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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cccgatctgcgttgtagtatttgcgcagtgtgttcttgttgctgtctcttagcatctgcaccgtagagcgttttttgaggcgtgttcgttgatggcgcagATGGACCCCAAGTTCTTGAGGAACCAGAGGTATGCCAAGAAGCATAACCGATCGGGTGCCGCCGACGAAGTTGAGTCTGCGGAGGAGTAGATCTTGTACT

Basic information

species Physcomitrella patens
transcript PP1S58_102V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S58_102V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os01g19840.1 (Oryza sativa), 3'ss of exon 2
----cccgatctgcgttgtagtatttgcgcagtgtgttcttgttgctgtctcttagcatctgcaccgtagagcgttttttgaggcgtgttcgttgatggcgcagATGGACCCCAAGTTCTTGAGGAACCAGAGGTATGCCAAGAAGCATAACCGATCGGGTGCCGCCGACGAAGTTGAGTCTGCGGAGGAG--TAGATCTTGTACT----
    |  ||  ||  |   | |   |  | | ||||  |   |       | ||  |  ||  ||  |      | |       | | |||           |||||||||| |||||| ||||||||||||| ||| ||| ||||||||||     | |||        || | ||| || | |||| |   | ||  |||| ||    
ttatcttgaattgtttatcaatcaatcagtattgtgcacaaatccaaaatttttgcctcctttacact----tctctcactgatctttttcaccatgtttatagATGGACCCAAAGTTCCTGAGGAACCAGAGATATTCCAGGAAGCATAACAAGAAGAGTG------GTGAGGCTGAATCCGAGGAGTAAGATGGAAGTTGTCCTTTCG

upper sequence: PP1S58_102V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G147791_T03 (Zea mays), 3'ss of exon 2
cccgatctgcgttgtagtatttgcgcagtgtgttcttgttgctgtctcttagcatctgcaccgtagagcgttttttga--ggcgtgtt-cgttgatggcg----cagATGGACCCCAAGTTCTTGAGGAACCAGAGGTATGCCAAGAAGCATAACCGATCGGGTGCCGCCGACGAAGTTGAGTCTGCGGAGGAGTAGATCTTGTACT-
      |     |||     ||||  | | | |  |     | |  ||||   ||    |  ||     | | ||  |  | | | || | ||||    |    |||||||||||||||||| ||||||||| ||||||| | | ||||   |||  |  | |||  |  |  |||| ||||   |  |    | |    | |   | 
------cacaactgttactgttgccaaattt-tcatctccacagcatcttgagatgcatattgtttcttgctcttaaactgaccttttgctttgaccatgtttgcagATGGACCCCAAGTTCCTGAGGAACCTGAGGTATTCTAGGAAGGGCAACAAAAAGAGTGGTGAGGCTGAAGCTGAGGA-GTAGGAAGGAAAGCATGGCTTTG

upper sequence: PP1S58_102V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G009894_T01 (Zea mays), 3'ss of exon 2
-----cccgatctgcgttgtagtatttgcgcagtgtgttcttgttgctgtctcttagcatctgcaccgtagagcgttttttgaggcgtgttcgttgatggcgcagATGGACCCCAAGTTCTTGAGGAACCAGAGGTATGCCAAGAAGCATAACCGATCGGGTGCCGCCGACGAAGTTGAGTCTGCGGAGGAGTA-GATCTTGTACT--
         |  |  |      | |   | |     | |  |   | ||   ||| |  | ||| |   |        ||||    |     |||      ||||||||||||||||||| ||||||||| ||||||| | | ||||   |||     | |||  |  |  || |   |||  |  |   || | | |  |||     
acaactgttacttttgccaatttttcatctctaacagctgcttgagatgcaccttggtttttgctctacaactgaccctttgcattgaccatgtt-----tgcagATGGACCCCAAGTTCCTGAGGAACCTGAGGTATTCAAGGAAGGGCAACAAGAAGAGTGGTGAGGCTGAGG---AGTAGGAAGGAAAGCATGGTTGTGTTTCCT

upper sequence: PP1S58_102V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT3G06700.3 (Arabidopsis thaliana), 3'ss of exon 2
-cccgatctgcgttgtagtatttgcgcagtgtgttcttgttgctgtctcttagcatctgcaccgtagagcgttttttgaggcgtgttcgttgatggcgcagATGGACCCCAAGTTCTTGAGGAACCAGAGGTATGCCAAGAAGCATAACCGATCGGGTGCCGCCGACGAAGTTGAGTCTGCGGAGGAGTAGATCTTGTACT---
    |       ||  |||  |  |  |     ||   | | | |  | | ||  |  |     |      || ||       |||    |||||   ||||||||||| |||||| |||||||||||||||| || | |||||| |||   ||  | |||| |||  | | |    |||  ||  |   | | |  |  |   
gtaagtctcttattacagttctaacctaactgatttcagattcgggttat-agtgttggaggtttga----ttattgcgtttatgtgaaatgatgtttcagATGGACCCTAAGTTCCTGAGGAACCAGAGGTACGCAAGGAAGCACAAC--GTCAAG-GCCGGCGAGAATGCTAGCGCTGAAGAATAAGTGTTTTGATTATCTG

upper sequence: PP1S58_102V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: Vv07s0005g01340.t01 (Vitis vinifera), 3'ss of exon 2
---------------------------cccgatc-tgcgttgtagtatttgcgcagt-gtgttcttgttgctgtctcttagcatctgcaccgtagagcgttttttgaggcgtgttcgttgatggcgcagATGGACCCCAAGTTCTTGAGGAACCAGAGGTATGCCAAGAAGCATAACCGATCGGGTGCCGCCGACGAAGTTGAGTCTGCGGAGGAGTAGATCTTGTACT---
                            || ||| |  ||| |  |  ||   |  | ||| |||  ||| ||  | ||    | ||     ||  | ||||  |      | || |    ||||| ||||||| |||||||| ||||||||||| |||||||| | ||||||||||     | |||  |     | |  ||||   | ||||| |||||  |||  ||   
gtttgatttctctctgttttaatctcttccaatcgtttgtttttttccttttacttttgtgatctccttggtgggttttctggtttgagtgctatggtgtttgatttcttttatttgc-attggcgtagATGGATCCCAAGTTTTTGAGGAACCAAAGGTATGCGAGGAAGCATAACAAGAAGAGTGAAGGGTCTGCAACTGAG---GAGGAGGCGTAGACATTGCGCTGTT

upper sequence: PP1S58_102V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: Vv05s0077g01220.t01 (Vitis vinifera), 3'ss of exon 1
cccgatctgcgttgtagtatttgcgcagtgtgttcttgttgctgtctcttagcatctgc-accgtagagcgttttttgaggcgtgttcgttgatg-gcgcagATGGACCCCAAGTTCTTGAGGAACCAGAGGTATGCCAAGAAGCATAACCGATCGGGTGCCGCCGACGAAGTTGAGTCTGCGGAGGAGTAGATCTTGTACT------
           |   |   ||     | | | |||       | |     || || ||  |  |  | |     |||| |   ||     |||   |  ||||||||||| ||||||||||||||||||||||| || | |||||| |||     | |      ||  |||   |   | | ||| || |||| |    |        
-----gtaatttctcaactttgatttactcttttccccccttttttctgaagaatatgtgattgatgcgatgaatttgtgttttgaaatctgaaatgaacagATGGACCCGAAGTTCTTGAGGAACCAGAGGTACGCGAGGAAGCACAACAAGAAGAG------CGGTGAATCCGCCACCGAGGAAGAATAGACCAACAATGATTAGG

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|67573419|gb|BJ946243.1|BJ946243
EST:     AGAATGGTATCAAGAAGGTTAAGAAACACAAATATGCCTCAAGGAAGGGG                         ATGGACCCCAAGTTCTTGAGGAACCAGAGGTATGCCAAGAAGCATAACCGA
genomic: AGAATGGTATCAAGAAGGTTAAGAAACACAAATATGCCTCAAGGAAGGGGgtgagtatct ... gatggcgcagATGGACCCCAAGTTCTTGAGGAACCAGAGGTATGCCAAGAAGCATAACCGA
EST: gi|37846542|gb|BJ604550.1|BJ604550
EST:     AGAATGGTATCAAGAAGGTTAAGAAACACAAATATGCCTCAAGGAAGGGG                         ATGGACCCCAAGTTCTTGAGGAACCAGAGGTATGCCAAGAAGCATAACCGA
genomic: AGAATGGTATCAAGAAGGTTAAGAAACACAAATATGCCTCAAGGAAGGGGgtgagtatct ... gatggcgcagATGGACCCCAAGTTCTTGAGGAACCAGAGGTATGCCAAGAAGCATAACCGA
EST: gi|7287210|gb|AW599697.1|AW599697
EST:     AGAATGGTATCAAGAAGGTTAAGAAACACAAATATGCCTCAAGGAAGGGG                         ATGGACCCCAAGTTCTTGAGGAACCAGAGGTATGCCAAGAAGCATAACCGA
genomic: AGAATGGTATCAAGAAGGTTAAGAAACACAAATATGCCTCAAGGAAGGGGgtgagtatct ... gatggcgcagATGGACCCCAAGTTCTTGAGGAACCAGAGGTATGCCAAGAAGCATAACCGA
EST: gi|19789288|gb|BQ041216.1|BQ041216
EST:     AGAATGGTATCAAGAAGGTTAAGAAACACAAATATGCCTCAAGGAAGGGG                         ATGGACCCCAAGTTCTTGAGGAACCAGAGGTATGCCAAGAAGCATAACCGA
genomic: AGAATGGTATCAAGAAGGTTAAGAAACACAAATATGCCTCAAGGAAGGGGgtgagtatct ... gatggcgcagATGGACCCCAAGTTCTTGAGGAACCAGAGGTATGCCAAGAAGCATAACCGA
EST: gi|15730302|gb|BI741779.1|BI741779
EST:     AGAATGGTATCAAGAAGGTTAAGAAACACAAATATGCCTCAAGGAAGGGG                         ATGGACCCCAAGTTCTTGAGGAACCAGAGGTATGCCAAGAAGCATAACCGA
genomic: AGAATGGTATCAAGAAGGTTAAGAAACACAAATATGCCTCAAGGAAGGGGgtgagtatct ... gatggcgcagATGGACCCCAAGTTCTTGAGGAACCAGAGGTATGCCAAGAAGCATAACCGA
EST: gi|162164575|gb|FC341870.1|FC341870
EST:     AGAATGGTATCAAGAAGGTTAAGAAACACAAATATGCCTCAAGGAAGGGG                         ATGGACCCCAAGTTCTTGAGGAACCAGAGGTATGCCAAGAAGCATAACCGA
genomic: AGAATGGTATCAAGAAGGTTAAGAAACACAAATATGCCTCAAGGAAGGGGgtgagtatct ... gatggcgcagATGGACCCCAAGTTCTTGAGGAACCAGAGGTATGCCAAGAAGCATAACCGA
EST: gi|67572465|gb|BJ945289.1|BJ945289
EST:     AGAATGGTATCAAGAAGGTTAAGAAACACAAATATGCCTCAAGGAAGGGG                         ATGGACCCCAAGTTCTTGAGGAACCAGAGGTATGCCAAGAAGCATAACCGA
genomic: AGAATGGTATCAAGAAGGTTAAGAAACACAAATATGCCTCAAGGAAGGGGgtgagtatct ... gatggcgcagATGGACCCCAAGTTCTTGAGGAACCAGAGGTATGCCAAGAAGCATAACCGA
EST: gi|19778970|gb|BQ039392.1|BQ039392
EST:     AGAATGGTATCAAGAAGGTTAAGAAACACAAATATGCCTCAAGGAAGGGG                         ATGGACCCCAAGTTCTTGAGGAACCAGAGGTATGCCAAGAAGCATAACCGA
genomic: AGAATGGTATCAAGAAGGTTAAGAAACACAAATATGCCTCAAGGAAGGGGgtgagtatct ... gatggcgcagATGGACCCCAAGTTCTTGAGGAACCAGAGGTATGCCAAGAAGCATAACCGA
EST: gi|15320243|gb|BI488010.1|BI488010
EST:     AGAATGGTATCAAGAAGGTTAAGAAACACAAATATGCCTCAAGGAAGGGG                         ATGGACCCCAAGTTCTTGAGGAACCAGAGGTATGCCAAGAAGCATAACCGA
genomic: AGAATGGTATCAAGAAGGTTAAGAAACACAAATATGCCTCAAGGAAGGGGgtgagtatct ... gatggcgcagATGGACCCCAAGTTCTTGAGGAACCAGAGGTATGCCAAGAAGCATAACCGA
EST: gi|7583210|gb|AW699374.1|AW699374
EST:     AGAATGGTATCAAGAAGGTTAAGAAACACAAATATGCCTCAAGGAAGGGG                         ATGGACCCCAAGTTCTTGAGGAACCAGAGGTATGCCAAGAAGCATAACCGA
genomic: AGAATGGTATCAAGAAGGTTAAGAAACACAAATATGCCTCAAGGAAGGGGgtgagtatct ... gatggcgcagATGGACCCCAAGTTCTTGAGGAACCAGAGGTATGCCAAGAAGCATAACCGA
EST: gi|6167022|gb|AW145341.1|AW145341
EST:     AGAATGGTATCAAGAAGGTTAAGAAACACAAATATGCCTCAAGGAAGGGG                         ATGGACCCCAAGTTCTTGAGGAACCAGAGGTATGCCAAGAAGCATAACCGA
genomic: AGAATGGTATCAAGAAGGTTAAGAAACACAAATATGCCTCAAGGAAGGGGgtgagtatct ... gatggcgcagATGGACCCCAAGTTCTTGAGGAACCAGAGGTATGCCAAGAAGCATAACCGA
EST: gi|67695837|gb|BJ956070.1|BJ956070
EST:     AGAATGGTATCAAGAAGGTTAAGAAACACAAATATGCCTCAAGGAAGGGG                         ATGGACCCCAAGTTCTTGAGGAACCAGAGGTATGCCAAGAAGCATAACCGA
genomic: AGAATGGTATCAAGAAGGTTAAGAAACACAAATATGCCTCAAGGAAGGGGgtgagtatct ... gatggcgcagATGGACCCCAAGTTCTTGAGGAACCAGAGGTATGCCAAGAAGCATAACCGA
EST: gi|67696777|gb|BJ957010.1|BJ957010
EST:     AGAATGGTATCAAGAAGGTTAAGAAACACAAATATGCCTCAAGGAAGGGG                         ATGGACCCCAAGTTCTTGAGGAACCAGAGGTATGCCAAGAAGCATAACCGA
genomic: AGAATGGTATCAAGAAGGTTAAGAAACACAAATATGCCTCAAGGAAGGGGgtgagtatct ... gatggcgcagATGGACCCCAAGTTCTTGAGGAACCAGAGGTATGCCAAGAAGCATAACCGA
EST: gi|7583640|gb|AW699548.1|AW699548
EST:     AAAATGGTATCAAGAAGGTTAAGAAACACAAATATGCCTCAAGGAAGGGG                         ATGGACCCCAAGTTCTTGAAGAACCAGAGGTATGCCAAGAAGCATAACCGA
genomic: AGAATGGTATCAAGAAGGTTAAGAAACACAAATATGCCTCAAGGAAGGGGgtgagtatct ... gatggcgcagATGGACCCCAAGTTCTTGAGGAACCAGAGGTATGCCAAGAAGCATAACCGA
EST: gi|67573396|gb|BJ946220.1|BJ946220
EST:     AGAATGGTATCAAGAAGGTTAAGAAACACAAATATGCCTCAAGGAAGGGG                         ATGGACCCCAAGTTCTTGAGGAACCAGAGGTATGCCAAGAAGCATAACCGA
genomic: AGAATGGTATCAAGAAGGTTAAGAAACACAAATATGCCTCAAGGAAGGGGgtgagtatct ... gatggcgcagATGGACCCCAAGTTCTTGAGGAACCAGAGGTATGCCAAGAAGCATAACCGA
EST: gi|67696800|gb|BJ957033.1|BJ957033
EST:     AGAATGGTATCAAGAAGGTTAAGAAACACAAATATGCCTCAAGGAAGGGG                         ATGGACCCCAAGTTCTTGAGGAACCAGAGGTATGCCAAGAAGCATAACCGA
genomic: AGAATGGTATCAAGAAGGTTAAGAAACACAAATATGCCTCAAGGAAGGGGgtgagtatct ... gatggcgcagATGGACCCCAAGTTCTTGAGGAACCAGAGGTATGCCAAGAAGCATAACCGA
EST: gi|18366165|gb|BJ198243.1|BJ198243
EST:     AGAATGGTATCAAGAAGGTTAAGAAACACAAATATGCCTCAAGGAAGGGG                         ATGGACCCCAAGTTCTTGAGGAACCAGAGGTATGCCAAGAAGCATAACCGA
genomic: AGAATGGTATCAAGAAGGTTAAGAAACACAAATATGCCTCAAGGAAGGGGgtgagtatct ... gatggcgcagATGGACCCCAAGTTCTTGAGGAACCAGAGGTATGCCAAGAAGCATAACCGA
EST: gi|7584218|gb|AW700115.1|AW700115
EST:     AGAATGGTATCAAGAAGGTTAAGAAACACAAATATGCCTCAAGGAAGGGG                         ATGGACCCCAAGTTCTTGAGGAACCAGAGGTATGCCAAGAAGCATAACCGA
genomic: AGAATGGTATCAAGAAGGTTAAGAAACACAAATATGCCTCAAGGAAGGGGgtgagtatct ... gatggcgcagATGGACCCCAAGTTCTTGAGGAACCAGAGGTATGCCAAGAAGCATAACCGA
EST: gi|7583020|gb|AW699184.1|AW699184
EST:     AGAATGGTATCAAGAAGGTTAAGAAACACAAATATGCCTCAAGGAAGGGG                         ATGGACCCCAAGTTCTTGAGGAACCAGAGGTATGCCAAGAAGCATAACCGA
genomic: AGAATGGTATCAAGAAGGTTAAGAAACACAAATATGCCTCAAGGAAGGGGgtgagtatct ... gatggcgcagATGGACCCCAAGTTCTTGAGGAACCAGAGGTATGCCAAGAAGCATAACCGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcttagcatctgcaccgtagagcgttttttgaggcgtgttcgttgatggcgcagATGGACCCCAAGTTCTTGAGGAACCAGAGGTATGCCAAGAAGCATAACCGATCGGGTGCCGCCGACGAAGTTGAGTCTGCGGAGGAGTAGATCTTGTACT
                                         cgttgat  putative branch site (score: 5)
                         ttttttga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cccgatctgcgttgtagtatttgcgcagtgtgttcttgttgctgtctcttagcatctgcaccgtagagcgttttttgaggcgtgttcgttgatggcgcagATGGACCCCAAGTTCTTGAGGAACCAGAGGTATGCCAAGAAGCATAACCGATCGGGTGCCGCCGACGAAGTTGAGTCTGCGGAGGAGTAGATCTTGTACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgcacc