Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGACCGTTGGATTCGAATATGGGTGAAGAAGGGAGACATGATTGTGTTGCCTGCAGGGAGTTACCACCGCTTTACTCTTGATGAAAACAATTATCTCAAGgtacacatagctacctatcagtagccccattctaaaaaacagtgactgcagatatgaataagatagcttattcagtgtttaaaattgtccaatccaatagaactctgaaaccctgtattattatattcgtggcag

Basic information

species Physcomitrella patens
transcript PP1S69_28V6.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S69_28V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: LOC_Os10g28350.1 (Oryza sativa), 5'ss of exon 5
AGACCGTTGGATTCGAATATGGGTGAAGAAGGGAGACATGATTGTGTTGCCTGCAGGGAGTTACCACCGCTTTACTCTTGATGAAAACAATTATCTCAAGgtacacatagctacctatcagtagccccattctaaaaaacagtgactgcagatatgaataagatagcttattcagtgtttaaaattgtccaatccaatagaactctgaaaccctgtattattatattcgtggcag
 || |  |||||||| |||    ||||||| |||| |||||||||  ||||||||||||  ||||||||||||||  | ||     |||| ||| ||||||||| | |  ||||||      |||    | || |  | |    | |||| | || | |    |   | ||| |      |||  || | |      |  || |  | ||                         
TGATCAGTGGATTCGTATAGCACTGAAGAAAGGAGGCATGATTGTTCTGCCTGCAGGGATGTACCACCGCTTTACGTTGGACACCGACAACTATATCAAGgtactcct--ctacct--tgtcagctttgt-ctgatcatc--ccattgcacacatcatttg--tcattaattaaaaaa--aaatgtgacgacgttgttccaaatgggtaat------------------------

upper sequence: PP1S69_28V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: EFJ16843 (Selaginella moellendorffii), 5'ss of exon 4
AGACCGTTGGATTCGAATATGGGTGAAGAAGGGAGACATGATTGTGTTGCCTGCAGGGAGTTACCACCGCTTTACTCTTGATGAAAACAATTATCTCAAGgtacacatagctacctatcagtagccccattctaaaaaacagtgactgcagatatgaataagatagcttattcagtgtttaaaattgtccaatccaatagaactctgaaaccctgtattattatattcgtggcag
    || |||||||| || ||||||||||||||||||||||| ||| | ||||| || || ||||| ||||| ||||| ||| | ||||||||  |||||||    || |  | |   ||  |     ||  |   |  |   |  | |    |                                                                                 
---TCGGTGGATTCGTATTTGGGTGAAGAAGGGAGACATGATCGTGCTTCCTGCTGGAAGCTACCATCGCTTCACTCTGGATAACAACAATTACATCAAGGTG-

upper sequence: PP1S69_28V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: EFJ32152 (Selaginella moellendorffii), 5'ss of exon 4
AGACCGTTGGATTCGAATATGGGTGAAGAAGGGAGACATGATTGTGTTGCCTGCAGGGAGTTACCACCGCTTTACTCTTGATGAAAACAATTATCTCAAGgtacacatagctacctatcagtagccccattctaaaaaacagtgactgcagatatgaataagatagcttattcagtgtttaaaattgtccaatccaatagaactctgaaaccctgtattattatattcgtggcag
 || || |||||||| || ||||||||||||||||||||||| ||| | ||||| || || ||||| ||||| ||||| ||| | | ||||||  |||||||   ||| |  | |   ||  |     ||  |   |  |   |  | |    |                                                                                 
CGATCGGTGGATTCGTATTTGGGTGAAGAAGGGAGACATGATCGTGCTTCCTGCTGGAAGCTACCATCGCTTCACTCTGGATAACAGCAATTACATCAAGgtg-gcattgagatcgcacacgaattt-atcttctgatgcttcggtttcgagcag--------------------------------------------------------------------------------

upper sequence: PP1S69_28V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: EFJ32151 (Selaginella moellendorffii), 5'ss of exon 3
----AGACCGTTGGATTCGAATATGGGTGAAGAAGGGAGACATGATTGTGTTGCCTGCAGGGAGTTACCACCGCTTTACTCTTGATGAAAACAATTATCTCAAGgtacacatagctacctatcagtagccccattctaaaaaacagtgactgcagatatgaataagatagcttattcagtgtttaaaattgtccaatccaatagaactctgaaaccctgtattattatattcgtggcag
     || |  |||||    || ||||||||||||||||||||||| ||  | ||||| || || ||||| ||||| ||||| ||| | ||||||||  |||||||    || |  | | |           ||      |  |   |  | |    |                                                                                 
TTTGCGATCAGTGGAT----ATTTGGGTGAAGAAGGGAGACATGATCGTACTTCCTGCTGGAAGCTACCATCGCTTCACTCTGGATAACAACAATTACGTCAAGgtg-gtattgagatc-acacacgaatttatctcctgatgcttcggtttcgagcag--------------------------------------------------------------------------------

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|208385965|gb|DC956803.1|DC956803
EST:     CTGCAGGGAGTTACCACCGCTTTACTCTTGATGAAAACAATTATCTCAAG                         GCAATGAGGCTGTTTGTAGGTGAACCTGTCTGGACCCCATATAACCGACCC
genomic: CTGCAGGGAGTTACCACCGCTTTACTCTTGATGAAAACAATTATCTCAAGgtacacatag ... ttcgtggcagGCAATGAGGCTGTTTGTAGGTGAACCTGTCTGGACCCCATATAACCGACCC
EST: gi|100407256|gb|BY974081.1|BY974081
EST:     CTGCAGGGAGTTACCACCGCTTTACTCTTGATGAATACA-TTATCTCAAG                         GCAATGACGCTGTTTGTAGGTGA
genomic: CTGCAGGGAGTTACCACCGCTTTACTCTTGATGAAAACAATTATCTCAAGgtacacatag ... ttcgtggcagGCAATGAGGCTGTTTGTAGGTGA
EST: gi|162263751|gb|FC440157.1|FC440157
EST:     CTGCAGGGAGTTACCACCGCTTTACTCTTGATGAAAACAATTATCTCAAG                         GCAATGAGGCTGTTTGTAGGTGAACCTGTCTGGACCCCATATAACCGACCC
genomic: CTGCAGGGAGTTACCACCGCTTTACTCTTGATGAAAACAATTATCTCAAGgtacacatag ... ttcgtggcagGCAATGAGGCTGTTTGTAGGTGAACCTGTCTGGACCCCATATAACCGACCC
EST: gi|162233761|gb|FC410027.1|FC410027
EST:     CTGCAGGGAGTTACCACCGCTTTACTCTTGATGAAAACAATTATCTCAAG                         GCAATGAGGCTGTTTGTAGGTGAACCTGTCTGGACCCCATATAACCGACCC
genomic: CTGCAGGGAGTTACCACCGCTTTACTCTTGATGAAAACAATTATCTCAAGgtacacatag ... ttcgtggcagGCAATGAGGCTGTTTGTAGGTGAACCTGTCTGGACCCCATATAACCGACCC
EST: gi|162187912|gb|FC364486.1|FC364486
EST:     CTGCAGGGAGTTACCACCGCTTTACTCTTGATGAAAACAATTATCTCAAG                         GCAATGAGGCTGTTTGTAGGTGAACCTGTCTGGACCCCATATAACCGACCC
genomic: CTGCAGGGAGTTACCACCGCTTTACTCTTGATGAAAACAATTATCTCAAGgtacacatag ... ttcgtggcagGCAATGAGGCTGTTTGTAGGTGAACCTGTCTGGACCCCATATAACCGACCC
EST: gi|162233762|gb|FC410028.1|FC410028
EST:     CTGCAGGGAGTTACCACCGCTTTACTCTTGATGAAAACAATTATCTCAAG                         GCAATGAGGCTGTTTGTAGGTGAACCTGTCTGGACCCCATATAACCGACCC
genomic: CTGCAGGGAGTTACCACCGCTTTACTCTTGATGAAAACAATTATCTCAAGgtacacatag ... ttcgtggcagGCAATGAGGCTGTTTGTAGGTGAACCTGTCTGGACCCCATATAACCGACCC
EST: gi|208378344|gb|DC923015.1|DC923015
EST:     CTGCAGGGAGTTACCACCGCTTTACTCTTGATGAAAACAATTATCTCAAG                         GCAATGAGGCTGTTTGTAGGTGAACCTGTCTGGACCCCATATAACCGACCC
genomic: CTGCAGGGAGTTACCACCGCTTTACTCTTGATGAAAACAATTATCTCAAGgtacacatag ... ttcgtggcagGCAATGAGGCTGTTTGTAGGTGAACCTGTCTGGACCCCATATAACCGACCC
EST: gi|162187911|gb|FC364485.1|FC364485
EST:     NTGCAGGGAGTTACCACCGCTTTACTCTTGATGAAAACAATTATCTCAAG                         GCAATGAGGCTGTTTGTAGGTGAACCTGTCTGGACCCCATATAACCGACCC
genomic: CTGCAGGGAGTTACCACCGCTTTACTCTTGATGAAAACAATTATCTCAAGgtacacatag ... ttcgtggcagGCAATGAGGCTGTTTGTAGGTGAACCTGTCTGGACCCCATATAACCGACCC
EST: gi|100388684|gb|BY970832.1|BY970832
EST:     CTGCAGGGAGTTACCACCGCTTTACTCTTGATGAAA-CAATTATCTCA-G                         GCAATGAGGCTGTTT
genomic: CTGCAGGGAGTTACCACCGCTTTACTCTTGATGAAAACAATTATCTCAAGgtacacatag ... ttcgtggcagGCAATGAGGCTGTTT
EST: gi|208344591|gb|DC909150.1|DC909150
EST:     CTGCAGGGAGTTACCACCGCTTTACTCTTGATGAAA-CANT-ATCTCANG                         -CAATGAGGCTGTT
genomic: CTGCAGGGAGTTACCACCGCTTTACTCTTGATGAAAACAATTATCTCAAGgtacacatag ... ttcgtggcagGCAATGAGGCTGTT
EST: gi|100405835|gb|BY973878.1|BY973878
EST:     TGCAGGGAGTTACCACCGCTTTACTNCT-GATGAAAACA-TTATCTCAAG                         GCA-TGAGGCTG
genomic: TGCAGGGAGTTACCACCGCTTTACT-CTTGATGAAAACAATTATCTCAAGgtacacatag ... ttcgtggcagGCAATGAGGCTG
EST: gi|162265235|gb|FC440158.1|FC440158
EST:     CTGCAGGGAGTTACCACCGCTTTACTCTTGATGAAAACAATTATCTCAAG                         GCAATGAGGCTGTTTGTAGGTGAACCTGTCTGGACCCCATATAACCGACCC
genomic: CTGCAGGGAGTTACCACCGCTTTACTCTTGATGAAAACAATTATCTCAAGgtacacatag ... ttcgtggcagGCAATGAGGCTGTTTGTAGGTGAACCTGTCTGGACCCCATATAACCGACCC

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), 35 (downstream exon)
Score: 33

AGACCGTTGGATTCGAATATGGGTGAAGAAGGGAGACATGATTGTGTTGCCTGCAGGGAGTTACCACCGCTTTACTCTTGATGAAAACAATTATCTCAAGgtacacatag ... ttcgtggcagGCAATGAGGCTGTTTGTAGGTGAACCTGTCTGGACCCCATATAACCGACCCCAAGATGAACACCCTGTGAG




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGACCGTTGGATTCGAATATGGGTGAAGAAGGGAGACATGATTGTGTTGCCTGCAGGGAGTTACCACCGCTTTACTCTTGATGAAAACAATTATCTCAAGgtacacatagctacctatcagtagccccattctaaaaaacagtgactgcagatatgaataagatagcttattcagtgtttaaaattgtccaatccaatagaactctgaaaccctgtattattatattcgtggcag

- - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG