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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctcggtagagaatatctaacattatccgctaccaactaaatagcctactgaacaggcgagattgtgagaaagcaccatgacttgttttggaaccatccagGTGCTTTCGAGATGAAGACTTAAGGGCGGATAGGCAACCAGAGTTTACACAGCTAGATTTGGAGCTTTCTTTTACACCTCTTGAGGATATGCTGGAGCTC

Basic information

species Physcomitrella patens
transcript PP1S9_39V6.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S9_39V6.3 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GRMZM2G378717_T01 (Zea mays), 3'ss of exon 6
-----ctcggtagagaatatctaacattatccgctaccaactaaatagcctactgaacaggcgagattgtgagaaagcaccatgacttgttttggaaccatccagGTGCTTTCGAGATGAAGACTTAAGGGCGGATAGGCAACCAGAGTTTACACAGCTAGATTTGGAGCTTTCTTTTACACCTCTTGAGGATATGCTGGAGCTC
      | |   ||| |||| | |   |||||  |     ||| |||   |  | ||        | |      ||   |      |  |    |   | |  |||||||| |||||||||||  |  | ||||| |||||||||||||||||||| || ||| ||||| || |||||||| || | ||||||||| || || | 
atctcattgcatgagcatatatgatcatatccagt-tggcctatatattatttttaatccaattaactactcagaaaagctgcacttcat----ggttcttatagGTGCTTCCGAGATGAAGATCTGCGTGCGGACAGGCAACCAGAGTTTACACAACTTGATATGGAGGTTGCTTTTACATCTATGGAGGATATGTTGAAGTTG
















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|162226283|gb|FC402991.1|FC402991
EST:     AAGCAGATGCTCATGGTTTCAGGGTTCAACAGATACTATCAACTAGCCAG                         GTGCTTTCGAGATGAAGACTTAAGGGCTGATAGGCAACCAGAGTTTACACA
genomic: AAGCAGATGCTCATGGTTTCAGGGTTCAACAGATACTATCAACTAGCCAGgtaacttttt ... aaccatccagGTGCTTTCGAGATGAAGACTTAAGGGCGGATAGGCAACCAGAGTTTACACA
EST: gi|162174743|gb|FC352159.1|FC352159
EST:     AAGCAGATGCTCATGGTTTCAGGGTTCAACAGATACTATCAACTAGCCAG                         GTGCTTTCGAGATGAAGACTTAAGGGCTGATAGGCAACCAGAGTTTACACA
genomic: AAGCAGATGCTCATGGTTTCAGGGTTCAACAGATACTATCAACTAGCCAGgtaacttttt ... aaccatccagGTGCTTTCGAGATGAAGACTTAAGGGCGGATAGGCAACCAGAGTTTACACA
EST: gi|162149974|gb|FC326505.1|FC326505
EST:     AAGCAGATGCTCATGGTTTCAGGGTTCAACAGATACTATCAACTAGCCAG                         GTGCTTTCGAGATGAAGACTTAAGGGCTGATAGGCAACCAGAGTTTACACA
genomic: AAGCAGATGCTCATGGTTTCAGGGTTCAACAGATACTATCAACTAGCCAGgtaacttttt ... aaccatccagGTGCTTTCGAGATGAAGACTTAAGGGCGGATAGGCAACCAGAGTTTACACA
EST: gi|162175866|gb|FC351544.1|FC351544
EST:     AAGCAGATGCTCATGGTTTCAGGGTTCAACAGATACTATCAACTAGCCAG                         GTGCTTTCGAGATGAAGACTTAAGGGCTGATAGGCAACCAGAGTTTACACA
genomic: AAGCAGATGCTCATGGTTTCAGGGTTCAACAGATACTATCAACTAGCCAGgtaacttttt ... aaccatccagGTGCTTTCGAGATGAAGACTTAAGGGCGGATAGGCAACCAGAGTTTACACA
EST: gi|162195380|gb|FC369822.1|FC369822
EST:     AAGCAGATGCTCATGGTTTCAGGGTTCAACAGATACTATCAACTAGCCAG                         GTGCTTTCGAGATGAAGACTTAAGGGCTGATAGGCAACCAGAGTTTACACA
genomic: AAGCAGATGCTCATGGTTTCAGGGTTCAACAGATACTATCAACTAGCCAGgtaacttttt ... aaccatccagGTGCTTTCGAGATGAAGACTTAAGGGCGGATAGGCAACCAGAGTTTACACA
EST: gi|162185588|gb|FC362014.1|FC362014
EST:     AAGCAGATGCTCATGGTTTCAGGGTTCAACAGATACTATCAACTAGCCAG                         GTGCTTTCGAGATGAAGACTTAAGGGCTGATAGGCAACCAGAGTTTACACA
genomic: AAGCAGATGCTCATGGTTTCAGGGTTCAACAGATACTATCAACTAGCCAGgtaacttttt ... aaccatccagGTGCTTTCGAGATGAAGACTTAAGGGCGGATAGGCAACCAGAGTTTACACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tactgaacaggcgagattgtgagaaagcaccatgacttgttttggaaccatccagGTGCTTTCGAGATGAAGACTTAAGGGCGGATAGGCAACCAGAGTTTACACAGCTAGATTTGGAGCTTTCTTTTACACCTCTTGAGGATATGCTGGAGCTC
                                    ttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctcggtagagaatatctaacattatccgctaccaactaaatagcctactgaacaggcgagattgtgagaaagcaccatgacttgttttggaaccatccagGTGCTTTCGAGATGAAGACTTAAGGGCGGATAGGCAACCAGAGTTTACACAGCTAGATTTGGAGCTTTCTTTTACACCTCTTGAGGATATGCTGGAGCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - -ctgaaca