGCAGACTTTGGCAAGGACTAAGGACATTTTTTTCTTCCTTTATGCT-

upper sequence: PP1S47_46V6.3 (Physcomitrella patens), 3'ss of exon 8
lower sequence: EFJ13668 (Selaginella moellendorffii), 3'ss of exon 9
gactgcttccagttgtaagcttcagcggcgttgaggttctgatgtttaaaggtttctagctacgattatactgttcttactcaact-tgtggtttctttagGCTGTTCGAAAGCTTACAGATGCAAAGAAGTTGGAATCAAGTGCTCATTATAGCACAGATTTTGGCAAGGAGTAGGATGTTCAAATCCTCTCGTCCCCAT
                                              |||| |      | |   ||||| || ||| | ||||| | ||||  |||   |||| ||  | ||||| |  || || |||||| |||||||||| ||||| |||||| |||| ||||||||||| || |    |    | ||  | |     |
---------------------------------------------gtaaatgcc----gttcatattatccttttcattctcaaatgtgtgacttcc--agGCCGTGAGGAAGCTAAACGACGCCAAGAAGCTGGAATCAAGCGCTCACTATAGCGCAGACTTTGGCAAGGACTAAGGAAATTTTTTTCTTCCTTTATGCT

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|162266638|gb|FC441998.1|FC441998
EST:     TTGCTATCCGGGCTGATCGGGACTATGTTGTACAAGAAGACTTTATGAAG                         GCTGTTCGAAAGCTTACAGATGCAAAGAAGTTGGAATCAAGTGCTCATTAT
genomic: TTGCTATCCGGGCTGATCGGGACTATGTTGTACAAGAAGACTTTATGAAGgtattctctc ... gtttctttagGCTGTTCGAAAGCTTACAGATGCAAAGAAGTTGGAATCAAGTGCTCATTAT
EST: gi|162266639|gb|FC441999.1|FC441999
EST:     TTGCTATCCGGGCTGATCGGGACTATGTTGTACAAGAAGACTTTATGAAG                         GCTGTTCGAAAGCTTACAGATGCAAAGAAGTTGGAATCAAGTGCTCATTAT
genomic: TTGCTATCCGGGCTGATCGGGACTATGTTGTACAAGAAGACTTTATGAAGgtattctctc ... gtttctttagGCTGTTCGAAAGCTTACAGATGCAAAGAAGTTGGAATCAAGTGCTCATTAT
EST: gi|37837457|gb|BJ595465.1|BJ595465
EST:     TTGCTATCCGGGCTGATCGGGACTATGTTGTACAAGAAGACTTTATGAAG                         GCTGTTCGAAAGCTTACAGATGCAAAGAAGTTGGAATCAAGTGCTCATTAT
genomic: TTGCTATCCGGGCTGATCGGGACTATGTTGTACAAGAAGACTTTATGAAGgtattctctc ... gtttctttagGCTGTTCGAAAGCTTACAGATGCAAAGAAGTTGGAATCAAGTGCTCATTAT
EST: gi|37836411|gb|BJ594419.1|BJ594419
EST:     TTGCTATCCGGGCTGATCGGGACTATGTTGTACAAGAAGACTTTATGAAG                         GCTGTTCGAAAGCTTACAGATGCAAAGAAGTTGGAATCAAGTGCTCATTAT
genomic: TTGCTATCCGGGCTGATCGGGACTATGTTGTACAAGAAGACTTTATGAAGgtattctctc ... gtttctttagGCTGTTCGAAAGCTTACAGATGCAAAGAAGTTGGAATCAAGTGCTCATTAT
EST: gi|162269526|gb|FC445082.1|FC445082
EST:     TTGCTATCCGGGCTGATCGGGACTATGTTGTACAAGAAGACTTTATGAAG                         GCTGTTCGAAAGCTTACAGATGCAAAGAAGTTGGAATCAAGTGCTCATTAT
genomic: TTGCTATCCGGGCTGATCGGGACTATGTTGTACAAGAAGACTTTATGAAGgtattctctc ... gtttctttagGCTGTTCGAAAGCTTACAGATGCAAAGAAGTTGGAATCAAGTGCTCATTAT
EST: gi|37834916|gb|BJ592928.1|BJ592928
EST:     TTGCTATCCGGGCTGATCGGGACTATGTTGTACAAGAAGACTTTATGAAG                         GCTGTTCGAAAGCTTACAGATGCAAAGAAGTTGGAATCAAGTGCTCATTAT
genomic: TTGCTATCCGGGCTGATCGGGACTATGTTGTACAAGAAGACTTTATGAAGgtattctctc ... gtttctttagGCTGTTCGAAAGCTTACAGATGCAAAGAAGTTGGAATCAAGTGCTCATTAT
EST: gi|208353233|gb|DC926158.1|DC926158
EST:     TTGCTATCCGGGCTGATCGGGACTATGTTGTACAAGAAGACTTTATGAAG                         GCTGTTCGAAAGCTTACAGATGCAAAGAAGTTGGAATCAAGTGCTCATTAT
genomic: TTGCTATCCGGGCTGATCGGGACTATGTTGTACAAGAAGACTTTATGAAGgtattctctc ... gtttctttagGCTGTTCGAAAGCTTACAGATGCAAAGAAGTTGGAATCAAGTGCTCATTAT
EST: gi|37823384|gb|BJ581450.1|BJ581450
EST:     TTGCTATCCGGGCTGATCGGGACTATGTTGTACAAGAAGACTTTATGAAG                         GCTGTTCGAAAGCTTACAGATGCAAAGAAGTTGGAATCAAGTGCTCATTAT
genomic: TTGCTATCCGGGCTGATCGGGACTATGTTGTACAAGAAGACTTTATGAAGgtattctctc ... gtttctttagGCTGTTCGAAAGCTTACAGATGCAAAGAAGTTGGAATCAAGTGCTCATTAT
EST: gi|37833453|gb|BJ591465.1|BJ591465
EST:     TTGCTATCCGGGCTGATCGGGACTATGTTGTACAAGAAGACTTTATGAAG                         GCTGTTCGAAAGCTTACAGATGCAAAGAAGTTGGAATCAAGTGCTCATTAT
genomic: TTGCTATCCGGGCTGATCGGGACTATGTTGTACAAGAAGACTTTATGAAGgtattctctc ... gtttctttagGCTGTTCGAAAGCTTACAGATGCAAAGAAGTTGGAATCAAGTGCTCATTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaaaggtttctagctacgattatactgttcttactcaacttgtggtttctttagGCTGTTCGAAAGCTTACAGATGCAAAGAAGTTGGAATCAAGTGCTCATTATAGCACAGATTTTGGCAAGGAGTAGGATGTTCAAATCCTCTCGTCCCCAT
                            ttcttac  putative branch site (score: 2)
                                              tttcttt  putative PPT
                   attatact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gactgcttccagttgtaagcttcagcggcgttgaggttctgatgtttaaaggtttctagctacgattatactgttcttactcaacttgtggtttctttagGCTGTTCGAAAGCTTACAGATGCAAAGAAGTTGGAATCAAGTGCTCATTATAGCACAGATTTTGGCAAGGAGTAGGATGTTCAAATCCTCTCGTCCCCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG