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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttttattacagtttcttattggttttgtgacgtaatcaaagggtctcgtttataaacagattaacaatggttcggtattcgtgaatgaatcatgtgcagGCTGTCATGGCTCTTCGTGATTCAATTAAGCGGCACCTTCATTTGCCTATTGGATATATGATGGAGTACAAACCTCACGATGCTTCGTTGCGTGACAATT

Basic information

species Physcomitrella patens
transcript PP1S6_173V6.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S6_173V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: EFJ13594 (Selaginella moellendorffii), 3'ss of exon 5
tttttattacagtttcttattggttttgtgacgtaatcaaagggtctcgtttataaacagattaacaatggttcggtattcgtgaatgaatcatgtgcagGCTGTCATGGCTCTTCGTGATTCAATTAAGCGGCACCTTCATTTGCCTATTGGATATATGATGGAGTACAAACCTCACGATGCTTCGTTGCGTGACAATT
                      || | ||   | | | ||  |    | |   |   |   |  ||| | || |  || | |||         | | |||||||| ||||||||||| ||||| || ||||||||||| ||| | || |   | ||  |||||||||||||||| ||||| ||||| ||||| ||||| |
----------------------gtatggtttggaagtgaactgtctgcttcgctgttcttctccacagtcgtgct-tacttgtg---------tttacagGCTGTGATGGCTCTTCGCGATTCCATCAAGCGGCACCTCCATCTCCCCACCAGTTACGTGATGGAGTACAAACCACACGACGCTTCCTTGCGAGACAACT

upper sequence: PP1S6_173V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: EFJ19220 (Selaginella moellendorffii), 3'ss of exon 5
tttttattacagtttcttattggttttgtgacgtaatcaaagggtctcgtttataaacagattaacaatggttcggtat--tcgtgaatgaat-catgtgcagGCTGTCATGGCTCTTCGTGATTCAATTAAGCGGCACCTTCATTTGCCTATTGGATATATGATGGAGTACAAACCTCACGATGCTTCGTTGCGTGACAATT
                                           || | |||||    | | ||  |  |  |||   |   |||||  |   |   | | |||||||| ||||||||||| ||||| || ||||||||||| ||| | || |   | ||  |||||||||||||||| ||||| ||||| ||||| ||||| |
-------------------------------------------gtatggtttactgtctgcttcgctgttcttctccacagtcgtgcttacttgtgtttacagGCTGTGATGGCTCTTCGCGATTCCATCAAGCGGCACCTCCATCTCCCCACCAGTTACGTGATGGAGTACAAACCACACGACGCTTCCTTGCGAGACAACT
















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|208374177|gb|DC945223.1|DC945223
EST:     TTGGGGAGGACATCCTTAGCATATGGAACCGCAATGCTTCTGATAATCAG                         GCTGTCATGGCTCTTCGTGATTCAATTAAGCGGCACCTTCATTTGCCTATT
genomic: TTGGGGAGGACATCCTTAGCATATGGAACCGCAATGCTTCTGATAATCAGgtacagcgtc ... tcatgtgcagGCTGTCATGGCTCTTCGTGATTCAATTAAGCGGCACCTTCATTTGCCTATT
EST: gi|67726582|gb|BJ976841.1|BJ976841
EST:     TTGGGGAGGACATCCTTAGCATATGGAACCGCAATGCTTCTGATAATCAG                         GCTGTCATGGCTCTTCGTGATTCAATTAAGCGGCACCTTCATTTGCCTATT
genomic: TTGGGGAGGACATCCTTAGCATATGGAACCGCAATGCTTCTGATAATCAGgtacagcgtc ... tcatgtgcagGCTGTCATGGCTCTTCGTGATTCAATTAAGCGGCACCTTCATTTGCCTATT
EST: gi|208346475|gb|DC917428.1|DC917428
EST:     TTGGGGAGGACATCCTTAGCATATGGAACCGCAATGCTTCTGATAATCAG                         GCTGTCATGGCTCTTCGTGATTCAATTAAGCGGCACCTTCATTTGCCTATT
genomic: TTGGGGAGGACATCCTTAGCATATGGAACCGCAATGCTTCTGATAATCAGgtacagcgtc ... tcatgtgcagGCTGTCATGGCTCTTCGTGATTCAATTAAGCGGCACCTTCATTTGCCTATT
EST: gi|208395942|gb|DC915702.1|DC915702
EST:     TTGGGGAGGACATCCTTAGCATATGGAACCGCAATGCTTCTGATAATCAG                         GCTGTCATGGCTCTTCGTGATTCAATTAAGCGGCACCTTCATTTGCCTATT
genomic: TTGGGGAGGACATCCTTAGCATATGGAACCGCAATGCTTCTGATAATCAGgtacagcgtc ... tcatgtgcagGCTGTCATGGCTCTTCGTGATTCAATTAAGCGGCACCTTCATTTGCCTATT
EST: gi|208370208|gb|DC952030.1|DC952030
EST:     TTGGGGAGGACATCCTTAGCATATGGAACCGCAATGCTTCTGATAATCAG                         GCTGTCATGGCTCTTCGTGATTCAATTAAGCGGCACCTTCATTTGCCTATT
genomic: TTGGGGAGGACATCCTTAGCATATGGAACCGCAATGCTTCTGATAATCAGgtacagcgtc ... tcatgtgcagGCTGTCATGGCTCTTCGTGATTCAATTAAGCGGCACCTTCATTTGCCTATT
EST: gi|67696865|gb|BJ957098.1|BJ957098
EST:     TTGGGGAGGACATCCTTAGCATATGGAACCGCAATGCTTCTGATAATCAG                         GCTGTCATGGCTCTTCGTGATTCAATTAAGCGGCACCTTCATTTGCCTATT
genomic: TTGGGGAGGACATCCTTAGCATATGGAACCGCAATGCTTCTGATAATCAGgtacagcgtc ... tcatgtgcagGCTGTCATGGCTCTTCGTGATTCAATTAAGCGGCACCTTCATTTGCCTATT
EST: gi|67725755|gb|BJ976014.1|BJ976014
EST:     TTGGGGAGGACATCCTTAGCATATGGAACCGCAATGCTTCTGATAATCAG                         GCTGTCATGGCTCTTCGTGATTCAATTAAGCGGCACCTTCATTTGCCTATT
genomic: TTGGGGAGGACATCCTTAGCATATGGAACCGCAATGCTTCTGATAATCAGgtacagcgtc ... tcatgtgcagGCTGTCATGGCTCTTCGTGATTCAATTAAGCGGCACCTTCATTTGCCTATT
EST: gi|162232709|gb|FC408116.1|FC408116
EST:     TTGGGGAGGACATCCTTAGCATATGGAACCGCAATGCTTCTGATAATCAG                         GCTGTCATGGCTCTTCGTGATTCAATTAAGCGGCACCTTCATTTGCCTATT
genomic: TTGGGGAGGACATCCTTAGCATATGGAACCGCAATGCTTCTGATAATCAGgtacagcgtc ... tcatgtgcagGCTGTCATGGCTCTTCGTGATTCAATTAAGCGGCACCTTCATTTGCCTATT
EST: gi|37824112|gb|BJ582178.1|BJ582178
EST:     TTGGGGAGGACATCCTTAGCATATGGAACCGCAATGCTTCTGATAATCAG                         GCTGTCATGGCTCTTCGTGATTCAATTAAGCGGCACCTTCATTTGCCTATT
genomic: TTGGGGAGGACATCCTTAGCATATGGAACCGCAATGCTTCTGATAATCAGgtacagcgtc ... tcatgtgcagGCTGTCATGGCTCTTCGTGATTCAATTAAGCGGCACCTTCATTTGCCTATT
EST: gi|208393913|gb|DC946123.1|DC946123
EST:     TTGGGGAGGACATCCTTAGCATATGGAACCGCAATGCTTCTGATAATCAG                         GCTGTCATGGCTCTTCGTGATTCAATTAAGCGGCACCTTCATTTGCCTATT
genomic: TTGGGGAGGACATCCTTAGCATATGGAACCGCAATGCTTCTGATAATCAGgtacagcgtc ... tcatgtgcagGCTGTCATGGCTCTTCGTGATTCAATTAAGCGGCACCTTCATTTGCCTATT
EST: gi|208399428|gb|DC924858.1|DC924858
EST:     TTGGGGAGGACATCCTTAGCATATGGAACCGCAATGCTTCTGATAATCAG                         GCTGTCATGGCTCTTCGTGATTCAATTAAGCGGCACCTTCATTTGCCTATT
genomic: TTGGGGAGGACATCCTTAGCATATGGAACCGCAATGCTTCTGATAATCAGgtacagcgtc ... tcatgtgcagGCTGTCATGGCTCTTCGTGATTCAATTAAGCGGCACCTTCATTTGCCTATT
EST: gi|162232708|gb|FC408115.1|FC408115
EST:     TTGGGGAGGACATCCTTAGCATATGGAACCGCAATGCTTCTGATAATCAG                         GCTGTCATGGCTCTTCGTGATTCAATTAAGCGGCACCTTCATTTGCCTATT
genomic: TTGGGGAGGACATCCTTAGCATATGGAACCGCAATGCTTCTGATAATCAGgtacagcgtc ... tcatgtgcagGCTGTCATGGCTCTTCGTGATTCAATTAAGCGGCACCTTCATTTGCCTATT
EST: gi|37826519|gb|BJ584531.1|BJ584531
EST:     TTGGGGAGGACATCCTTAGCATATGGAACCGCAATGCTTCTGATAATCAG                         GCTGTCATGGCTCTTCGTGATTCAATTAAGCGGCACCTTCATTTGCCTATT
genomic: TTGGGGAGGACATCCTTAGCATATGGAACCGCAATGCTTCTGATAATCAGgtacagcgtc ... tcatgtgcagGCTGTCATGGCTCTTCGTGATTCAATTAAGCGGCACCTTCATTTGCCTATT
EST: gi|208349443|gb|DC921931.1|DC921931
EST:     TTGGGGAGGACATCCTTAGCATATGGAACCGCAATGCTTCTGATAATCAG                         GCTGTCATGGCTCTTCGTGATTCAATTAAGCGGCACCTTCATTTGCCTATT
genomic: TTGGGGAGGACATCCTTAGCATATGGAACCGCAATGCTTCTGATAATCAGgtacagcgtc ... tcatgtgcagGCTGTCATGGCTCTTCGTGATTCAATTAAGCGGCACCTTCATTTGCCTATT
EST: gi|208373323|gb|DC944966.1|DC944966
EST:     TTGGGGAGGACATCCTTAGCATATGGAACCGCAATGCTTCTGATAATCAG                         GCTGTCATGGCTCTTCGTGATTCAATTAAGCGGCACCTTCATTTGCCTATT
genomic: TTGGGGAGGACATCCTTAGCATATGGAACCGCAATGCTTCTGATAATCAGgtacagcgtc ... tcatgtgcagGCTGTCATGGCTCTTCGTGATTCAATTAAGCGGCACCTTCATTTGCCTATT
EST: gi|37846680|gb|BJ604688.1|BJ604688
EST:     TTGGGGAGGACATCCTTAGCATATGGAACCGCAATGCTTCTGATAATCAG                         GCTGTCATGGCTCTTCGTGATTCAATTAAGCGGCACCTTCATTTGCCTATT
genomic: TTGGGGAGGACATCCTTAGCATATGGAACCGCAATGCTTCTGATAATCAGgtacagcgtc ... tcatgtgcagGCTGTCATGGCTCTTCGTGATTCAATTAAGCGGCACCTTCATTTGCCTATT
EST: gi|37826548|gb|BJ584560.1|BJ584560
EST:     TTGGGGAGGACATCCTTAGCATATGGAACCGCAATGCTTTTGATAATCAG                         GCTGTCATGGCTCTTCGTGATTCAATTAAGCGGCACCTTCATTTGCCTATN
genomic: TTGGGGAGGACATCCTTAGCATATGGAACCGCAATGCTTCTGATAATCAGgtacagcgtc ... tcatgtgcagGCTGTCATGGCTCTTCGTGATTCAATTAAGCGGCACCTTCATTTGCCTATT
EST: gi|37850883|gb|BJ608891.1|BJ608891
EST:     TGGGGAGGACATCCTTAGCATATGGAACCGCAATGCTTTCTGATAATCAG                         GCTGTCATGGCTCTTCGTGATTCAATTAAGCGGCACCTTCATTTGCCTATT
genomic: TGGGGAGGACATCCTTAGCATATGGAACCGCAATGCTT-CTGATAATCAGgtacagcgtc ... tcatgtgcagGCTGTCATGGCTCTTCGTGATTCAATTAAGCGGCACCTTCATTTGCCTATT
EST: gi|67726544|gb|BJ976803.1|BJ976803
EST:     TTGGGGAGGACATCCTTAGCATATGGAACCGCAATGCTTCTGATAATCAG                         GCTGTCATGGCTCTTCGTGATTCAATTAAGCGGCACCTTCATTTGCCTATT
genomic: TTGGGGAGGACATCCTTAGCATATGGAACCGCAATGCTTCTGATAATCAGgtacagcgtc ... tcatgtgcagGCTGTCATGGCTCTTCGTGATTCAATTAAGCGGCACCTTCATTTGCCTATT
EST: gi|208397369|gb|DC916323.1|DC916323
EST:     TTGGGGAGGACATCCTTAGCATATGGAACCGCAATGCTTCTGATAATCAG                         GCTGTCATGGCTCTTCGTGATTCAATTAAGCGGCACCTTCATTTGCCTATT
genomic: TTGGGGAGGACATCCTTAGCATATGGAACCGCAATGCTTCTGATAATCAGgtacagcgtc ... tcatgtgcagGCTGTCATGGCTCTTCGTGATTCAATTAAGCGGCACCTTCATTTGCCTATT
EST: gi|208382280|gb|DC919268.1|DC919268
EST:     TTGGGGAGGACATCCTTAGCATATGGAACCGCAATGCTTCTGATAATCAG                         GCTGTCATGGCTCTTCGTGATTCAATTAAGCGGCACCTTCATTTGCCTATT
genomic: TTGGGGAGGACATCCTTAGCATATGGAACCGCAATGCTTCTGATAATCAGgtacagcgtc ... tcatgtgcagGCTGTCATGGCTCTTCGTGATTCAATTAAGCGGCACCTTCATTTGCCTATT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 33 (upstream exon), 32 (downstream exon)
Score: 10

TCAGTTGGATTTCGGCGACAGTGTCTGTGGTGCTGTTTTGAGCATTCGTTTTGGGGAGGACATCCTTAGCATATGGAACCGCAATGCTTCTGATAATCAGgtacagcgtc ... tcatgtgcagGCTGTCATGGCTCTTCGTGATTCAATTAAGCGGCACCTTCATTTGCCTATTGGATATATGATGGAGTACAAACCTCACGATGCTTCGTTGCGTGACAATT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcgtttataaacagattaacaatggttcggtattcgtgaatgaatcatgtgcagGCTGTCATGGCTCTTCGTGATTCAATTAAGCGGCACCTTCATTTGCCTATTGGATATATGATGGAGTACAAACCTCACGATGCTTCGTTGCGTGACAATT
              gattaac  putative branch site (score: 10)
     ttataaacagattaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttttattacagtttcttattggttttgtgacgtaatcaaagggtctcgtttataaacagattaacaatggttcggtattcgtgaatgaatcatgtgcagGCTGTCATGGCTCTTCGTGATTCAATTAAGCGGCACCTTCATTTGCCTATTGGATATATGATGGAGTACAAACCTCACGATGCTTCGTTGCGTGACAATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA