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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCATGACAATGTCAACATTGTGGTTATTCGGGAGAATACCGAAGGGGAGTATTCTGGTCTTGAGCACGAGGTCGTCCCCGGGGTCGTCGAGAGCCTTAAGgtacatatttcgttttctgacctgaaaaataacactactctatgttgtgcctagtgattgtaatattttctgtccaagcatttttttcacgcctttgttt...

Basic information

species Physcomitrella patens
transcript PP1S101_151V6.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S101_151V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: LOC_Os02g38200.1 (Oryza sativa), 5'ss of exon 1
CCATGACAATGTCAACATTGTGGTTATTCGGGAGAATACCGAAGGGGAGTATTCTGGTCTTGAGCACGAGGTCGTCCCCGGGGTCGTCGAGAGCCTTAAGgta---catatttcgttttctgacctgaaaaataacactactcta-tgttgtgcctagtgattgtaatattttctgt-ccaagcatttttttcacgcctttgttt
 || ||||| ||| ||||||| || ||  ||||||| ||||| || ||||| || || |||||||||||||||||||| || ||||| |||||||||||||||   |  ||| || || |||  || |   |      |  | || ||||   |   ||| |||   || |   ||| || ||          | ||   |    
GCACGACAACGTCGACATTGTCGTCATCAGGGAGAACACCGAGGGCGAGTACTCCGGGCTTGAGCACGAGGTCGTCCCTGGCGTCGTGGAGAGCCTTAAGgtatggcgaattccgcttgctg--ctaactcacctagttgatgtagtgtttgccagggtgcttgggttaatgcgtgtgccgagagaaccccaaatgcaactt---

upper sequence: PP1S101_151V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: LOC_Os04g40310.2 (Oryza sativa), 5'ss of exon 1
CCATGACAATGTCAACATTGTGGTTATTCGGGAGAATACCGAAGGGGAGTATTCTGGTCTTGAGCACGAGGTCGTCCCCGGGGTCGTCGAGAGCCTTAAGgtacatatttcgttttctgacctgaaaaataacactactctat-gttgtgcctagtgattgtaatattttctgtccaagcattt-ttttcacgcctt-tgttt-----
 ||  |  | ||| |||| || || ||  ||||||| ||||| |||||||| || || || |||||||||||||| ||||| |||||||||||||| |||||||           |||  | |||       |  | |||| | ||||||  |  || ||| |  ||   |   ||  ||||   |||| ||| ||  ||| |     
GCACCAGGACGTCGACATCGTCGTCATCAGGGAGAACACCGAGGGGGAGTACTCGGGGCTCGAGCACGAGGTCGTGCCCGGCGTCGTCGAGAGCCTCAAGgtacgggccaa----tctcgcgtgacgcgcg-ctttgctctgttgttgtgtgt--tggttggagaatcgcc-acccgtgcatcgattttgacgtctaatgtgttcctt

upper sequence: PP1S101_151V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GRMZM2G025366_T02 (Zea mays), 5'ss of exon 1
CCATGACAATGTCAACATTGTGGTTATTCGGGAGAATACCGAAGGGGAGTATTCTGGTCTTGAGCACGAGGTCGTCCCCGGGGTCGTCGAGAGCCTTAAGgtacatatttcgttttctgacctgaaaaataacactactctatgttgtgcctagtgattgtaatattttctgtccaagcatttttttcacgcctttgttt-----
 || ||   |||| |||| || || ||  ||||||| ||||| || ||||| || || || |||||||||||||| ||||||||||| |||||||| |||||||    | ||   | |    ||        |     |  |||||     |  |  ||   |||| || |   |   | |||| |  | |  | ||        
GCACGAGGGTGTCGACATCGTCGTAATCAGGGAGAACACCGAGGGCGAGTACTCGGGGCTCGAGCACGAGGTCGTACCCGGGGTCGTTGAGAGCCTCAAGgtac----tacggagtgtcggttggggt-cggctgcgtttcatgtttattatgatttttccgatatgttatactccctccttttatataagtatatgacaccgtt

upper sequence: PP1S101_151V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GLYMA11G08920.1 (Glycine max), 5'ss of exon 1
CCATGACAATGTCAACATTGTGGTTATTCGGGAGAATACCGAAGGGGAGTATTCTGGTCTTGAGCACGAGGTCGTCCCCGGGGTCGTCGAGAGCCTTAAGgtacatattt-cgttttctgac-ctgaaaaataacactactctatgttgtgcctagtgattgtaatattttctgtccaagcatttttttcacgcctttgttt
||| ||||| ||  |||| || || ||  ||||||| ||||| || ||||| || || || || ||||||||||||||||| || ||||| ||||| |||||||  | |  ||||  | |   ||      | |  |||    ||     ||  | | |||    | | |  | |  |   | |    | | |    ||   
CCACGACAACGTTGACATCGTCGTCATCAGGGAGAACACCGAGGGCGAGTACTCCGGCCTCGAACACGAGGTCGTCCCCGGCGTGGTCGAAAGCCTCAAGgtactcactcacgttcacggtttctttctgctcaagctaaataatagca-gctgaataattaggttttatgatcttaataaaatgaaattaagagaatgaa-

upper sequence: PP1S101_151V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GLYMA16G22640.1 (Glycine max), 5'ss of exon 1
CCATGACAATGTCAACATTGTGGTTATTCGGGAGAATACCGAAGGGGAGTATTCTGGTCTTGAGCACGAGGTCGTCCCCGGGGTCGTCGAGAGCCTTAAGgtacatatttcgttttctgacctgaaaaataacactactc-tatgttgtgcctagtgattgtaatattttctgtccaagcatttttttcacgcctttgttt-
|||||| |||||  | || || || ||  ||||||| |||||||| || || ||||| || || ||||||||||| ||||| || || || ||||||||||| | |  |||   | |   |  |     | || ||  |  ||| || |      || ||   || ||||      |   |||| |||          ||  
CCATGATAATGTGGATATCGTTGTCATCAGGGAGAACACCGAAGGCGAATACTCTGGCCTCGAACACGAGGTCGTTCCCGGCGTTGTTGAAAGCCTTAAGgtgcgttcttccactccc--ctcgctttctcacgctttttatatattatcaaatttgttttctatgtttttctattatttatttatttgtttttgaaattag

upper sequence: PP1S101_151V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GLYMA02G04780.1 (Glycine max), 5'ss of exon 1
CCATGACAATGTCAACATTGTGGTTATTCGGGAGAATACCGAAGGGGAGTATTCTGGTCTTGAGCACGAGGTCGTCCCCGGGGTCGTCGAGAGCCTTAAGgtacatatttcgttttctgacctgaaaaataacactactc-tatgttgtgcctagtgattgtaatattttctgtccaagcatttttttcacgcctttgttt---
|||||| |||||  | ||||| || ||  ||||||| |||||||| ||||| || || || || ||||||||||| ||||| || || || |||||||||||      ||| | | ||  |  |     | |||||  |   || | | | ||  || |     || |   |  | ||  |        |  | |||  ||   
CCATGATAATGTTGATATTGTTGTCATCAGGGAGAACACCGAAGGCGAGTACTCCGGCCTCGAACACGAGGTCGTTCCCGGCGTTGTTGAAAGCCTTAAGgtgtgctcttcctctcct--ctcgctttctcacactttttacatatagggtct--tgctaagggtactagttaacgaactaaaaagagaaatcatttactttga

upper sequence: PP1S101_151V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: Vv04s0210g00180.t01 (Vitis vinifera), 5'ss of exon 1
CCATGACAATGTCAACATTGTGGTTATTCGGGAGAATACCGAAGGGGAGTATTCTGGTCTTGAGCACGAGGTCGTCCCCGGGGTCGTCGAGAGCCTTAAGgtacatatttcgttttctgacctgaaaaataacactactctatgttgtgcctagtgat-tgtaatattttctgtccaagcatttttttcacgcctttgttt---
 ||  | |||||  | || || || |||||||||||||| ||||| ||||| || || || |||||||||||||| ||||| ||||| || |||||||||||    ||||   ||  |  | ||    ||     || | |      | || | || | |  ||| ||   | ||      ||      |     |  |||   
GCACCAGAATGTGGATATAGTCGTGATTCGGGAGAATACGGAAGGCGAGTACTCGGGGCTCGAGCACGAGGTCGTTCCCGGTGTCGTGGAAAGCCTTAAGgttttgatttg--ttattaccttgtctgatggt--tattttggccgtttcccaatgctgttcaattttccttttctcgattttagaggtagaggatcatttggt

upper sequence: PP1S101_151V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: Vv03s0038g03120.t01 (Vitis vinifera), 5'ss of exon 1
CCATGACAATGTCAACATTGTGGTTATTCGGGAGAATACCGAAGGGGAGTATTCTGGTCTTGAGCACGAGGTCGTCCCCGGGGTCGTCGAGAGCCTTAAGgtacatatttcgttttctgacctgaaaaataacactactctatgttgtgcctagtgattgtaatattttc-tgtccaagcatttttttcacgcctttgttt
 ||  |  ||||  | ||||| ||  |  ||||||| || || || |||||  |||| ||||||||||||||||| ||||| || ||||| |||||||||||| |  | |  ||   || |  || || |      ||   |          | |  | ||  | ||||  |    ||  |  | |   | ||      | 
GCACAATGATGTTGATATTGTTGTGGTGAGGGAGAACACGGAGGGCGAGTACGCTGGGCTTGAGCACGAGGTCGTTCCCGGCGTGGTCGAAAGCCTTAAGgta-acgtctgtttggatgcctagagaactggtggaacataaaagaaaatagacttttggttctgttttggtaagaaaaaaaatataaaatgcgaccccta

upper sequence: PP1S101_151V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: EFJ13705 (Selaginella moellendorffii), 5'ss of exon 1
CCATGACAATGTCAACATTGTGGTTATTCGGGAGAATACCGAAGGGGAGTATTCTGGTCTTGAGCACGAGGTCGTCCCCGGGGTCGTCGAGAGCCTTAAGgtac----atatttcgttttctgacctgaaaaataacactactctatgttgtgcctagtgattgtaatattttctgtccaagcatttttttcacgcctttgttt
||||||||| ||||||||||| || || |||||||| ||||| ||||||||  | || || ||||||||||||||||| || || ||||||   || |||||||    || | |  |  ||||   ||        | | |  ||| |||    || | |                                            
CCATGACAACGTCAACATTGTTGTGATCCGGGAGAACACCGAGGGGGAGTACGCCGGCCTGGAGCACGAGGTCGTCCCGGGTGTTGTCGAGTCTCTCAAGgtactccaatttcttctcctctgctttgctcggccgctccag-ctacgtttcttcttgcgcaccag--------------------------------------

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|208383014|gb|DC927764.1|DC927764
EST:     ATTCTGGTCTTGAGCACGAGGTCGTCCCCGGGGTCGTCGAGAGCCTTAAG                         GTAATCACCAAGTTCTGCTCGGAGCGCATTGCGAAATACGCCTTTGAGTAT
genomic: ATTCTGGTCTTGAGCACGAGGTCGTCCCCGGGGTCGTCGAGAGCCTTAAGgtacatattt ... agatgttcagGTAATCACCAAGTTCTGCTCGGAGCGCATTGCGAAATACGCCTTTGAGTAT
EST: gi|162238353|gb|FC417338.1|FC417338
EST:     ATTCTGGTCTTGAGCACGAGGTCGTCCCCGGGGTCGTCGAGAGCCTTAAG                         GTAATCACCAAGTTCTGCTCGGAGCGCATTGCGAAATACGCCTTTGAGTAT
genomic: ATTCTGGTCTTGAGCACGAGGTCGTCCCCGGGGTCGTCGAGAGCCTTAAGgtacatattt ... agatgttcagGTAATCACCAAGTTCTGCTCGGAGCGCATTGCGAAATACGCCTTTGAGTAT
EST: gi|208387364|gb|DC933115.1|DC933115
EST:     ATTCTGGTCTTGAGCACGAGGTCGTCCCCGGGGTCGTCGAGAGCCTTAAG                         GTAATCACCAAGTTCTGCTCGGAGCGCATTGCGAAATACGCCTTTGAGTAT
genomic: ATTCTGGTCTTGAGCACGAGGTCGTCCCCGGGGTCGTCGAGAGCCTTAAGgtacatattt ... agatgttcagGTAATCACCAAGTTCTGCTCGGAGCGCATTGCGAAATACGCCTTTGAGTAT
EST: gi|208357601|gb|DC914015.1|DC914015
EST:     ATTCTGGTCTTGAGCACGAGGTCGTCCCCGGGGTCGTCGAGAGCCTTAAG                         GTAATCACCAAGTTCTGCTCGGAGCGCATTGCNAAATACGCCTTTGAGTAT
genomic: ATTCTGGTCTTGAGCACGAGGTCGTCCCCGGGGTCGTCGAGAGCCTTAAGgtacatattt ... agatgttcagGTAATCACCAAGTTCTGCTCGGAGCGCATTGCGAAATACGCCTTTGAGTAT
EST: gi|208385560|gb|DC937105.1|DC937105
EST:     ATTCTGGTCTTGAGCACGAGGTCGTCCCCGGGGTCGTCGAGAGCCTTAAG                         GTAATCACCAAGTTCTGCTCGGAGCGCATTGCGAAATACGCCTTTGAGTAT
genomic: ATTCTGGTCTTGAGCACGAGGTCGTCCCCGGGGTCGTCGAGAGCCTTAAGgtacatattt ... agatgttcagGTAATCACCAAGTTCTGCTCGGAGCGCATTGCGAAATACGCCTTTGAGTAT
EST: gi|100356963|gb|BY965366.1|BY965366
EST:     ATTCTGGTCTTGAGCACGAGGTCGTCCCCGGGGTCGTCGAGAGCCTTAAG                         GTAATCACCAAGTTCTGCTCGGAGCGCATTGCGAAATACGCCTTTGAGTAT
genomic: ATTCTGGTCTTGAGCACGAGGTCGTCCCCGGGGTCGTCGAGAGCCTTAAGgtacatattt ... agatgttcagGTAATCACCAAGTTCTGCTCGGAGCGCATTGCGAAATACGCCTTTGAGTAT
EST: gi|162195565|gb|FC371866.1|FC371866
EST:     ATTCTGGTCTTGAGCACGAGGTCGTCCCCGGGGTCGTCGAGAGCCTTAAG                         GTAATCACCAAGTTCTGCTCGGAGCGCATTGCGAAATACGCCTTTGAGTAT
genomic: ATTCTGGTCTTGAGCACGAGGTCGTCCCCGGGGTCGTCGAGAGCCTTAAGgtacatattt ... agatgttcagGTAATCACCAAGTTCTGCTCGGAGCGCATTGCGAAATACGCCTTTGAGTAT
EST: gi|100358833|gb|BY946711.1|BY946711
EST:     ATTCTGGTCTTGAGCACGAGGTCGTCCCCNGGGTCGTCGAGAGCCTTAAG                         GTAATCACCAAGTTCTGCTCGGAGCGCATTGCGAAATACGCCTTTGAGTAT
genomic: ATTCTGGTCTTGAGCACGAGGTCGTCCCCGGGGTCGTCGAGAGCCTTAAGgtacatattt ... agatgttcagGTAATCACCAAGTTCTGCTCGGAGCGCATTGCGAAATACGCCTTTGAGTAT
EST: gi|100359663|gb|BY947090.1|BY947090
EST:     ATTCTGGTCTTGAGCACGAGGTCGTCCGCGTGGTCGTCGAGAGCCTTAAG                         GTAATCACCAAGTTCTGCTCGGAGCGCATTGCGAAATACGCCTTTGAGTAT
genomic: ATTCTGGTCTTGAGCACGAGGTCGTCCCCGGGGTCGTCGAGAGCCTTAAGgtacatattt ... agatgttcagGTAATCACCAAGTTCTGCTCGGAGCGCATTGCGAAATACGCCTTTGAGTAT

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: 34 (upstream exon), 35 (downstream exon)
Score: 10

CCATGACAATGTCAACATTGTGGTTATTCGGGAGAATACCGAAGGGGAGTATTCTGGTCTTGAGCACGAGGTCGTCCCCGGGGTCGTCGAGAGCCTTAAGgtacatattt ... agatgttcagGTAATCACCAAGTTCTGCTCGGAGCGCATTGCGAAATACGCCTTTGAGTATGCTTATCTCAACAACCGCAAGACAGTAACAGCAGTGCACAAGGCCAACA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCATGACAATGTCAACATTGTGGTTATTCGGGAGAATACCGAAGGGGAGTATTCTGGTCTTGAGCACGAGGTCGTCCCCGGGGTCGTCGAGAGCCTTAAGgtacatatttcgttttctgacctgaaaaataacactactctatgttgtgcctagtgattgtaatattttctgtccaagcatttttttcacgcctttgttt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaataa