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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atttttaaatgatttgcgttggctgtattaactcattcaatttctgaaccttgattttctaaaaatgttctaatattagtctttgttgtggttttcttagTACATTCTAAAAATTGGGGAAGGACCCGAGAAACAGTGCGTCAGTGGTTTCTTGGGACTTGATGTGCCGCCTCCAGCAGGACCCCTCTGGATTTTAGGAG

Basic information

species Physcomitrella patens
transcript PP1S113_31V6.1
intron # 8
splice site 3'
intron type U2

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|162235502|gb|FC411832.1|FC411832
EST:     ACGTCGGCTTTACCATTGCTGGAAAGTCTTTTGAGCTCACACCAGAGCAG                         TACATTCTAAAAATTGGGGAAGGACCCGAGAAACAGTGCGTCAGTGGTTTC
genomic: ACGTCGGCTTTACCATTGCTGGAAAGTCTTTTGAGCTCACACCAGAGCAGgttagtattt ... gttttcttagTACATTCTAAAAATTGGGGAAGGACCCGAGAAACAGTGCGTCAGTGGTTTC
EST: gi|37825124|gb|BJ583190.1|BJ583190
EST:     ACGTCGGCTTTACCATTGCTGGAAAGTCTTTTGAGCTCACACCAGAGCAG                         TACATTCTAAAAATTGGGGAAGGACCCGAGAAACAGTGCGTCAGTGGTTTC
genomic: ACGTCGGCTTTACCATTGCTGGAAAGTCTTTTGAGCTCACACCAGAGCAGgttagtattt ... gttttcttagTACATTCTAAAAATTGGGGAAGGACCCGAGAAACAGTGCGTCAGTGGTTTC
EST: gi|67727315|gb|BJ977574.1|BJ977574
EST:     ACGTCGGCTTTACCATTGCTGGAAAGTCTTTTGAGCTCACACCAGAGCAG                         TACATTCTAAAAATTGGGGAAGGACCCGAGAAACAGTGCGTCAGTGGTTTC
genomic: ACGTCGGCTTTACCATTGCTGGAAAGTCTTTTGAGCTCACACCAGAGCAGgttagtattt ... gttttcttagTACATTCTAAAAATTGGGGAAGGACCCGAGAAACAGTGCGTCAGTGGTTTC
EST: gi|162211128|gb|FC387152.1|FC387152
EST:     ACGTCGGCTTTACCATTGCTGGAAAGTCTTTTGAGCTCACACCAGAGCAG                         TACATTCTAAAAATTGGGGAAGGACCCGAGAAACAGTGCGTCAGTGGTTTC
genomic: ACGTCGGCTTTACCATTGCTGGAAAGTCTTTTGAGCTCACACCAGAGCAGgttagtattt ... gttttcttagTACATTCTAAAAATTGGGGAAGGACCCGAGAAACAGTGCGTCAGTGGTTTC
EST: gi|67723726|gb|BJ973985.1|BJ973985
EST:     ACGTCGGCTTTACCATTGCTGGAAAGTCTTTTGAGCTCACACCAGAGCAG                         TACATTCTAAAAATTGGGGAAGGACCCGAGAAACAGTGCGTCAGTGGTTTC
genomic: ACGTCGGCTTTACCATTGCTGGAAAGTCTTTTGAGCTCACACCAGAGCAGgttagtattt ... gttttcttagTACATTCTAAAAATTGGGGAAGGACCCGAGAAACAGTGCGTCAGTGGTTTC
EST: gi|162151132|gb|FC327651.1|FC327651
EST:     ACGTCGGCTTTACCATTGCTGGAAAGTCTTTTGAGCTCACACCAGAGCAG                         TACATTCTAAAAATTGGGGAAGGACCCGAGAAACAGTGCGTCAGTGGTTTC
genomic: ACGTCGGCTTTACCATTGCTGGAAAGTCTTTTGAGCTCACACCAGAGCAGgttagtattt ... gttttcttagTACATTCTAAAAATTGGGGAAGGACCCGAGAAACAGTGCGTCAGTGGTTTC
EST: gi|162156150|gb|FC332525.1|FC332525
EST:     ACGTCGGCTTTACCATTGCTGGAAAGTCTTTTGAGCTCACACCAGAGCAG                         TACATTCTAAAAATTGGGGAAGGACCCGAGAAACAGTGCGTCAGTGGTTTC
genomic: ACGTCGGCTTTACCATTGCTGGAAAGTCTTTTGAGCTCACACCAGAGCAGgttagtattt ... gttttcttagTACATTCTAAAAATTGGGGAAGGACCCGAGAAACAGTGCGTCAGTGGTTTC
EST: gi|67725928|gb|BJ976187.1|BJ976187
EST:     ACGTCGGCTTTACCATTGCTGGAAAGTCTTTTGAGCTCACACCAGAGCAG                         TACATTCTAAAAATTGGGGAAGGACCCGAGAAACAGTGCGTCAGTGGTTTC
genomic: ACGTCGGCTTTACCATTGCTGGAAAGTCTTTTGAGCTCACACCAGAGCAGgttagtattt ... gttttcttagTACATTCTAAAAATTGGGGAAGGACCCGAGAAACAGTGCGTCAGTGGTTTC
EST: gi|162157105|gb|FC333675.1|FC333675
EST:     ACGTCGGCTTTACCATTGCTGGAAAGTCTTTTGAGCTCACACCAGAGCAG                         TACATTCTAAAAATTGGGGAAGGACCCGAGAAACAGTGCGTCAGTGGTTTC
genomic: ACGTCGGCTTTACCATTGCTGGAAAGTCTTTTGAGCTCACACCAGAGCAGgttagtattt ... gttttcttagTACATTCTAAAAATTGGGGAAGGACCCGAGAAACAGTGCGTCAGTGGTTTC
EST: gi|37844744|gb|BJ602752.1|BJ602752
EST:     ACGTCGGCTTTACCATTGCTGGAAAGTCTTTTGAGCTCACACCAGAGCAG                         TACATTCTAAAAATTGGGGAAGGACCCGAGAAACAGTGCGTCAGTGGTTTC
genomic: ACGTCGGCTTTACCATTGCTGGAAAGTCTTTTGAGCTCACACCAGAGCAGgttagtattt ... gttttcttagTACATTCTAAAAATTGGGGAAGGACCCGAGAAACAGTGCGTCAGTGGTTTC

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: 8 (upstream exon), 28 (downstream exon)
Score: 1

TCCAAACGGCGAATCAGCTGTGGATTGCAATGCGCTTTCTTATATGCCAAACGTCGGCTTTACCATTGCTGGAAAGTCTTTTGAGCTCACACCAGAGCAGgttagtattt ... gttttcttagTACATTCTAAAAATTGGGGAAGGACCCGAGAAACAGTGCGTCAGTGGTTTCTTGGGACTTGATGTGCCGCCTCCAGCAGGACCCCTCTGGATTTTAGGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaccttgattttctaaaaatgttctaatattagtctttgttgtggttttcttagTACATTCTAAAAATTGGGGAAGGACCCGAGAAACAGTGCGTCAGTGGTTTCTTGGGACTTGATGTGCCGCCTCCAGCAGGACCCCTCTGGATTTTAGGAG
                      ttctaat  putative branch site (score: 1)
 ttttctt  putative PPT
 ttgattttctaaaaat  TA-rich tract