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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtttgctttttaagtatttcccacttaacgtttaggtgtgattgagttatgtatcatttcgatttggttgggactaactgagttccttcactcctgcagAGTGCTATTGGACAGGGAATGACTCGAAAGGATCATTCTGAAGTCTCTAACCAG

Basic information

species Physcomitrella patens
transcript PP1S100_117V6.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S100_117V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: LOC_Os01g51380.2 (Oryza sativa), 3'ss of exon 12
----------------tgtttgctttttaagtatttcccacttaacgtttaggtgtgattgagttatgtatcatttcgatttggttgggactaactgagttccttcac------tcctgcagAGTGCTATTGGACAGGGAATGACTCGAAAGGATCATTCTGAAGTCTCTAACCAG
                |         |   | | |   ||    || ||   || |    | |      ||| |    ||  |||||  | |       |  ||| ||      || ||||||||||||||||  | || |||||||| | |||||||||||| ||||| ||||||
gtaaggtttttggcaataaagaaagctgccgcactctacatcctactttagagttttgcagggactgacatcgtcaatataaggttgataatttgcttataacttgaccggatctcttgcagAGTGCTATTGGTGAAGGCATGACTCGCAGGGATCATTCTGATGTCTCGAACCAG

upper sequence: PP1S100_117V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: GLYMA10G42940.2 (Glycine max), 3'ss of exon 12
-------------tgtttgctttttaagtatttcccacttaacgtt-taggtgtgattgagttatgtatcatttcgatttggttggg-actaactgagttcctt----cactcctgcagAGTGCTATTGGACAGGGAATGACTCGAAAGGATCATTCTGAAGTCTCTAACCAG
              ||||| ||  ||   |  | |   |||| ||  ||  | |  |    || |  || |   | | | | |     |||||  | |   | |    ||||  ||||||||||||||||  ||||||||||| |||||||||||||||| || || ||||||
gtaaggttaatctcgtttgtttgatatcaaggtgct--ttaaagtgataaatattttctgtttcttaattaaagcaagtggttcacacactaaaggtgcatcattggtcacttttgcagAGTGCTATTGGTGAGGGAATGACTAGAAAGGATCATTCTGATGTGTCCAACCAG

upper sequence: PP1S100_117V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: GLYMA20G24070.1 (Glycine max), 3'ss of exon 13
---------tgtttgctttttaagtatttc--ccacttaacgtt-taggtgtgattgagttatgtatcatttcgatttggttgggact--aactgagttcctt----cactcctgcagAGTGCTATTGGACAGGGAATGACTCGAAAGGATCATTCTGAAGTCTCTAACCAG
            |||||| ||   ||| |       |||| ||  ||  | |  |    || |  || | | | |  |||||    ||  ||  | |   | |    |||| |||||||||||||||||  ||||||||||| ||| |||||||||||| || || ||||||
gtaaggataatcttgcttgtttgatatctaggtgctttaaagtgataaatattttctgattcttaattaatgcaaagtggttcacgctctaatggtgcatcattggtcacttctgcagAGTGCTATTGGTGAGGGAATGACTAGAAGGGATCATTCTGATGTGTCCAACCAG

upper sequence: PP1S100_117V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: GLYMA18G48280.1 (Glycine max), 3'ss of exon 12
---------------------------------------------------------------------------tgtttgctttttaagtatttcc------cacttaacgtttag------gtgtgattgagttatgtatcatttcgatt--tggttgggactaactgagttcct-----tcactcctgcagAGTGCTATTGGACAGGGAATGACTCGAAAGGATCATTCTGAAGTCTCTAACCAG-
                                                                           ||  | |   |  | |   |||      |||| ||   |  |      || |   ||  | | | | |||| |  ||  | |||   |  || | | ||  |     |  ||  |||||||||| |||||  |||||||||| ||||||||||||||||| || || |||||| 
taaggttaatcttgttcgtttgatgtcaaaatggcaccaacagataaatttgtgacgttttggatgggtgagtggtgcctaccactggattccatccaacaatcactaaagactctgcaacttgttttcctggctaaagcagcattacccttattagttcaaa--aagtaaatttttaaggtttgcttatgcagaGTGCCATTGGTGAGGGAATGACACGAAAGGATCATTCTGATGTGTCCAACCAGG

upper sequence: PP1S100_117V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: GLYMA09G38110.1 (Glycine max), 3'ss of exon 12
--------------------------------------------------------------------------------------tgtttgctttttaagtatttccca-----cttaacgtttaggtgtgattgagttatgtatcatttcgatttggttgggactaactgagttc--cttcactcctgcagAGTGCTATTGGACAGGGAATGACTCGAAAGGATCATTCTGAAGTCTCTAACCAG
                                                                                      ||  | |  |  ||  ||  |  |        ||| |||     ||  | |   | | || |      || | |    |   |   | ||    ||  ||  |||||||||| |||||  |||||||||| |||||||||||||| || || || ||||||
gtgaggttaatcttgttagtttgatgtcaaaatgccatcaactgataaaattgtgactttttggttcggtgagtggtccctaccactggattccatccaacaatcactaaaactctgcaactttttttcctggctaaagca-gcattacccttgttagttcaaaaagtaaatatttgaggtttgcttatgcagAGTGCCATTGGTGAGGGAATGACACGAAAGGATCATTCCGATGTGTCCAACCAG

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|208395424|gb|DC924478.1|DC924478
EST:     ATTTATCCTCCTATTAATGTTTTGCCGTCTCTGTCACGGTTGATGAAG                         AGTGCTATTGGACAGGGAATGACTCGAAAGGATCATTCTGAAGTCTCTAAC
genomic: ATTTATCCTCCTATTAATGTTTTGCCGTCTCTGTCACGGTTGATGAAGgtactacact ... actcctgcagAGTGCTATTGGACAGGGAATGACTCGAAAGGATCATTCTGAAGTCTCTAAC
EST: gi|37837091|gb|BJ595099.1|BJ595099
EST:     ATTTATCCTCCTATTAATGTTTTGCCGTCTCTGTCACGGTTGATGAAG                         AGTGCTATTGGACAGGGAATGACTCGAAAGGATCATTCTGAAGTCTCTAAC
genomic: ATTTATCCTCCTATTAATGTTTTGCCGTCTCTGTCACGGTTGATGAAGgtactacact ... actcctgcagAGTGCTATTGGACAGGGAATGACTCGAAAGGATCATTCTGAAGTCTCTAAC
EST: gi|162153494|gb|FC329380.1|FC329380
EST:     ATTTATCCTCCTATTAATGTTTTGCCGTCTCTGTCACGGTTGATGAAG                         AGTGCTATCGGACAGGGAATGACTCGAAAGGATCATTCTGAAGTCTCTAAC
genomic: ATTTATCCTCCTATTAATGTTTTGCCGTCTCTGTCACGGTTGATGAAGgtactacact ... actcctgcagAGTGCTATTGGACAGGGAATGACTCGAAAGGATCATTCTGAAGTCTCTAAC
EST: gi|162278566|gb|FC454028.1|FC454028
EST:     ATTTATCCTCCTATTAATGTTTTGCCGTCTCTGTCACGGTTGATGAAG                         AGTGCTATTGGACAGGGAATGACTCGAAAGGATCATTCTGAAGTCTCTAAC
genomic: ATTTATCCTCCTATTAATGTTTTGCCGTCTCTGTCACGGTTGATGAAGgtactacact ... actcctgcagAGTGCTATTGGACAGGGAATGACTCGAAAGGATCATTCTGAAGTCTCTAAC
EST: gi|162230898|gb|FC406737.1|FC406737
EST:     ATTTATCCTCCTATTAATGTTTTGCCGTCTCTGTCACGGTTGATGAAG                         AGTGCTATCGGACAGGGAATGACTCGAAAGGATCATTCTGAAGTCTCTAAC
genomic: ATTTATCCTCCTATTAATGTTTTGCCGTCTCTGTCACGGTTGATGAAGgtactacact ... actcctgcagAGTGCTATTGGACAGGGAATGACTCGAAAGGATCATTCTGAAGTCTCTAAC
EST: gi|67698241|gb|BJ958474.1|BJ958474
EST:     ATTTATCCTCCTATTAATGTTTTGCCGTCTCTGTCACGGTTGATGAAG                         AGTGCTATTGGACAGGGAATGACTCGAAAGGATCATTCTGAAGTCTCTAAC
genomic: ATTTATCCTCCTATTAATGTTTTGCCGTCTCTGTCACGGTTGATGAAGgtactacact ... actcctgcagAGTGCTATTGGACAGGGAATGACTCGAAAGGATCATTCTGAAGTCTCTAAC
EST: gi|162209307|gb|FC385227.1|FC385227
EST:     ATTTATCCTCCTATTAATGTTTTGCCGTCTCTGTCACGGTTGATGAAG                         AGTGCTATCGGACAGGGAATGACTCGAAAGGATCATTCTGAAGTCTCTAAC
genomic: ATTTATCCTCCTATTAATGTTTTGCCGTCTCTGTCACGGTTGATGAAGgtactacact ... actcctgcagAGTGCTATTGGACAGGGAATGACTCGAAAGGATCATTCTGAAGTCTCTAAC
EST: gi|162153495|gb|FC329381.1|FC329381
EST:     ATTTATCCTCCTATTAATGTTTTGCCGTCTCTGTCACGGTTGATGAAG                         AGTGCTATCGGACAGGGAATGACTCGAAAGGATCATTCTGAAGTCTCTAAC
genomic: ATTTATCCTCCTATTAATGTTTTGCCGTCTCTGTCACGGTTGATGAAGgtactacact ... actcctgcagAGTGCTATTGGACAGGGAATGACTCGAAAGGATCATTCTGAAGTCTCTAAC
EST: gi|162221565|gb|FC397582.1|FC397582
EST:     ATTTATCCTCCTATTAATGTTTTGCCGTCTCTGTCACGGTTGATGAAG                         AGTGCTATCGGACAGGGAATGACTCGAAAGGATCATTCTGAAGTCTCTAAC
genomic: ATTTATCCTCCTATTAATGTTTTGCCGTCTCTGTCACGGTTGATGAAGgtactacact ... actcctgcagAGTGCTATTGGACAGGGAATGACTCGAAAGGATCATTCTGAAGTCTCTAAC
EST: gi|162232324|gb|FC408667.1|FC408667
EST:     ATTTATCCTCCTATTAATGTTTTGCCGTCTCTGTCACGGTTGATGAAG                         AGTGCTATCGGACAGGGAATGACTCGAAAGGATCATTCTGAAGTCTCTAAC
genomic: ATTTATCCTCCTATTAATGTTTTGCCGTCTCTGTCACGGTTGATGAAGgtactacact ... actcctgcagAGTGCTATTGGACAGGGAATGACTCGAAAGGATCATTCTGAAGTCTCTAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttatgtatcatttcgatttggttgggactaactgagttccttcactcctgcagAGTGCTATTGGACAGGGAATGACTCGAAAGGATCATTCTGAAGTCTCTAACCAG
                           gactaac  putative branch site (score: 1)
                                      ttccttcactcctgc  putative PPT
       tatcattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtttgctttttaagtatttcccacttaacgtttaggtgtgattgagttatgtatcatttcgatttggttgggactaactgagttccttcactcctgcagAGTGCTATTGGACAGGGAATGACTCGAAAGGATCATTCTGAAGTCTCTAACCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG