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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTATTGCCGGTGTGGCGGATGACCAAGGTTTTGGCTGGGCCATTGCCAAAGCTCTGGCAGCAGCTGGAGCTGAAATTCTTGTCGGAACCTGGGTGCCGgtaagctattttaaccttgttgaatttgattattcatcaccacttgaattgccactcttaggttattatgacaagtttaatttgatcgagcctctttttggacaatgcag

Basic information

species Physcomitrella patens
transcript PP1S29_256V6.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S29_256V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: LOC_Os08g23810.2 (Oryza sativa), 5'ss of exon 3
GTTTATTGCCGGTGTGGCGGATGACCAAGGTTTTGGCTGGGCCATTGCCAAAGCTCTGGCAGCAGCTGGAGCTGAAATTCTTGTCGGAACCTGGGTGCCGgtaagctattttaaccttgttgaatttgattattcatcaccacttgaattgccactcttaggttatt--atgacaagtttaatttgatcgagcctctttttggacaatgcag
||| ||||| || || || |||||| | || | ||||||||| ||||| || ||||| || || ||||| |||||||||||||| || || |||||||| |||||    |  |||  |       || | ||   ||||    ||   || |   |  |   | | |  |||   ||||  |  ||  |                       
GTTCATTGCTGGAGTTGCTGATGACAATGGCTATGGCTGGGCAATTGCAAAGGCTCTTGCTGCTGCTGGTGCTGAAATTCTTGTTGGTACATGGGTGCCTgtaagtggatccaactcttgcagtgttcaatagggatcatttttttttttcctctttgtcattcacttaatggagagttctacctgcacag---------------------

upper sequence: PP1S29_256V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GLYMA08G45990.1 (Glycine max), 5'ss of exon 3
GTTTATTGCCGGTGTGGCGGATGACCAAGGTTTTGGCTGGGCCATTGCCAAAGCTCTGGCAGCAGCTGGAGCTGAAATTCTTGTCGGAACCTGGGTGCCGgtaagctattttaac-----cttgttgaatttgattattcatcacc-acttgaattgccactcttaggttat---tatgacaagtttaatttgatcgagcctctttttggaca-----atgcag
 || ||||| |||||||| |||||| | || | ||||||||| || || ||| |||| |||||||| |||||||||||||||||||| || ||||| || |||||  | | | ||     || ||  | | || ||   |||     ||||  |   |     | | |||||   | ||  |  |  || | |   |   ||   || | |||     ||||||
TTTCATTGCTGGTGTGGCTGATGACAATGGATATGGCTGGGCAATAGCAAAATCTCTTGCAGCAGCAGGAGCTGAAATTCTTGTCGGCACATGGGTACCTgtaagtaaatatcactgattctggtgtagtgtgtttgcacattgtttacttttacc-ctgaaatcatgttatctctgtgtaatatacaagtggtcaggttctaacttcgaacattttcatgcag

upper sequence: PP1S29_256V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GLYMA18G31780.1 (Glycine max), 5'ss of exon 2
GTTTATTGCCGGTGTGGCGGATGACCAAGGTTTTGGCTGGGCCATTGCCAAAGCTCTGGCAGCAGCTGGAGCTGAAATTCTTGTCGGAACCTGGGTGCCGgtaagc---tatt-ttaaccttgttg-aatttgattattcatcac---cacttgaattgccactcttaggttattatgacaagtttaatttgatcgagcctctttttggaca-----atgcag
 || ||||| |||||||| |||||| | || | ||||||||| || || ||| |||| |||||||| |||||||||||||||||||| || ||||| || |||||    ||||  | |   || || | | || || | |||      |  ||    ||  |   |    |   | ||| |  |  || | |   |   ||   |||| |||     ||||||
TTTCATTGCTGGTGTGGCTGATGACAATGGATATGGCTGGGCAATAGCAAAATCTCTCGCAGCAGCAGGAGCTGAAATTCTTGTCGGCACATGGGTACCTgtaagtaaatattactgattctggtgtagtgtgtttgtacattgtttacttttaccctgaaatgatggcatctctgtgaaatatacaagtggtcaggtactaactttgaacattttcatgcag

upper sequence: PP1S29_256V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GLYMA11G10770.1 (Glycine max), 5'ss of exon 3
GTTTATTGCCGGTGTGGCGGATGACCAAGGTTTTGGCTGGGCCATTGCCAAAGCTCTGGCAGCAGCTGGAGCTGAAATTCTTGTCGGAACCTGGGTGCCGgtaagctattttaaccttgttga-atttgattattcatcaccacttgaattgccactct--taggttattatgacaagtttaatttgatcgagcctctttttggacaatgcag--------------------------------------------------------
 |||||||| ||||| || |||||| | || | ||| ||||| ||||| ||| |||| || ||||| ||||||||||||||||| || || ||||| || ||||| |||||     || | || |    ||   |    | || ||||  | | | |     ||||| |     |    ||  || || | |  |          || ||||                                                         
TTTTATTGCTGGTGTTGCTGATGACAATGGATATGGATGGGCAATTGCAAAATCTCTTGCTGCAGCCGGAGCTGAAATTCTTGTTGGCACATGGGTACCTgtaagttatttgtttattttggataaaaaatgggtacctatcagttgatatacaaattcacgaggttctgtctgctgactt--ttggaacaacacctcccccctccagtgcatatgttttccagtccttttacggtgatacatttactaactgtgaactatttctatag

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|100389328|gb|BY971078.1|BY971078
EST:     AAGCTCTGGCAGCAGCTGGAGCTGAAATTCTTGTCGGAACCTGGGTGCCG                         GCTCTTAACATCTTCGAGACCAGTCTCAGGAGAGGCAAGTTCGACGAGTCC
genomic: AAGCTCTGGCAGCAGCTGGAGCTGAAATTCTTGTCGGAACCTGGGTGCCGgtaagctatt ... gacaatgcagGCTCTTAACATCTTCGAGACCAGTCTCAGGAGAGGCAAGTTCGACGAGTCC
EST: gi|162171618|gb|FC347559.1|FC347559
EST:     AAGCTCTGGCAGCAGCTGGAGCTGAAATTCTTGTCGGAACCTGGGTGCCG                         GCTCTTAACATCTTCGAGACCAGTCTCAGGAGAGGCAAGTTCGACGAGTCC
genomic: AAGCTCTGGCAGCAGCTGGAGCTGAAATTCTTGTCGGAACCTGGGTGCCGgtaagctatt ... gacaatgcagGCTCTTAACATCTTCGAGACCAGTCTCAGGAGAGGCAAGTTCGACGAGTCC
EST: gi|19777824|gb|BQ039232.1|BQ039232
EST:     AAGCTCTGGCAGCAGCTGGAGCTGAAATTCTTGTCGGAACCTGGGTGCCG                         GCTCTTAACATCTTCGAGACCAGTCTCAGGAGAGGCAAGTTCGACGAGTCC
genomic: AAGCTCTGGCAGCAGCTGGAGCTGAAATTCTTGTCGGAACCTGGGTGCCGgtaagctatt ... gacaatgcagGCTCTTAACATCTTCGAGACCAGTCTCAGGAGAGGCAAGTTCGACGAGTCC
EST: gi|18345650|gb|BJ177693.1|BJ177693
EST:     AAGCTCTGGCAGCAGCTGGAGCTGAAATTCTTGTCGGAACCTGGGTGCCG                         GCTCTTAACATCTTC
genomic: AAGCTCTGGCAGCAGCTGGAGCTGAAATTCTTGTCGGAACCTGGGTGCCGgtaagctatt ... gacaatgcagGCTCTTAACATCTTC
EST: gi|67717450|gb|BJ967709.1|BJ967709
EST:     AAGCTCTGGCAGCAGCTGGAGCTGAAATTCTTGTCGGAACCTGGGTGCCG                         GCTCTTAACATCTTCGAGACCAGTCTCAGGAGAGGCAAGTTCGACGAGTCC
genomic: AAGCTCTGGCAGCAGCTGGAGCTGAAATTCTTGTCGGAACCTGGGTGCCGgtaagctatt ... gacaatgcagGCTCTTAACATCTTCGAGACCAGTCTCAGGAGAGGCAAGTTCGACGAGTCC
EST: gi|18351024|gb|BJ183075.1|BJ183075
EST:     AAGCTCTGGCAGCAGCTGGAGCTGAAATTCTTGTCGGAACCTGGGTGCCG                         GCTCTTAACATCTTCGAGACCAGTCTCA
genomic: AAGCTCTGGCAGCAGCTGGAGCTGAAATTCTTGTCGGAACCTGGGTGCCGgtaagctatt ... gacaatgcagGCTCTTAACATCTTCGAGACCAGTCTCA
EST: gi|67719586|gb|BJ969845.1|BJ969845
EST:     AAGCTCTGGCAGCAGCTGGAGCTGAAATTCTTGTCGGAACCTGGGTGCCG                         GCTCTTAACATCTTCGAGACCAGTCTCAGGAGAGGCAAGTTCGACGAGTCC
genomic: AAGCTCTGGCAGCAGCTGGAGCTGAAATTCTTGTCGGAACCTGGGTGCCGgtaagctatt ... gacaatgcagGCTCTTAACATCTTCGAGACCAGTCTCAGGAGAGGCAAGTTCGACGAGTCC
EST: gi|100368841|gb|BY984912.1|BY984912
EST:     AAGCTCTGGCAGCAGCTGGAGCTGAAATTCTTGTCGGAACCTGGGTGCCG                         GCTCTTAACGTCTTCAAGACCAGTCTCAGGAGAGGCAAGTTCGACGAGTCC
genomic: AAGCTCTGGCAGCAGCTGGAGCTGAAATTCTTGTCGGAACCTGGGTGCCGgtaagctatt ... gacaatgcagGCTCTTAACATCTTCGAGACCAGTCTCAGGAGAGGCAAGTTCGACGAGTCC
EST: gi|67718262|gb|BJ968521.1|BJ968521
EST:     AAGCTCTGGCAGCAGCTGGAGCTGAAATTCTTGTCGGAACCTGGGTGCCG                         GCTCTTAACATCTTCGAGACCAGTCTCAGGAGAGGCAAGTTCGACGAGTCC
genomic: AAGCTCTGGCAGCAGCTGGAGCTGAAATTCTTGTCGGAACCTGGGTGCCGgtaagctatt ... gacaatgcagGCTCTTAACATCTTCGAGACCAGTCTCAGGAGAGGCAAGTTCGACGAGTCC
EST: gi|162176349|gb|FC353534.1|FC353534
EST:     AAGCTCTGGCAGCAGCTGGAGCTGAAATTCTTGTCGGAACCTGGGTGCCG                         GCTCTTAACATCTTCGAGACCAGTCTCAGGAGAGGCAAGTTCGACGAGTCC
genomic: AAGCTCTGGCAGCAGCTGGAGCTGAAATTCTTGTCGGAACCTGGGTGCCGgtaagctatt ... gacaatgcagGCTCTTAACATCTTCGAGACCAGTCTCAGGAGAGGCAAGTTCGACGAGTCC
EST: gi|18350765|gb|BJ182816.1|BJ182816
EST:     AAGCTCTGGCAGCAGCTGGAGCTGAAATTCTTGTCGGAACCTGGGTGCCG                         GCTCTTAACATCTTCGAGACCAGTCTCAGGAGANGCAAGTTCGACGAGTCC
genomic: AAGCTCTGGCAGCAGCTGGAGCTGAAATTCTTGTCGGAACCTGGGTGCCGgtaagctatt ... gacaatgcagGCTCTTAACATCTTCGAGACCAGTCTCAGGAGAGGCAAGTTCGACGAGTCC
EST: gi|208359693|gb|DC930283.1|DC930283
EST:     AAGCTCTGGCAGCAGCTGGAGCTGAAATTCTTGTCGGAACCTGGGTGCCG                         GCTCTTAACATCTTCNAGACCAGTCTCAGGAGAGGCAAGTTCGACGAGTCC
genomic: AAGCTCTGGCAGCAGCTGGAGCTGAAATTCTTGTCGGAACCTGGGTGCCGgtaagctatt ... gacaatgcagGCTCTTAACATCTTCGAGACCAGTCTCAGGAGAGGCAAGTTCGACGAGTCC
EST: gi|162167232|gb|FC342797.1|FC342797
EST:     AAGCTCTGGCAGCAGCTGGAGCTGAAATTCTTGTCGGAACCTGGGTGCCG                         GCTCTTAACATCTTCGAGACCAGTCTCAGGAGAGGCAAGTTCGACGAGTCC
genomic: AAGCTCTGGCAGCAGCTGGAGCTGAAATTCTTGTCGGAACCTGGGTGCCGgtaagctatt ... gacaatgcagGCTCTTAACATCTTCGAGACCAGTCTCAGGAGAGGCAAGTTCGACGAGTCC
EST: gi|100386758|gb|BY970299.1|BY970299
EST:     AAGCTCTGGCAGCAGCTGGAGCTGAAATTCTTGTCGGAACCTGGGTGCCG                         GCTCTTAACATCTTCGAGACCAGTCTCAGGAGAGGCAAGTTCGACGAGTCC
genomic: AAGCTCTGGCAGCAGCTGGAGCTGAAATTCTTGTCGGAACCTGGGTGCCGgtaagctatt ... gacaatgcagGCTCTTAACATCTTCGAGACCAGTCTCAGGAGAGGCAAGTTCGACGAGTCC
EST: gi|162169525|gb|FC346089.1|FC346089
EST:     AAGCTCTGGCAGCAGCTGGAGCTGAAATTCTTGTCGGAACCTGGGTGCCG                         GCTCTTAACATCTTCGAGACCAGTCTCAGGAGAGGCAAGTTCGACGAGTCC
genomic: AAGCTCTGGCAGCAGCTGGAGCTGAAATTCTTGTCGGAACCTGGGTGCCGgtaagctatt ... gacaatgcagGCTCTTAACATCTTCGAGACCAGTCTCAGGAGAGGCAAGTTCGACGAGTCC
EST: gi|162169758|gb|FC345295.1|FC345295
EST:     AAGCTCTGGCAGCAGCTGGAGCTGAAATTCTTGTCGGAACCTGGGTGCCG                         GCTCTTAACATCTTCGAGACCAGTCTCAGGAGAGGCAAGTTCGACGAGTCC
genomic: AAGCTCTGGCAGCAGCTGGAGCTGAAATTCTTGTCGGAACCTGGGTGCCGgtaagctatt ... gacaatgcagGCTCTTAACATCTTCGAGACCAGTCTCAGGAGAGGCAAGTTCGACGAGTCC
EST: gi|100418707|gb|BY975701.1|BY975701
EST:     AAGCTCTGGCAGCAGCTGGAGCTGAAATTCTTGTCGGAACCTGGGTGCCG                         GCTCTTAACATCTTCGAGACCAGTCTCAGGAGAGGCAAGTTCGACGAGTCC
genomic: AAGCTCTGGCAGCAGCTGGAGCTGAAATTCTTGTCGGAACCTGGGTGCCGgtaagctatt ... gacaatgcagGCTCTTAACATCTTCGAGACCAGTCTCAGGAGAGGCAAGTTCGACGAGTCC
EST: gi|162176594|gb|FC353063.1|FC353063
EST:     AAGCTCTGGCAGCAGCTGGAGCTGAAATTCTTGTCGGAACCTGGGTGCCG                         GCTCTTAACATCTTCGAGACCAGTCTCAGGAGAGGCAAGTTCGACGAGTCC
genomic: AAGCTCTGGCAGCAGCTGGAGCTGAAATTCTTGTCGGAACCTGGGTGCCGgtaagctatt ... gacaatgcagGCTCTTAACATCTTCGAGACCAGTCTCAGGAGAGGCAAGTTCGACGAGTCC
EST: gi|162181164|gb|FC357609.1|FC357609
EST:     AAGCTCTGGCAGCAGCTGGAGCTGAAATTCTTGTCGGAACCTGGGTGCCG                         GCTCTTAACATCTTCGAGACCAGTCTCAGGAGAGGCAAGTTCGACGAGTCC
genomic: AAGCTCTGGCAGCAGCTGGAGCTGAAATTCTTGTCGGAACCTGGGTGCCGgtaagctatt ... gacaatgcagGCTCTTAACATCTTCGAGACCAGTCTCAGGAGAGGCAAGTTCGACGAGTCC
EST: gi|67718833|gb|BJ969092.1|BJ969092
EST:     AAGCTCTGGCAGCAGCTGGAGCTGAAATTCTTGTCGGAACCTGGGTGCCG                         GCTCTTAACATCTTCGAGACCAGTCTCAGGAGAGGCAAGTTCGACGAGTCC
genomic: AAGCTCTGGCAGCAGCTGGAGCTGAAATTCTTGTCGGAACCTGGGTGCCGgtaagctatt ... gacaatgcagGCTCTTAACATCTTCGAGACCAGTCTCAGGAGAGGCAAGTTCGACGAGTCC
EST: gi|18361236|gb|BJ193301.1|BJ193301
EST:     AAGCTCTGGCAGCAGCTGGAGCTGAAATTCTTGTCGGAACCTGGGTGCCG                         GCTCTTAACATCTTCGAGAC
genomic: AAGCTCTGGCAGCAGCTGGAGCTGAAATTCTTGTCGGAACCTGGGTGCCGgtaagctatt ... gacaatgcagGCTCTTAACATCTTCGAGAC
EST: gi|18325596|gb|BJ157593.1|BJ157593
EST:     AAGCTCTGGCAGCAGCTGGAGCTGAAATTCTTGTCGGAACCTGGGTGCCG                         GCTCTTAACATCTTCGAGACCAGTCTCAGGAGAGGCAAGTTCGACGAGTCC
genomic: AAGCTCTGGCAGCAGCTGGAGCTGAAATTCTTGTCGGAACCTGGGTGCCGgtaagctatt ... gacaatgcagGCTCTTAACATCTTCGAGACCAGTCTCAGGAGAGGCAAGTTCGACGAGTCC
EST: gi|100384688|gb|BY950678.1|BY950678
EST:     AAGCTCTGGCAGCAGCTGGAGCTGAAATTCTTGTCGGAACCTGGGTGCCG                         GCTCTTAACATCTTCGAGACCAGTCTCAGGAGAGGCAAGTTCGACGAGTCC
genomic: AAGCTCTGGCAGCAGCTGGAGCTGAAATTCTTGTCGGAACCTGGGTGCCGgtaagctatt ... gacaatgcagGCTCTTAACATCTTCGAGACCAGTCTCAGGAGAGGCAAGTTCGACGAGTCC
EST: gi|100429370|gb|BY978077.1|BY978077
EST:     AAGCTCTGGCAGCAGCTGGAGCTGAAATTCTTGTCGGAACCTGGGTGCCG                         GCTCTTAACATCTTCGAGACCAGTCTCAGGAGAGGCAAGTTCGACGAGTCC
genomic: AAGCTCTGGCAGCAGCTGGAGCTGAAATTCTTGTCGGAACCTGGGTGCCGgtaagctatt ... gacaatgcagGCTCTTAACATCTTCGAGACCAGTCTCAGGAGAGGCAAGTTCGACGAGTCC
EST: gi|100403476|gb|BY991219.1|BY991219
EST:     AAGCTCTGGCAGCAGCTGGAGCTGAAATTCTTGTCGGAACCTGGGTGCCG                         GCTCTTAACATCTTCGAGACCAGTCTCAGGAGAGGCAAGTTCGACGAGTCC
genomic: AAGCTCTGGCAGCAGCTGGAGCTGAAATTCTTGTCGGAACCTGGGTGCCGgtaagctatt ... gacaatgcagGCTCTTAACATCTTCGAGACCAGTCTCAGGAGAGGCAAGTTCGACGAGTCC
EST: gi|162241271|gb|FC416902.1|FC416902
EST:     AAGCTCTGGCAGCAGCTGGAGCTGAAATTCTTGTCGGAACCTGGGTGCCG                         GCTCTTAACATCTTCGAGACCAGTCTCAGGAGAGGCAAGTTCGACGAGTCC
genomic: AAGCTCTGGCAGCAGCTGGAGCTGAAATTCTTGTCGGAACCTGGGTGCCGgtaagctatt ... gacaatgcagGCTCTTAACATCTTCGAGACCAGTCTCAGGAGAGGCAAGTTCGACGAGTCC

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: 35 (upstream exon), 33 (downstream exon)
Score: 9

GTTTATTGCCGGTGTGGCGGATGACCAAGGTTTTGGCTGGGCCATTGCCAAAGCTCTGGCAGCAGCTGGAGCTGAAATTCTTGTCGGAACCTGGGTGCCGgtaagctatt ... gacaatgcagGCTCTTAACATCTTCGAGACCAGTCTCAGGAGAGGCAAGTTCGACGAGTCCCGGCA




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Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTTATTGCCGGTGTGGCGGATGACCAAGGTTTTGGCTGGGCCATTGCCAAAGCTCTGGCAGCAGCTGGAGCTGAAATTCTTGTCGGAACCTGGGTGCCGgtaagctattttaaccttgttgaatttgattattcatcaccacttgaattgccactcttaggttattatgacaagtttaatttgatcgagcctctttttggacaatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA