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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

atatccttttttgtgcgagatcttgtgtgttatgaatctgaaatccccttgcgtttttcctatgaatgtctcacgttttgtttgctgtagagaagatgttttcgattcgtcattcgtgcggcccccttaatcttcctacacAAGACCAACGTGGTGGGGACCTTGAACATGCTGGGATTGGCGAAGCGCATTGGAGCACGGTTCTTGTTGACCAGTACGAGTGAGGTTTATGGTGATCCTT

Basic information

species Physcomitrella patens
transcript PP1S209_52V6.1
intron # 1
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S209_52V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os03g17230.1 (Oryza sativa), 3'ss of exon 1
atatccttttttgtgcgagatcttgtgtgttatgaatctgaaatcccc--ttgcgtttttcctatgaatgtctcacgttttgtttgctgtagagaagatgttttcgattcgtcattcgtgcggcccccttaatcttcctacacAAGACCAACGTGGTGGGGACCTTGAACATGCTGGGATTGGCGAAGCGCATTGGAGCACGGTTCTTGTTGACCAGTACGAGTGAGGTTTATGGTGATCCTT
                                 ||||||     |  |  ||||  ||| |||   |    || |  |||||||  | ||        | ||||   ||    |||     ||  |||| | | ||     ||||||| || ||| |||||||||||||||||||||||||||| ||| |  | ||||| |||||||| ||||||||||| |||||||| || ||||||||| 
---------------------------------gaatcttgtgcctgcggttgccatttgcctggaagaacctgaaattttgttc-cagtcc------tatttttccttataaattt---tggttccctaactgttatagtacAAGACAAATGTGATGGGGACCTTGAACATGCTGGGATTGGCAAAGAGGGTGGGAGCCCGGTTCTTATTGACCAGTACCAGTGAGGTGTACGGTGATCCTC

upper sequence: PP1S209_52V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G347717_T01 (Zea mays), 3'ss of exon 1
atatccttttttgtgcgagatcttgtgtgttatgaatctgaaatccccttgcgtttttcctatgaatgtctcacgttttgtttgctgtagagaagatgttttcgattcgtcattcgtgcggcccccttaatcttcc-tacacAAGACCAACGTGGTGGGGACCTTGAACATGCTGGGATTGGCGAAGCGCATTGGAGCACGGTTCTTGTTGACCAGTACGAGTGAGGTTTATGGTGATCCTT---
                                           |    ||| | ||       ||||  |     |||   |   | ||       ||||||   ||  |  |||     |   | |||| |  |  |  ||||||| || ||  ||||||||||||| ||||| ||| |||| ||| |  |||| || |||||||||||||| ||||| ||||| || ||||||||||||    
------------------------------------------gtagttttgtgcttgcgtggggaatagcctgtatttacatctgtttattttgtctgttttt--ttttttcttca-attgtttctttaaccaactatgtacaagACAAATGTCATGGGGACCTTGAATATGCTTGGACTGGCTAAGAGGGTTGGGGCTCGGTTCTTGTTGACTAGTACCAGTGAAGTGTATGGTGATCCTCTTG

upper sequence: PP1S209_52V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G347717_T03 (Zea mays), 3'ss of exon 1
atatccttttttgtgcgagatcttgtgtgttatgaatctgaaatccccttgcgtttttcctatgaatgtctcacgttttgtttgctgtagagaagatgttttcgattcgtcattcgtgcggcccccttaatcttcc-tacacAAGACCAACGTGGTGGGGACCTTGAACATGCTGGGATTGGCGAAGCGCATTGGAGCACGGTTCTTGTTGACCAGTACGAGTGAGGTTTATGGTGATCCTT
                                    | || | |    ||| | ||       ||||  |     |||   |   | ||       ||||||   ||  |  |||     |   | |||| |  |  |  ||||||| || ||  ||||||||||||| ||||| ||| |||| ||| |  |||| || |||||||||||||| ||||| ||||| || |||||||||||| 
------------------------------------tttgtagtt---ttgtgcttgcgtggggaatagcctgtatttacatctgtttattttgtctgttttt--ttttttcttca-attgtttctttaaccaactatgtacAAGACAAATGTCATGGGGACCTTGAATATGCTTGGACTGGCTAAGAGGGTTGGGGCTCGGTTCTTGTTGACTAGTACCAGTGAAGTGTATGGTGATCCTC

upper sequence: PP1S209_52V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G359234_T03 (Zea mays), 3'ss of exon 1
atatccttttttgtgcgagatcttgtgtgttatgaatctgaaatccccttgcgtttttcctatgaatgtctcacgttttgtttgctgtagagaagatgttttcgattcgtcattcgtgcggcccccttaatcttcctacacAAGACCAACGTGGTGGGGACCTTGAACATGCTGGGATTGGCGAAGCGCATTGGAGCACGGTTCTTGTTGACCAGTACGAGTGAGGTTTATGGTGATCCTT---
                                         ||     | ||  ||||     | |||| || | ||  || | |  || ||| | ||| ||   || |||     |  || |  |||||   |  |  ||||||| || ||  |||| || ||||| ||| ||||  |||||||||| ||||| ||| |||| |||||||| || || ||||| ||||||||||||||     
-----------------------------------------aaggatgtcgccattttttgcagcatgtgtc-cattcagtat-ccatatagatggtgtgtttcttttgtctcgaatttggacttcttaacactt-tgtacaagACAAATGTCATGGGAACTTTGAATATGTTGGGTCTGGCGAAGCGAATTGGTGCAAGGTTTTTGTTGACTAGCACAAGTGAAGTTTATGGTGATCCGCTTG

upper sequence: PP1S209_52V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G359234_T01 (Zea mays), 3'ss of exon 1
atatccttttttgtgcgagatcttgtgtgttatgaatctgaaatccccttgcgtttttcctatgaatgtctcacgttttgtttgctgtagagaagatgttttcgattcgtcattcgtgcggcccccttaatcttcctacacAAGACCAACGTGGTGGGGACCTTGAACATGCTGGGATTGGCGAAGCGCATTGGAGCACGGTTCTTGTTGACCAGTACGAGTGAGGTTTATGGTGATCCTT
                                       | ||     | ||  ||||     | |||| || | ||  || | |  || ||| | ||| ||   || |||     |  || |  |||||   |  |  ||||||| || ||  |||| || ||||| ||| ||||  |||||||||| ||||| ||| |||| |||||||| || || ||||| ||||||||||||||  
--------------------------------------gggaaggatgtcgccattttttgcagcatgtgtc-cattcagtat-ccatatagatggtgtgtttcttttgtctcgaatttggacttcttaacactt-tgtacAAGACAAATGTCATGGGAACTTTGAATATGTTGGGTCTGGCGAAGCGAATTGGTGCAAGGTTTTTGTTGACTAGCACAAGTGAAGTTTATGGTGATCCGC

upper sequence: PP1S209_52V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ30517 (Selaginella moellendorffii), 3'ss of exon 2
atatccttttttgtgcgagatcttgtgtgttatgaatctgaaatccccttgcgtttttcctatgaatgtctcacgttttgtttgctgtagagaagatgttttcgattcgtcattcgtgcggcccccttaatctt-----cctacacAAGACCAACGTGGTGGGGACCTTGAACATGCTGGGATTGGCGAAGCGCATTGGAGCACGGTTCTTGTTGACCAGTACGAGTGAGGTTTATGGTGATCCTT---
                            || | ||   | | ||||       ||| | || ||  |||    ||||| ||||   | |   ||   || ||   ||  |  ||  ||  ||  ||||||   |     | | ||||||||||||||||| || ||  | |||||||| |||||||| ||||| ||||| || ||||| ||| ||||||| || || ||||||||||| |||||     
----------------------------gtcaagacgatcatatcct------tttcttctttgcttgttcttcgttt-gtttcgagcatctaacgcgtgtttt-ttttttttttttgttgcttccttaactcttggagctttcacaagACCAACGTGGTTGGAACACTCAACATGCTCGGATTGGCCAAGCGAATTGGTGCTCGGTTTTTGCTGACCAGCACAAGCGAGGTTTATGGAGATCCGCTGG

upper sequence: PP1S209_52V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ23020 (Selaginella moellendorffii), 3'ss of exon 1
atatccttttttgtgcgagatcttgtgtgttatgaatctgaaatccccttgcgtttttcctatgaatgtctcacgttttgtttgctgtagagaagatgttttcgatt-cgtcattcgtgcggcccccttaatcttcctacacAAGACCAACGTGGTGGGGACCTTGAACATGCTGGGATTGGCGAAGCGCATTGGAGCACGGTTCTTGTTGACCAGTACGAGTGAGGTTTATGGTGATCCTT---
                            || | ||   | | ||||       ||| | || ||  |||    |||||  || |  | |   ||   |||||   || |||   |       | |    |   |||    |||||||||||||||| || ||  | |||||||| |||||||| ||||| || || || ||||| ||| ||||||| || || ||||||||||| |||||     
----------------------------gtcaagacgatcatatcct------tttcttctttgcttgttcttcgtttctttcga-gcatctaacgcgttttttttttcgttgcttccttaactcttggagctttc----acaagACCAACGTGGTTGGAACACTCAACATGCTCGGATTGGCCAAGCGAATCGGTGCTCGGTTTTTGCTGACCAGCACAAGCGAGGTTTATGGAGATCCGCTGG

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|162196627|gb|FC374917.1|FC374917
EST:     CGTGTCCGGCGTCGCCCGTGCATTACAAGTTCAACCCCATCAAGACAATC                         AAGACCAACGTGGTGGGGACCTTGAACATGCTGGGATTGGCGAAGCGCATT
genomic: CGTGTCCGGCGTCGCCCGTGCATTACAAGTTCAACCCCATCAAGACAATCatatcctttt ... cttcctacacAAGACCAACGTGGTGGGGACCTTGAACATGCTGGGATTGGCGAAGCGCATT
EST: gi|162245553|gb|FC424107.1|FC424107
EST:     CGTGTCCGGCGTCGCCCGTGCATTACAAGTTCAACCCCATCAAGACCATC                         AAGACCAACGTGGTGG
genomic: CGTGTCCGGCGTCGCCCGTGCATTACAAGTTCAACCCCATCAAGACAATCatatcctttt ... cttcctacacAAGACCAACGTGGTGG
EST: gi|162194370|gb|FC371088.1|FC371088
EST:     CGTGTCCGGCGTCGCCCGTGCATTACAAGTTCAACCCCATCAAGACAATC                         AAGACCAACGTGGTGGGGACCTTGAACATGCTGGGATTGGCGAAGCGCATT
genomic: CGTGTCCGGCGTCGCCCGTGCATTACAAGTTCAACCCCATCAAGACAATCatatcctttt ... cttcctacacAAGACCAACGTGGTGGGGACCTTGAACATGCTGGGATTGGCGAAGCGCATT
EST: gi|162155079|gb|FC330873.1|FC330873
EST:     CGTGTCCGGCGTCGCCCGTGCATTACAAGTTCAACCCCATCAAGACAATC                         AAGACCAACGTGGTGGGGACCTTGAACATGCTGGGATTGGCGAAGCGCATT
genomic: CGTGTCCGGCGTCGCCCGTGCATTACAAGTTCAACCCCATCAAGACAATCatatcctttt ... cttcctacacAAGACCAACGTGGTGGGGACCTTGAACATGCTGGGATTGGCGAAGCGCATT
EST: gi|162181366|gb|FC358435.1|FC358435
EST:     CGTGTCCGGCGTCGCCCGTGCATTACAAGTTCAACCCCATCAAGACAATC                         AAGACCAACGTGGTGGGGACCTTGAACATGCTGGGATTGGCGAAGCGCATT
genomic: CGTGTCCGGCGTCGCCCGTGCATTACAAGTTCAACCCCATCAAGACAATCatatcctttt ... cttcctacacAAGACCAACGTGGTGGGGACCTTGAACATGCTGGGATTGGCGAAGCGCATT

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: 31 (upstream exon), 35 (downstream exon)
Score: 16

CGATGTGGTGGAGCCTTTGTTGCTGGAGGTGGACCAGATTTATCACCTTGCGTGTCCGGCGTCGCCCGTGCATTACAAGTTCAACCCCATCAAGACAATCatatcctttt ... cttcctacacAAGACCAACGTGGTGGGGACCTTGAACATGCTGGGATTGGCGAAGCGCATTGGAGCACGGTTCTTGTTGACCAGTACGAGTGAGGTTTATGGTGATCCTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtagagaagatgttttcgattcgtcattcgtgcggcccccttaatcttcctacacAAGACCAACGTGGTGGGGACCTTGAACATGCTGGGATTGGCGAAGCGCATTGGAGCACGGTTCTTGTTGACCAGTACGAGTGAGGTTTATGGTGATCCTT
 ccccttaat  putative branch site 
                                   cccccttaatcttcct  putative PPT
                                        ttaatctt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atatccttttttgtgcgagatcttgtgtgttatgaatctgaaatccccttgcgtttttcctatgaatgtctcacgttttgtttgctgtagagaagatgttttcgattcgtcattcgtgcggcccccttaatcttcctacacAAGACCAACGTGGTGGGGACCTTGAACATGCTGGGATTGGCGAAGCGCATTGGAGCACGGTTCTTGTTGACCAGTACGAGTGAGGTTTATGGTGATCCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA