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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcaattgaagtgagttgtgattggatttgtttctttgaccaaagttttctcaagtaaactgccacaatatttcatttttgggtgtcacaaacccgttatgctagttaccatcatgatttgcgtctagctaatgtcatcggtcgttgtttaatagtatttggcttgtcaagtacagATGAGGACCTTTGGAACTTGGAGATGTATCCGCCGGAGGCTATGGCTACCAGCAATGACTTTGTATCGAATATACTTAACG

Basic information

species Physcomitrella patens
transcript PP1S473_1V6.2
intron # 3
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|67694722|gb|BJ954955.1|BJ954955
EST:     CCGACA-TTTCATCGCCTCAGTCCTGGTCACTGAAG                         ATGAGGACCTTTGGAACTTGGAGATGTATCCGCCGGAGGCTATGGCTACCA
genomic: CCGACATTTTCATCGCCTCAGTCCTGGTCACTGAAGgtgagcaatt ... tcaagtacagATGAGGACCTTTGGAACTTGGAGATGTATCCGCCGGAGGCTATGGCTACCA
EST: gi|162265407|gb|FC440733.1|FC440733
EST:     GCCTTGACCGACATTTTCATCGCCTCAGTCCTGGTCACTGAAG                         ATGAGGACCTTTGGAACTTGGAGATGTATCCGCCGGAGGCTATGGCTACCA
genomic: GCCTTGACCGACATTTTCATCGCCTCAGTCCTGGTCACTGAAGgtgagcaatt ... tcaagtacagATGAGGACCTTTGGAACTTGGAGATGTATCCGCCGGAGGCTATGGCTACCA
EST: gi|162151453|gb|FC326958.1|FC326958
EST:     TTCCTCTGCCTTGACCGACATTTTCATCGCCTCAGTCCTGGTCACTGAAG                         ATGAGGACCTTTGGAACTTGGAGATGTATCCGCCGGAGGCTATGGCTACCA
genomic: TTCCTCTGCCTTGACCGACATTTTCATCGCCTCAGTCCTGGTCACTGAAGgtgagcaatt ... tcaagtacagATGAGGACCTTTGGAACTTGGAGATGTATCCGCCGGAGGCTATGGCTACCA
EST: gi|162157013|gb|FC333375.1|FC333375
EST:     TTCCTCTGCCTTGACCGACATTTTCATCGCCTCAGTCCTGGTCACTGAAG                         ATGAGGACCTTTGGAACTTGGAGATGTATCCGCCGGAGGCTATGGCTACCA
genomic: TTCCTCTGCCTTGACCGACATTTTCATCGCCTCAGTCCTGGTCACTGAAGgtgagcaatt ... tcaagtacagATGAGGACCTTTGGAACTTGGAGATGTATCCGCCGGAGGCTATGGCTACCA
EST: gi|162266183|gb|FC441920.1|FC441920
EST:     TTCCTCTGCCTTGACCGACATNTTCATCGCCTCAGTCCTGGTCACTGAAG                         ATGAGGACCTTTGGAACTTGGAGATGTATCCGCCGGAGGCTATGGCTACCA
genomic: TTCCTCTGCCTTGACCGACATTTTCATCGCCTCAGTCCTGGTCACTGAAGgtgagcaatt ... tcaagtacagATGAGGACCTTTGGAACTTGGAGATGTATCCGCCGGAGGCTATGGCTACCA
EST: gi|162160847|gb|FC337669.1|FC337669
EST:     TTCCTCTGCCTTGACCGACATNTTCATCGCCTCAGTCCTGGTCACTGAAG                         ATGAGGACCTTTGGAACTTGGAGATGTATCCGCCGGAGGCTATGGCTACCA
genomic: TTCCTCTGCCTTGACCGACATTTTCATCGCCTCAGTCCTGGTCACTGAAGgtgagcaatt ... tcaagtacagATGAGGACCTTTGGAACTTGGAGATGTATCCGCCGGAGGCTATGGCTACCA
EST: gi|208358689|gb|DC942911.1|DC942911
EST:     TTCCTCTGCCTTGACCGACATTTTCATCGCCTCAGTCCTGGTCACTGAAG                         ATGAGGACCTTTGGAACTTGGAGATGTATCCGCCGGAGGCTATGGCTACCA
genomic: TTCCTCTGCCTTGACCGACATTTTCATCGCCTCAGTCCTGGTCACTGAAGgtgagcaatt ... tcaagtacagATGAGGACCTTTGGAACTTGGAGATGTATCCGCCGGAGGCTATGGCTACCA
EST: gi|162265408|gb|FC440734.1|FC440734
EST:     TTCCTCTGCCTTGACCGACATTTTCATCGCCTCAGTCCTGGTCACTGAAG                         ATGAGGACCTTTGGAACTTGGAGATGTATCCGCCGGAGGCTATGGCTACCA
genomic: TTCCTCTGCCTTGACCGACATTTTCATCGCCTCAGTCCTGGTCACTGAAGgtgagcaatt ... tcaagtacagATGAGGACCTTTGGAACTTGGAGATGTATCCGCCGGAGGCTATGGCTACCA
EST: gi|162185767|gb|FC362323.1|FC362323
EST:     CTCTGCCTTGACCGACATTTTCATCGCCTCAGTCCTGGTCACTGAAG                         ATGAGGACCTTTGGAACTTGGAGATGTATCCGCCGGAGGCTATGGCTACCA
genomic: CTCTGCCTTGACCGACATTTTCATCGCCTCAGTCCTGGTCACTGAAGgtgagcaatt ... tcaagtacagATGAGGACCTTTGGAACTTGGAGATGTATCCGCCGGAGGCTATGGCTACCA
EST: gi|162151452|gb|FC326957.1|FC326957
EST:     TTCCTCTGCCTTGACCGACATTTTCATCGCCTCAGTCCTGGTCACTGAAG                         ATGAGGACCTTTGGAACTTGGAGATGTATCCGCCGGAGGCTATGGCTACCA
genomic: TTCCTCTGCCTTGACCGACATTTTCATCGCCTCAGTCCTGGTCACTGAAGgtgagcaatt ... tcaagtacagATGAGGACCTTTGGAACTTGGAGATGTATCCGCCGGAGGCTATGGCTACCA

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: 15

TCTCATGTTGGGCGTAACGGATTTGATGAGAGGACGGAAGAGCCTAGTACTTCCTCTGCCTTGACCGACATTTTCATCGCCTCAGTCCTGGTCACTGAAGgtgagcaatt ... tcaagtacagATGAGGACCTTTGGAACTTGGAGATGTATCCGCCGGAGGCTATGGCTACCAGCAATGACTTTGTATCGAATATACTTAACG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgtctagctaatgtcatcggtcgttgtttaatagtatttggcttgtcaagtacagATGAGGACCTTTGGAACTTGGAGATGTATCCGCCGGAGGCTATGGCTACCAGCAATGACTTTGTATCGAATATACTTAACG
                       ttgtttaatagtattt  TA-rich tract