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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcaatgccgctgtcataaacaatcattcaactgtctatgctggcttagttgtatccatattgttatctcatccattttctacggtatggtctatttgcagATTGGATTGGCCATGTCTCCGCTAAGCAACAATTCTCTTTTCCTAGACTATCATCGCAACCCTTTTCCTATGTTTTTTGCCCGAGGTCTGAATGTATCGC

Basic information

species Physcomitrella patens
transcript PP1S77_89V6.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S77_89V6.1 (Physcomitrella patens), 3'ss of exon 15
lower sequence: Vv08s0105g00570.t01 (Vitis vinifera), 3'ss of exon 15
-tcaatgccgctgtcataaacaatcattcaactgtctatgctggcttagttgtatccatattgttatctcatccattttctacggtatggtctatttgcagATTGGATTGGCCATGTCTCCGCTAAGCAACAATTCTCTTTTCCTAGACTATCATCGCAACCCTTTTCCTATGTTTTTTGCCCGAGGTCTGAATGTATCGC
 | ||    |   | ||   |  |  |  |  | ||||  ||| |||  || | |||||| |   |||| ||    | |  |  | |||   |  || ||||||||  |||| |||||||| || |||||||||||  | ||  | ||||||||||| || |||||||||||||||||    || || || ||||| || |
gtaaaaagggagatgatg--ctgttttgaatatatctacactgacttgattat-tccatagt---atctgattggctgtg-attgcatg--ttggttacagATTGGTCTGGCTATGTCTCCTCTGAGCAACAATTCCTTGTTTTTGGACTATCATCGGAATCCTTTTCCTATGTTTTTCCTTCGGGGCCTCAATGTTTCCC
















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|162194297|gb|FC369520.1|FC369520
EST:     ACAATCTGCGTAAAACTCCTGGTCTACAGTATCTTTATTACCTTGCCCAG                         ATTGGATTGGCCATGTCTCCGCTAAGCAACAATTCTCTTTTCCTAGACTAT
genomic: ACAATCTGCGTAAAACTCCTGGTCTACAGTATCTTTATTACCTTGCCCAGgttttctttc ... ctatttgcagATTGGATTGGCCATGTCTCCGCTAAGCAACAATTCTCTTTTCCTAGACTAT
EST: gi|19779903|gb|BQ039488.1|BQ039488
EST:     ACAATCTGCGTAAAACTCCTGGTCTACAGTATCTTTATTACCTTGCCCAG                         ATTGGATTGGCCATGTCTCCGCTAAGCAACAATTCTCTTTTCCTAGACTAT
genomic: ACAATCTGCGTAAAACTCCTGGTCTACAGTATCTTTATTACCTTGCCCAGgttttctttc ... ctatttgcagATTGGATTGGCCATGTCTCCGCTAAGCAACAATTCTCTTTTCCTAGACTAT
EST: gi|7147916|gb|AW509838.1|AW509838
EST:     AATCTGCGTAAAACTCCTGGTCTACAGTATCTTTATTACCTTGCCCAG                         ATTGGATTGGCCATGTCTCCGCTAAGCAACAATTCTCTTTTCCTAGACTAT
genomic: AATCTGCGTAAAACTCCTGGTCTACAGTATCTTTATTACCTTGCCCAGgttttctttc ... ctatttgcagATTGGATTGGCCATGTCTCCGCTAAGCAACAATTCTCTTTTCCTAGACTAT
EST: gi|162268981|gb|FC445473.1|FC445473
EST:     ACAATCTGCGTAAAACTCCTGGTCTACAGTATCTTTATTACCTTGCCCAG                         ATTGGATTGGCCATGTCTCCGCTAAGCAACAATTCTCTTTTCCTAGACTAT
genomic: ACAATCTGCGTAAAACTCCTGGTCTACAGTATCTTTATTACCTTGCCCAGgttttctttc ... ctatttgcagATTGGATTGGCCATGTCTCCGCTAAGCAACAATTCTCTTTTCCTAGACTAT

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: 17 (upstream exon), 30 (downstream exon)
Score: 2

GGACCATTTAGCAGCATCCTTCTTGGTGGCACACAATATTGCGCATGGAAACAATCTGCGTAAAACTCCTGGTCTACAGTATCTTTATTACCTTGCCCAGgttttctttc ... ctatttgcagATTGGATTGGCCATGTCTCCGCTAAGCAACAATTCTCTTTTCCTAGACTATCATCGCAACCCTTTTCCTATGTTTTTTGCCCGAGGTCTGAATGTATCGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagttgtatccatattgttatctcatccattttctacggtatggtctatttgcagATTGGATTGGCCATGTCTCCGCTAAGCAACAATTCTCTTTTCCTAGACTATCATCGCAACCCTTTTCCTATGTTTTTTGCCCGAGGTCTGAATGTATCGC
                                            tctattt  CT-rich tract
           atattgttat  TA-rich tract