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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCATGATTGCTTGCGCTAAGGGTGGAACCAGCATAGAGGACCTTGCTGAGAAATATCCGGATCAGATTATCAAGgttttctttgtgttggtgtttgtatttgtgtttgatgtttgcagaatgtaattagagacttacaggccgttttttttttattattattattatcttgttctgggattatgcttccttgcatataacgatttagcagtagcatgtgaggtgaaattgtgagctctaagtgtgcag

Basic information

species Physcomitrella patens
transcript PP1S9_103V6.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S9_103V6.2 (Physcomitrella patens), 5'ss of exon 6
lower sequence: GLYMA10G04480.1 (Glycine max), 5'ss of exon 6
GTCATGATTGCTTGCGCTAAGGGTGGAACCAGCATAGAGGACCTTGCTGAGAAATATCCGGATCAGATTATCAAGgttttctttgtgttggtgtttgtatttgtgtttgatgtttgcagaatgtaattagagacttacaggccgttttttttttattattattattatcttgttctgggattatgcttccttgcatataacgatttagcagtagcatgtgaggtgaaattgtgagctctaagtgtgcag
 | || ||||||||   |||||| ||||||||||| || |||||||| ||||||| ||||||   |||||| |||||||  | |   ||||  ||| |  |  || || |  |||      ||           || || |   |   |  | || | ||  | |    | |                                                                             
ATTATAATTGCTTGTAGTAAGGGAGGAACCAGCATTGAAGACCTTGCAGAGAAATTTCCGGACATGATTATAAAGgtttgttgtcc-ttggcatttctcatcatggtttagttttttcacctgagcagtcttctttgcaagatatacctgatgtactctttctttctagtag-----------------------------------------------------------------------------
















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|208373828|gb|DC936599.1|DC936599
EST:     GAACCAGCATAGAGGACCTTGCTGAGAAATATCCGGATCAGATTATCAAG                         GTTCCAATCAACATCAACAAAGGTATTTCAGATG
genomic: GAACCAGCATAGAGGACCTTGCTGAGAAATATCCGGATCAGATTATCAAGgttttctttg ... aagtgtgcagGTTCCAATCAACATCAACAAAGGTATTTCAGATG
EST: gi|100379638|gb|BY949869.1|BY949869
EST:     AACCAGCATAGNAG-ACCTTGCTGAGAAATATCCGGATCAGATTATCANG                         GNTCCNANNTCA-CATCA-CAANGGTATTTCAGATGAAGAAGCCGAGAAAG
genomic: AACCAGCATAG-AGGACCTTGCTGAGAAATATCCGGATCAGATTATCAAGgttttctttg ... aagtgtgcagGTTCCAA--TCAACATCAACAAAGGTATTTCAGATGAAGAAGCCGAGAAAG
EST: gi|100395304|gb|BY953670.1|BY953670
EST:     GAACCAGCATAGAGGACCTTGCTGAGAAATATCCGGATCAGATTATCANG                         GTTCCAANNTCA-CATCA-CAAAGGTATTTCAGATGAAGAAGCCGAGAAAG
genomic: GAACCAGCATAGAGGACCTTGCTGAGAAATATCCGGATCAGATTATCAAGgttttctttg ... aagtgtgcagGTTCCAA--TCAACATCAACAAAGGTATTTCAGATGAAGAAGCCGAGAAAG
EST: gi|208369720|gb|DC932618.1|DC932618
EST:     GAACCAGCATANAGGACCTTGCTGAAAAATATCCGGATCANATTATCAAG                         GTTCCAATCAACATCAACAAAGGTATTTCAAATGA
genomic: GAACCAGCATAGAGGACCTTGCTGAGAAATATCCGGATCAGATTATCAAGgttttctttg ... aagtgtgcagGTTCCAATCAACATCAACAAAGGTATTTCAGATGA
EST: gi|208390018|gb|DC938073.1|DC938073
EST:     GAACCAGCATAGAGGACCTTGCTGAGAAATATCCGGATCAGATTATCAAG                         GTTCCAATCAACATCAACAAAGGTATTTC
genomic: GAACCAGCATAGAGGACCTTGCTGAGAAATATCCGGATCAGATTATCAAGgttttctttg ... aagtgtgcagGTTCCAATCAACATCAACAAAGGTATTTC
EST: gi|208354269|gb|DC902483.1|DC902483
EST:     GAACCAGCATAGAGGACCTTGCTGAGAAATATCCGGATCAGATTATCAAN                         GTTCCNATCAACATCAACAAAGGTATTTCAGATGAANAAGCCGAGAAN-TT
genomic: GAACCAGCATAGAGGACCTTGCTGAGAAATATCCGGATCAGATTATCAAGgttttctttg ... aagtgtgcagGTTCCAATCAACATCAACAAAGGTATTTCAGATGAAGAAGCCGAGAAAGTT
EST: gi|208386847|gb|DC941565.1|DC941565
EST:     GAACCAGCATAGAGGACCTTGCTGAGAAATATCCGGATCAGATTATCAAG                         GTTCCAATCAACATCAACAAAGGTATTTCAGATGAAGAAGCCGAGAAAGTT
genomic: GAACCAGCATAGAGGACCTTGCTGAGAAATATCCGGATCAGATTATCAAGgttttctttg ... aagtgtgcagGTTCCAATCAACATCAACAAAGGTATTTCAGATGAAGAAGCCGAGAAAGTT
EST: gi|100365282|gb|BY966901.1|BY966901
EST:     AACCAGCATAGAGGACCTTGCTGAGAAATATCGGGATCAGATTTATCA-G                         GNTCCAATCAACATCAACAAAGGTATTTCAGATGAAGAAACCGANGAAGG
genomic: AACCAGCATAGAGGACCTTGCTGAGAAATATCCGGATCAGATT-ATCAAGgttttctttg ... aagtgtgcagGTTCCAATCAACATCAACAAAGGTATTTCAGATGAAGAAGCCGA-GAAAG
EST: gi|100379592|gb|BY949846.1|BY949846
EST:     GAACCAGCATAGAGGACCTTGCTGAGAAATATCCGGATCAGATTATCAAG                         GTTCCAATCAACATCAACAAAGGTATTTCAGATGAAGAAGCCGAGAAANGT
genomic: GAACCAGCATAGAGGACCTTGCTGAGAAATATCCGGATCAGATTATCAAGgttttctttg ... aagtgtgcagGTTCCAATCAACATCAACAAAGGTATTTCAGATGAAGAAGCCGAGAAA-GT
EST: gi|67704790|gb|BJ965023.1|BJ965023
EST:     GAACCAGCATAGAGGACCTTGCTGAGAAATATCCGGATCAGATTATCAAG                         GTTCCAATCAACATCAACAAAGGTATTTCAG
genomic: GAACCAGCATAGAGGACCTTGCTGAGAAATATCCGGATCAGATTATCAAGgttttctttg ... aagtgtgcagGTTCCAATCAACATCAACAAAGGTATTTCAG
EST: gi|67719429|gb|BJ969688.1|BJ969688
EST:     GAACCAGCATAGAGGACCTTGCTGAGAAATATCCGGATCAGATTATCAAG                         GTTCCAATCAACATCAACAAAGGTATTTCAGATGAAGAAGCCGAGAAAGTT
genomic: GAACCAGCATAGAGGACCTTGCTGAGAAATATCCGGATCAGATTATCAAGgttttctttg ... aagtgtgcagGTTCCAATCAACATCAACAAAGGTATTTCAGATGAAGAAGCCGAGAAAGTT
EST: gi|208364000|gb|DC939593.1|DC939593
EST:     GAACCANCATAAAGGACCTTGCTGAAAAATATCCGGATCAAATNATCAAG                         GTTCCAATCAACATCAACAAAAGGTATTTCA
genomic: GAACCAGCATAGAGGACCTTGCTGAGAAATATCCGGATCAGATTATCAAGgttttctttg ... aagtgtgcagGTTCCAATCAACATCAACAAA-GGTATTTCA
EST: gi|208393623|gb|DC904339.1|DC904339
EST:     GAACCAGCATAGAGGACCTTGCTGAGAAATATCCGGATCAGATTATCAAG                         GTTCCAATCAACATCAANCAAAGGTATTTCAGATGA
genomic: GAACCAGCATAGAGGACCTTGCTGAGAAATATCCGGATCAGATTATCAAGgttttctttg ... aagtgtgcagGTTCCAATCAACATCAA-CAAAGGTATTTCAGATGA
EST: gi|100376654|gb|BY949400.1|BY949400
EST:     ACCAGCATAGNAG-ACCTTGCTGANGAA-TATCCGGATCAGAATATCAAG                         GTTCCANNNTCA-CATCA-CAAAGGTATTTCAGATGAAGAAGCCGAGAAAA
genomic: ACCAGCATAG-AGGACCTTGCTGA-GAAATATCCGGATCAGATTATCAAGgttttctttg ... aagtgtgcagGTTCCAA--TCAACATCAACAAAGGTATTTCAGATGAAGAAGCCGAGAAA-
EST: gi|100385264|gb|BY950856.1|BY950856
EST:     GAACCAGCATAGAGGACCTTGCTGAGAAATATCCGGATCAGATTATCAAG                         GTTCCAATCAACATCAACAAAGGTATTTCAGATGANGAAGCCGAGAAAGTT
genomic: GAACCAGCATAGAGGACCTTGCTGAGAAATATCCGGATCAGATTATCAAGgttttctttg ... aagtgtgcagGTTCCAATCAACATCAACAAAGGTATTTCAGATGAAGAAGCCGAGAAAGTT
EST: gi|100394556|gb|BY989846.1|BY989846
EST:     AACCAGCATAGAGGACCTTGCTGAGAAATATCCGGATCAGATTNATCA-G                         GTTCCAATCAACATCAACAAAGGTATTTCAGATGAAGAAGCCGAGAAAGT
genomic: AACCAGCATAGAGGACCTTGCTGAGAAATATCCGGATCAGATT-ATCAAGgttttctttg ... aagtgtgcagGTTCCAATCAACATCAACAAAGGTATTTCAGATGAAGAAGCCGAGAAAGT
EST: gi|100444730|gb|BY982559.1|BY982559
EST:     GA-CCAGCATAGAGGACCTTGCTGAGAA-TATCCGGATCAGATTATCA-G                         GTTCCCAATCA-CATCA
genomic: GAACCAGCATAGAGGACCTTGCTGAGAAATATCCGGATCAGATTATCAAGgttttctttg ... aagtgtgcagGTTCC-AATCAACATCA
EST: gi|100369353|gb|BY948059.1|BY948059
EST:     GAACCAGCATAGAGGACCTTGCTGAGAAATATCCGGATCAGATTATCANG                         GNTTCCAATCA-CATCAACAAAGGTATTTCAGATGAAGAAGCCGAGAAAGT
genomic: GAACCAGCATAGAGGACCTTGCTGAGAAATATCCGGATCAGATTATCAAGgttttctttg ... aagtgtgcagG-TTCCAATCAACATCAACAAAGGTATTTCAGATGAAGAAGCCGAGAAAGT
EST: gi|100356151|gb|BY946222.1|BY946222
EST:     GAACCAGCATAGAGGACCTTGCTGAGAAATATCCGGATCAGATTATCAAG                         GTTCCAATCAACATCAACAAAGGTATTTCAGATGAAGAACCCGAGAAAGTT
genomic: GAACCAGCATAGAGGACCTTGCTGAGAAATATCCGGATCAGATTATCAAGgttttctttg ... aagtgtgcagGTTCCAATCAACATCAACAAAGGTATTTCAGATGAAGAAGCCGAGAAAGTT
EST: gi|67508667|gb|BJ941528.1|BJ941528
EST:     GAACCAGCATAGAGGACCTTGCTGAGAAATATCCGGATCAGATTATCAAG                         GTTCCAATCAACATCAACAAAGGTATTTCAG
genomic: GAACCAGCATAGAGGACCTTGCTGAGAAATATCCGGATCAGATTATCAAGgttttctttg ... aagtgtgcagGTTCCAATCAACATCAACAAAGGTATTTCAG

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), 33 (downstream exon)
Score: 9

GTCATGATTGCTTGCGCTAAGGGTGGAACCAGCATAGAGGACCTTGCTGAGAAATATCCGGATCAGATTATCAAGgttttctttg ... aagtgtgcagGTTCCAATCAACATCAACAAAGGTATTTCAGATGAAGAAGCCGAGAAAGTTGTGAAAGGATTGGCTCCAAAGAAGGTCGACATGCAGCAAGGCATTGACC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCATGATTGCTTGCGCTAAGGGTGGAACCAGCATAGAGGACCTTGCTGAGAAATATCCGGATCAGATTATCAAGgttttctttgtgttggtgtttgtatttgtgtttgatgtttgcagaatgtaattagagacttacaggccgttttttttttattattattattatcttgttctgggattatgcttccttgcatataacgatttagcagtagcatgtgaggtgaaattgtgagctctaagtgtgcag

- - - - - - - - - - - - - - - - -  AGAGGA