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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagcagtcgtccttgttgaaggctggtcatacaaacaccttcaacggtcagctgatttctagcttggattcctatcagattgttttcggacttaaatcgcacaatatggggtacacaaatgctgaatttcatcacctagcagggtttgacttgtaattacgtgcaactttatggacgcagTTTTATGTGGCGAACGGGGAGCTCTCCTGTCAGATGTACCAGCGGTCCTGTGATATGGGATTGGGGGTGCCTTTCAATATTGCATCTTATGCACTTCTCA

Basic information

species Physcomitrella patens
transcript PP1S34_360V6.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S34_360V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GRMZM2G139880_T01 (Zea mays), 3'ss of exon 7
gtcagcagtcgtccttgttgaaggctggtcatacaaacaccttcaacggtcagctgatttctagcttggattcctatcagattgttttcggacttaaatcgcacaatatggggtacacaaatgctgaatttcatcacctagcagggtttgacttgtaattacgtgcaactttatggac--gcagTTTTATGTGGCGAACGGGGAGCTCTCCTGTCAGATGTACCAGCGGTCCTGTGATATGGGATTGGGGGTGCCTTTCAATATTGCATCTTATGCACTTCTCA
                                                                                 |||  || |    | |       || ||    | |    ||  |   ||  || || | |  |  |   |     | || | |||||| |  |   |   ||||||||||||| |||||||||||| ||||| |||||||| || || ||    || |||||  | || || || ||||| || ||||| ||| | ||| | |
------------------------------------------------------------------------------gttttgcctttgataattacctttgtaacatt---tgcttgcattttattttcgataacattgtcgact---aacaacatttgcatgcaacctattcaccttccagTTTTATGTGGAGAACGGGGAGCTATCCTGCCAGATGTATCAACGCTCTGCAGACATGGGGCTTGGTGTTCCATTCAACATCGCATCATATTCTCTTTTGA
















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|18340844|gb|BJ172875.1|BJ172875
EST:     CAGCTGACTTGAAGCTCATGGCTCTCCCACCCTGCCACATGTTTGCTCAG                         TTTTATGTGGCGAACGGGGAGCTCTCCTGTCAGATGTACCAGCGGTCCTGT
genomic: CAGCTGACTTGAAGCTCATGGCTCTCCCACCCTGCCACATGTTTGCTCAGgtcagcagtc ... atggacgcagTTTTATGTGGCGAACGGGGAGCTCTCCTGTCAGATGTACCAGCGGTCCTGT
EST: gi|162204721|gb|FC381429.1|FC381429
EST:     CAGCTGACTTGAAGCTCATGGCTCTCCCACCCTGCCACATGTTTGCTCAG                         TTTTATGTGGCGAACGGGGAGCTCTCCTGTCAGATGTACCAGCGGTCCTGT
genomic: CAGCTGACTTGAAGCTCATGGCTCTCCCACCCTGCCACATGTTTGCTCAGgtcagcagtc ... atggacgcagTTTTATGTGGCGAACGGGGAGCTCTCCTGTCAGATGTACCAGCGGTCCTGT
EST: gi|162256722|gb|FC433240.1|FC433240
EST:     CAGCTGACTTGAAGCTCATGGCTCTCCCACCCTGCCACATGTTTGCTCAG                         TTTTATGTGGCGAACGGGGAGCTCTCCTGTCAGATGTACCAGCGGTCCTGT
genomic: CAGCTGACTTGAAGCTCATGGCTCTCCCACCCTGCCACATGTTTGCTCAGgtcagcagtc ... atggacgcagTTTTATGTGGCGAACGGGGAGCTCTCCTGTCAGATGTACCAGCGGTCCTGT
EST: gi|162204720|gb|FC381428.1|FC381428
EST:     CAGCTGACTTGAAGCTCATGGCTCTCCCACCCTGCCACATGTTTGCTCAG                         TTTTATGTGGCGAACGGGGAGCTCTCCTGTCAGATGTACCAGCGGTCCTGT
genomic: CAGCTGACTTGAAGCTCATGGCTCTCCCACCCTGCCACATGTTTGCTCAGgtcagcagtc ... atggacgcagTTTTATGTGGCGAACGGGGAGCTCTCCTGTCAGATGTACCAGCGGTCCTGT

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: 25 (upstream exon), 27 (downstream exon)
Score: 4

AATCAAAACAGACCCAGATGATCGGCGCATCCTTCTGTCAGCTTGGAACCCAGCTGACTTGAAGCTCATGGCTCTCCCACCCTGCCACATGTTTGCTCAGgtcagcagtc ... atggacgcagTTTTATGTGGCGAACGGGGAGCTCTCCTGTCAGATGTACCAGCGGTCCTGTGATATGGGATTGGGGGTGCCTTTCAATATTGCATCTTATGCACTTCTCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttcatcacctagcagggtttgacttgtaattacgtgcaactttatggacgcagTTTTATGTGGCGAACGGGGAGCTCTCCTGTCAGATGTACCAGCGGTCCTGTGATATGGGATTGGGGGTGCCTTTCAATATTGCATCTTATGCACTTCTCA
                  gtttgac  putative branch site (score: 4)
                         ttgtaatta  TA-rich tract