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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattgttctcgtatttggtttaatttttcgatcctgaataagtacgttgcgacttatttactctggcaaggagaacttgggtaaagacaatgtgaatgactaccattgagttttgaagtggattttttgtggccagtagtagagtaatcagactgtctacacatcgtttatgcagTTGCAAAGCCATTGGTGGCTGATGGTTCTGCCAAGTCACATGCCATGTCACTTGCATATGACCGTTTTGGGCTATCTTCCCTGGACACTCCCCTTGTTCT

Basic information

species Physcomitrella patens
transcript PP1S46_310V6.1
intron # 7
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|162271516|gb|FC446465.1|FC446465
EST:     GTCCTGCATTCCATCCTCCGTAGCTGAAGCAGGATTGAAGCTGCCTTTGG                         TTGCAAAGCCATTGGTGGCTGATGGTTCTGCCAAGTCACATGCCATGTCAC
genomic: GTCCTGCATTCCATCCTCCGTAGCTGAAGCAGGATTGAAGCTGCCTTTGGgtaattgttc ... gtttatgcagTTGCAAAGCCATTGGTGGCTGATGGTTCTGCCAAGTCACATGCCATGTCAC
EST: gi|208370333|gb|DC931745.1|DC931745
EST:     GTCCTGCATTCCATCCTCCGTAGCTGAAGCAGGATTGAAGCTGCCTTTGG                         TTGCAA-GCCATTGGTGGCTGATGGTTCTGCCA-GTCACATGCCATGTCAC
genomic: GTCCTGCATTCCATCCTCCGTAGCTGAAGCAGGATTGAAGCTGCCTTTGGgtaattgttc ... gtttatgcagTTGCAAAGCCATTGGTGGCTGATGGTTCTGCCAAGTCACATGCCATGTCAC
EST: gi|100424319|gb|BY958425.1|BY958425
EST:     GTCCTGCATTCCATCCTCCGTAGCTGAAGCAGGATTGAAGCTGCCTTTGG                         TTGCAAAGCCATTGGTGGCTGATGGTTCTGCC
genomic: GTCCTGCATTCCATCCTCCGTAGCTGAAGCAGGATTGAAGCTGCCTTTGGgtaattgttc ... gtttatgcagTTGCAAAGCCATTGGTGGCTGATGGTTCTGCC
EST: gi|162230406|gb|FC407074.1|FC407074
EST:     GTCCTGCATTCCATCCTCCGTAGCTGAAGCAGGATTGAAGCTGCCTTTGG                         TTGCAAAGCCATTGGTGGCTGATGGTTCTGCCAAGTCACATGCCATGTCAC
genomic: GTCCTGCATTCCATCCTCCGTAGCTGAAGCAGGATTGAAGCTGCCTTTGGgtaattgttc ... gtttatgcagTTGCAAAGCCATTGGTGGCTGATGGTTCTGCCAAGTCACATGCCATGTCAC
EST: gi|67572564|gb|BJ945388.1|BJ945388
EST:     GTCCTGCATTCCATCCTCCGTAGCTGAAGCAGGATTGAAGCTGCCTTTGG                         TTGCAAAGCCATTGGTGGCTGATGGTTCTGCCAAGTCACATGCCATGTCAC
genomic: GTCCTGCATTCCATCCTCCGTAGCTGAAGCAGGATTGAAGCTGCCTTTGGgtaattgttc ... gtttatgcagTTGCAAAGCCATTGGTGGCTGATGGTTCTGCCAAGTCACATGCCATGTCAC

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: 28 (upstream exon), 21 (downstream exon)
Score: 5

GACAAGTACGAGTTCCAAAGCAACTGGTGGTTGTCGGTGATTCGTCCTGCATTCCATCCTCCGTAGCTGAAGCAGGATTGAAGCTGCCTTTGGgtaattgttc ... gtttatgcagTTGCAAAGCCATTGGTGGCTGATGGTTCTGCCAAGTCACATGCCATGTCACTTGCATATGACCGTTTTGGGCTATCTTCCCTGGACACTCCCCTTGTTCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattttttgtggccagtagtagagtaatcagactgtctacacatcgtttatgcagTTGCAAAGCCATTGGTGGCTGATGGTTCTGCCAAGTCACATGCCATGTCACTTGCATATGACCGTTTTGGGCTATCTTCCCTGGACACTCCCCTTGTTCT
                                              tttat  TA-rich tract