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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctctaccttaacattctgtcagtgatatgcctctggacgaactgtctgaaattgaaatacaatatacatgatgtagatacttatgttgtaagcttcagtgatcttcataattgagcacttgccatgccgctaacattggcacatggtgccgtctccagGGTCATTGGCCATTCCCTCGCGACAAATTGATGATGGGATATGCATACATTTTAACACACCCTGGAACT

Basic information

species Physcomitrella patens
transcript PP1S100_191V6.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S100_191V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: Vv14s0068g00420.t01 (Vitis vinifera), 3'ss of exon 12
gtctctaccttaacattctgtcagtgatatgcctctggacgaactgtctgaaattgaaatacaatatacatgatgtagatacttatgttgtaagcttcagtgatcttcataattgagcacttgccatgccgctaacat-tggcacatggtgccgtctccagGGTCATTGGCCATTCCCTCGCGACAAATTGATGATGGGATATGCATACATTTTAACACACCCTGGAACT
                                                           ||     ||| || | |   |||| ||||   | |    | | || |    |||  ||| |     |||   ||||| | |  ||  ||        | ||||||||||||||||| || || || ||  | |    ||||||||||||||||||||| || |||||||| 
-----------------------------------------------------------taatcagtacctgttttgcttactcatgtc-catgtcaaactaatgta-gcaatgaagctcgaaggatgagactaacttgtaacatttgtgttttatttcagGGTCATTGGCCATTTCCACGAGATAAGCTTACACAGGGATATGCATACATTTTAACCCATCCTGGAACG
















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|162169840|gb|FC346196.1|FC346196
EST:     CTTCTCGTGCAGTTACTTTCCTTGAGAATCACGATACCGGATCAACTCAG                         GGTCATTGGCCATTCCCTCGCGACAAATTGATGATGGGATATGCATACATT
genomic: CTTCTCGTGCAGTTACTTTCCTTGAGAATCACGATACCGGATCAACTCAGgtctctacct ... ccgtctccagGGTCATTGGCCATTCCCTCGCGACAAATTGATGATGGGATATGCATACATT
EST: gi|19780303|gb|BQ039545.1|BQ039545
EST:     CTTCTCGTGCAGTTACTTTCCTTGAGAATCACGATACCGGATCAACTCAG                         GGTCATTGGCCATTCCCT
genomic: CTTCTCGTGCAGTTACTTTCCTTGAGAATCACGATACCGGATCAACTCAGgtctctacct ... ccgtctccagGGTCATTGGCCATTCCCT
EST: gi|162166455|gb|FC342437.1|FC342437
EST:     CTTCTCGTGCAGTTACTTTCCTTGAGAATCACGATACCGGATCAACTCAG                         GGTCATTGGCCATTCCCTCGCGACAAATTGATGATGGGATATGCATACATT
genomic: CTTCTCGTGCAGTTACTTTCCTTGAGAATCACGATACCGGATCAACTCAGgtctctacct ... ccgtctccagGGTCATTGGCCATTCCCTCGCGACAAATTGATGATGGGATATGCATACATT
EST: gi|162167712|gb|FC344026.1|FC344026
EST:     CTTCTCGTGCAGTTACTTTCCTTGAGAATCACGATACCGGATCAACTCAG                         GGTCATTGGCCATTCCCTCGCGACAAATTGATGATGGGATATGCATACATT
genomic: CTTCTCGTGCAGTTACTTTCCTTGAGAATCACGATACCGGATCAACTCAGgtctctacct ... ccgtctccagGGTCATTGGCCATTCCCTCGCGACAAATTGATGATGGGATATGCATACATT
EST: gi|162245205|gb|FC422134.1|FC422134
EST:     CTTCTCGTGCAGTTACTTTCCTTGAGAATCACGATACCGGATCAACTCAG                         GGTCATTGGCCATTCCCTCGCGACAAATTGATGATGGGATATGCATACATT
genomic: CTTCTCGTGCAGTTACTTTCCTTGAGAATCACGATACCGGATCAACTCAGgtctctacct ... ccgtctccagGGTCATTGGCCATTCCCTCGCGACAAATTGATGATGGGATATGCATACATT
EST: gi|162184867|gb|FC361377.1|FC361377
EST:     CTTCTCGTGCAGTTACTTTCCTTGAGAATCACGATACCGGATCAACTCAG                         GGTCATTGGCCATTCCCTCGCGACAAATTGATGATGGGATATGCATACATT
genomic: CTTCTCGTGCAGTTACTTTCCTTGAGAATCACGATACCGGATCAACTCAGgtctctacct ... ccgtctccagGGTCATTGGCCATTCCCTCGCGACAAATTGATGATGGGATATGCATACATT
EST: gi|162171740|gb|FC348201.1|FC348201
EST:     CTTCTCGTGCAGTTACTTTCCTTGAGAATCACGATACCGGATCAACTCAG                         GGTCATTGGCCATTCCCTCGCGACAAATTGATGATGGGATATGCATACATT
genomic: CTTCTCGTGCAGTTACTTTCCTTGAGAATCACGATACCGGATCAACTCAGgtctctacct ... ccgtctccagGGTCATTGGCCATTCCCTCGCGACAAATTGATGATGGGATATGCATACATT
EST: gi|162254705|gb|FC430994.1|FC430994
EST:     CTTCTCGTGCAGTTACTTTCCTTGAGAATCACGATACCGGATCAACTCAG                         GGTCATTGGCCATTCCCTCGCGACAAATTGATGATGGGATATGCATACATT
genomic: CTTCTCGTGCAGTTACTTTCCTTGAGAATCACGATACCGGATCAACTCAGgtctctacct ... ccgtctccagGGTCATTGGCCATTCCCTCGCGACAAATTGATGATGGGATATGCATACATT
EST: gi|162169841|gb|FC346197.1|FC346197
EST:     CTTCTCGTGCAGTTACTTTCCTTGAGAATCACGATACCGGATCAACTCAG                         GGTCATTGGCCATTCCCTCGCGACAAATTGATGATGGGATATGCATACATT
genomic: CTTCTCGTGCAGTTACTTTCCTTGAGAATCACGATACCGGATCAACTCAGgtctctacct ... ccgtctccagGGTCATTGGCCATTCCCTCGCGACAAATTGATGATGGGATATGCATACATT
EST: gi|162150065|gb|FC326596.1|FC326596
EST:     CTTCTCGTGCAGTTACTTTCCTTGAGAATCACGATACCGGATCAACTCAG                         GGTCATTGGCCATTCCCTCGCGACAAATTGATGATGGGATATGCATACATT
genomic: CTTCTCGTGCAGTTACTTTCCTTGAGAATCACGATACCGGATCAACTCAGgtctctacct ... ccgtctccagGGTCATTGGCCATTCCCTCGCGACAAATTGATGATGGGATATGCATACATT
EST: gi|18338916|gb|BJ170942.1|BJ170942
EST:     CTTCTCGTGCAGTTACTTTCCTTGAGAATCACGATACCGGATCAACTCAG                         GGTCATTGGCCATTCCCTCGCGACAAATTGATGATGGGATATGCATACATT
genomic: CTTCTCGTGCAGTTACTTTCCTTGAGAATCACGATACCGGATCAACTCAGgtctctacct ... ccgtctccagGGTCATTGGCCATTCCCTCGCGACAAATTGATGATGGGATATGCATACATT
EST: gi|162171141|gb|FC347755.1|FC347755
EST:     CTTCTCGTGCAGTTACTTTCCTTGAGAATCACGATACCGGATCAACTCAG                         GGTCATTGGCCATTCCCTCGCGACAAATTGATGATGGGATATGCATACATT
genomic: CTTCTCGTGCAGTTACTTTCCTTGAGAATCACGATACCGGATCAACTCAGgtctctacct ... ccgtctccagGGTCATTGGCCATTCCCTCGCGACAAATTGATGATGGGATATGCATACATT
EST: gi|162164446|gb|FC341572.1|FC341572
EST:     CTTCTCGTGCAGTTACTTTCCTTGAGAATCACGATACCGGATCAACTCAG                         GGTCATTGGCCATTCCCTCGCGACAAATTGATGATGGGATATGCATACATT
genomic: CTTCTCGTGCAGTTACTTTCCTTGAGAATCACGATACCGGATCAACTCAGgtctctacct ... ccgtctccagGGTCATTGGCCATTCCCTCGCGACAAATTGATGATGGGATATGCATACATT
EST: gi|162183699|gb|FC359095.1|FC359095
EST:     CTTCTCGTGCAGTTACTTTCCTTGAGAATCACGATACCGGATCAACTCAG                         GGTCATTGGCCATTCCCTCGCGACAAATTGATGATGGGATATGCATACATT
genomic: CTTCTCGTGCAGTTACTTTCCTTGAGAATCACGATACCGGATCAACTCAGgtctctacct ... ccgtctccagGGTCATTGGCCATTCCCTCGCGACAAATTGATGATGGGATATGCATACATT
EST: gi|162164679|gb|FC340726.1|FC340726
EST:     CTTCTCGTGCAGTTACTTTCCTTGAGAATCACGATACCGGATCAACTCAG                         GGTCATTGGCCATTCCCTCGCGACAAATTGATGATGGGATATGCATACATT
genomic: CTTCTCGTGCAGTTACTTTCCTTGAGAATCACGATACCGGATCAACTCAGgtctctacct ... ccgtctccagGGTCATTGGCCATTCCCTCGCGACAAATTGATGATGGGATATGCATACATT
EST: gi|162171741|gb|FC348202.1|FC348202
EST:     CTTCTCGTGCAGTTACTTTCCTTGAGAATCACGATACCGGATCAACTCAG                         GGTCATTGGCCATTCCCTCGCGACAAATTGATGATGGGATATGCATACATT
genomic: CTTCTCGTGCAGTTACTTTCCTTGAGAATCACGATACCGGATCAACTCAGgtctctacct ... ccgtctccagGGTCATTGGCCATTCCCTCGCGACAAATTGATGATGGGATATGCATACATT
EST: gi|162167713|gb|FC344027.1|FC344027
EST:     CTTCTCGTGCAGTTACTTTCCTTGAGAATCACGATACCGGATCAACTCAG                         GGTCATTGGCCATTCCCTCGCGACAAATTGATGATGGGATATGCATACATT
genomic: CTTCTCGTGCAGTTACTTTCCTTGAGAATCACGATACCGGATCAACTCAGgtctctacct ... ccgtctccagGGTCATTGGCCATTCCCTCGCGACAAATTGATGATGGGATATGCATACATT
EST: gi|162191939|gb|FC366944.1|FC366944
EST:     CTTCTCGTGCAGTTACTTTCCTTGAGAATCACGATACCGGATCAACTCAG                         GGTCATTGGCCATTCCCTCGCGACAAATTGATGATGGGATATGCATACATT
genomic: CTTCTCGTGCAGTTACTTTCCTTGAGAATCACGATACCGGATCAACTCAGgtctctacct ... ccgtctccagGGTCATTGGCCATTCCCTCGCGACAAATTGATGATGGGATATGCATACATT

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: 33 (upstream exon), 35 (downstream exon)
Score: 6

GAGATTAATAGATCCTCAAGGAAAACCACCTGGAGTGATGGGTTGGTGGCCTTCTCGTGCAGTTACTTTCCTTGAGAATCACGATACCGGATCAACTCAGgtctctacct ... ccgtctccagGGTCATTGGCCATTCCCTCGCGACAAATTGATGATGGGATATGCATACATTTTAACACACCCTGGAACT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcataattgagcacttgccatgccgctaacattggcacatggtgccgtctccagGGTCATTGGCCATTCCCTCGCGACAAATTGATGATGGGATATGCATACATTTTAACACACCCTGGAACT
                        cgctaac  putative branch site (score: 6)
                                             ccgtctcc  putative PPT
                           taacatt  TA-rich tract