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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcctttccatcaaatccccttcccatacttttcgtaactcttgcctttgttgacaagactgtgagtaattcttagttagacatctcgtctttcttgatagggaatttcacgtgtttacatatgtacttcgcagGTGAAGATGATTCAGCTGCGGGTGGTAAGTCCAAGCAGAGCCGTGGTGAGAAGAAGAGCAGGAAGGCCATGCAAAAGCTTGGCATGAAGCCCGTGACTGA

Basic information

species Physcomitrella patens
transcript PP1S539_1V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S539_1V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os05g31000.1 (Oryza sativa), 3'ss of exon 2
gtcctttccatcaaatccccttcccatacttttcgtaactcttgcctttgttgacaagactgtgagtaa-ttcttagttagacatctcgtctttcttgatagggaatttcacgtgtttacatatg-tacttcgcagGTGAAGATGATTCAGCTGCGGGTGGTAAGTCCAAGCAGAGCCGTGGTGAGAAGAAGAGCAGGAAGGCCATGCAAAAGCTTGGCATGAAGCCCGTGACTGA---------
                                       | | || ||| |  | | ||  |   |||  || ||||||  |  |   ||    | |||     | |  |  || | || | |   ||||   |   | |  | ||      |||  |||| |  || |||||||| ||| ||||||| || |||||||||||||||   ||||||||||||||| |  | ||||          
---------------------------------------tttagcttttttccaaatgatcgattgtagctttttagttcaaactgcagtggagcctga-----actgacttgtttctaaacacaatactctcctttttaccagGAGGTGA-TGCAAGTGGAAGATCTAAGCAGAGTCGTAGTGAGAAAAAAAGCAGGAAGGCCATGGTGAAGCTTGGCATGAAGTCTATCACTGGTGTGAGCCG

upper sequence: PP1S539_1V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os01g71230.1 (Oryza sativa), 3'ss of exon 2
gtcctttccatcaaatccccttcccatacttttcgtaactcttgcctttgttgacaagactgtgagtaattcttagttagacatctcgtctttcttgatagggaatttcacgtgtttacatatgtacttcgcagGTGAAGATGATTCAGCTGCGGGTGGTAAGTCCAAGCAGAGCCGTGGTGAGAAGAAGAGCAGGAAGGCCATGCAAAAGCTTGGCATGAAGCCCGTGACTGA---
                       | |||||| |         ||   |||| |||         |||  ||  || |||    ||  || |||  | |  |   ||       | || | | | | ||| ||||| | ||  | |   | |||  |||| | ||| ||||||||  |  | ||||| ||||||||||| |||||||| || |||||||||||| || | ||||    
---------------------aactatacttcta------tgtggtattgtagacttactgtccagtgtttgctacttac-tgtccagtgtttgctaaatgctgatg------gctttcctttatgctttgcagGAGCAGGAGGT---GATGCTAGTGGAAGGTCTAAGCAGAGTAGGAGCGAGAAAAAGAGCAGGAAAGCCATGCAGAAACTTGGCATGAAGACCATCACTGGTGT

upper sequence: PP1S539_1V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os01g71230.2 (Oryza sativa), 3'ss of exon 2
gtcctttccatcaaatccccttcccatacttttcgtaactcttgcctttgttgacaagactgtgagtaattcttagttagacatctcgtctttcttgatagggaatttcacgtgtttacatatgtacttcgcagGTGAAGATGATTCAGCTGCGGGTGGTAAGTCCAAGCAGAGCCGTGGTGAGAAGAAGAGCAGGAAGGCCATGCAAAAGCTTGGCATGAAGCCCGTGACTGA---------
                                     |||  |   |    |   |    |       | | || | ||   |        |  ||| ||   |||       | || | | | | ||| ||||| | ||  | |   | |||  |||| | ||| ||||||||  |  | ||||| ||||||||||| |||||||| || |||||||||||| || | ||||          
-------------------------------------acttctatgtggtattgtagacttactgtccagtgtttgctacttactgtccagtgtttgcta---aatgctgatggctttcctttatgctttgcaggagcagGAGGT---GATGCTAGTGGAAGGTCTAAGCAGAGTAGGAGCGAGAAAAAGAGCAGGAAAGCCATGCAGAAACTTGGCATGAAGACCATCACTGGTGTGAGCCG

upper sequence: PP1S539_1V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G000923_T01 (Zea mays), 3'ss of exon 2
gtcctttccatcaaatccccttcccatacttttcgtaactcttgcctttgttgacaagactgtgagtaattcttagttagacatctcgtctttcttgatagggaatttcacgtgtttacatatgtacttcgcagGTGAAGATGATTCAGCTGCGGGTGGTAAGTCCAAGCAGAGCCGTGGTGAGAAGAAGAGCAGGAAGGCCATGCAAAAGCTTGGCATGAAGCCCGTGACTGA---------
                     |||  | |  || | |  |  || || | || |     || ||        |  || | |||  |       | ||| | | | |||  |   ||| ||| |    ||||| |   |  | |     | |||  |||| ||||| ||||| ||| |  |||||||||||||| | ||||||||||  |||||||||||||||||| | ||||          
---------------------tcctgtgcgctttgaatttgctgtctgtttttat----ctctgg-------tatgtgaaacaatt-acaacacctgacaagta-tttgtctcattttcatct----ttcgc-gacaagAAGGG----GATGCCAGTGGCAAGTCAAAGCAAAGCAGGAGTGAGAAGAAGAGCCGCAAGGCCATGCTGAAGCTTGGCATGAAGCCCATCACTGGTGTCAGCCG

upper sequence: PP1S539_1V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G000923_T02 (Zea mays), 3'ss of exon 2
gtcctttccatcaaatccccttcccatacttttcgtaactcttgcctttgttgacaagactgtgagtaattcttagttagacatctcgtctttcttgatagggaatttcacgtgtttacatatgtacttcgcagGTGAAGATGATTCAGCTGCGGGTGGTAAGTCCAAGCAGAGCCGTGGTGAGAAGAAGAGCAGGAAGGCCATGCAAAAGCTTGGCATGAAGCCCGTGACTGA------------
                                  ||     |||  |||| || |     | | |    |  |  || | |||  |       | ||| | | | |||  |   ||| ||| |    ||||| |   |  | |     | |||  |||| ||||| ||||| ||| |  |||||||||||||| | ||||||||||  |||||||||||||||||| | ||||             
---------------------------------tgtgcgctttgaatttgctgtctg--tttttatctctggtatgtgaaacaatt-acaacacctgacaagta-tttgtctcattttcatct----ttcgc-gacaagaagGG----GATGCCAGTGGCAAGTCAAAGCAAAGCAGGAGTGAGAAGAAGAGCCGCAAGGCCATGCTGAAGCTTGGCATGAAGCCCATCACTGGTGTCAGCCGCGT

upper sequence: PP1S539_1V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G465333_T01 (Zea mays), 3'ss of exon 2
gtcctttccatcaaatccccttcccatacttttcgtaactcttgcct-ttgttgacaagactgtgagtaattcttagttagacatctcgtctttcttgatagggaatttcacgtgtttacatatgtacttcgcagGTGAAGATGATTCAGCTGCGGGTGGTAAGTCCAAGCAGAGCCGTGGTGAGAAGAAGAGCAGGAAGGCCATGCAAAAGCTTGGCATGAAGCCCGTGACTGA---
                      ||   ||  || | |  |  || || || ||  |     |||| | ||     | ||  | | ||     |   ||| | | | |     ||||   ||| |  |  |  ||||  |||| |     | |||  | || ||||| ||||| ||| |  |||||||||||||| | || |||||||  |||||||||||||||||| | ||||    
-------------------taacctgcaccctttgaatttgctgtctgtttttatctctggtgtgtgaaac----aattgcagacctg----tatctgacaagtattg----gtgt---cattttcatctt-cagGACAAGAAGG---GGATGCCAGCGGCAAGTCAAAGCAAAGCAGGAGTGAGAAGAAGAGCCGCAAAGCCATGCTGAAGCTTGGCATGAAGCCCATCACTGGTGT

upper sequence: PP1S539_1V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EDO97954 (Chlamydomonas reinhardtii), 3'ss of exon 1
gtcctttccatcaaatccccttcccatacttttcgtaactcttgcctttgttgacaagactgtgagtaattcttagttagacatctcgtctttcttgataggga-atttcacgtgtttacatatgtacttcgcagGTGAAGATGATTCAGCTGCGGGTGGTAAGTCCAAGCAGAGCCGTGGTGAGAAGAAGAGCAGGAAGGCCATGCAAAAGCTTGGCATGAAGCCCGTGACTGA------
                                 |  | |   || |  ||| | |  | |   |||  || |    ||     | |||||   |   | |||||   |  || ||    ||| |||  |     | || ||||||    | ||  | |||      ||||||||||||  | |||||||||||| | ||||||||||| ||||| |||||||||||||| ||||       
--------------------------------gctcagcgtctggcgctgtcggctgggc---gagcgatgccagctttag--tttcgtcggccc--acagggatgctgaacatggc-gcatgtgtgatgt-tggctgcagATGAGGAGGGTGGCGCTGGCCGCGGCAAGCAGAGCCGCAGCGAGAAGAAGAGCCGCAAGGCCATGCAGAAGCTGGGCATGAAGCCCGTCACTGGCGTGAC

upper sequence: PP1S539_1V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ23805 (Selaginella moellendorffii), 3'ss of exon 2
gtcctttccatcaaatccccttcccatacttttcgtaactcttgcctttgttgacaagactgtgagtaattcttagttagacatctcgtctttcttgatagggaatttcacgtgtttacatatgtacttcgcagGTGAAGATGATTCAGCTGCGGGTGGTAAGTCCAAGCAGAGCCGTGGTGAGAAGAAGAGCAGGAAGGCCATGCAAAAGCTTGGCATGAAGCCCGTGACTGA--------------
                                                                                                          |||     |||   |||||   |  |||| || ||||   | |         | || || ||||| |||||  | |||||||||||| ||||||| ||||| ||||| || ||||||||||||||||               
---------------------------------------------------------------------------------------------------------gttcctac-tttctttatgtttcttccaggcgagGATGGAACGG---------GGAAATCGAAGCAAAGCCGGAGCGAGAAGAAGAGCCGGAAGGCAATGCAGAAGCTCGGGATGAAGCCCGTGACTGGAGTAACGAGGGTGA

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|37839794|gb|BJ597802.1|BJ597802
EST:     TGGAGACGATGGTCATGGCGAAG                         GTGAAGATGATTCAGCTGCGGGTGGTAAGTCCAAGCAGAGCCGTGGTGAGA
genomic: TGGAGACGATGGTCATGGCGAAGgtcctttcca ... tacttcgcagGTGAAGATGATTCAGCTGCGGGTGGTAAGTCCAAGCAGAGCCGTGGTGAGA
EST: gi|37824901|gb|BJ582967.1|BJ582967
EST:     GTCATGGCGAAG                         GTGAAGATGATTCAGCTGCGGGTGGTAAGTCCAAGCAGAGCCGTGGTGAGA
genomic: GTCATGGCGAAGgtcctttcca ... tacttcgcagGTGAAGATGATTCAGCTGCGGGTGGTAAGTCCAAGCAGAGCCGTGGTGAGA
EST: gi|37821412|gb|BJ579478.1|BJ579478
EST:     TGATGACGACGAGTTTGACGCCCTTGATGGAGACGATGGTCATGGCGAAG                         GTGAAGATGATTCAGCTGCGGGTGGTAAGTCCAAGCAGAGCCGTGGTGAGA
genomic: TGATGACGACGAGTTTGACGCCCTTGATGGAGACGATGGTCATGGCGAAGgtcctttcca ... tacttcgcagGTGAAGATGATTCAGCTGCGGGTGGTAAGTCCAAGCAGAGCCGTGGTGAGA
EST: gi|37832326|gb|BJ590338.1|BJ590338
EST:     GTCATGGCGAAG                         GTGAAGATGATTCAGCTGCGGGTGGTAAGTCCAAGCAGAGCCGTGGTGAGA
genomic: GTCATGGCGAAGgtcctttcca ... tacttcgcagGTGAAGATGATTCAGCTGCGGGTGGTAAGTCCAAGCAGAGCCGTGGTGAGA

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: 35 (upstream exon), 34 (downstream exon)
Score: 38

GATGAGCCCACCATAGAGGACGCCAAGGACGACGACGACGATGAAGACGATGATGACGACGAGTTTGACGCCCTTGATGGAGACGATGGTCATGGCGAAGgtcctttcca ... tacttcgcagGTGAAGATGATTCAGCTGCGGGTGGTAAGTCCAAGCAGAGCCGTGGTGAGAAGAAGAGCAGGAAGGCCATGCAAAAGCTTGGCATGAAGCCCGTGACTGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gacatctcgtctttcttgatagggaatttcacgtgtttacatatgtacttcgcagGTGAAGATGATTCAGCTGCGGGTGGTAAGTCCAAGCAGAGCCGTGGTGAGAAGAAGAGCAGGAAGGCCATGCAAAAGCTTGGCATGAAGCCCGTGACTGA
             tcttgat  putative branch site (score: 38)
                                   tttacatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcctttccatcaaatccccttcccatacttttcgtaactcttgcctttgttgacaagactgtgagtaattcttagttagacatctcgtctttcttgatagggaatttcacgtgtttacatatgtacttcgcagGTGAAGATGATTCAGCTGCGGGTGGTAAGTCCAAGCAGAGCCGTGGTGAGAAGAAGAGCAGGAAGGCCATGCAAAAGCTTGGCATGAAGCCCGTGACTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC