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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgatcttactttgaattctgatggtttgtactggcctcttggtaaatgatatgttttggtatcaccagtctctctctaatttatggttactccacgcagTTCTTCTATCTTTACTGGTGATGGAGAAGGTGGAAGTGGATTTGCTGCAGCTGCTGCCGCATCTGCTGCCGCGGCTGCCGTTGGTGGTGGAGGTGGTGCA

Basic information

species Physcomitrella patens
transcript PP1S14_318V6.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S14_318V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA02G05250.2 (Glycine max), 3'ss of exon 5
-------atgatcttactttgaattctgatggtttgtactggcctcttggtaaatgatatgttttggtatcaccagtctctctctaatttatggttactccacgcagTTCTTCTATCTTTACTGGTGATGGAGAAGGTGGAAGTGGATTTGCTGCAGCTGCTGCCGCATCTGCTGCCGCGGCTGCCGTTGGTGGTGGAGGTGGTGCA
          || || |||  ||  ||||  |       ||  || | |     || |   ||||  | | |        ||| | |    |||   ||    ||||| || |||| |||||||||||||| |||||||||||||| ||||| ||||||||||| ||| | || || |  | ||    |||   ||    |||||  
aattctgcccatttttcttctaaccctgaaaggagagtttgaactttggactcttg-tgcattttcttttaaat------tctttgaaccttggactcttgtggcagTACTCCTATTTTTACTGGTGATGGGGAAGGTGGAAGTGGTTTTGCAGCAGCTGCTGCTGCAGCAGCAGCAGGCGGTGTATCTGGATTTGAGTTTGGTGTT

upper sequence: PP1S14_318V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA11G08290.1 (Glycine max), 3'ss of exon 5
--------------------------atgatcttactttgaattctgatggtttgtactggcctcttggtaaatgatatgttttggtatcaccagtctctctctaatttatggttactccacg-cagTTCTTCTATCTTTACTGGTGATGGAGAAGGTGGAAGTGGATTTGCTGCAGCTGCTGCCGCATCTGCTGCCGCGGCTGCCGTTGGTGGTGGAGGTGGTGCA
                           |  | ||   |     | |  |    | |  |   |||||  || | | |   | |  || || |   |       | || | | ||| ||    | |||| |  |||| |||||||||||||| |||||||||||||| |||||||| ||||| ||| |  |||| || |  | ||     ||   ||    ||| |  
gtttgtgggcttaatttcatcttcttttttttttctctctttcttttttatcctttgtttctctcttaatataagttcaatctatgtttctctcttaagatattcatgtgttgttgctttgtggcagTACGCCTATTTTTACTGGTGATGGGGAAGGTGGAAGTGGTTTTGCTGCTGCTGCCGCCACCGCTGCAGCTGGTGGTGTATCCGGATTTGAGTTTGGCGTG

upper sequence: PP1S14_318V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA16G23590.1 (Glycine max), 3'ss of exon 5
-------atgatcttactttgaattctgatggtttgtactggcctcttggtaaatgatatgttttggtatcaccagtctctctctaatttatggttactccacgcagTTCTTCTATCTTTACTGGTGATGGAGAAGGTGGAAGTGGATTTGCTGCAGCTGCTGCCGCATCTGCTGCCGCGGCTGCCGTTGGTGGTGGAGGTGGTGCA----
          || || |||  || |||||| |       ||  || ||||    | ||   ||||  | | |        ||| | |    |||   ||    ||||| || |||| ||||||||||| || |||||||||||||| ||||||||||    ||    |||||     | |  ||  |||| |     |  |||  |     
aattctacccatttttcttctaactctgataggagagtttgaact-ttggactcttatgcattttcttttaaat------tctttgaaccttggactcttgtggcagTACTCCTATTTTTACTGGTGACGGGGAAGGTGGAAGTGGTTTTGCTGCAGGCAGTGT---ATCTGGATTTGAGTTTGGTGTTGATC-CAAACTTGGACCCTGAA

upper sequence: PP1S14_318V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA01G36990.1 (Glycine max), 3'ss of exon 5
------------------atgatcttactttgaattctgatggtttgtactggcctcttggtaaat--gatatgttttggtatcaccagtctc--tctctaatttatggttactccacgcagTTCTTCTATCTTTACTGGTGATGGAGAAGGTGGAAGTGGATTTGCTGCAGCTGCTGCCGCATCTGCTGCCGCGGCTGCCGTTGGTGGTGGAGGTGGTGCA
                  ||  | |   |||   || |  |   ||||      ||   | ||| |   || |   ||  |    | | | |   | |  |    ||| |   | |  ||||| |  |||| || ||||||||||| |||||||||||||| ||||| || |||||||| ||  |||| || |  | ||     ||   ||    ||| |  
gttcgtgggctcaatttcatcgtgtgttttttcttttttgtcccttgtttctctcttaagataagttcaatgtaacttttttgatctaattttgatattcatgcgatgttgctttctggcagTACACCTATTTTCACTGGTGATGGGGAAGGTGGAAGTGGTTTTGCAGCTGCTGCTGCTGCCGCTGCAGCTGGTGGTGTATCAGGATTTGAGTTTGGCGTG

upper sequence: PP1S14_318V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: Vv04s0023g03620.t01 (Vitis vinifera), 3'ss of exon 5
---------atgatcttactttgaattctgatggtttgtac-tggcctcttggtaaatgat-atgttttggtatcacca-gtctctctctaatttatggttactccacgcagTTCTTCTATCTTTACTGGTGATGGAGAAGGTGGAAGTGGATTTGCTGCAGCTGCTGCCGCATCTGCTGCCGCGGCTGCCGTTGGTGGTGGAGGTGGTGCA
             | | | |||   || |  |  ||    | || | |  | | |||| || |   | |  | ||| |   | | |   |   || || || |||   ||||| |  | ||||| || || ||||| |||||||||||||| ||||| |||||||| |||||| | || || |  | ||  | ||||  ||    |||||  
gtaactggtcaactttcattttttttttttttcattctcgcatgacattgtagaaaattatgacagtgtaatttcatcttatatattcttttgttttgtttcctcatggcagTACACCCATCTTCACAGGGGATGGGGAAGGTGGAAGTGGTTTTGCAGCAGCTGCCGCCGCAGCAGCAGCTGGTGGTGTGGCTGGTTTTGATTTTGGTGTG

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|162270585|gb|FC446510.1|FC446510
EST:     ATCGTACATATTCCAGGAGGAGAAAGAGTACTTTCTGACGTATTGATCAG                         TTCTTCTATCTTTACTGGTGATGGAGAAGGTGGAAGTGGATTTGCTGCAGC
genomic: ATCGTACATATTCCAGGAGGAGAAAGAGTACTTTCTGACGTATTGATCAGgtaaaattgg ... ctccacgcagTTCTTCTATCTTTACTGGTGATGGAGAAGGTGGAAGTGGATTTGCTGCAGC
EST: gi|162235944|gb|FC411687.1|FC411687
EST:     ATCGTACATATTCCAGGAGGAGAAAGAGTACTTTCTGACGTATTGATCAG                         TTCTTCTATCTTTACTGGTGATGGAGAAGGTGGAAGTGGATTTGCTGCAGC
genomic: ATCGTACATATTCCAGGAGGAGAAAGAGTACTTTCTGACGTATTGATCAGgtaaaattgg ... ctccacgcagTTCTTCTATCTTTACTGGTGATGGAGAAGGTGGAAGTGGATTTGCTGCAGC
EST: gi|162159573|gb|FC335751.1|FC335751
EST:     ATCGTACATATTCCAGGAGGAGAAAGAGTACTTTCTGACGTATTGATCAG                         TTCTTCTATCTTTACTGGTGATGGAGAAGGTGGAAGTGGATTTGCTGCAGC
genomic: ATCGTACATATTCCAGGAGGAGAAAGAGTACTTTCTGACGTATTGATCAGgtaaaattgg ... ctccacgcagTTCTTCTATCTTTACTGGTGATGGAGAAGGTGGAAGTGGATTTGCTGCAGC
EST: gi|100400831|gb|BY972965.1|BY972965
EST:     ATCGTACATATTCCAGGAGGAGAAAGAGTACTTTCTGACGGATTGATCAG                         TTCTTCTATCTTTACTGGGGATGGAG
genomic: ATCGTACATATTCCAGGAGGAGAAAGAGTACTTTCTGACGTATTGATCAGgtaaaattgg ... ctccacgcagTTCTTCTATCTTTACTGGTGATGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgatatgttttggtatcaccagtctctctctaatttatggttactccacgcagTTCTTCTATCTTTACTGGTGATGGAGAAGGTGGAAGTGGATTTGCTGCAGCTGCTGCCGCATCTGCTGCCGCGGCTGCCGTTGGTGGTGGAGGTGGTGCA
                             ctctaat  putative branch site (score: 3)
                                          ttactcc  putative PPT
                              tctaatttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgatcttactttgaattctgatggtttgtactggcctcttggtaaatgatatgttttggtatcaccagtctctctctaatttatggttactccacgcagTTCTTCTATCTTTACTGGTGATGGAGAAGGTGGAAGTGGATTTGCTGCAGCTGCTGCCGCATCTGCTGCCGCGGCTGCCGTTGGTGGTGGAGGTGGTGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG