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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTACGACTATGAAGACAAAATTAATGCTGCTGTTTTTCCAGGACTACAAGGGGGTCCTCACAACCACACCATTGCAGGACTTGCTGTTGCCTTGAAACAGgtaaactttcgtcatgcgatcatttaacgaggagcataactcatcgatattggaaagaggtttaagcgaatcaaaatgcaaaacttcaccttttttaatg...

Basic information

species Physcomitrella patens
transcript PP1S79_54V6.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S79_54V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: GLYMA18G27710.1 (Glycine max), 5'ss of exon 11
CTACGACTATGAAGACAAAATTAATGCTGCTGTTTTTCCAGGACTACAAGGGGGTCCTCACAACCACACCATTGCAGGACTTGCTGTTGCCTTGAAACAGgtaaactttcgtcatgcgatcatttaacgaggagcataactcatcgatattggaaagaggtttaagcgaatcaaaa------tgcaaaacttcaccttttttaatg
 || |||||||| |||||||| ||    |||||||| || ||||| |||||||| |||||||||||||| ||| | ||  | |||||||| ||||| |||||| ||    |  |   ||||||   | ||  |  |    | |||  | ||  ||    |    |  ||     ||      ||  | |||| |  |||||     
GTATGACTATGAGGACAAAATCAACCAAGCTGTTTTCCCTGGACTGCAAGGGGGCCCTCACAACCACACTATTACTGGTTTAGCTGTTGCATTGAAGCAGgtacacaagtgg-agatgatcataatatgataattact-tttatcagtgtttcaatagtgacagactgagatggaaaggatctgtgacactttatgtttttc----

upper sequence: PP1S79_54V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: GLYMA14G36280.1 (Glycine max), 5'ss of exon 10
CTACGACTATGAAGACAAAATTAATGCTGCTGTTTTTCCAGGACTACAAGGGGGTCCTCACAACCACACCATTGCAGGACTTGCTGTTGCCTTGAAACAGgtaaact--ttcgtcatgcgatcatttaacgaggagcataactcatcgatattggaaagaggtttaagcgaatcaaaatgcaaaacttcaccttttttaatg---------------------------------------------------
 || ||||||||||||||||| ||    ||||||||||| ||||| ||||| ||||| ||||| ||||| ||| ||||  | || |||||  |||| |||||    |  ||    | || |  |          |  |||  |  ||    | | ||| |  |||      || ||||   ||   | ||   || | |||                                                    
GTATGACTATGAAGACAAAATAAACCAGGCTGTTTTTCCTGGACTTCAAGGTGGTCCACACAATCACACTATTTCAGGCTTAGCAGTTGCACTGAAGCAGgttctttaattgactaggcaaagaaactgtagttattatagtttctcc---tagtaaacatttttttctctataaaaacataatggt-cattcttgtaaatctgttgccaggcttatgtaagtccagttctttcttcatttctgtaaatgtag

upper sequence: PP1S79_54V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: GLYMA02G38160.2 (Glycine max), 5'ss of exon 10
CTACGACTATGAAGACAAAATTAATGCTGCTGTTTTTCCAGGACTACAAGGGGGTCCTCACAACCACACCATTGCAGGACTTGCTGTTGCCTTGAAACAGgt--aaactttcgtcatgcgatcatttaacgaggagcataactcatcgatattggaaa--gaggtttaagcgaatcaaaatg--caaaacttcaccttttttaatg---------------------------------------
 || ||||||||||||| ||| |||   ||||||||||| ||||| ||||| ||||| ||||| ||||| ||| | ||  | || |||||  |||| |||||   |   ||    | || |  |          |  |||  |  || || |    |    |  ||  |   || || ||||  ||    |  || | | ||                                           
GTATGACTATGAAGACAGAATAAATCAGGCTGTTTTTCCTGGACTTCAAGGTGGTCCACACAATCACACTATTTCTGGCTTAGCAGTTGCACTGAAGCAGgttctataattgactaggcaaagaaactgtagttattatagttt-tccatgtaaacatttcattttctataaaaacataatgatcattcttgtacatctgttgccaggcttaagttcagttctttcttcatttctgtaaatgtag

upper sequence: PP1S79_54V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: AT4G37930.1 (Arabidopsis thaliana), 5'ss of exon 10
CTACGACTATGAAGACAAAATTAATGCTGCTGTTTTTCCAGGACTACAAGGGGGTCCTCACAACCACACCATTGCAGGACTTGCTGTTGCCTTGAAACAGgtaaactttcgtcatgcgatc-atttaacgaggagcat-aactcatcgatattggaaagaggtttaagcgaatc-aaaatgcaaaacttcaccttttttaatg
 || || | ||||||||| || ||    ||||| || || || || ||||| ||||| ||||||||||| ||  ||||||| |||||||| ||||||||||||   |   | || |  ||  |  |||||  |   ||    |   || | |  | ||    || ||  |  |  ||||||||                    
GTATGATTTTGAAGACAAGATCAACCAAGCTGTCTTCCCTGGTCTTCAAGGTGGTCCACACAACCACACTATCACAGGACTAGCTGTTGCTTTGAAACAGgtacggtgagg-cacggaatggaactaacgttgcttattggatttgcggtttctgtaacc--ttcaaatggtttgaaaatgcag-------------------

upper sequence: PP1S79_54V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: Vv00s0211g00080.t01 (Vitis vinifera), 5'ss of exon 3
CTACGACTATGAAGACAAAATTAATGCTGCTGTTTTTCCAGGACTACAAGGGGGTCCTCACAACCACACCATTGCAGGACTTGCTGTTGCCTTGAAACAGgtaaactttc--gtcatgcgat---catttaacgaggagcataactcatcgatattggaaagaggtttaagcgaatcaaaatgcaaaacttcaccttttttaatg
 || ||||||||||||||||| |||   ||||| ||||| ||||| ||||| || |||||||| ||||| ||||| ||  | |||||||| |||||||||||    | ||  |       ||   ||| ||   | | |||| ||   |   | ||     | ||   ||  |||  |    |         |            
GTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTTCAAGGTGGCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGAAACAGgtctgttctctggctggataattttcatatattaatgcgcattacatttttttttttttttgtggcaaaaaggaaagaggggggggggggggaaaaaaga-----

upper sequence: PP1S79_54V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: Vv00s0211g00120.t01 (Vitis vinifera), 5'ss of exon 10
CTACGACTATGAAGACAAAATTAATGCTGCTGTTTTTCCAGGACTACAAGGGGGTCCTCACAACCACACCATTGCAGGACTTGCTGTTGCCTTGAAACAGgtaaactttc--gtcatgcgat---catttaacgaggagcataac--tcatcgatattggaaagaggtttaagcgaatcaaaatgcaaaacttcaccttttttaatg
 || ||||||||||||||||| |||   ||||| ||||| ||||| ||||| || |||||||| ||||| ||||| ||  | |||||||| |||||||||||    | ||  |       ||   ||| ||   | | |||| ||  |  |   | ||     | ||   ||  |||  |    |         |            
GTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTTCAAGGTGGCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGAAACAGgtctgttctctggctggataattttcatatattaatgcgcattacatttttttttttttttttgtggcaaaaaggaaagagggggggggggaagaatgaa-------

upper sequence: PP1S79_54V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: Vv00s0211g00070.t01 (Vitis vinifera), 5'ss of exon 10
CTACGACTATGAAGACAAAATTAATGCTGCTGTTTTTCCAGGACTACAAGGGGGTCCTCACAACCACACCATTGCAGGACTTGCTGTTGCCTTGAAACAGgtaaactttc--gtcatgcgat---catttaacgaggagcataac-tcatcgatattggaaagaggtttaagcgaatcaaaatgcaaaacttcaccttttttaatg
 || ||||||||||||||||| |||   ||||| ||||| ||||| ||| | |  |||||||| ||||| ||||| ||  | |||||||| |||||||||||    || |  |       ||   ||| ||   | | |||| || |  |   | | | ||| |||     | | |  | |||| ||||  | |  |         
GTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTTCAAAGTGCCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGAAACAGgtctgtttgctggctggataattttcatatattaatgcgcattacattttttttgtggcaaaaaggaagggggggagaagaatg-aaaatctaatatgcca-----

upper sequence: PP1S79_54V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: Vv00s0211g00090.t01 (Vitis vinifera), 5'ss of exon 2
CTACGACTATGAAGACAAAATTAATGCTGCTGTTTTTCCAGGACTACAAGGGGGTCCTCACAACCACACCATTGCAGGACTTGCTGTTGCCTTGAAACAGgtaaactttc--gtcatgcgat---catttaacgaggagcataactcatcgatattggaaagaggtttaagcgaatcaaaatgcaaaacttcaccttttttaatg
 || ||||||||||||||||| |||   ||||| ||||| ||||| ||| | |  |||||||| ||||| ||||| ||  | |||||||| |||||||||||    || |  |       ||   ||| ||   | | |||| ||   |   |  ||| || | |   | | |       | | || |    | ||  | |    
GTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTTCAAAGTGCCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGAAACAGgtctgtttgctggctggataattttcatatattaatgcgcattacattttttttgtggcaaaaaggaaagggggggggggaagaaagaaa--atctaatatg---

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|37851231|gb|BJ609239.1|BJ609239
EST:     TTGCTGTTGCCTTGAAACAG                         GCAGCTACGCCAGAGTTCAAGGCGTACCAGGAACAAGTTCTGAGCAACTCT
genomic: TTGCTGTTGCCTTGAAACAGgtaaactttc ... gtggttacagGCAGCTACGCCAGAGTTCAAGGCGTACCAGGAACAAGTTCTGAGCAACTCT
EST: gi|162182304|gb|FC357175.1|FC357175
EST:     GGGGTCCTCACAACCACACCATTGCAGGACTTGCTGTTGCCTTGAAACAG                         GCAGCTACGCCAGAGTTCAAGGCGTACCAGGAACAAGTTCTGAGCAACTCT
genomic: GGGGTCCTCACAACCACACCATTGCAGGACTTGCTGTTGCCTTGAAACAGgtaaactttc ... gtggttacagGCAGCTACGCCAGAGTTCAAGGCGTACCAGGAACAAGTTCTGAGCAACTCT
EST: gi|37852647|gb|BJ610655.1|BJ610655
EST:     CTTGCTGTTGCCTTGAAACAG                         GCAGCTACGCCAGAGTTCAAGGCGTACCAGGAACAAGTTCTGAGCAACTCT
genomic: CTTGCTGTTGCCTTGAAACAGgtaaactttc ... gtggttacagGCAGCTACGCCAGAGTTCAAGGCGTACCAGGAACAAGTTCTGAGCAACTCT
EST: gi|37845693|gb|BJ603701.1|BJ603701
EST:     TTGCTGTTGCCTTGAAACAG                         GCAGCTACGCCAGAGTTCAAGGCGTACCAGGAACAAGTTCTGAGCAACTCT
genomic: TTGCTGTTGCCTTGAAACAGgtaaactttc ... gtggttacagGCAGCTACGCCAGAGTTCAAGGCGTACCAGGAACAAGTTCTGAGCAACTCT
EST: gi|37850584|gb|BJ608592.1|BJ608592
EST:     ATTGCAGGACTTGCTGTTGCCTTGAAACAG                         GCAGCTACGCCAGAGTTCAAGGCGTACCAGGAACAAGTTCTGAGCAACTCT
genomic: ATTGCAGGACTTGCTGTTGCCTTGAAACAGgtaaactttc ... gtggttacagGCAGCTACGCCAGAGTTCAAGGCGTACCAGGAACAAGTTCTGAGCAACTCT
EST: gi|37847210|gb|BJ605218.1|BJ605218
EST:     CACCATTGCAGGACTTGCTGTTGCCTTGAAACAG                         GCAGCTACGCCAGAGTTCAAGGCGTACCAGGAACAAGTTCTGAGCAACTCT
genomic: CACCATTGCAGGACTTGCTGTTGCCTTGAAACAGgtaaactttc ... gtggttacagGCAGCTACGCCAGAGTTCAAGGCGTACCAGGAACAAGTTCTGAGCAACTCT
EST: gi|37850496|gb|BJ608504.1|BJ608504
EST:     CTTGCTGTTGCCTTGAAACAG                         GCAGCTACGCCAGAGTTCAAGGCGTACCAGGAACAAGTTCTGAGCAACTCT
genomic: CTTGCTGTTGCCTTGAAACAGgtaaactttc ... gtggttacagGCAGCTACGCCAGAGTTCAAGGCGTACCAGGAACAAGTTCTGAGCAACTCT
EST: gi|67698707|gb|BJ958940.1|BJ958940
EST:     GGGGTCCTCACAACCACACCATTGCAGGACTTGCTGTTGCCTTGAAACAG                         GCAGCTACGCCAGAGTTCAAGGCGTACCAGGAACAAGTTCTGAGCAACTCT
genomic: GGGGTCCTCACAACCACACCATTGCAGGACTTGCTGTTGCCTTGAAACAGgtaaactttc ... gtggttacagGCAGCTACGCCAGAGTTCAAGGCGTACCAGGAACAAGTTCTGAGCAACTCT
EST: gi|208388379|gb|DC949323.1|DC949323
EST:     GGGGTCCTCACAACCACACCATTGCAGGACTTGCTGTTGCCTTGAAACAG                         GCAGNTACGCCAGAGTTCAAGGCGTACCAGGAACAAGTTCTGAGCAACTCT
genomic: GGGGTCCTCACAACCACACCATTGCAGGACTTGCTGTTGCCTTGAAACAGgtaaactttc ... gtggttacagGCAGCTACGCCAGAGTTCAAGGCGTACCAGGAACAAGTTCTGAGCAACTCT
EST: gi|37840030|gb|BJ598038.1|BJ598038
EST:     GCAGGACTTGCTGTTGCCTTGAAACAG                         GCAGCTACGCCAGAGTTCCAAGGCGTACCAGGAACAAGTTCTGAGCAACTC
genomic: GCAGGACTTGCTGTTGCCTTGAAACAGgtaaactttc ... gtggttacagGCAGCTACGCCAGAGTT-CAAGGCGTACCAGGAACAAGTTCTGAGCAACTC
EST: gi|37838492|gb|BJ596500.1|BJ596500
EST:     TGCAGGACTTGCTGTTGCCTTGAAACAG                         GCAGCTACGCCAGAGTTCCAAGGCGTACCAGGAACAAGTTCTGAGCAACTC
genomic: TGCAGGACTTGCTGTTGCCTTGAAACAGgtaaactttc ... gtggttacagGCAGCTACGCCAGAGTT-CAAGGCGTACCAGGAACAAGTTCTGAGCAACTC
EST: gi|67575248|gb|BJ948072.1|BJ948072
EST:     GGGGTCCTCACAACCACACCATTGCAGGACTTGCTGTTGCCTTGAAACAG                         GCAGCTACGCCAGAGTTCAAGGCGTACCAGGAACAAGTTCTGAGCAACTCT
genomic: GGGGTCCTCACAACCACACCATTGCAGGACTTGCTGTTGCCTTGAAACAGgtaaactttc ... gtggttacagGCAGCTACGCCAGAGTTCAAGGCGTACCAGGAACAAGTTCTGAGCAACTCT
EST: gi|37838309|gb|BJ596317.1|BJ596317
EST:     GGGGTCCTCACAACCACACCATTGCAGGACTTGCTGTTGCCTTGAAACAG                         GCAGCTACGCCAGAGTTCAAGGCGTACCAGGAACAAGTTCTGAGCAACTCT
genomic: GGGGTCCTCACAACCACACCATTGCAGGACTTGCTGTTGCCTTGAAACAGgtaaactttc ... gtggttacagGCAGCTACGCCAGAGTTCAAGGCGTACCAGGAACAAGTTCTGAGCAACTCT
EST: gi|162179834|gb|FC355905.1|FC355905
EST:     GGGGTCCTCACAACCACACCATTGCAGGACTTGCTGTTGCCTTGAAACAG                         GCAGCTACGCCAGAGTTCAAGGCGTACCAGGAACAAGTTCTGAGCAACTCT
genomic: GGGGTCCTCACAACCACACCATTGCAGGACTTGCTGTTGCCTTGAAACAGgtaaactttc ... gtggttacagGCAGCTACGCCAGAGTTCAAGGCGTACCAGGAACAAGTTCTGAGCAACTCT

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), 26 (downstream exon)
Score: 8

CTACGACTATGAAGACAAAATTAATGCTGCTGTTTTTCCAGGACTACAAGGGGGTCCTCACAACCACACCATTGCAGGACTTGCTGTTGCCTTGAAACAGgtaaactttc ... gtggttacagGCAGCTACGCCAGAGTTCAAGGCGTACCAGGAACAAGTTCTGAGCAACTCTGCACGTTTTGCCAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTACGACTATGAAGACAAAATTAATGCTGCTGTTTTTCCAGGACTACAAGGGGGTCCTCACAACCACACCATTGCAGGACTTGCTGTTGCCTTGAAACAGgtaaactttcgtcatgcgatcatttaacgaggagcataactcatcgatattggaaagaggtttaagcgaatcaaaatgcaaaacttcaccttttttaatg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aatcaaaa