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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcccttatttgctcctctgatgttttttgtggccttgagctggaggcatgttaccactgcgtcgcccaagttattttcttatttcaagtctctccttgaaggtcacataccatagaggtcatataccagaaatttacattccgcatacttgtggatgttcgtgcagGTGCACAGCAGACTGTGGGTGGATTACTGGTCACAGCTACCTGACATATGGCCCTCTTCTCAACGGTGCTAGCATGGTTGTCTTTGAAGGG

Basic information

species Physcomitrella patens
transcript PP1S398_15V6.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S398_15V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: LOC_Os04g33190.1 (Oryza sativa), 3'ss of exon 8
gtgagcccttatttgctcctctgatgttttttgtggccttgagctggaggcatgttaccactgcgtcgcccaagttattttcttatttcaagtctctccttgaaggtcacataccatagaggtcatataccagaaatttacattccgcatacttgtggatgttcgtgcagGTGCACAGCAGACTGTGGGTGGATTACTGGTCACAGCTACCTGACATATGGCCCTCTTCTCAACGGTGCTAGCATGGTTGTCTTTGAAGGG
                                                 | ||| | | |    ||     |   | |||   || |  ||   | | | | | | | | |    ||      ||     ||  | ||   |||     | | |||     ||    ||||||||| ||||||||||||||||||||||| || || ||  |||||||||| ||||| || || || || |   |  |||| |  ||||||
-------------------------------------------------gtatgatgcta----gttttttagcatctttgggtagtataaacttgttcctaatgttaataggaaattttctgcaagctgcattatttcttattagatttccctgtttgacttgcatcagGTGCACTGCAGACTGTGGGTGGATTACTGGGCATAGTTATGTGACATATGGTCCTCTCCTGAATGGAGCCACAGTTCTTGTTTACGAAGGG

upper sequence: PP1S398_15V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: LOC_Os02g32490.2 (Oryza sativa), 3'ss of exon 8
gtgagcccttatttgctcctctgatgttttttgtggccttgagctggaggcatgttaccactgcgtcgcccaagttattttcttatttcaagtctctccttgaaggtcacataccatagaggtcatataccagaaatttacattccgcatacttgtggatgttcgtg-cagGTGCACAGCAGACTGTGGGTGGATTACTGGTCACAGCTACCTGACATATGGCCCTCTTCTCAACGGTGCTAGCATGGTTGTCTTTGAAGGG
                                            |  || || |||    ||   |      |   |  |  ||||  ||  |   |  ||   ||    |  ||    |  |  |||  |   |    |  ||  || |   ||||  | |      ||||||||| ||||||||||| ||||||||||| ||||||||  |||| ||||| || || || || || || |   |  | || |||||||||
-------------------------------------------gtaaagacaagtt----ctttttttttttaaggagatggttatggcattttcatattttggggaactactccgagaaacttctatttcctcatacaatctttggcctgtgtgtgtgtctcaacatcagGTGCACTGCAGACTGTGGCTGGATTACTGGACACAGCTATGTGACGTATGGTCCACTCCTGAATGGAGCAACAGTTCTCGTTTTTGAAGGG

upper sequence: PP1S398_15V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GRMZM2G162663_T03 (Zea mays), 3'ss of exon 7
gtgagcccttatttgctcctctgatgttttttgtggccttgagctggaggcatgttaccactgcgtcgcccaagttattttcttatttcaagtctctccttgaaggtcacataccatagaggtcatataccagaaatttacattccgcatacttgtggatgttcgtg-cagGTGCACAGCAGACTGTGGGTGGATTACTGGTCACAGCTACCTGACATATGGCCCTCTTCTCAACGGTGCTAGCATGGTTGTCTTTGAAGGG
                                             | |||  || || |||     | |  | ||| ||  | | |  |     || | |||  ||  |     |||||| |     | | |   |||||   ||| ||  |       |||| |   ||||||||| ||||||||||| ||||||||||| || || ||  | |||||||| ||||| || || |||||||   |  | || |||||||||
---------------------------------------------gtagg--tggtagcacataagctcttatgtttttagcatgtaccctcattc-ctttgtggggaattattcatagaagc----tgctatttattta---tccacacccactgttttgtttgcaacagGTGCACTGCAGACTGTGGCTGGATTACTGGACATAGTTATGTAACATATGGTCCTCTCCTGAATGGTGCTACGGTTCTCGTTTTTGAAGGG

upper sequence: PP1S398_15V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: EFJ36126 (Selaginella moellendorffii), 3'ss of exon 8
gtgagcccttatttgctcctctgatgttttttgtggccttgagctggaggcatgttaccactgcgtcgcccaagttattttcttatttcaagtctctccttgaaggtcacataccatagaggtcatataccagaaatttacattccgcatacttgtggatgttcgtg-cagGTGCACAGCAGACTGTGGGTGGATTACTGGTCACAGCTACCTGACATATGGCCCTCTTCTCAACGGTGCTAGCATGGTTGTCTTTGAAGGG
                                                                                                      |||   || |  ||   | || ||||        ||    || | |        | |    | || |||||| || ||||| ||||| ||||| ||||||||||||||| | || ||||||||| |  | |||   || |   |  |  ||||||| |||
----------------------------------------------------------------------------------------------------gtaagtatacttttcaacaatgttatat-ttttttgttactgtttcacgcgtcaaggtaatgccatgtcagGTGTACTGCAGATTGTGGATGGATCACTGGTCACAGCTACGTCACTTATGGCCCTTTATTGAACAAAGCGACTGTCTTGATCTTTGAGGGG

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|162163342|gb|FC339668.1|FC339668
EST:     GCTACAACCTTCAAGTATGCATTTAATTACCACGATGATGACGTCTACTG                         GTGCACAGCAGACTGTGGGTGGATTACTGGTCACAGCTACCTGACATATGG
genomic: GCTACAACCTTCAAGTATGCATTTAATTACCACGATGATGACGTCTACTGgtgagccctt ... gttcgtgcagGTGCACAGCAGACTGTGGGTGGATTACTGGTCACAGCTACCTGACATATGG
EST: gi|162197340|gb|FC372302.1|FC372302
EST:     GCTACAACCTTCAAGTATGCATTTAATTACCACGATGATGACGTCTACTG                         GTGCACAGCAGACTGTGGGTGGATTACTGGTCACAGCTACCTGACATATGG
genomic: GCTACAACCTTCAAGTATGCATTTAATTACCACGATGATGACGTCTACTGgtgagccctt ... gttcgtgcagGTGCACAGCAGACTGTGGGTGGATTACTGGTCACAGCTACCTGACATATGG
EST: gi|162208860|gb|FC384996.1|FC384996
EST:     GCTACAACCTTCAAGTATGCATTTAATTACCACGATGATGACGTCTACTG                         GTGCACAGCAGACTGTGGGTGGATTACTGGTCACAGCTACCTGACATATGG
genomic: GCTACAACCTTCAAGTATGCATTTAATTACCACGATGATGACGTCTACTGgtgagccctt ... gttcgtgcagGTGCACAGCAGACTGTGGGTGGATTACTGGTCACAGCTACCTGACATATGG
EST: gi|162255648|gb|FC431646.1|FC431646
EST:     GCTACAACCTTCAAGTATGCATTTAATTACCACGATGATGACGTCTACTG                         GTGCACAGCAGACTGTGGGTGGATTACTGGTCACAGCTACCTGACATATGG
genomic: GCTACAACCTTCAAGTATGCATTTAATTACCACGATGATGACGTCTACTGgtgagccctt ... gttcgtgcagGTGCACAGCAGACTGTGGGTGGATTACTGGTCACAGCTACCTGACATATGG
EST: gi|162257811|gb|FC434009.1|FC434009
EST:     GCTACAACCTTCAAGTATGCATTTAATTACCACGATGATGACGTCTACTG                         GTGCACAGCAGACTGTGGGTGGATTACTGGTCACAGCTACCTGACATATGG
genomic: GCTACAACCTTCAAGTATGCATTTAATTACCACGATGATGACGTCTACTGgtgagccctt ... gttcgtgcagGTGCACAGCAGACTGTGGGTGGATTACTGGTCACAGCTACCTGACATATGG
EST: gi|162178871|gb|FC354803.1|FC354803
EST:     GCTACAACCTTCAAGTATGCATTTAATTACCACGATGATGACGTCTACTG                         GTGCACAGCAGACTGTGGGTGGATTACTGGTCACAGCTACCTGACATATGG
genomic: GCTACAACCTTCAAGTATGCATTTAATTACCACGATGATGACGTCTACTGgtgagccctt ... gttcgtgcagGTGCACAGCAGACTGTGGGTGGATTACTGGTCACAGCTACCTGACATATGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atagaggtcatataccagaaatttacattccgcatacttgtggatgttcgtgcagGTGCACAGCAGACTGTGGGTGGATTACTGGTCACAGCTACCTGACATATGGCCCTCTTCTCAACGGTGCTAGCATGGTTGTCTTTGAAGGG
                  aaatttacatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagcccttatttgctcctctgatgttttttgtggccttgagctggaggcatgttaccactgcgtcgcccaagttattttcttatttcaagtctctccttgaaggtcacataccatagaggtcatataccagaaatttacattccgcatacttgtggatgttcgtgcagGTGCACAGCAGACTGTGGGTGGATTACTGGTCACAGCTACCTGACATATGGCCCTCTTCTCAACGGTGCTAGCATGGTTGTCTTTGAAGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG