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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttttctggcaagttctgactattttctgcatatttgttagattgtatatttctttcatatcttcaacctcttaaggataagaaaaagttgtaggggaactcaagaactttgaaaagctttcttgcacatgtcatcaaagtttcgatgactttgtatgattaattcgcatgctcggcagGGTAAGAATGCACTATGGTCATCCCGATGTTTTCGATCGGATATTCCACATAACAAGGGGAGGTATCAGCAAATCTTCAAAAGAGATCAATCTGAGTAAA

Basic information

species Physcomitrella patens
transcript PP1S40_186V6.2
intron # 22
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S40_186V6.2 (Physcomitrella patens), 3'ss of exon 22
lower sequence: GRMZM2G326643_T01 (Zea mays), 3'ss of exon 37
gtgagttttctggcaagttctgactattttctgcatatttgttagattgtatatttctttcatatcttcaacctcttaaggataagaaaaagttgtaggggaactcaagaactttgaaaagctttcttgcacatgtcatcaaagtttcgatgactttgtatgattaattcgcatgctcggcagGGTAAGAATGCACTATGGTCATCCCGATGTTTTCGATCGGATATTCCACATAACAAGGGGAGGTATCAGCAAATCTTCAAAAGAGATCAATCTGAGTAAA
                             |  | | ||||     |   |||  |    |  |||    ||| | ||  |  |   |     || ||  | |        | |||   | | | | ||  |||     | | |  |  | | ||||    || |  | |  | |  |   ||| ||  ||||||||||||| ||||| |||||||| ||||||||||| ||||||||  | || || || |||||  | ||   || ||| ||| | ||  ||
----------------------------gtgagtaaattttaccaaccatatggtagcatgctatagggaacatgttctg--ttgcactctcttatactgcagtc-----attttattatgatatatttgacaataatttagaactgagctaacttctggtggtatactatccttgtt--cagAGTTCGAATGCACTATGGACATCCTGATGTTTTTGATCGGATATTTCACATAACCCGAGGTGGCATTAGCAAGGCGTCTCGAGTGATTAATATAAGCGAA

upper sequence: PP1S40_186V6.2 (Physcomitrella patens), 3'ss of exon 22
lower sequence: GRMZM2G453794_T01 (Zea mays), 3'ss of exon 3
gtgagttttctggcaagttctgactattttctgcatatttgttagattgtatatttctttcatatcttcaacctcttaaggataagaaaaagttgtaggggaactcaagaactttgaaaagc-tttcttgcacatgtcatcaaagtttcgatgactttgtatgattaattcgcatgctcggcagGGTAAGAATGCACTATGGTCATCCCGATGTTTTCGATCGGATATTCCACATAACAAGGGGAGGTATCAGCAAATCTTCAAAAGAGATCAATCTGAGTAAA
                                                                                              ||| | |   | |   | | ||       ||||         ||| | ||  ||   ||   ||     || ||  |   |  |  | || || |||||||||||||||||||| |||||||| ||| | || || || ||||||||||| || || || ||  | ||       |||||| | ||| | 
----------------------------------------------------------------------------------------------gtaagtgcttttacatagtatgttttctgtttcacatgaggatcagctaaaattgtgtgtagttaatacatgaaaccttttcttttgtagAGTGAGAATGCACTATGGTCATCCAGATGTTTTTGATAGAATTTTTCATATAACAAGGGGTGGAATTAGTAAGGCCTCTCGCAGCATCAATATCAGTGAG

upper sequence: PP1S40_186V6.2 (Physcomitrella patens), 3'ss of exon 22
lower sequence: GLYMA20G38860.1 (Glycine max), 3'ss of exon 40
gtgagttttctggcaagttctgactattttctgcatatttgttagattgtatatttctttcatatcttcaacctcttaaggataagaaaaagttgtaggggaactcaagaactttgaaaagctttcttgcacatgtcatcaaagtttcgatgactttgtatgattaattcgcatgctcggcagGGTAAGAATGCACTATGGTCATCCCGATGTTTTCGATCGGATATTCCACATAACAAGGGGAGGTATCAGCAAATCTTCAAAAGAGATCAATCTGAGTAAA
                                                                                                          |||  | ||  |||          |  | || ||||  ||   |   ||  ||||||  |  |      ||   ||||||  | ||||||||||| ||||| |||||||| ||| | ||||||||||||||  | || |||||||||||  ||||    |  |||||  | ||| ||
--------------------------------------------------------------------------------------------------------gtaagcccattttaaattaaataatgatttctcgtcaagattcaaa---ctaagtatgacaa--tgatgctctattcagGGTCCGCATGCACTATGGGCATCCTGATGTTTTTGATAGAATATTCCACATAACCCGTGGTGGTATCAGCAAGGCTTCCCGTGTTATCAACATTAGTGAA

upper sequence: PP1S40_186V6.2 (Physcomitrella patens), 3'ss of exon 22
lower sequence: EFJ07568 (Selaginella moellendorffii), 3'ss of exon 37
gtgagttttctggcaagttctgactattttctgcatatttgttagattgtatatttctttcatatcttcaacctcttaaggataagaaaaagttgtaggggaactcaagaactttgaaaagctttcttgcacatgtcatcaaagtttcgat-gactttgtatgattaattcgcatgctcggcagGGTAAGAATGCACTATGGTCATCCCGATGTTTTCGATCGGATATTCCACATAACAAGGGGAGGTATCAGCAAATCTTCAAAAGAGATCAATCTGAGTAAA
                                                                                                                                      || |    | | | | | ||  |||||   ||||  |   |  |   |||||| |||||||| || |||||||| |||||||||||| | || ||||| ||||||||||| || || || ||| | ||    |  || ||  | ||| | 
--------------------------------------------------------------------------------------------------------------------------------------gtaagtctactcttggtagaacttgtagtgttaa--cagtttttatccagGGTGAGAATGCATTACGGTCATCCAGATGTTTTCGATAGAATCTTCCATATAACAAGGGGGGGCATTAGTAAAGCCTCTCGGGTCATAAACATTAGTGAG

upper sequence: PP1S40_186V6.2 (Physcomitrella patens), 3'ss of exon 22
lower sequence: EFJ05083 (Selaginella moellendorffii), 3'ss of exon 37
gtgagttttctggcaagttctgactattttctgcatatttgttagattgtatatttctttcatatcttcaacctcttaaggataagaaaaagttgtaggggaactcaagaactttgaaaagctttcttgcacatgt-catcaaagtttcgatgactttgtatgattaattcgcatgctcggcagGGTAAGAATGCACTATGGTCATCCCGATGTTTTCGATCGGATATTCCACATAACAAGGGGAGGTATCAGCAAATCTTCAAAAGAGATCAATCTGAGTAAA
                                                                                                                                      || | || |   || |  ||  |||||   ||||  |   |  |  ||||||| |||||||| || |||||||| |||||||||||| | || ||||| ||||||||||| || || || ||| | ||    |  || ||  | ||| | 
--------------------------------------------------------------------------------------------------------------------------------------gtacgtctattcttggtagaacttgtagtgttaa--cagtttttatgcagGGTGAGAATGCATTACGGTCATCCAGATGTTTTCGATAGAATCTTCCATATAACAAGGGGGGGCATTAGTAAAGCCTCTCGGGTCATAAACATTAGTGAG

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|162190969|gb|FC368375.1|FC368375
EST:     GAAAGGAGCTTTGTTACCCTTGGGCAACGAGTCCTGGCGAAGTCACTTAA                         GGTAAGAATGCACTATGGTCATCCCGATGTTTTCGATCGGATATTCCACAT
genomic: GAAAGGAGCTTTGTTACCCTTGGGCAACGAGTCCTGGCGAAGTCACTTAAgtgagttttc ... tgctcggcagGGTAAGAATGCACTATGGTCATCCCGATGTTTTCGATCGGATATTCCACAT
EST: gi|162169262|gb|FC345424.1|FC345424
EST:     GAAAGGAGCTTTGTTACCCTTGGGCAACGAGTCCTGGCGAAGTCACTTAA                         GGTAAGAATGCACTATGGTCATCCCGATGTTTTCGATCGGATATTCCACAT
genomic: GAAAGGAGCTTTGTTACCCTTGGGCAACGAGTCCTGGCGAAGTCACTTAAgtgagttttc ... tgctcggcagGGTAAGAATGCACTATGGTCATCCCGATGTTTTCGATCGGATATTCCACAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcacatgtcatcaaagtttcgatgactttgtatgattaattcgcatgctcggcagGGTAAGAATGCACTATGGTCATCCCGATGTTTTCGATCGGATATTCCACATAACAAGGGGAGGTATCAGCAAATCTTCAAAAGAGATCAATCTGAGTAAA
                                 gattaat  putative branch site (score: 3)
                          tttgtatgattaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagttttctggcaagttctgactattttctgcatatttgttagattgtatatttctttcatatcttcaacctcttaaggataagaaaaagttgtaggggaactcaagaactttgaaaagctttcttgcacatgtcatcaaagtttcgatgactttgtatgattaattcgcatgctcggcagGGTAAGAATGCACTATGGTCATCCCGATGTTTTCGATCGGATATTCCACATAACAAGGGGAGGTATCAGCAAATCTTCAAAAGAGATCAATCTGAGTAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA