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

GGCAACAACATTCGATATTATATCTTGCCTGACAGCTTGAATCTTGACACGCTTCTTGTTGACGATACACCGCGCGTGAAAGTCAAGAAACCTGTTGCAGgtctctttgttaaaccctttgagtcagaagtcttatctagtactctttttttattccttggctttactagaattgttacattgtatcccagcacgttgtg...

Basic information

species Physcomitrella patens
transcript PP1S37_118V6.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S37_118V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA03G30880.1 (Glycine max), 5'ss of exon 3
GGCAACAACATTCGATATTATATCTTGCCTGACAGCTTGAATCTTGACACGCTTCTTGTTGACGATACACCGCGCGTGAAAGTCAAGAAACCTGTTGCAGgtctc-tttgttaaaccctttgagtcagaagtcttatctagtactctttttttattccttggct-ttactagaattgttacattgtatcccagcacgttgtg-----------
|||||||||||||||||||||||| | |||||||||||||||||||| ||  | || ||||| ||  | ||     | ||    ||||| ||   ||| ||| |  | | |||      |      | ||   |||||      |  || | |     ||| || |||  |     | ||  | || || ||     |||             
GGCAACAACATTCGATATTATATCCTTCCTGACAGCTTGAATCTTGAGACTTTACTGGTTGAAGAGGCTCCTAAGATCAAGCCTAAGAAGCCAACTGCTGgtattgtatattatttgactgtcactaaaatgtttatcagaagttaattatgttcaggttgactgttatcaagg--gatatctggt-tctcaaagttttgattttatttgcag

upper sequence: PP1S37_118V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA19G33700.1 (Glycine max), 5'ss of exon 3
GGCAACAACATTCGATATTATATCTTGCCTGACAGCTTGAATCTTGACACGCTTCTTGTTGACGATACACCGCGCGTGAAAGTCAAGAAACCTGTTGCAGgtctc-tttgttaaaccctttgagtcagaagtcttatctagtactctttttttattccttggct-tta-ctagaattgttacattgt--atcccagcacgttgtg-----
|||||||||||||||||||||||| | |||||||||||||||||||| ||  | || ||||| ||  | ||     | ||    ||||| ||   ||| ||| |  | | |||      ||     ||||   |||||     |   || | |     ||| || ||| |||| | | |    || |  |       |  || |      
GGCAACAACATTCGATATTATATCCTTCCTGACAGCTTGAATCTTGAGACTTTACTGGTTGAAGAGGCTCCTAAGATCAAGCCTAAGAAGCCAACTGCTGgtattgtatattatttgactttcactagaatgtttatcagaggccaattatgttcaggttgactgttatctaggaatatctggttctcaaagttttgattttatttacag

upper sequence: PP1S37_118V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: Vv07s0104g00160.t01 (Vitis vinifera), 5'ss of exon 5
GGCAACAACATTCGATATTATATCTTGCCTGACAGCTTGAATCTTGACACGCTTCTTGTTGACGATACACCGCGCGTGAAAGTCAAGAAACCTGTTGCAGgtctctttgttaaaccctttgagtcagaagtcttatctagtactctttttttattccttggctttactagaattgttacattgtatcccagcacgttgtg
|||||||||||||| ||||||||| | || ||||||||||||||||| || ||| | || || || |||||  | || ||   |||||| ||    |||||| |   | |  | | |||||  ||  |  |  |||  | |    | |  ||  |  |   |||   |  | || ||  | ||  |     ||  |    
GGCAACAACATTCGGTATTATATCCTTCCCGACAGCTTGAATCTTGAGACCCTTTTGGTGGAAGAGACACCTAGGGTCAAGCCCAAGAAGCCAACCGCAGgtattgctct--atctctttggctctaa--ttctatgcattttcgtatgatttatgttccccttgttttaattttttttaatgcttttttccatttcag-

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|162210344|gb|FC386224.1|FC386224
EST:     GCTTCTTGTTGACGATACACCGCGCGTGAAAGTCAAGAAACCTGTTGCAG                         GCAAACCCGTTGGAAGGGGAAGAGGGCGCGGTCGTGGCAGAGGGCGTGGAC
genomic: GCTTCTTGTTGACGATACACCGCGCGTGAAAGTCAAGAAACCTGTTGCAGgtctctttgt ... tcgtatgcagGCAAACCCGTTGGAAGGGGAAGAGGGCGCGGTCGTGGCAGAGGGCGTGGAC
EST: gi|208364908|gb|DC947050.1|DC947050
EST:     GCTTCTTGTTGACGATACACCGCGCGTGAAAGTCAAGAAACCTGTTGCAG                         GCAAACCCGTTGGAAGGGGAAGAGGGCGCGGTCGTGGCAGAGGGCGTGGAC
genomic: GCTTCTTGTTGACGATACACCGCGCGTGAAAGTCAAGAAACCTGTTGCAGgtctctttgt ... tcgtatgcagGCAAACCCGTTGGAAGGGGAAGAGGGCGCGGTCGTGGCAGAGGGCGTGGAC
EST: gi|37824593|gb|BJ582659.1|BJ582659
EST:     GCTTCTTGTTGACGATACACCGCGCGTGAAAGTCAAGAAACCTGTTGCAG                         GCAAACCCGTTGGAAGGGGAAGAGGGCGCGGTCGTGGCAGAGGGCGTGGAC
genomic: GCTTCTTGTTGACGATACACCGCGCGTGAAAGTCAAGAAACCTGTTGCAGgtctctttgt ... tcgtatgcagGCAAACCCGTTGGAAGGGGAAGAGGGCGCGGTCGTGGCAGAGGGCGTGGAC
EST: gi|162210343|gb|FC386223.1|FC386223
EST:     GCTTCTTGTTGACGATACACCGCGCGTGAAAGTCAAGAAACCTGTTGCAG                         GCAAACCCGTTGGAAGGGGAAGAGGGCGCGGTCGTGGCAGAGGGCGTGGAC
genomic: GCTTCTTGTTGACGATACACCGCGCGTGAAAGTCAAGAAACCTGTTGCAGgtctctttgt ... tcgtatgcagGCAAACCCGTTGGAAGGGGAAGAGGGCGCGGTCGTGGCAGAGGGCGTGGAC
EST: gi|18345230|gb|BJ177271.1|BJ177271
EST:     GCTTCTTGTTGACGATACACCGCGCGTGAAAGTCAAGAAACCTGTTGCAG                         GCAAACCCGTTGGAAGGGGAAGAGGGCGCGGTCGTGGCAGAGGGCGTGGAC
genomic: GCTTCTTGTTGACGATACACCGCGCGTGAAAGTCAAGAAACCTGTTGCAGgtctctttgt ... tcgtatgcagGCAAACCCGTTGGAAGGGGAAGAGGGCGCGGTCGTGGCAGAGGGCGTGGAC
EST: gi|162217222|gb|FC391962.1|FC391962
EST:     GCTTCTTGTTGACGATACACCGCGCGTGAAAGTCAAGAAACCTGTTGCAG                         GCAAACCCGTTGGAAGGGGAAGAGGGCGCGGTCGTGGCAGAGGGCGTGGAC
genomic: GCTTCTTGTTGACGATACACCGCGCGTGAAAGTCAAGAAACCTGTTGCAGgtctctttgt ... tcgtatgcagGCAAACCCGTTGGAAGGGGAAGAGGGCGCGGTCGTGGCAGAGGGCGTGGAC
EST: gi|208375129|gb|DC956469.1|DC956469
EST:     GCTTCTTGTTGACGATACACCGCGCGTGAAAGTCAAGAAACCTGTTGCAG                         GCAAACCCGTTGGAAGGGGAAGAGGGCGCGGTCGTGGCAGAGGGCGTGGAC
genomic: GCTTCTTGTTGACGATACACCGCGCGTGAAAGTCAAGAAACCTGTTGCAGgtctctttgt ... tcgtatgcagGCAAACCCGTTGGAAGGGGAAGAGGGCGCGGTCGTGGCAGAGGGCGTGGAC
EST: gi|208369557|gb|DC932539.1|DC932539
EST:     GCTTCTTGTTGACGATACACCGCGCGTGAAAGTCAAGAAACCTGTTGCAG                         GCAAACCCGTTGGAAGGGGAAGAGGGCGCGGTCGTGGCAGAGGGCGTGGAC
genomic: GCTTCTTGTTGACGATACACCGCGCGTGAAAGTCAAGAAACCTGTTGCAGgtctctttgt ... tcgtatgcagGCAAACCCGTTGGAAGGGGAAGAGGGCGCGGTCGTGGCAGAGGGCGTGGAC
EST: gi|162217223|gb|FC391963.1|FC391963
EST:     GCTTCTTGTTGACGATACACCGCGCGTGAAAGTCAAGAAACCTGTTGCAG                         GCAAACCCGTTGGAAGGGGAAGAGGGCGCGGTCGTGGCAGAGGGCGTGGAC
genomic: GCTTCTTGTTGACGATACACCGCGCGTGAAAGTCAAGAAACCTGTTGCAGgtctctttgt ... tcgtatgcagGCAAACCCGTTGGAAGGGGAAGAGGGCGCGGTCGTGGCAGAGGGCGTGGAC
EST: gi|208388874|gb|DC932902.1|DC932902
EST:     GCTTCTTGTTGACGATACACCGCGCGTGAAAGTCAAGAAACCTGTTGCAG                         GCAAACCCGTTGGAAGGGGAAGAGGGCGCGGTCGTGGCAGAGGGCGTGGAC
genomic: GCTTCTTGTTGACGATACACCGCGCGTGAAAGTCAAGAAACCTGTTGCAGgtctctttgt ... tcgtatgcagGCAAACCCGTTGGAAGGGGAAGAGGGCGCGGTCGTGGCAGAGGGCGTGGAC

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: 32 (upstream exon), 12 (downstream exon)
Score: 4

GGCAACAACATTCGATATTATATCTTGCCTGACAGCTTGAATCTTGACACGCTTCTTGTTGACGATACACCGCGCGTGAAAGTCAAGAAACCTGTTGCAGgtctctttgt ... tcgtatgcagGCAAACCCGTTGGAAGGGGAAGAGGGCGCGGTCGTGGCAGAGGGCGTGGACGTGGGCGATAGTTTGTGGTTCATATCCCTCATTAGGGTTTCCAGTGTTG




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCAACAACATTCGATATTATATCTTGCCTGACAGCTTGAATCTTGACACGCTTCTTGTTGACGATACACCGCGCGTGAAAGTCAAGAAACCTGTTGCAGgtctctttgttaaaccctttgagtcagaagtcttatctagtactctttttttattccttggctttactagaattgttacattgtatcccagcacgttgtg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA