Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttagttcggagatgatttagttgaattttggaggattctgggtagttagcattggagcttctccatgtttcctgcattgagtttttcattcgctcgatagCAGGTAAGATGGCCAAGTCCAAGAATCACACCGCACACAACCAGTCCTACAAGAACCACAAGAATGGTATCAAGAAGGTTAAGAAACACAAATATGCCTC

Basic information

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

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S58_102V6.2 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os01g19840.1 (Oryza sativa), 3'ss of exon 1
--------ttagttcggagatgatttagttgaattttggaggattctgggtagttagcattggagcttctcca-tgtttcctgcattgagtttttcattcg-----ctcgatag-
          | | |     |    | |    |||         | ||  |  |     || |   |  |||  || ||||||  ||   |  ||  ||||      | ||  |   | ||  ||||||||||||| ||||| ||||| || ||||||||||| ||||||   |||||||| || |||||||||   |||   |||    |      
gtaaccgacgattcctccatttccatcgcctcattcgatgtctctttgatttatcgatcttcgttttcttcccctgattcctgatttttttcgtttgttcgtcgtctttgaagGATTCGGGGGAGATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTCGTACAAGGCGCACAAGAACGGGATCAAGAAGCCCAAGCGCCACCGCCAGA----

upper sequence: PP1S58_102V6.2 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G009894_T01 (Zea mays), 3'ss of exon 1
--------ttagttcggagatgatttagttgaattttggaggattctgggtagttagcattggagcttctccatgtttcctgcattgagtttttcattcgctcgatagCAGGTAAGATGGCCAAGTCCAAGAATCACACCGCACACAACCAGTCCTACAAGAACCACAAGAATGGTATCAAGAAGGTTAAGAAACACAAATATGCCTC
           |  |   | |   |  |||     | |  |  || |  ||  | | | |     |  ||||   || |    | |  |  |||  || ||  |    | |   ||||||||||||| ||||| ||||| || ||||||||||| ||||||   |||||||| || |||||||||   |||   |||    |      
gtaactctccggcactccgctcgatctgttcctactagatgtgttgttcgtcttcaccgtcaatccacctcccccttactctgagtc-gccttttgtttgcagGGATCCGGAAGAGATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTCGTACAAGGCGCACAAGAACGGCATCAAGAAGCCCAAGCGCCACCGGCAG-----

upper sequence: PP1S58_102V6.2 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA07G37060.1 (Glycine max), 3'ss of exon 1
ttagttcggagatgatttagttgaattttggaggattctgggtagttagcattggagcttctccatgtttcctgcattgagtt---tttcattcgctcgatagCAGGTAAGATGGCCAAGTCCAAGAATCACACCGCACACAACCAGTCCTACAAGAACCACAAGAATGGTATCAAGAAGGTTAAGAAACACAAATATGCCTC------
          | |   |  ||| |||||        |||     |||   | |     || |   || |  || |||||  ||   ||   | |  |  || ||||   ||||||| ||||| ||||| |||||||| ||||||||||||||||||  |||||||||||| ||||| |||   ||||  |||    |  | ||      
----------gttcgctctgttcaatttc-------tctaacacgttcttact-----tttttgctgctctcttcattgtcttacattgtgtgcattgaattgcag-

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

upper sequence: PP1S58_102V6.2 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA09G04280.1 (Glycine max), 3'ss of exon 1
--ttagttcggagatgatttagttgaat--tttggaggattctgggtagttagcattggagcttctccatgtttcctgcattgagtttttcattcgctcgatagCAGGTAAGATGGCCAAGTCCAAGAATCACACCGCACACAACCAGTCCTACAAGAACCACAAGAATGGTATCAAGAAGGTTAAGAAACACAAATATGCCTC------
  |   |||    ||   |  |   ||   ||      ||| || |   ||    |  |  ||||||      || | | || | |||||    | || ||| ||||   ||||||| ||||| ||||||||||| |||||||| ||||||||||||  |||||| || || ||||||||    ||||  ||     |  | ||      
gttcgtttcttcaatttctgtgacaaaaaattcttctaattttgtgctttt--tttctgttcttctcttcccatcgt-cttttaatttttgtgccacttgattgcag-

upper sequence: PP1S58_102V6.2 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA15G15320.1 (Glycine max), 3'ss of exon 1
ttagttcggagatgatttagttgaattttggag--gattctgggtagttagcattggagcttctccatgtttcctgcattgagtttttcattcgctcgatagCA--GGTAAGATGGCCAAGTCCAAGAATCACACCGCACACAACCAGTCCTACAAGAACCACAAGAATGGTATCAAGAAGGTTAAGAAACACAAATATGCCTC------
          | |  | |  |  | || || |    |||||    | || ||  |      | | | |        ||| |   |||   || |||| ||   |  |   ||||||| ||||| ||||||||||| || ||||| ||||||||||||  |||||| || || ||||||||    ||||  ||     |  | ||      
----------gttcgtatcttcaatttctgtaacaaattcttctaattttgcgctttgttctattctttcccttctcatcgtcctttcattttgctctattttattgcagAGATGGCAAAGTCTAAGAATCACACAGCGCACAATCAGTCCTACAAGGCCCACAAAAACGGCATCAAGAAACCCAAGAGGCATCGCCACACTTCCACCAA

upper sequence: PP1S58_102V6.2 (Physcomitrella patens), 3'ss of exon 1
lower sequence: Vv07s0005g01340.t01 (Vitis vinifera), 3'ss of exon 1
ttagttcggagatgatttagttgaattttggaggattctgggtagttagcattggagcttctccatgtttcctgcattgagtttttcattcgctcgatagCAGGTAAGATGGCCAAGTCCAAGAATCACACCGCACACAACCAGTCCTACAAGAACCACAAGAATGGTATCAAGAAGGTTAAGAAACACAAATATGCCTC----
                   ||  |   |  |    || |||  |     |   |    | ||||    |  ||| |||     || || |  |      | ||| || ||||| ||||| ||||| ||||| || |||||||||||||||||   |||||||||||| ||||||||       || |||    |  ||||    
-------------------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|162164575|gb|FC341870.1|FC341870
EST:     TTTATTGTGTTCCTCGCGTTTCTGCCGGTGTTGAGAGGCTGCCT-CA-A-                         CAGGTAAGATGGCCAAGTCCAAGAATCACACCGCACACAACCAGTCCTACA
genomic: TTTTTTGTGTTCCTCGCGTTTCTGCCGGTGTTGATAGGCTGCCTCCACAGgtaaatttct ... cgctcgatagCAGGTAAGATGGCCAAGTCCAAGAATCACACCGCACACAACCAGTCCTACA
EST: gi|7583020|gb|AW699184.1|AW699184
EST:     TTTTTTGTGTTCCTCGCGTTTCTGCCGGTGTTGATAGGCTGCCTCCACAG                         CAGGTAAGATGGCCAAGTCCAAGAATCACACCGCACACAACCAGTCCTACA
genomic: TTTTTTGTGTTCCTCGCGTTTCTGCCGGTGTTGATAGGCTGCCTCCACAGgtaaatttct ... cgctcgatagCAGGTAAGATGGCCAAGTCCAAGAATCACACCGCACACAACCAGTCCTACA
EST: gi|67695837|gb|BJ956070.1|BJ956070
EST:     TTTTTTGTGTTCCTCGCGTTTCTGCCGGTGTTGATAGGCTGCCTCCACAG                         CAGGTAAGATGGCCAAGTCCAAGAATCACACCGCACACAACCAGTCCTACA
genomic: TTTTTTGTGTTCCTCGCGTTTCTGCCGGTGTTGATAGGCTGCCTCCACAGgtaaatttct ... cgctcgatagCAGGTAAGATGGCCAAGTCCAAGAATCACACCGCACACAACCAGTCCTACA
EST: gi|67696800|gb|BJ957033.1|BJ957033
EST:     TTTTTTGTGTTCCTCGCGTTTCTGCCGGTGTTGATAGGCTGCCT-C-CA-                         CAGGTAAGATGGCCAAGTCCAAGAATCACACCGCACACAACCAGTCCTACA
genomic: TTTTTTGTGTTCCTCGCGTTTCTGCCGGTGTTGATAGGCTGCCTCCACAGgtaaatttct ... cgctcgatagCAGGTAAGATGGCCAAGTCCAAGAATCACACCGCACACAACCAGTCCTACA
EST: gi|19789288|gb|BQ041216.1|BQ041216
EST:     TTTTTTGTGTTCCTCGCGTTTCTGCCGGTGTTGATAGGCTGCCTCCACAG                         CAGGTAAGATGGCCAAGTCCAAGAATCACACCGCACACAACCAGTCCTACA
genomic: TTTTTTGTGTTCCTCGCGTTTCTGCCGGTGTTGATAGGCTGCCTCCACAGgtaaatttct ... cgctcgatagCAGGTAAGATGGCCAAGTCCAAGAATCACACCGCACACAACCAGTCCTACA
EST: gi|67572465|gb|BJ945289.1|BJ945289
EST:     TTTTTTGTGTTCCTCGCGTTTCTGCCGGTGTTGATAGGCTGCCTCCACAG                         CAGGTAAGATGGCCAAGTCCAAGAATCACACCGCACACAACCAGTCCTACA
genomic: TTTTTTGTGTTCCTCGCGTTTCTGCCGGTGTTGATAGGCTGCCTCCACAGgtaaatttct ... cgctcgatagCAGGTAAGATGGCCAAGTCCAAGAATCACACCGCACACAACCAGTCCTACA
EST: gi|7583210|gb|AW699374.1|AW699374
EST:     TTTTTTGTGTTCCTCGCGTTTCTGCCGGTGTTGATAGGCTGCCTCCACAG                         CAGGTAAGATGGCCAAGTCCAAGAATCACACCGCACACAACCAGTCCTACA
genomic: TTTTTTGTGTTCCTCGCGTTTCTGCCGGTGTTGATAGGCTGCCTCCACAGgtaaatttct ... cgctcgatagCAGGTAAGATGGCCAAGTCCAAGAATCACACCGCACACAACCAGTCCTACA
EST: gi|19778970|gb|BQ039392.1|BQ039392
EST:     TTTTTTGTGTTCCTCGCGTTTCTGCCGGTGTTGATAGGCTGCCTCCACAG                         CAGGTAAGATGGCCAAGTCCAAGAATCACACCGCACACAACCAGTCCTACA
genomic: TTTTTTGTGTTCCTCGCGTTTCTGCCGGTGTTGATAGGCTGCCTCCACAGgtaaatttct ... cgctcgatagCAGGTAAGATGGCCAAGTCCAAGAATCACACCGCACACAACCAGTCCTACA
EST: gi|67573419|gb|BJ946243.1|BJ946243
EST:     TTTTTTGTGTTCCTCGCGTTTCTGCCGGTGTTGATAGGCTGCCT-C-CA-                         CAGGTAAGATGGCCAAGTCCAAGAATCACACCGCACACAACCAGTCCTACA
genomic: TTTTTTGTGTTCCTCGCGTTTCTGCCGGTGTTGATAGGCTGCCTCCACAGgtaaatttct ... cgctcgatagCAGGTAAGATGGCCAAGTCCAAGAATCACACCGCACACAACCAGTCCTACA
EST: gi|7287210|gb|AW599697.1|AW599697
EST:     TTTTTTGTGTTCCTCGCGTTTCTGCCGGTGTTGATAGGCTGCCTCCACAG                         CAGGTAAGATGGCCAAGTCCAAGAATCACACCGCACACAACCAGTCCTACA
genomic: TTTTTTGTGTTCCTCGCGTTTCTGCCGGTGTTGATAGGCTGCCTCCACAGgtaaatttct ... cgctcgatagCAGGTAAGATGGCCAAGTCCAAGAATCACACCGCACACAACCAGTCCTACA
EST: gi|7584218|gb|AW700115.1|AW700115
EST:     GTTGATAGGCTGCCT-C-CA-                         CAGGTAAGATGGCCAAGTCCAAGAATCACACCGCACACAACCAGTCCTACA
genomic: GTTGATAGGCTGCCTCCACAGgtaaatttct ... cgctcgatagCAGGTAAGATGGCCAAGTCCAAGAATCACACCGCACACAACCAGTCCTACA
EST: gi|15730302|gb|BI741779.1|BI741779
EST:     ATAGGCTGCCTCCACAG                         CAGGTAAGATGGCCAAGTCCAAGAATCACACCGCACACAACCAGTCCTACA
genomic: ATAGGCTGCCTCCACAGgtaaatttct ... cgctcgatagCAGGTAAGATGGCCAAGTCCAAGAATCACACCGCACACAACCAGTCCTACA
EST: gi|6167022|gb|AW145341.1|AW145341
EST:     TTGATAGGCTGCCT-C-CA-                         CAGGTAAGATGGCCAAGTCCAAGAATCACACCGCACACAACCAGTCCTACA
genomic: TTGATAGGCTGCCTCCACAGgtaaatttct ... cgctcgatagCAGGTAAGATGGCCAAGTCCAAGAATCACACCGCACACAACCAGTCCTACA
EST: gi|67696777|gb|BJ957010.1|BJ957010
EST:     TTTTTTGTGTTCCTCGCGTTTCTGCCGGTGTTGATAGGCTGCCT-C-CA-                         CAGGTAAGATGGCCAAGTCCAAGAATCACACCGCACACAACCAGTCCTACA
genomic: TTTTTTGTGTTCCTCGCGTTTCTGCCGGTGTTGATAGGCTGCCTCCACAGgtaaatttct ... cgctcgatagCAGGTAAGATGGCCAAGTCCAAGAATCACACCGCACACAACCAGTCCTACA
EST: gi|67573396|gb|BJ946220.1|BJ946220
EST:     TTTTTTGTGTTCCTCGCGTTTCTGCCGGTGTTGATAGGCTGCCT-C-CA-                         CAGGTAAGATGGCCAAGTCCAAGAATCACACCGCACACAACCAGTCCTACA
genomic: TTTTTTGTGTTCCTCGCGTTTCTGCCGGTGTTGATAGGCTGCCTCCACAGgtaaatttct ... cgctcgatagCAGGTAAGATGGCCAAGTCCAAGAATCACACCGCACACAACCAGTCCTACA

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: 27 (upstream exon), 35 (downstream exon)
Score: 5

GTCCCGTATACAGTTCTTTCGGGCGCCGCACTCAGTATTTTTTGTGTTCCTCGCGTTTCTGCCGGTGTTGATAGGCTGCCTCCACAGgtaaatttct ... cgctcgatagCAGGTAAGATGGCCAAGTCCAAGAATCACACCGCACACAACCAGTCCTACAAGAACCACAAGAATGGTATCAAGAAGGTTAAGAAACACAAATATGCCTC




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagcattggagcttctccatgtttcctgcattgagtttttcattcgctcgatagCAGGTAAGATGGCCAAGTCCAAGAATCACACCGCACACAACCAGTCCTACAAGAACCACAAGAATGGTATCAAGAAGGTTAAGAAACACAAATATGCCTC
                                    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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttagttcggagatgatttagttgaattttggaggattctgggtagttagcattggagcttctccatgtttcctgcattgagtttttcattcgctcgatagCAGGTAAGATGGCCAAGTCCAAGAATCACACCGCACACAACCAGTCCTACAAGAACCACAAGAATGGTATCAAGAAGGTTAAGAAACACAAATATGCCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA