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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcaccgcttgagttgaaggagacaagccggagttgatttatcttcctcgataattgaagttttcctctaacacttgtggttttgcaatgtgatgtgcagCCGGAGCCCGAGTTCCGACCCCCGATGTCTGAAGTGGTGCAGGCACTTGTAAGGCTGATGCAGCGTGCGAGTCTGAGCAAACGCAGATCGGAGTCCGCTG

Basic information

species Physcomitrella patens
transcript PP1S204_22V6.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S204_22V6.1 (Physcomitrella patens), 3'ss of exon 14
lower sequence: GLYMA19G45130.1 (Glycine max), 3'ss of exon 15
-----------------------------------------ttcaccgcttgagttgaaggagacaagc--cggagttgatttatcttcctcgataattgaagttttcctctaacacttgtggttttgcaatgtgatgtgcagCCGGAGCCCGAGTTCCGACCCCCGATGTCTGAAGTGGTGCAGGCACTTGTAAGGCTGATGCAGCGTGCGAGTCTGAGCAAACGCAGATCGGAGTCCGCTG
                                         ||      |   | || |   |  || |  ||| | ||  |        |   |   ||   | ||| | | |   || || || |   || ||  | |||||||||||| || |||||||| |||||||| |||||||| || ||||| ||  | ||  ||||||| || |   ||||||| || | ||          ||
gtactgtcagacacgttttgattcacccaaaatttattgattttgtaaatatggatggatttgggaaaccacgggggtggatgggaaatatttgtgcatggcttgttcatgtgattttt-tgtttatattatttg--gggcagCCGGAGCCAGAATTCCGACCACCGATGTCAGAAGTGGTTCAAGCACTGGTGCGACTAGTGCAGCGAGCTAACATGAGCAAGCGAACATTTAGTAGTAGTG

upper sequence: PP1S204_22V6.1 (Physcomitrella patens), 3'ss of exon 14
lower sequence: Vv10s0116g00100.t01 (Vitis vinifera), 3'ss of exon 15
ttcaccgcttgagttgaaggagacaagccggagttg----atttatcttcctcgat---aattgaagttttcctc-taacacttgtggttttgcaatgtgatgtgcagCCGGAGCCCGAGTTCCGACCCCCGATGTCTGAAGTGGTGCAGGCACTTGTAAGGCTGATGCAGCGTGCGAGTCTGAGCAAACGCAGATCGGAGTCCGCTG
        |  |  | ||     ||  | | ||||     |||||| |  |  |||   || | |||  || ||| | |  | | ||   ||   || | ||   ||||||||||| ||||| ||||| || ||||||||||| ||||| ||||| ||  || |  | ||  | || ||| ||  ||| ||  | ||       |   
------agtccacataaaatgctcattctgtagttattcaatttatatgacctgattctaagtaaagcatttctcatcattcctatgtcgttttcatttcata--cagCCGGAGCCAGAGTTTCGACCTCCAATGTCTGAAGTTGTGCAAGCACTGGTTCGGTTAGTACAAAGAGCAAGTGTGGTCAAGCGGCGCTCAAGTGATGAAT

upper sequence: PP1S204_22V6.1 (Physcomitrella patens), 3'ss of exon 14
lower sequence: Vv10s0116g00050.t01 (Vitis vinifera), 3'ss of exon 3
ttcaccgcttgagttgaaggagacaagccggagttg----atttatcttcctcgat---aattgaagttttcctc-taacacttgtggttttgcaatgtgatgtgcagCCGGAGCCCGAGTTCCGACCCCCGATGTCTGAAGTGGTGCAGGCACTTGTAAGGCTGATGCAGCGTGCGAGTCTGAGCAAACGCAGATCGGAGTCCGCTG
        |  |  | ||     ||  | | ||||     |||||| |  |  |||   || | | |  || ||| | |  | ||||   ||   || | ||   ||||||||||| ||||| ||||| || ||||||||||| ||||| ||||| ||  || |  | ||  | || ||| ||  |||  |  | ||       |   
------agtccacataaaatgctcattctgcagttattcaatttatatgacctgattctaagtaatgcatttctcatcattcctgtgtggttttcatttcata--cagCCGGAGCCAGAGTTTCGACCTCCAATGTCTGAAGTTGTGCAAGCACTGGTTCGGTTAGTACAAAGAGCAAGTGTGGTCAAGAGGCGCTCAAGTGATGAAT

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|162155036|gb|FC331454.1|FC331454
EST:     CTGCTAAATCACTCTCTCGGTTTGCTGATATAGTCGCCCTTTGCGTCCAG                         CCGGAGCCCGAGTTCCGACCCCCGATGTCTGAAGTGGTGCANGCACTTGTA
genomic: CTGCTAAATCACTCTCTCGGTTTGCTGATATAGTCGCCCTTTGCGTCCAGgtattctctt ... tgatgtgcagCCGGAGCCCGAGTTCCGACCCCCGATGTCTGAAGTGGTGCAGGCACTTGTA
EST: gi|162267430|gb|FC443973.1|FC443973
EST:     CTGCTAAATCACTCTCTCGGTTTGCTGATATAGTCGCCCTTTGCGTCCAG                         CCGGAGCCCGAGTTCCGACCCCCGATGTCTGAAGTGGTGCAGGCACTTGTA
genomic: CTGCTAAATCACTCTCTCGGTTTGCTGATATAGTCGCCCTTTGCGTCCAGgtattctctt ... tgatgtgcagCCGGAGCCCGAGTTCCGACCCCCGATGTCTGAAGTGGTGCAGGCACTTGTA
EST: gi|162260498|gb|FC435085.1|FC435085
EST:     CTGCTAAATCACTCTCTCGGTTTGCTGATATAGTCGCCCTTTGCGTCCAG                         CCGGAGCCCGAGTTCCGACCCCCGATGTCTGAAGTGGTGCAGGCACTTGTA
genomic: CTGCTAAATCACTCTCTCGGTTTGCTGATATAGTCGCCCTTTGCGTCCAGgtattctctt ... tgatgtgcagCCGGAGCCCGAGTTCCGACCCCCGATGTCTGAAGTGGTGCAGGCACTTGTA
EST: gi|162267588|gb|FC444651.1|FC444651
EST:     CTGCTAAATCACTCTCTCGGTTTGCTGATATAGTCGCCCTTTGCGTCCAG                         CCGGAGCCCGAGTTCCGACCCCCGATGTCTGAAGTGGTGCAGGCACTTGTA
genomic: CTGCTAAATCACTCTCTCGGTTTGCTGATATAGTCGCCCTTTGCGTCCAGgtattctctt ... tgatgtgcagCCGGAGCCCGAGTTCCGACCCCCGATGTCTGAAGTGGTGCAGGCACTTGTA
EST: gi|15261634|gb|BI436944.1|BI436944
EST:     CTGCTAAATCACTCTCTCGGTTTGCTGATATAGTCGCCCTTTGCGTCCAG                         CCGGAGCCCGAGTTCCGACCCCCGATGTCTGAAGTGGTGCAGGCACTTGTA
genomic: CTGCTAAATCACTCTCTCGGTTTGCTGATATAGTCGCCCTTTGCGTCCAGgtattctctt ... tgatgtgcagCCGGAGCCCGAGTTCCGACCCCCGATGTCTGAAGTGGTGCAGGCACTTGTA
EST: gi|162166497|gb|FC343194.1|FC343194
EST:     CTGCTAAATCACTCTCTCGGTTTGCTGATATAGTCGCCCTTTGCGTCCAG                         CCGGAGCCCGAGTTCCGACCCCCGATGTCTGAAGTGGTGCAGGCACTTGTA
genomic: CTGCTAAATCACTCTCTCGGTTTGCTGATATAGTCGCCCTTTGCGTCCAGgtattctctt ... tgatgtgcagCCGGAGCCCGAGTTCCGACCCCCGATGTCTGAAGTGGTGCAGGCACTTGTA
EST: gi|162194242|gb|FC369504.1|FC369504
EST:     CTGCTAAATCACTCTCTCGGTTTGCTGATATAGTCGCCCTTTGCGTCCAG                         CCGGAGCCCGAGTTCCGACCCCCGATGTCTGAAGTGGTGCAGGCACTTGTA
genomic: CTGCTAAATCACTCTCTCGGTTTGCTGATATAGTCGCCCTTTGCGTCCAGgtattctctt ... tgatgtgcagCCGGAGCCCGAGTTCCGACCCCCGATGTCTGAAGTGGTGCAGGCACTTGTA
EST: gi|162243391|gb|FC417092.1|FC417092
EST:     CTGCTAAATCACTCTCTCGGTTTGCTGATATAGTCGCCCTTTGCGTCCAG                         CCGGAGCCCGAGTTCCGACCCCCGATGTCTGAAGTGGTGCAGGCACTTGTA
genomic: CTGCTAAATCACTCTCTCGGTTTGCTGATATAGTCGCCCTTTGCGTCCAGgtattctctt ... tgatgtgcagCCGGAGCCCGAGTTCCGACCCCCGATGTCTGAAGTGGTGCAGGCACTTGTA
EST: gi|162248155|gb|FC419705.1|FC419705
EST:     CTGCTAAATCACTCTCTCGGTTTGCTGATATAGTCGCCCTTTGCGTCCAG                         CCGGAGCCCGAGTTCCGACCCCCGATGTCTGAAGTGGTGCAGGCACTTGTA
genomic: CTGCTAAATCACTCTCTCGGTTTGCTGATATAGTCGCCCTTTGCGTCCAGgtattctctt ... tgatgtgcagCCGGAGCCCGAGTTCCGACCCCCGATGTCTGAAGTGGTGCAGGCACTTGTA
EST: gi|162248154|gb|FC419704.1|FC419704
EST:     CTGCTAAATCACTCTCTCGGTTTGCTGATATAGTCGCCCTTTGCGTCCAG                         CCGGAGCCCGAGTTCCGACCCCCGATGTCTGAAGTGGTGCAGGCACTTGTA
genomic: CTGCTAAATCACTCTCTCGGTTTGCTGATATAGTCGCCCTTTGCGTCCAGgtattctctt ... tgatgtgcagCCGGAGCCCGAGTTCCGACCCCCGATGTCTGAAGTGGTGCAGGCACTTGTA
EST: gi|162194241|gb|FC369503.1|FC369503
EST:     CTGCTAAATCACTCTCTCGGTTTGCTGATATAGTCGCCCTTTGCGTCCAG                         CCGGAGCCCGAGTTCCGACCCCCGATGTCTGAAGTGGTGCAGGCACTTGTA
genomic: CTGCTAAATCACTCTCTCGGTTTGCTGATATAGTCGCCCTTTGCGTCCAGgtattctctt ... tgatgtgcagCCGGAGCCCGAGTTCCGACCCCCGATGTCTGAAGTGGTGCAGGCACTTGTA
EST: gi|37850223|gb|BJ608231.1|BJ608231
EST:     AATCACTCTCTCGGTTTGCTGATATAGTCGCCCTTTGCGTCCAG                         CCGGAGCCCGAGTTCCGACCCCCGATGTCTGAAGTGGTGCAGGCACTTGTA
genomic: AATCACTCTCTCGGTTTGCTGATATAGTCGCCCTTTGCGTCCAGgtattctctt ... tgatgtgcagCCGGAGCCCGAGTTCCGACCCCCGATGTCTGAAGTGGTGCAGGCACTTGTA

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), 32 (downstream exon)
Score: 12

CATCGACGCCCTTGCACGAATGGTGGATCCGTCGTTGAAGGGCATCTACCCTGCTAAATCACTCTCTCGGTTTGCTGATATAGTCGCCCTTTGCGTCCAGgtattctctt ... tgatgtgcagCCGGAGCCCGAGTTCCGACCCCCGATGTCTGAAGTGGTGCAGGCACTTGTAAGGCTGATGCAGCGTGCGAGTCTGAGCAAACGCAGATCGGAGTCCGCTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctcgataattgaagttttcctctaacacttgtggttttgcaatgtgatgtgcagCCGGAGCCCGAGTTCCGACCCCCGATGTCTGAAGTGGTGCAGGCACTTGTAAGGCTGATGCAGCGTGCGAGTCTGAGCAAACGCAGATCGGAGTCCGCTG
                    ctctaac  putative branch site (score: 12)
     ataattgaagtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcaccgcttgagttgaaggagacaagccggagttgatttatcttcctcgataattgaagttttcctctaacacttgtggttttgcaatgtgatgtgcagCCGGAGCCCGAGTTCCGACCCCCGATGTCTGAAGTGGTGCAGGCACTTGTAAGGCTGATGCAGCGTGCGAGTCTGAGCAAACGCAGATCGGAGTCCGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT