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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttcggagatgatttagttgaattttggaggattctgggtagttagcattggagcttctccatgtttcctgcattgagtttttcattcgctcgatagcagGTAAGATGGCCAAGTCCAAGAATCACACCGCACACAACCAGTCCTACAAGAACCACAAGAATGGTATCAAGAAGGTTAAGAAACACAAATATGCCTCAAG

Basic information

species Physcomitrella patens
transcript PP1S58_102V6.1
intron # 1
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 1
lower sequence: LOC_Os01g19840.1 (Oryza sativa), 3'ss of exon 1
----------gttcggagatgatt-tagttgaattttggaggattctgggtagttagcattggagcttctcca-tgtttcctgcattgagtttttcattcg-----ctcgatag---cagGTAAGATGGCCAAGTCCAAGAATCACACCGCACACAACCAGTCCTACAAGAACCACAAGAATGGTATCAAGAAGGTTAAGAAACACAAATATGCCTCAAG
           |||    ||     | |    |||         | ||  |  |     || |   |  |||  || ||||||  ||   |  ||  ||||      | ||  |   | ||  ||||||||||||| ||||| ||||| || ||||||||||| ||||||   |||||||| || |||||||||   |||   |||    |         
gtaaccgacgattcctccatttccatcgcctcattcgatgtctctttgatttatcgatcttcgttttcttcccctgattcctgatttttttcgtttgttcgtcgtctttgaagGATTCGGGGGAGATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTCGTACAAGGCGCACAAGAACGGGATCAAGAAGCCCAAGCGCCACCGCCAGA-------

upper sequence: PP1S58_102V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G009894_T01 (Zea mays), 3'ss of exon 1
------gttcgg-agatgatttagttgaattttggaggat-tctgggtagttagcattggagcttctccatgtttcctgcattgagtt---tttcattcgctcgatagcagGTAAGATGGCCAAGTCCAAGAATCACACCGCACACAACCAGTCCTACAAGAACCACAAGAATGGTATCAAGAAGGTTAAGAAACACAAATATGCCTCAAG
       | ||| |      |   |    |  |    ||| | | | | ||   ||  |    | | || |    | | |  |||||    |||  || ||  |    | |   ||||||||||||| ||||| ||||| || ||||||||||| ||||||   |||||||| || |||||||||   |||   |||    |         
gtaactctccggcactccgctcgatctgttcctactagatgtgttgttcgtcttcaccgtcaatccacc-tcccccttactctgagtcgccttttgtttgcagGGATCCGGAAGAGATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTCGTACAAGGCGCACAAGAACGGCATCAAGAAGCCCAAGCGCCACCGGCAG--------

upper sequence: PP1S58_102V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA07G37060.1 (Glycine max), 3'ss of exon 1
gttcggagatgatttagttgaattttggaggattctgggtagttagcattggagcttctccatgtttcctgcattgagtt---tttcattcgctcgatagcagGTAAGATGGCCAAGTCCAAGAATCACACCGCACACAACCAGTCCTACAAGAACCACAAGAATGGTATCAAGAAGGTTAAGAAACACAAATATGCCTCAAG---
       | |   |  ||| |||||        |||     |||   | |     || |   || |  || |||||  ||   ||   | |  |  || ||||   ||||||| ||||| ||||| |||||||| ||||||||||||||||||  |||||||||||| ||||| |||   ||||  |||    |  | || |    
-------gttcgctctgttcaatttc-------tctaacacgttcttact-----tttttgctgctctcttcattgtcttacattgtgtgcattgaattgcag-

upper sequence: PP1S58_102V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA17G03550.2 (Glycine max), 3'ss of exon 1
gttcggagatgatttagttgaattttggaggattctgggtagttagcattggagcttctccatgtttcctgcattgagt---ttttcattcgctcgatagcagGTAAGATGGCCAAGTCCAAGAATCACACCGCACACAACCAGTCCTACAAGAACCACAAGAATGGTATCAAGAAGGTTAAGAAACACAAATATGCCTCAAG---
                |||   | |  |   |||||   ||  | |   |  |  || |  || |   || ||||  ||    |||  | |  |  || ||||   ||||||| ||||| ||||| |||||||| ||||||||||||||||||  ||| |||||||| ||||| |||   ||||  ||     |  | || |    
----------------gttcgctctgtgcaaattctc--taacttgttctc-actttgttgatttcctcttcatttcgtaacattttgtgcattgaattgcag-

upper sequence: PP1S58_102V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA09G04280.1 (Glycine max), 3'ss of exon 1
gttcggagatgatttagttgaattttggaggattct--gggtagttagcattggagcttctccatgtttcctg----cattgagtttttcattcgctcgatagcagGTAAGATGGCCAAGTCCAAGAATCACACCGCACACAACCAGTCCTACAAGAACCACAAGAATGGTATCAAGAAGGTTAAGAAACACAAATATGCCTCAAG---
|||||    |  |  | ||   |     |  |||||     |  |  || ||    ||  ||     ||||      | || | |||||    | || ||| ||||   ||||||| ||||| ||||||||||| |||||||| ||||||||||||  |||||| || || ||||||||    ||||  ||     |  | || |    
gttcgtttct--tcaatttctgtgacaaaaaattcttctaattttgtgctttttttctgttcttctcttcccatcgtcttttaatttttgtgccacttgattgcag-

upper sequence: PP1S58_102V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA15G15320.1 (Glycine max), 3'ss of exon 1
gttcggagatgatttagttgaattttggag--gattctgggtagttagcattggagcttctccatgtttcctgcattgagtttttcattcgctcgatagca--gGTAAGATGGCCAAGTCCAAGAATCACACCGCACACAACCAGTCCTACAAGAACCACAAGAATGGTATCAAGAAGGTTAAGAAACACAAATATGCCTCAAG---
       | |  | |  |  | || || |    |||||    | || ||  |      | | | |        ||| |   |||   || |||| ||   |  |   ||||||| ||||| ||||||||||| || ||||| ||||||||||||  |||||| || || ||||||||    ||||  ||     |  | || |    
-------gttcgtatcttcaatttctgtaacaaattcttctaattttgcgctttgttctattctttcccttctcatcgtcctttcattttgctctattttattgcagAGATGGCAAAGTCTAAGAATCACACAGCGCACAATCAGTCCTACAAGGCCCACAAAAACGGCATCAAGAAACCCAAGAGGCATCGCCACACTTCCACCAA

upper sequence: PP1S58_102V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: Vv07s0005g01340.t01 (Vitis vinifera), 3'ss of exon 1
gttcggagatgatttagttgaattttggaggattctgggtagttagcattggagcttctccatgtttcctgcattgagtttttcattcgctcgatagcagGTAAGATGGCCAAGTCCAAGAATCACACCGCACACAACCAGTCCTACAAGAACCACAAGAATGGTATCAAGAAGGTTAAGAAACACAAATATGCCTCAAG-
                ||  |   |  |    || |||  |     |   |    | ||||    |  ||| |||     || || |  |      | ||| || ||||| ||||| ||||| ||||| || |||||||||||||||||   |||||||||||| ||||||||       || |||    |  |||| |  
----------------gtacagcctctgcatcttttggtaaaacgacgccgtttttgctcccatctcactgaatt----cttccactttcaatgctgtagGGAA-ATGGCGAAGTCGAAGAACCACACTGCCCACAACCAGTCCTACAAAGCCCACAAGAATGGAATCAAGAAACCCCGAAAGCACCGCCACACCTCCACC

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:     TTTTTTGTGTTCCTCGCGTTTCTGCCGGTGTTGATAGGCTGCCTCCACAG                         GTAAGATGGCCAAGTCCAAGAATCACACCGCACACAACCAGTCCTACAAGA
genomic: TTTTTTGTGTTCCTCGCGTTTCTGCCGGTGTTGATAGGCTGCCTCCACAGgtaaatttct ... tcgatagcagGTAAGATGGCCAAGTCCAAGAATCACACCGCACACAACCAGTCCTACAAGA
EST: gi|37846542|gb|BJ604550.1|BJ604550
EST:     TNTTTTGTGTTCCTCGCGTTTCTGCCGGTGTTGATAGGCTGCCTCCACAG                         GTAAGATGGCCAAGTCCAAGAATCACACCGCACACANCCAGTCCTACAAGA
genomic: TTTTTTGTGTTCCTCGCGTTTCTGCCGGTGTTGATAGGCTGCCTCCACAGgtaaatttct ... tcgatagcagGTAAGATGGCCAAGTCCAAGAATCACACCGCACACAACCAGTCCTACAAGA
EST: gi|7287210|gb|AW599697.1|AW599697
EST:     TTTTTTGTGTTCCTCGCGTTTCTGCCGGTGTTGATAGGCTGCCTCCACAGCAG                       
genomic: TTTTTTGTGTTCCTCGCGTTTCTGCCGGTGTTGATAGGCTGCCT-C-CA-CAGgtaaatttct ... tcgatagc
EST: gi|19789288|gb|BQ041216.1|BQ041216
EST:     TTTTTTGTGTTCCTCGCGTTTCTGCCGGTGTTGATAGGCTGCCTCCACAGCAG                       
genomic: TTTTTTGTGTTCCTCGCGTTTCTGCCGGTGTTGATAGGCTGCCT-C-CA-CAGgtaaatttct ... tcgatagc
EST: gi|15730302|gb|BI741779.1|BI741779
EST:     ATAGGCTGCCTCCACAGCAG                       
genomic: ATAGGCTGCCT-C-CA-CAGgtaaatttct ... tcgatagc
EST: gi|162164575|gb|FC341870.1|FC341870
EST:     TTTATTGTGTTCCTCGCGTTTCTGCCGGTGTTGAGAGGCTGCCTCAACAG                         GTAAGATGGCCAAGTCCAAGAATCACACCGCACACAACCAGTCCTACAAGA
genomic: TTTTTTGTGTTCCTCGCGTTTCTGCCGGTGTTGATAGGCTGCCTCCACAGgtaaatttct ... tcgatagcagGTAAGATGGCCAAGTCCAAGAATCACACCGCACACAACCAGTCCTACAAGA
EST: gi|67572465|gb|BJ945289.1|BJ945289
EST:     TTTTTTGTGTTCCTCGCGTTTCTGCCGGTGTTGATAGGCTGCCTCCACAGCAG                       
genomic: TTTTTTGTGTTCCTCGCGTTTCTGCCGGTGTTGATAGGCTGCCT-C-CA-CAGgtaaatttct ... tcgatagc
EST: gi|19778970|gb|BQ039392.1|BQ039392
EST:     TTTTTTGTGTTCCTCGCGTTTCTGCCGGTGTTGATAGGCTGCCTCCACAGCAG                       
genomic: TTTTTTGTGTTCCTCGCGTTTCTGCCGGTGTTGATAGGCTGCCT-C-CA-CAGgtaaatttct ... tcgatagc
EST: gi|7583210|gb|AW699374.1|AW699374
EST:     TTTTTTGTGTTCCTCGCGTTTCTGCCGGTGTTGATAGGCTGCCTCCACAGCAG                       
genomic: TTTTTTGTGTTCCTCGCGTTTCTGCCGGTGTTGATAGGCTGCCT-C-CA-CAGgtaaatttct ... tcgatagc
EST: gi|6167022|gb|AW145341.1|AW145341
EST:     TTGATAGGCTGCCTCCACAG                         GTAAGATGGCCAAGTCCAAGAATCACACCGCACACAACCAGTCCTACAAGA
genomic: TTGATAGGCTGCCTCCACAGgtaaatttct ... tcgatagcagGTAAGATGGCCAAGTCCAAGAATCACACCGCACACAACCAGTCCTACAAGA
EST: gi|67695837|gb|BJ956070.1|BJ956070
EST:     TTTTTTGTGTTCCTCGCGTTTCTGCCGGTGTTGATAGGCTGCCTCCACAGCAG                       
genomic: TTTTTTGTGTTCCTCGCGTTTCTGCCGGTGTTGATAGGCTGCCT-C-CA-CAGgtaaatttct ... tcgatagc
EST: gi|67696777|gb|BJ957010.1|BJ957010
EST:     TTTTTTGTGTTCCTCGCGTTTCTGCCGGTGTTGATAGGCTGCCTCCACAG                         GTAAGATGGCCAAGTCCAAGAATCACACCGCACACAACCAGTCCTACAAGA
genomic: TTTTTTGTGTTCCTCGCGTTTCTGCCGGTGTTGATAGGCTGCCTCCACAGgtaaatttct ... tcgatagcagGTAAGATGGCCAAGTCCAAGAATCACACCGCACACAACCAGTCCTACAAGA
EST: gi|67573396|gb|BJ946220.1|BJ946220
EST:     TTTTTTGTGTTCCTCGCGTTTCTGCCGGTGTTGATAGGCTGCCTCCACAG                         GTAAGATGGCCAAGTCCAAGAATCACACCGCACACAACCAGTCCTACAAGA
genomic: TTTTTTGTGTTCCTCGCGTTTCTGCCGGTGTTGATAGGCTGCCTCCACAGgtaaatttct ... tcgatagcagGTAAGATGGCCAAGTCCAAGAATCACACCGCACACAACCAGTCCTACAAGA
EST: gi|67696800|gb|BJ957033.1|BJ957033
EST:     TTTTTTGTGTTCCTCGCGTTTCTGCCGGTGTTGATAGGCTGCCTCCACAG                         GTAAGATGGCCAAGTCCAAGAATCACACCGCACACAACCAGTCCTACAAGA
genomic: TTTTTTGTGTTCCTCGCGTTTCTGCCGGTGTTGATAGGCTGCCTCCACAGgtaaatttct ... tcgatagcagGTAAGATGGCCAAGTCCAAGAATCACACCGCACACAACCAGTCCTACAAGA
EST: gi|18366165|gb|BJ198243.1|BJ198243
EST:     TTTTTTGTGTTCCTCGCGTTTCTGCCGGTGTTGATAGGCTGCCTCCACAG                         GTAAGATGGCCAAGTCCAAGAATCACACCGCACACAACCAGTCCTACAAGA
genomic: TTTTTTGTGTTCCTCGCGTTTCTGCCGGTGTTGATAGGCTGCCTCCACAGgtaaatttct ... tcgatagcagGTAAGATGGCCAAGTCCAAGAATCACACCGCACACAACCAGTCCTACAAGA
EST: gi|7584218|gb|AW700115.1|AW700115
EST:     GTTGATAGGCTGCCTCCACAG                         GTAAGATGGCCAAGTCCAAGAATCACACCGCACACAACCAGTCCTACAAGA
genomic: GTTGATAGGCTGCCTCCACAGgtaaatttct ... tcgatagcagGTAAGATGGCCAAGTCCAAGAATCACACCGCACACAACCAGTCCTACAAGA
EST: gi|7583020|gb|AW699184.1|AW699184
EST:     TTTTTTGTGTTCCTCGCGTTTCTGCCGGTGTTGATAGGCTGCCTCCACAGCAG                       
genomic: TTTTTTGTGTTCCTCGCGTTTCTGCCGGTGTTGATAGGCTGCCT-C-CA-CAGgtaaatttct ... tcgatagc

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 26 (upstream exon), 35 (downstream exon)
Score: 16

TGAGGTGAGCTTCGTCCCGTATACAGTTCTTTCGGGCGCCGCACTCAGTATTTTTTGTGTTCCTCGCGTTTCTGCCGGTGTTGATAGGCTGCCTCCACAGgtaaatttct ... tcgatagcagGTAAGATGGCCAAGTCCAAGAATCACACCGCACACAACCAGTCCTACAAGAACCACAAGAATGGTATCAAGAAGGTTAAGAAACACAAATATGCCTCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcattggagcttctccatgtttcctgcattgagtttttcattcgctcgatagcagGTAAGATGGCCAAGTCCAAGAATCACACCGCACACAACCAGTCCTACAAGAACCACAAGAATGGTATCAAGAAGGTTAAGAAACACAAATATGCCTCAAG
                                 tttttcattcgctc  CT-rich tract
                                 tttttcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcggagatgatttagttgaattttggaggattctgggtagttagcattggagcttctccatgtttcctgcattgagtttttcattcgctcgatagcagGTAAGATGGCCAAGTCCAAGAATCACACCGCACACAACCAGTCCTACAAGAACCACAAGAATGGTATCAAGAAGGTTAAGAAACACAAATATGCCTCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA