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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTATCAGACGTGCGCATGCGGTCCACCCCATCACTGCTGTGCAGATTGAGTGGTCTCTTTGGTCTCGAGACATTGAAGAAGAAATCATCCCTCTTTGTAGgtaaattcataatatcgagctgctatttctcttgctcgatcccagttgatgatggtatccctgaataagttgaaatgttcatacaacttggcaatctcac...

Basic information

species Physcomitrella patens
transcript PP1S309_8V6.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S309_8V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: LOC_Os01g43090.1 (Oryza sativa), 5'ss of exon 4
CTATCAGACGTGCGCATGCGGTCCACCCCATCACTGCTGTGCAGATTGAGTGGTCTCTTTGGTCTCGAGACATTGAAGAAGAAATCATCCCTCTTTGTAGgtaaattcataatatcgagctgctatttctcttgctcgatcccagttgatgatggtatccctgaataagttgaaatgttcatacaacttggcaatctcac
| ||||| || || ||||| || ||||| |||||||| || ||||| ||||||||||| ||| |||| |||||||||   |||||  | || || || |||| |||||   ||  |  | |    || ||  || | |||  |   ||    |    ||   |   ||         | ||| | |              
CCATCAGGCGAGCTCATGCCGTGCACCCAATCACTGCAGTTCAGATGGAGTGGTCTCTCTGGGCTCGTGACATTGAACCCGAAATTGTGCCGCTCTGCAGgtgaattccgcatcgcaggtt----ttactaatgattgattgctcatgcaagtaaactcatcg--caatccatggactccattccag-------------

upper sequence: PP1S309_8V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: GRMZM2G024315_T01 (Zea mays), 5'ss of exon 4
CTATCAGACGTGCGCATGCGGTCCACCCCATCACTGCTGTGCAGATTGAGTGGTCTCTTTGGTCTCGAGACATTGAAGAAGAAATCATCCCTCTTTGTAGgtaaattcataatatcgagctgctatttctcttgctcgatcccagttgatgatgg-tatccctgaataagttgaaatgttcatacaacttggcaatctcac---
| ||||| ||||| ||||| || ||||| ||||| || |||||||| ||||||||||| |||||||| ||||||||    |||||  | || || || |||| | |||||    |  ||   || ||  ||  || |      ||    | | || | |   || |||   |   ||   |  |  ||      ||        
CCATCAGGCGTGCACATGCTGTGCACCCGATCACCGCGGTGCAGATGGAGTGGTCTCTCTGGTCTCGCGACATTGAGCCCGAAATTGTGCCGCTCTGCAGgtga-ttcatggattgcagactcttttgttccagccca---tgaggccctcacggctttgtttggatactctagtattacctcaatacacatagattgaggtgg

upper sequence: PP1S309_8V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: GLYMA03G40860.1 (Glycine max), 5'ss of exon 4
CTATCAGACGTGCGCATGCGGTCCACCCCATCACTGCTGTGCAGATTGAGTGGTCTCTTTGGTCTCGAGACATTGAAGAAGAAATCATCCCTCTTTGTAGgtaaattcataat-atcgagctgctatttctcttgctcgatcccagttgatgatggt------atccctgaataagttgaaatgttcatacaacttggcaatctcac------------------
| || ||  | || || ||  | || |||||||| |||||||| || ||||||||| | ||| |||| |||||||||||||| ||  ||||||| || |||| | ||||   | || |  ||||   |  |||||   |     |   ||   ||||       |   ||  |   ||    |||| || | ||||     | | |                   
CAATAAGGAGAGCACACGCAATTCATCCCATCACAGCTGTGCAAATAGAGTGGTCTTTGTGGACTCGTGACATTGAAGAAGAGATAGTCCCTCTCTGCAGgttagttcaagttcatggcactgcagctcttcttgaaaggagggaaaagaaagtggtttagttgttgttggctgtatttttgtgttaatgcgacttcaattttttaatgcttatattggtttcag

upper sequence: PP1S309_8V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: Vv14s0030g02060.t01 (Vitis vinifera), 5'ss of exon 4
CTATCAGACGTGCGCATGCGGTCCACCCCATCACTGCTGTGCAGATTGAGTGGTCTCTTTGGTCTCGAGACATTGAAGAAGAAATCATCCCTCTTTGTAGgtaaattcataatatcgagctgctatttctcttgctcgatcccagttgatgatggtatccctgaataag---ttgaaatgttcatacaacttggcaatctcac-------------------------
| || ||  | || ||||| || || ||||| |||||  |  | || ||||||||||||||| ||||||| ||||||||||||||  |||| ||||| ||||   |||||| |  | | |    |    |  |  || |||  |    ||  |    | | || || ||    | ||   || || |    |||    |||                           
CAATAAGGAGGGCTCATGCAGTTCATCCCATTACTGCCATAGAAATGGAGTGGTCTCTTTGGACTCGAGAAATTGAAGAAGAAATTCTCCCACTTTGCAGgt---ttcatatttcctatccttaacgattgattttctatcataaaacattctatagttcttgcattagatccttaatccttaatccttaatggaggactcggttacacttgggatatatttttatag

upper sequence: PP1S309_8V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: Vv14s0030g01990.t01 (Vitis vinifera), 5'ss of exon 4
CTATCAGACGTGCGCATGCGGTCCACCCCATCACTGCTGTGCAGATTGAGTGGTCTCTTTGGTCTCGAGACATTGAAGAAGAAATCATCCCTCTTTGTAGgt---aaattcataatatcgagctgctatttctcttgctcga------tcccagttgatg-atggtatccctga--ataagttgaaatgttcatacaacttggca-atctcac-----
| || ||  | || ||||| || || ||||| |||||  |  | || |||||||| |||||| ||||||| ||||||||||||||  |||| ||||| ||||     |||    ||    | |   |  || |||  |   |          ||||  || ||   |||| | |   | | | ||    ||  |   |||||| | || |        
CAATAAGGAGGGCTCATGCAGTTCATCCCATTACTGCCATAGAAATGGAGTGGTCCCTTTGGACTCGAGAAATTGAAGAAGAAATTCTCCCACTTTGCAGgtttcgtatttcctatccttaacgattgattttctatcataaaacattctatagttcttgcattagatccttaatccttaatggaggacttggttacacttgggatatatttttatag

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|208392632|gb|DC933990.1|DC933990
EST:     TGGTCTCTTTGGTCTCGAGACATTGAAGAAGAAATCATCCCTCTTTGTAG                         AGAGCTGGGAATTGGGATTGTGTCATACAGCCCACTTGGACGA
genomic: TGGTCTCTTTGGTCTCGAGACATTGAAGAAGAAATCATCCCTCTTTGTAGgtaaattcat ... tttgacgcagAGAGCTGGGAATTGGGATTGTGTCATACAGCCCACTTGGACGA
EST: gi|208387836|gb|DC941405.1|DC941405
EST:     TGGTCTCTTTGGTCTCGAGACATTGAAGAAGAAATCATCCCTCTTTGTAG                         AGAGCTGGGAATTGGGATTGTGTCATACAGCCCACTTGGACGANGTTTTTT
genomic: TGGTCTCTTTGGTCTCGAGACATTGAAGAAGAAATCATCCCTCTTTGTAGgtaaattcat ... tttgacgcagAGAGCTGGGAATTGGGATTGTGTCATACAGCCCACTTGGACGAGGTTTTTT
EST: gi|100395116|gb|BY953607.1|BY953607
EST:     TGGTCTCTTTGGTCTCGAGACATTGAAGAAGAAATCATCCCTCTTTGTAG                         AGAGCTGGGAATTGGGATTGTGTCATACAGCCCACTTGGACGAGNNNNNNN
genomic: TGGTCTCTTTGGTCTCGAGACATTGAAGAAGAAATCATCCCTCTTTGTAGgtaaattcat ... tttgacgcagAGAGCTGGGAATTGGGATTGTGTCATACAGCCCACTTGGACGAGGTTTTTT
EST: gi|208372043|gb|DC940225.1|DC940225
EST:     TGGTCTCTTTGGTCTCGAGACATTGAAGAAGAAATCATCCCTCTTTGTAG                         AGAGCTGGGAATTGGGATTGTGTCATACAGCCCACTTGGACNAGNTTTTT-
genomic: TGGTCTCTTTGGTCTCGAGACATTGAAGAAGAAATCATCCCTCTTTGTAGgtaaattcat ... tttgacgcagAGAGCTGGGAATTGGGATTGTGTCATACAGCCCACTTGGACGAGGTTTTTT

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: 33 (upstream exon), 35 (downstream exon)
Score: 16

CTATCAGACGTGCGCATGCGGTCCACCCCATCACTGCTGTGCAGATTGAGTGGTCTCTTTGGTCTCGAGACATTGAAGAAGAAATCATCCCTCTTTGTAGgtaaattcat ... tttgacgcagAGAGCTGGGAATTGGGATTGTGTCATACAGCCCACTTGGACGAGGTTTTTTCTCTGGGAAAGCAGTTCTGGAGAAGCTAGAAGAGACAGATCTTAGGCCT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTATCAGACGTGCGCATGCGGTCCACCCCATCACTGCTGTGCAGATTGAGTGGTCTCTTTGGTCTCGAGACATTGAAGAAGAAATCATCCCTCTTTGTAGgtaaattcataatatcgagctgctatttctcttgctcgatcccagttgatgatggtatccctgaataagttgaaatgttcatacaacttggcaatctcac

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA