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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caagagggcttgtcagtgtcatgtgtatgatcgtatctgcaggtttcctacttgccatctatgagattgatgagattcctaatggtgccaaaattgtcagGTGATTACAAAATTCTGCTCCGAGCGCATAGCAAAATATGCTTTTGAATATGCATATCTTAACAACCGCAAGACGGTTACAGCAGTGCACAAGGCGAACA

Basic information

species Physcomitrella patens
transcript PP1S152_81V6.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S152_81V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os04g40310.2 (Oryza sativa), 3'ss of exon 1
caagagggcttgtcagtgtcatgtgtatgatcgtatctgcaggtttcctacttgccatctatgagattgatgagattcctaatggtgccaaaattgtcagGTGATTACAAAATTCTGCTCCGAGCGCATAGCAAAATATGCTTTTGAATATGCATATCTTAACAACCGCAAGACGGTTACAGCAGTGCACAAGGCGAACA------------
         ||| || ||  |||      | | | | |     |||||   |  |      |    |  ||   | ||  | ||     |   |||||||||||| ||||| || ||||| ||| | || || |||||||||||||| ||||| || ||||||||||| ||||  || ||||||||||| || || ||||            
--------attgccaatggaatgaaatgcacccttttttt---tttccagttctctgagcttcttttccatcttagtctcactgac-taacttttgtcaggtgataacaaagTTTTGCTCTGAGAGGATTGCCAAATATGCTTTTGAGTATGCTTACCTTAACAACCGAAAGAAAGTCACAGCAGTGCATAAAGCAAACATCATGAAGCTTG

upper sequence: PP1S152_81V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os04g40310.1 (Oryza sativa), 3'ss of exon 1
caagagggcttgtcagtgtcatgtgtatgatcgtatctgcaggtttcctacttgcca--tctatgagattgatgagattcctaatggtgccaa--aa---ttgtcagGTGATTACAAAATTCTGCTCCGAGCGCATAGCAAAATATGCTTTTGAATATGCATATCTTAACAACCGCAAGACGGTTACAGCAGTGCACAAGGCGAACA
          ||| |      ||   |||     |  ||||   ||  |  || |||  ||| |||| ||  |     || || |    |  |  ||   |||||||||||| ||||| || ||||| ||| | || || |||||||||||||| ||||| || ||||||||||| ||||  || ||||||||||| || || ||||
-------ttgtgttacatgattgccaatggaatgaaatgcacccttttttttttccagttctctgagcttcttttccatcttagtctcactgactaacttttgtcagGTGATAACAAAGTTTTGCTCTGAGAGGATTGCCAAATATGCTTTTGAGTATGCTTACCTTAACAACCGAAAGAAAGTCACAGCAGTGCATAAAGCAAACA

upper sequence: PP1S152_81V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G006672_T02 (Zea mays), 3'ss of exon 1
caagagggcttgtcagtgtcatgtgtatg-atcgtatctgcaggtttcctacttgccatctatgaga---------ttgatgagattcctaatggtgcca--aaattgtcagGTGATTACAAAATTCTGCTCCGAGCGCATAGCAAAATATGCTTTTGAATATGCATATCTTAACAACCGCAAGACGGTTACAGCAGTGCACAAGGCGAACA
            | | |   | ||| ||| |   |  ||||   ||||    ||||||||||  ||          ||  |   |||    ||          | |||  ||||||| |||||||||||||| ||  | || ||||| ||||||||||| |||||||| |||||||| || ||||  || ||||||||||| || || || |
------------taatttgaaagtgcatgcaatattgctgctcctttctattttgccatctaaaaggcatttctccttattactatttactataactttgttgatttgctagGTGATAACAAAATTCTGCTCTGAAAGAATTGCAAAGTATGCTTTTGAGTATGCATACCTTAACAATCGAAAGAAAGTGACAGCAGTGCATAAAGCCAATA

upper sequence: PP1S152_81V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA11G08920.1 (Glycine max), 3'ss of exon 1
-caagagggcttgtcagtg-tcatgtgtatgatcgtatctgcaggtttcctacttgccatctatgagattgatgagattcctaatggtgccaaaatt--gtcagGTGATTACAAAATTCTGCTCCGAGCGCATAGCAAAATATGCTTTTGAATATGCATATCTTAACAACCGCAAGACGGTTACAGCAGTGCACAAGGCGAACA
         ||  ||     | || | | | ||    |  ||   ||  |   |||  | || |||| || |||   || |   |  | | ||  ||  |  |||| || ||||| |||||||| |||||||| || |||||||||||||| ||||| || || || ||| | |||| ||| || || |||||||| || ||||
ctttttcatctaatcttcaattatatatctcatgaagttagcgccttgaca--ttgtgaactgtgagttttatgt--ttgcacctcatactaatcttttgctagGTAATAACAAAGTTCTGCTCAGAGCGCATTGCTAAATATGCTTTTGAGTATGCTTACCTAAATAACAGAAAGAAGGTGACTGCTGTGCACAAAGCAAACA

upper sequence: PP1S152_81V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: AT2G17130.1 (Arabidopsis thaliana), 3'ss of exon 1
---------------------------------caagagggcttgtcagtgtcat-gtg-tatgatcgtatctgcaggtttcctacttgccatctatgagattgatgagattcctaatggtgccaaaattgtcagGTGATTACAAAATTCTGCTCCGAGCGCATAGCAAAATATGCTTTTGAATATGCATATCTTAACAACCGCAAGACGGTTACAGCAGTGCACAAGGCGAACA
                                   | |    |  |  |  |||| ||| | || | |||  ||      |   |  ||     | | | ||  | ||  |  || ||| |       |||  ||||||||||||| ||||| || ||||| || ||||| ||||| ||||| ||||| ||  | |||||| | ||||  |||||||||||||||||||| || |
gtgcaatttctcagtttttgttgattgttttggttacaaatgtgatttgattcatagtgatttggtagtagatgtgaaagttggagatgtt-catgttatatcaaagatgtctctgatgctaatgtt-ttggtagGTGATTACAAAGTTCTGTTCAGAGCGTATTGCAAAGTATGCGTTTGAGTATGCCTACTTGAACAACAGGAAGAAAGTTACAGCAGTGCACAAGGCTAATA

upper sequence: PP1S152_81V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: AT2G17130.2 (Arabidopsis thaliana), 3'ss of exon 1
---------------------------------caagagggcttgtcagtgtcat-gtg-tatgatcgtatctgcaggtttcctacttgccatctatgagattgatgagattcctaatggtgccaaaattgtcagGTGATTACAAAATTCTGCTCCGAGCGCATAGCAAAATATGCTTTTGAATATGCATATCTTAACAACCGCAAGACGGTTACAGCAGTGCACAAGGCGAACA------------
                                   | |    |  |  |  |||| ||| | || | |||  ||      |   |  ||     | | | ||  | ||  |  || ||| |       |||  ||||||||||||| ||||| || ||||| || ||||| ||||| ||||| ||||| ||  | |||||| | ||||  |||||||||||||||||||| || |            
gtgcaatttctcagtttttgttgattgttttggttacaaatgtgatttgattcatagtgatttggtagtagatgtgaaagttggagatgtt-catgttatatcaaagatgtctctgatgctaatgtt-ttggtaggtgattacaaagTTCTGTTCAGAGCGTATTGCAAAGTATGCGTTTGAGTATGCCTACTTGAACAACAGGAAGAAAGTTACAGCAGTGCACAAGGCTAATATCATGAAATTGG

upper sequence: PP1S152_81V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: AT4G35260.1 (Arabidopsis thaliana), 3'ss of exon 1
--------caagagggcttgtcagtgtcatgtgtatgatc-gtatctgcag----------gtttcctacttgccatc-tatgagattgatgagattcctaatggtgccaaaattgtcagGTGATTACAAAATTCTGCTCCGAGCGCATAGCAAAATATGCTTTTGAATATGCATATCTTAACAACCGCAAGACGGTTACAGCAGTGCACAAGGCGAACA
           ||   ||  ||   ||  ||  |   ||| |||| ||  |          |||| | | | | | |  ||||  ||   |||   | || ||  |      ||  | ||||||| || || ||||| || ||||| || ||||| ||||||||||| ||||| || || |||||| | ||||  |||||||| ||||| ||||| ||||
gtgagaattccgatttctgctcctcgttttggattcaatctgtatttgtggaatcatcttcgtttgcaagtggtctttgtatgttatgtgtgattgttctgatcctatttctatgcttagGTGATCACGAAGTTCTGTTCGGAGCGTATTGCAAAGTATGCTTTTGAGTATGCCTACCTGAACAACAGGAAGAAAGTTACAGCGGTGCATAAGGCTAACA

upper sequence: PP1S152_81V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: Vv04s0210g00180.t01 (Vitis vinifera), 3'ss of exon 1
----caagagggcttgtcagtgtcatgtgtatgatcgtatctgcaggtttcctact-tgccatctatgagattgatgagattcctaatggtgccaaaattgtcagGTGATTACAAAATTCTGCTCCGAGCGCATAGCAAAATATGCTTTTGAATATGCATATCTTAACAACCGCAAGACGGTTACAGCAGTGCACAAGGCGAACA
      |     ||  ||  ||  |||  | | || | |  ||||  ||    | |   |  ||| |   ||   || |  || | ||| |     | |||  |||| || ||||| ||||| || |||||||| ||||||||||||||||| |||||||| || |||||| | ||||  || ||||| |||||||| || ||||
gaggttaccttcctattctttgctatgcttttcat-gaacttgcatcttgggcattgcacagtctgtagtatgtttgtggctcatgatgctc----atttgctagGTAATAACAAAGTTCTGTTCAGAGCGCATTGCAAAATATGCTTTTGAGTATGCATACCTAAACAACAGAAAGAAAGTGACAGCTGTGCACAAAGCAAACA

upper sequence: PP1S152_81V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: Vv03s0038g03120.t01 (Vitis vinifera), 3'ss of exon 1
-caagagggc-ttgtcagtgtcatgtgtatgatcgtatctgcaggtttcctacttgccatctatgagattgatgagattcctaatggtgccaaaattgtcagGTGATTACAAAATTCTGCTCCGAGCGCATAGCAAAATATGCTTTTGAATATGCATATCTTAACAACCGCAAGACGGTTACAGCAGTGCACAAGGCGAACA
   |||  || || | | | |  ||| || |||  |        |||   |    | ||  ||||  ||||      || || ||   ||     |||  ||||||||||||| ||||||||||| || || ||||||||||| ||||| ||| | || || |||||||| ||||  || ||||| |||||||| || ||||
tttagatagcattataaatttagtgtttaagatttttataaagtgttgtttttccgacag-tatggaattgtgtctgtttctgatccagctgct-ttgctagGTGATTACAAAGTTCTGCTCCGAACGAATTGCAAAATATGCCTTTGAGTATTCTTACCTAAACAACCGAAAGAAAGTGACAGCTGTGCACAAAGCCAACA

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|162191774|gb|FC367507.1|FC367507
EST:     ACTCTGGTCTTGAACACGAGGTCGTCCCTGGGGTCGTGGAGAGCCTGAAA                         GTGATTACAAAATTCTGCTCCGAGCGCATAGCAAAATATGCTTTTGAATAT
genomic: ACTCTGGTCTTGAACACGAGGTCGTCCCTGGGGTCGTGGAGAGCCTGAAAgtacctatct ... aaattgtcagGTGATTACAAAATTCTGCTCCGAGCGCATAGCAAAATATGCTTTTGAATAT
EST: gi|162251760|gb|FC427492.1|FC427492
EST:     ACTCTGGTCTTGAACACGAGGTCGTCCCTGGGGTCGTGGAGAGCCTGANA                         GTGATTACAAAATTCTGCTCCGAGCGCATAGCANAATATGCTTTTGAATAT
genomic: ACTCTGGTCTTGAACACGAGGTCGTCCCTGGGGTCGTGGAGAGCCTGAAAgtacctatct ... aaattgtcagGTGATTACAAAATTCTGCTCCGAGCGCATAGCAAAATATGCTTTTGAATAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcctacttgccatctatgagattgatgagattcctaatggtgccaaaattgtcagGTGATTACAAAATTCTGCTCCGAGCGCATAGCAAAATATGCTTTTGAATATGCATATCTTAACAACCGCAAGACGGTTACAGCAGTGCACAAGGCGAACA
                               tcctaat  putative branch site (score: 2)
                                            aaaattgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caagagggcttgtcagtgtcatgtgtatgatcgtatctgcaggtttcctacttgccatctatgagattgatgagattcctaatggtgccaaaattgtcagGTGATTACAAAATTCTGCTCCGAGCGCATAGCAAAATATGCTTTTGAATATGCATATCTTAACAACCGCAAGACGGTTACAGCAGTGCACAAGGCGAACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA