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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAGGACTGTTCATATACGACATCTTCTGGGTGTTCTTCACGCCTGTAATGGTGAGCGTGGCAAAGTCGTTCGATGCTCCCATCAAGgtactaagccccttatctgtttcttcgtggatggtgcatggcaagctgtgttatgagagagctacttgacaacaatggaatgagacatgtttcgtgagct...

Basic information

species Physcomitrella patens
transcript PP1S47_4V6.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S47_5V6.2 (Physcomitrella patens), 5'ss of exon 8
lower sequence: GRMZM2G044348_T04 (Zea mays), 5'ss of exon 8
GCAGGACTGTTCATATACGACATCTTCTGGGTGTTCTTCACGCCTGTAATGGTGAGCGTGGCAAAGTCGTTCGATGCTCCCATCAAGgtactaagccccttatctgtttcttcgtggatggtgcatggcaa-gctgtgttatgagagagctacttgacaacaatggaatgagacatgtttcgtgagct----
|  ||||| ||  | || ||||| ||||||||||||||||| || || ||||| || ||||| || || ||||||||||| || ||||| |   | | |||  ||  |     |    ||||   ||  ||  |  | ||  |  ||  | |  || |  ||   ||    |   || || || |  |    
GGTGGACTTTTTGTGTATGACATTTTCTGGGTGTTCTTCACTCCAGTTATGGTCAGTGTGGCTAAATCTTTCGATGCTCCAATAAAGgt-cggtggctctttcctact-----gaacttggtctttgttaataccattttcagttagttccatatg-cttcagctgatctcgctttgcttggttatgtacag

upper sequence: PP1S47_5V6.2 (Physcomitrella patens), 5'ss of exon 8
lower sequence: Vv06s0009g03520.t01 (Vitis vinifera), 5'ss of exon 8
GCAGGACTGTTCATATACGACATCTTCTGGGTGTTCTTCACGCCTGTAATGGTGAGCGTGGCAAAGTCGTTCGATGCTCCCATCAAGgtactaagccccttatctgtttcttcgtggatggtgcatggcaagctgtgttatgagagagctacttgacaacaatggaatgagacat---gtttcgtgagct-----------------------------------------
|||||||| ||  | || || || |||||||| |||||||| || || ||||| || || |||||||| ||||||||||| || ||||| |      ||   ||   |      |  ||  || ||     |  || ||  |    |  || ||  |     || ||| |  |||   ||||  |   ||                                         
GCAGGACTTTTTGTTTATGATATTTTCTGGGTCTTCTTCACTCCAGTGATGGTCAGTGTTGCAAAGTCCTTCGATGCTCCTATTAAGgt-cagttatccaggtcaactgagatattaatcctggatattctg--gtttttggttcaatttatttcgctctgttgtaattaatcattaagtttaatttactttattattctaaatgtaataacagttcaattctttttgcag

upper sequence: PP1S47_5V6.2 (Physcomitrella patens), 5'ss of exon 8
lower sequence: EFJ18240 (Selaginella moellendorffii), 5'ss of exon 7
GCAGGACTGTTCATATACGACATCTTCTGGGTGTTCTTCACGCCTGTAATGGTGAGCGTGGCAAAGTCGTTCGATGCTCCCATCAAGgtactaagccccttatctgtttcttcgtggatggtgcatggcaagctgtgttatgagagagctacttgacaacaatggaatgagacatgtttcgtgagct
|| || || ||| |||| |||||||||||||| |||||||| ||||| ||||| | ||| || ||||| || |||||||||||||||||  |   | |    |    | | || |        |    || || |                                                    
GCCGGGCTATTCGTATATGACATCTTCTGGGTATTCTTCACTCCTGTGATGGTCACCGTTGCGAAGTCCTTTGATGCTCCCATCAAGgt-ttgctctctcagtgcaatgcatccttctctaatccctccatgcag----------------------------------------------------

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|37850221|gb|BJ608229.1|BJ608229
EST:     CACGCCTGTAATGGTGAGCGTGGCAAAGTCGTTCGATGCTCCCATCAAG                         CTGATTTTTCCAACTGGTGATGTTACCCGGCCTTTCTCTATGCTGGGACTA
genomic: CACGCCTGTAATGGTGAGCGTGGCAAAGTCGTTCGATGCTCCCATCAAGgtactaagcc ... gactgtgcagCTGATTTTTCCAACTGGTGATGTTACCCGGCCTTTCTCTATGCTGGGACTA
EST: gi|162242980|gb|FC417620.1|FC417620
EST:     TCACGCCTGTAATGGTGAGCGTGGCAAAGTCGTTCGATGCTCCCATCAAG                         CTGATTTTTCCAACTGGTGATGTTACCCGGCCTTTCTCTATGCTGGGACTA
genomic: TCACGCCTGTAATGGTGAGCGTGGCAAAGTCGTTCGATGCTCCCATCAAGgtactaagcc ... gactgtgcagCTGATTTTTCCAACTGGTGATGTTACCCGGCCTTTCTCTATGCTGGGACTA
EST: gi|37833593|gb|BJ591605.1|BJ591605
EST:     TCACGCCTGTAATGGTGAGCGTGGCAAAGTCGTTCGATGCTCCCATCAAG                         CTGATTTTTCCAACTGGTGATGTTACCCGGCCTTTCTCTATGCTGGGACTA
genomic: TCACGCCTGTAATGGTGAGCGTGGCAAAGTCGTTCGATGCTCCCATCAAGgtactaagcc ... gactgtgcagCTGATTTTTCCAACTGGTGATGTTACCCGGCCTTTCTCTATGCTGGGACTA
EST: gi|162241570|gb|FC414692.1|FC414692
EST:     TCACGCCTGTAATGGTGAGCGTGGCAAAGTCGTTCGATGCTCCCATCAAG                         CTGATTTTTCCAACTGGTGATGTTACCCGGCCTTTCTCTATGCTGGGACTA
genomic: TCACGCCTGTAATGGTGAGCGTGGCAAAGTCGTTCGATGCTCCCATCAAGgtactaagcc ... gactgtgcagCTGATTTTTCCAACTGGTGATGTTACCCGGCCTTTCTCTATGCTGGGACTA
EST: gi|208358879|gb|DC957651.1|DC957651
EST:     TCACGCCTGTAATGGTGAGCGTGGCAAAGTCGTTCGATGCTCCCATCAAG                         CTGATTTTTCCAACTGGTGATGTTACTCGGCCTTTCTCTATGCTGGGACTA
genomic: TCACGCCTGTAATGGTGAGCGTGGCAAAGTCGTTCGATGCTCCCATCAAGgtactaagcc ... gactgtgcagCTGATTTTTCCAACTGGTGATGTTACCCGGCCTTTCTCTATGCTGGGACTA
EST: gi|162241571|gb|FC414693.1|FC414693
EST:     TCACGCCTGTAATGGTGAGCGTGGCAAAGTCGTTCGATGCTCCCATCAAG                         CTGATTTTTCCAACTGGTGATGTTACCCGGCCTTTCTCTATGCTGGGACTA
genomic: TCACGCCTGTAATGGTGAGCGTGGCAAAGTCGTTCGATGCTCCCATCAAGgtactaagcc ... gactgtgcagCTGATTTTTCCAACTGGTGATGTTACCCGGCCTTTCTCTATGCTGGGACTA
EST: gi|162248337|gb|FC422552.1|FC422552
EST:     TCACGCCTGTAATGGTGAGCGTGGCAAAGTCGTTCGATGCTCCCATCAAG                         CTGATTTTTCCAACTGGTGATGTTACCCGGCCTTTCTCTATGCTGGGACTA
genomic: TCACGCCTGTAATGGTGAGCGTGGCAAAGTCGTTCGATGCTCCCATCAAGgtactaagcc ... gactgtgcagCTGATTTTTCCAACTGGTGATGTTACCCGGCCTTTCTCTATGCTGGGACTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAGGACTGTTCATATACGACATCTTCTGGGTGTTCTTCACGCCTGTAATGGTGAGCGTGGCAAAGTCGTTCGATGCTCCCATCAAGgtactaagccccttatctgtttcttcgtggatggtgcatggcaagctgtgttatgagagagctacttgacaacaatggaatgagacatgtttcgtgagct

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