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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAGAAAAGAAGCCGCCGACCAATCTTTGAAGGCGTACCAGgtgcgatgcacaggatgacatggtgtgcagttggggacggagtgagtttgtggagatggatagatatgtggcgcaggctgggtagaaagtcggcgttggacgtcgaggcagggagtgacgtatgtgtgttgtgcgcgggggttgcgaggagatctgaaatgtgaggtgcgatgtatgtgcgcag

Basic information

species Physcomitrella patens
transcript PP1S348_9V6.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S348_9V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: Vv19s0014g01420.t01 (Vitis vinifera), 5'ss of exon 3
GAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAGAAAAGAAGCCGCCGACCAATCTTTGAAGGCGTACCAGgtgcgatgcacaggatgacatggtgtgcagttggggacggagtgagtttgtggagatggatagatatgtggcgcaggctgggtagaaagtcggcgttggacgtcgaggcagggagtgacgtatgtgtgttgtgcgcgggggttgcgaggagatctgaaatgtgaggtgcgatgtatgtgcgcag
||| || ||||| ||||||||  ||||||||||||||||||| |||||||| ||||| || || || || ||| | ||||| ||||||||            |||   | || | || ||| |  ||   ||   || |    ||| ||   | |      | |  ||  | | | || ||   |      |  |  | |||                                                                      
GAAAGGGGATTATTATCGGTACCTGGCGGAGTTCAAGACCGGCAATGAGAGGAAAGAGGCGGCTGATCAGTCTCTTAAGGCATACCAGgtatat--------atgcttttgttt-catttgagctcgtgatgttctttt----atgaattt-tgtccatttctgtttgcttcgcatgtgggaagtatctagcatgctaagga----------------------------------------------------------------------

upper sequence: PP1S348_9V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: EFJ35972 (Selaginella moellendorffii), 5'ss of exon 3
GAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAGAAAAGAAGCCGCCGACCAATCTTTGAAGGCGTACCAGgtgcgatgcacaggatgacatg-gtg--tgcagttggggacggagtgagtttgtggagatggatagatatgtggcgcaggctgggtagaaagtcggcgttggacgtcgaggcagggagtgacgtatgtgtgttgtgcgcgggggttgcgaggagatctgaaatgtgaggtgcgatgtatgtgcgcag
||| || || ||||  || ||| | ||||||||||||||||| || || ||||| || || ||||| ||||| || ||||| ||||||||  | | | ||        || |||   |  |||  ||      | ||||| |||   ||  | | |                                                                                                                       
GAAAGGAGACTACTTCCGTTATCTCGCGGAGTTCAAGACCGGTAACGAAAGAAAGGAGGCGGCCGATCAATCATTCAAGGCTTACCAGgtaagct-cgcaaatctctttgcgtgatcgttgttttggtttctataagttt-tgggtgtgcgttgtttcag-------------------------------------------------------------------------------------------------------------------
















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|208389853|gb|DC937684.1|DC937684
EST:     CCGGGAATGAGAGAAAANAAGCCGCCGACCAATCTTTGAAGGCGTACCAG                         GCCGCGTCNAACACAGCTACGACGGATTTGGCGCCCACGCATCCGATCCGA
genomic: CCGGGAATGAGAGAAAAGAAGCCGCCGACCAATCTTTGAAGGCGTACCAGgtgcgatgca ... atgtgcgcagGCCGCGTCGAACACAGCTACGACGGATTTGGCGCCCACGCATCCGATCCGA
EST: gi|208395820|gb|DC911857.1|DC911857
EST:     CCGGGAATGAGAGAAAAGAAGCCGCCGACCAATCTTTGAAGGCGTACCAG                         GCCGCGTCGAACACAGCTACGACGGATTTGGCGCCCACGCATCCGATCCGA
genomic: CCGGGAATGAGAGAAAAGAAGCCGCCGACCAATCTTTGAAGGCGTACCAGgtgcgatgca ... atgtgcgcagGCCGCGTCGAACACAGCTACGACGGATTTGGCGCCCACGCATCCGATCCGA
EST: gi|67717893|gb|BJ968152.1|BJ968152
EST:     CCGGGAATGAGAGAAAAGAAGCCGCCGACCAATCTTTGAAGGCGTACCAG                         GCCGCGTCGAACACAGCTACGACGGATTTGGCGCCCACGCATCCGATCCGA
genomic: CCGGGAATGAGAGAAAAGAAGCCGCCGACCAATCTTTGAAGGCGTACCAGgtgcgatgca ... atgtgcgcagGCCGCGTCGAACACAGCTACGACGGATTTGGCGCCCACGCATCCGATCCGA
EST: gi|67704802|gb|BJ965035.1|BJ965035
EST:     CCGGGAATGAGAGAAAAGAAGCCGCCGACCAATCTTTGAAGGCGTACCAG                         GCCGCGTCGAACACAGCTACGACGGATTTGGCGCCCACGCATCCGATCCGA
genomic: CCGGGAATGAGAGAAAAGAAGCCGCCGACCAATCTTTGAAGGCGTACCAGgtgcgatgca ... atgtgcgcagGCCGCGTCGAACACAGCTACGACGGATTTGGCGCCCACGCATCCGATCCGA
EST: gi|67508215|gb|BJ941086.1|BJ941086
EST:     CCGGGAATGAGAGAAAAGAAGCCGCCGACCAATCTTTGAAGGCGTACCAG                         GCCGCGTCGAACACAGCTACGACGGATTTGGCGCCCACGCATCCGATCCGA
genomic: CCGGGAATGAGAGAAAAGAAGCCGCCGACCAATCTTTGAAGGCGTACCAGgtgcgatgca ... atgtgcgcagGCCGCGTCGAACACAGCTACGACGGATTTGGCGCCCACGCATCCGATCCGA
EST: gi|208361629|gb|DC942858.1|DC942858
EST:     CCGGGAATGAGAGAAAAGAAGCCGCCGACCAATCTTTGAAGGCGTATCAG                         GCCGCGTCGAACACAGCTACGACGGATTTGGCGCCCACGCATCCGATCCGA
genomic: CCGGGAATGAGAGAAAAGAAGCCGCCGACCAATCTTTGAAGGCGTACCAGgtgcgatgca ... atgtgcgcagGCCGCGTCGAACACAGCTACGACGGATTTGGCGCCCACGCATCCGATCCGA
EST: gi|162249894|gb|FC425695.1|FC425695
EST:     CCGGGAATGAGAGAAAAGAAGCCGCCGACCAATCTTTGAAGGCGTACCAG                         GCCGCGTCGAACACAGCTACGACGGATTTGGCGCCCACGCATCCGATCCGA
genomic: CCGGGAATGAGAGAAAAGAAGCCGCCGACCAATCTTTGAAGGCGTACCAGgtgcgatgca ... atgtgcgcagGCCGCGTCGAACACAGCTACGACGGATTTGGCGCCCACGCATCCGATCCGA
EST: gi|208377815|gb|DC940927.1|DC940927
EST:     CCGGGAATGAGAGAAAAGAAGCCGCCGACCAATCTTTGAAGGCGTACCAG                         GCCGCGTCGAACACAGCTACGACGGATTTGGCGCCCACGCATCCGATCCGA
genomic: CCGGGAATGAGAGAAAAGAAGCCGCCGACCAATCTTTGAAGGCGTACCAGgtgcgatgca ... atgtgcgcagGCCGCGTCGAACACAGCTACGACGGATTTGGCGCCCACGCATCCGATCCGA
EST: gi|67717603|gb|BJ967862.1|BJ967862
EST:     CCGGGAATGAGAGAAAAGAAGCCGCCGACCAATCTTTGAAGGCGTACCAG                         GCCGCGTCGAACACAGCTACGACGGATTTGGCGCCCACGCATCCGATCCGA
genomic: CCGGGAATGAGAGAAAAGAAGCCGCCGACCAATCTTTGAAGGCGTACCAGgtgcgatgca ... atgtgcgcagGCCGCGTCGAACACAGCTACGACGGATTTGGCGCCCACGCATCCGATCCGA
EST: gi|100444344|gb|BY982373.1|BY982373
EST:     CCGGGAATGAGAGAAAAGAAGCCGCCGACCAATCTTTGAAGGCGTACCAG                         GCCGCGTCGAACACAGCTACGACGGATTTGGCGCCCACGCATCCGATCCGA
genomic: CCGGGAATGAGAGAAAAGAAGCCGCCGACCAATCTTTGAAGGCGTACCAGgtgcgatgca ... atgtgcgcagGCCGCGTCGAACACAGCTACGACGGATTTGGCGCCCACGCATCCGATCCGA

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), 32 (downstream exon)
Score: 43

GAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAGAAAAGAAGCCGCCGACCAATCTTTGAAGGCGTACCAGgtgcgatgca ... atgtgcgcagGCCGCGTCGAACACAGCTACGACGGATTTGGCGCCCACGCATCCGATCCGACTGGGGCTGGCGTTGAATTTTTCGGTGTTTTATTACGAGATTTTGAACT




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAGAAAAGAAGCCGCCGACCAATCTTTGAAGGCGTACCAGgtgcgatgcacaggatgacatggtgtgcagttggggacggagtgagtttgtggagatggatagatatgtggcgcaggctgggtagaaagtcggcgttggacgtcgaggcagggagtgacgtatgtgtgttgtgcgcgggggttgcgaggagatctgaaatgtgaggtgcgatgtatgtgcgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG