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

...gaagtgtttttttttttttttttttttttttttttttgtgtgtgtgtgttgtgtttgctgaggtggtgatggggtggatatgtgatgggcgggatatcagGAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAGAAAAGAAGCCGCCGACCAATCTTTGAAGGCGTACCAG

Basic information

species Physcomitrella patens
transcript PP1S348_9V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S348_9V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: Vv19s0014g01420.t01 (Vitis vinifera), 3'ss of exon 2
gaagtgtttttttttttttttttttttttttttttttgtgtgtgtgtgttgtgtttgctgaggtggtgatggggtggatatgtgatgggcgggatatcagGAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAGAAAAGAAGCCGCCGACCAATCTTTGAAGGCGTACCAG
   ||      | | |||   |||  |   |||| ||   | || ||| | || ||  ||  ||  |    ||||       || | |      | ||||||| || ||||| ||||||||  ||||||||||||||||||| |||||||| ||||| || || || || ||| | ||||| ||||||
---gtaaggaatatgtttgagtttggtgcattttatttcatttgagtgctttgatttttgtagtaatttcagggtt------tggttg------tttcagGAAAGGGGATTATTATCGGTACCTGGCGGAGTTCAAGACCGGCAATGAGAGGAAAGAGGCGGCTGATCAGTCTCTTAAGGCATACCAG
















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|18331317|gb|BJ163327.1|BJ163327
EST:     TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGAT                         GAAGGGTGATTACTATCGGTATTTGGCGGA
genomic: TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGATgtacgtgatg ... gggatatcagGAAGGGTGATTACTATCGGTATTTGGCGGA
EST: gi|208389853|gb|DC937684.1|DC937684
EST:     TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGAT                         GAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
genomic: TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGATgtacgtgatg ... gggatatcagGAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
EST: gi|208395820|gb|DC911857.1|DC911857
EST:     TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGAT                         GAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
genomic: TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGATgtacgtgatg ... gggatatcagGAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
EST: gi|18350889|gb|BJ182940.1|BJ182940
EST:     TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGAT                         GAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
genomic: TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGATgtacgtgatg ... gggatatcagGAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
EST: gi|18359345|gb|BJ191406.1|BJ191406
EST:     TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGAT                         GAAGGGTGATTACTATCGGTATTTGGCCGGAGTTCAAGACCGGGAATGAGA
genomic: TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGATgtacgtgatg ... gggatatcagGAAGGGTGATTACTATCGGTATTTGGC-GGAGTTCAAGACCGGGAATGAGA
EST: gi|18375345|gb|BJ206923.1|BJ206923
EST:     TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGAT                         GAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
genomic: TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGATgtacgtgatg ... gggatatcagGAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
EST: gi|67717893|gb|BJ968152.1|BJ968152
EST:     TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGAT                         GAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
genomic: TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGATgtacgtgatg ... gggatatcagGAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
EST: gi|67704802|gb|BJ965035.1|BJ965035
EST:     TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGAT                         GAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
genomic: TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGATgtacgtgatg ... gggatatcagGAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
EST: gi|67508215|gb|BJ941086.1|BJ941086
EST:     TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGAT                         GAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
genomic: TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGATgtacgtgatg ... gggatatcagGAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
EST: gi|208361629|gb|DC942858.1|DC942858
EST:     TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGAT                         GAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
genomic: TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGATgtacgtgatg ... gggatatcagGAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
EST: gi|162249894|gb|FC425695.1|FC425695
EST:     TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGAT                         GAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
genomic: TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGATgtacgtgatg ... gggatatcagGAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
EST: gi|208377815|gb|DC940927.1|DC940927
EST:     TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGAT                         GAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
genomic: TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGATgtacgtgatg ... gggatatcagGAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
EST: gi|67717603|gb|BJ967862.1|BJ967862
EST:     TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGAT                         GAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
genomic: TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGATgtacgtgatg ... gggatatcagGAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
EST: gi|100444344|gb|BY982373.1|BY982373
EST:     TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGAT                         GAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
genomic: TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGATgtacgtgatg ... gggatatcagGAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG

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: 17

AAGAGCTTTCGAAGATTTGTCAGGACATACTGACGATCATCGACGAGCACTTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGATgtacgtgatg ... gggatatcagGAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAGAAAAGAAGCCGCCGACCAATCTTTGAAGGCGTACCAG




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaagtgtttttttttttttttttttttttttttttttgtgtgtgtgtgttgtgtttgctgaggtggtgatggggtggatatgtgatgggcgggatatcagGAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAGAAAAGAAGCCGCCGACCAATCTTTGAAGGCGTACCAG

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