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

ATCGCTATGAAAGAACTTCGGGAGCGGAAAATTCCCTTCACCATTCGTCGCTATCTGCCCGATGGGAGgtacgtctcatactagaataaagtacaaccaagtagcaagaagtgcaaaatatttttgaggttgacgtgaacatttttttatcttctgttttgttggtcaagttgctgaaatgcaatctgcggcagtctaatattttgtgccgtattgttccag

Basic information

species Physcomitrella patens
transcript PP1S197_12V6.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S197_12V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: Vv12s0028g01210.t01 (Vitis vinifera), 5'ss of exon 5
ATCGCTATGAAAGAACTTCGGGAGCGGAAAATTCCCTTCACCATTCGTCGCTATCTGCCCGATGGGAGgtacgtctcatactagaataaagtac-aaccaagtagcaagaagtgcaaaatatttttgaggttgacgtgaacatttttttatcttctgttttgttggtcaagttgctgaaatgcaatctgcggcagtctaatattttgtgccgtattgttccag
|| || |||||||||||||| ||| |||| || |||||||||||||| ||||| ||||| ||||| ||||| |  || || |   |  |  |||   ||   |    ||    || | |  |  ||||  |    |      || | || || |||| |||  |  || |  |  |||||    | ||  ||   | | | ||  |                 
ATTGCGATGAAAGAACTTCGTGAGAGGAAGATACCCTTCACCATTCGGCGCTACCTGCCTGATGGAAGgtaagggtcttagtttga--agttactggccttctttttaggttagccatacttagttgaactccctgctctttttctgttttcatctgcttttct--tcta--tattgaaa----acctttggttctgtgacatgctccag-------------

upper sequence: PP1S197_12V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: Vv16s0100g00530.t01 (Vitis vinifera), 5'ss of exon 7
ATCGCTATGAAAGAACTTCGGGAGCGGAAAATTCCCTTCACCATTCGTCGCTATCTGCCCGATGGGAGgtacgtctcatactagaataaagtacaaccaagtagcaagaagtgcaaaatatttttgaggttgacgtgaacatttttttatcttctgttttgttggtcaagttgctgaaatgcaatctgcggcagtctaatattttgtgccgtattgttccag
|| || ||||| |||||||| |||||||| || ||||||||||| || ||||| ||||| ||||| |||||           | |||||    ||  |   |    | ||||  |  ||  | ||   ||||           || |  | |||| ||   ||  |||  | | ||    |   | | | |                               
ATTGCAATGAAGGAACTTCGTGAGCGGAAGATACCCTTCACCATCCGCCGCTACCTGCCTGATGGAAGgta-----------acaataa----cattcttattttgaaaagt-tactattgtcttattgttgcttctgtttggttctcgttttct-ttacattaatcat-tggttgtgggggtttttccag-------------------------------
















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|37853644|gb|BJ611652.1|BJ611652
EST:     CGGGAGCGGAAAATCCCCTTCACCATTCGTCGCTATCTGCCCGATGGGAG                         TTATGAAGATTGGGGCGTGGACGAGTTGATCGTAGAAGATTCTTGGAGGCG
genomic: CGGGAGCGGAAAATTCCCTTCACCATTCGTCGCTATCTGCCCGATGGGAGgtacgtctca ... attgttccagTTATGAAGATTGGGGCGTGGACGAGTTGATCGTAGAAGATTCTTGGAGGCG
EST: gi|6102256|gb|AW126726.1|AW126726
EST:     CGGGAGCGGAAAATTCCCTTCACCATTCGTCGCTATCTGCCCGATGGGAG                         TTATGAAGATTGGGGCGTGGACGAGTTGATCGTAGAAGATTCTTGGAGGCG
genomic: CGGGAGCGGAAAATTCCCTTCACCATTCGTCGCTATCTGCCCGATGGGAGgtacgtctca ... attgttccagTTATGAAGATTGGGGCGTGGACGAGTTGATCGTAGAAGATTCTTGGAGGCG
EST: gi|67691341|gb|BJ951574.1|BJ951574
EST:     CGGGAGCGGAAAATTCCCTTCACCATTCGTCGCTATCTGCCCGATGGGAG                         TTATGAAGATTGGGGCGTGGACGAGTTGATCGTAGAAGATTCTTGGAGGCG
genomic: CGGGAGCGGAAAATTCCCTTCACCATTCGTCGCTATCTGCCCGATGGGAGgtacgtctca ... attgttccagTTATGAAGATTGGGGCGTGGACGAGTTGATCGTAGAAGATTCTTGGAGGCG
EST: gi|208399259|gb|DC912460.1|DC912460
EST:     CGGGAGCGGAAAATTCCCTTCACCATTCGTCGCTATCTGCCCGATGGGAG                         TTATGAAGATTGGGGCGTGGACGAGTTGATCGTAGAAGATTCTTGGAGGCG
genomic: CGGGAGCGGAAAATTCCCTTCACCATTCGTCGCTATCTGCCCGATGGGAGgtacgtctca ... attgttccagTTATGAAGATTGGGGCGTGGACGAGTTGATCGTAGAAGATTCTTGGAGGCG
EST: gi|37833887|gb|BJ591899.1|BJ591899
EST:     CGGGAGCGGAAAATTCCCTTCACCATTCGTCGCTATCTGCCCGATGGGAG                         TTATGAAGATTGGGGCGTGGACGAGTTGATCGTAGAAGATTCTTGGAGGCG
genomic: CGGGAGCGGAAAATTCCCTTCACCATTCGTCGCTATCTGCCCGATGGGAGgtacgtctca ... attgttccagTTATGAAGATTGGGGCGTGGACGAGTTGATCGTAGAAGATTCTTGGAGGCG
EST: gi|162199893|gb|FC376459.1|FC376459
EST:     CGGGAGCGGAAAATTCCCTTCACCATTCGTCGCTATCTGCCCGATGGGAG                         TTATGAAGATTGGGGCGTGGACGAGTTGATCGTAGAAGATTCTTGGAGGCG
genomic: CGGGAGCGGAAAATTCCCTTCACCATTCGTCGCTATCTGCCCGATGGGAGgtacgtctca ... attgttccagTTATGAAGATTGGGGCGTGGACGAGTTGATCGTAGAAGATTCTTGGAGGCG
EST: gi|67717109|gb|BJ967368.1|BJ967368
EST:     CGGGAGCGGAAAATTCCCTTCACCATTCGTCGCTATCTGCCCGATGGGAG                         TTATGAAGATTGGGGCGTGGACGAGTTGATCGTAGAAGATTCTTGGAGGCG
genomic: CGGGAGCGGAAAATTCCCTTCACCATTCGTCGCTATCTGCCCGATGGGAGgtacgtctca ... attgttccagTTATGAAGATTGGGGCGTGGACGAGTTGATCGTAGAAGATTCTTGGAGGCG
EST: gi|37841975|gb|BJ599983.1|BJ599983
EST:     CGGGAGCGGAAAATCCCCTTCACCATTCGTCGCTATCTGCCCGATGGGAG                         TTATGAAGATTGGGGCGTGGACGAGTTGATCGTAGAAGATTCTTGGAGGCG
genomic: CGGGAGCGGAAAATTCCCTTCACCATTCGTCGCTATCTGCCCGATGGGAGgtacgtctca ... attgttccagTTATGAAGATTGGGGCGTGGACGAGTTGATCGTAGAAGATTCTTGGAGGCG
EST: gi|162251127|gb|FC426404.1|FC426404
EST:     CGGGAGCGGAAAATTCCCTTCACCATTCGTCGCTATCTGCCCGATGGGAG                         TTATGAAGATTGGGGCGTGGACGAGTTGATCGTAGAAGATTCTTGGAGGCG
genomic: CGGGAGCGGAAAATTCCCTTCACCATTCGTCGCTATCTGCCCGATGGGAGgtacgtctca ... attgttccagTTATGAAGATTGGGGCGTGGACGAGTTGATCGTAGAAGATTCTTGGAGGCG
EST: gi|67508124|gb|BJ940995.1|BJ940995
EST:     CGGGAGCGGAAAATTCCCTTCACCATTCGTCGCTATCTGCCCGATGGGAG                         TTATGAAGATTGGGGCGTGGACGAGTTGATCGTAGAAGATTCTTGGAGGCG
genomic: CGGGAGCGGAAAATTCCCTTCACCATTCGTCGCTATCTGCCCGATGGGAGgtacgtctca ... attgttccagTTATGAAGATTGGGGCGTGGACGAGTTGATCGTAGAAGATTCTTGGAGGCG
EST: gi|162251128|gb|FC426405.1|FC426405
EST:     CGGGAGCGGAAAATTCCCTTCACCATTCGTCGCTATCTGCCCGATGGGAG                         TTATGAAGATTGGGGCGTGGACGAGTTGATCGTAGAAGATTCTTGGAGGCG
genomic: CGGGAGCGGAAAATTCCCTTCACCATTCGTCGCTATCTGCCCGATGGGAGgtacgtctca ... attgttccagTTATGAAGATTGGGGCGTGGACGAGTTGATCGTAGAAGATTCTTGGAGGCG
EST: gi|18352449|gb|BJ184503.1|BJ184503
EST:     CGGGAGCGGAAAATTCCCTTCACCATTCGTCGCTATCTGCCCGATGGGAG                         TTATGAAGATTGGGGCGTGGACGAGTTGATCGTAGAAG
genomic: CGGGAGCGGAAAATTCCCTTCACCATTCGTCGCTATCTGCCCGATGGGAGgtacgtctca ... attgttccagTTATGAAGATTGGGGCGTGGACGAGTTGATCGTAGAAG
EST: gi|162199892|gb|FC376458.1|FC376458
EST:     CGGGAGCGGAAAATTCCCTTCACCATTCGTCGCTATCTGCCCGATGGGAG                         TTATGAAGATTGGGGCGTGGACGAGTTGATCGTAGAAGATTCTTGGAGGCG
genomic: CGGGAGCGGAAAATTCCCTTCACCATTCGTCGCTATCTGCCCGATGGGAGgtacgtctca ... attgttccagTTATGAAGATTGGGGCGTGGACGAGTTGATCGTAGAAGATTCTTGGAGGCG
EST: gi|37848516|gb|BJ606524.1|BJ606524
EST:     CGGGAGCGGAAAATTCCCTTCACCATTCGTCGCTATCTGCCCGATGGGAG                         TTATGAAGATTGGGGCGTGGACGAGTTGATCGTAGAAGATTCTTGGAGGCG
genomic: CGGGAGCGGAAAATTCCCTTCACCATTCGTCGCTATCTGCCCGATGGGAGgtacgtctca ... attgttccagTTATGAAGATTGGGGCGTGGACGAGTTGATCGTAGAAGATTCTTGGAGGCG
EST: gi|208350547|gb|DC926238.1|DC926238
EST:     CGGGAGCGGAAAATTCCCTTCACCATTCGTCGCTATCTGCCCGATGGGAG                         TTATGAAGATTGGGGCGTGGACGAGTTGATCGTAGAAGATTCTTGGAGGCG
genomic: CGGGAGCGGAAAATTCCCTTCACCATTCGTCGCTATCTGCCCGATGGGAGgtacgtctca ... attgttccagTTATGAAGATTGGGGCGTGGACGAGTTGATCGTAGAAGATTCTTGGAGGCG
EST: gi|18360281|gb|BJ192343.1|BJ192343
EST:     CGGGAGCGGAAAATCCCCTTCACCATTCGTCGCTATCTGCCCGATGGGAG                         TTATGAAGATTGGGGCGTGGACGAGTTGATCGTAGAAGATTCTTGGAGGGC
genomic: CGGGAGCGGAAAATTCCCTTCACCATTCGTCGCTATCTGCCCGATGGGAGgtacgtctca ... attgttccagTTATGAAGATTGGGGCGTGGACGAGTTGATCGTAGAAGATTCTTGGAGG-C
EST: gi|67725632|gb|BJ975891.1|BJ975891
EST:     CGGGAGCGGAAAATTCCCTTCACCATTCGTCGCTATCTGCCCGATGGGAG                         TTATGAAGATTGGGGCGTGGACGAGTTGATCGTAGAAGATTCTTGGAGGCG
genomic: CGGGAGCGGAAAATTCCCTTCACCATTCGTCGCTATCTGCCCGATGGGAGgtacgtctca ... attgttccagTTATGAAGATTGGGGCGTGGACGAGTTGATCGTAGAAGATTCTTGGAGGCG

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: 34 (upstream exon), 35 (downstream exon)
Score: 44

ATCGCTATGAAAGAACTTCGGGAGCGGAAAATTCCCTTCACCATTCGTCGCTATCTGCCCGATGGGAGgtacgtctca ... attgttccagTTATGAAGATTGGGGCGTGGACGAGTTGATCGTAGAAGATTCTTGGAGGCGCCAGGTCGGCTGAGAATTTTCTTTCCAACGGGGACGAGTTGGACATCTC




<











<


<