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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttccttgatatcgaattgtttctgctatttgcggtcttgttcacgccgtttgcattttcaacatacataactaactcattcacaattcgatttgcacagATGCCACTGCATACTATTATTGAGATTCAAATGGGAGTTACTGGTGTTCAGGAGAAGCGATACAAGCTCATGGAGACCCAGA

Basic information

species Physcomitrella patens
transcript PP1S242_66V6.1
intron # 23
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S242_66V6.1 (Physcomitrella patens), 3'ss of exon 23
lower sequence: LOC_Os05g07130.2 (Oryza sativa), 3'ss of exon 22
tttccttgatatcgaattgtttctgctatttgcggtcttgttcacgccgtttgcattttcaacatacataactaactcattcacaattcgatttgcacagATGCCACTGCATACTATTATTGAGATTCAAATGGGAGTTACTGGTGTTCAGGAGAAGCGATACAAGCTCATGGA---GACCCAGA---------------
           ||  |   | |   ||  |   | || |  |   ||      | |    || | | | | | |||| || | |  |    ||     ||||||| || || || || |||||||| ||||||||||| || |||||| |||||||| | ||||||||||||||    |   | |               
----------gtcacac-atatgatcttctcttgttcattattgtgctagaaacctaagaaatacatagaccaaactaataccctttaatcttcatgtagATGCCTCTCCACACCATAATTGAGATACAAATGGGAGTCACAGGTGTTGAGGAGAAGAGGTACAAGCTCATGGACTGAATATACATACATCTAGGCTCAG

upper sequence: PP1S242_66V6.1 (Physcomitrella patens), 3'ss of exon 23
lower sequence: GLYMA14G37520.1 (Glycine max), 3'ss of exon 33
---tttccttgatatcgaattgtttctgctatttgcggtcttgttcacgccgtttgcattttcaacatacataactaactcattcacaattcgatt-tgcacagATGCCACTGCATACTATTATTGAGATTCAAATGGGAGTTACTGGTGTTCAGGAGAAGCGATACAAGCTCATGGA--GACCCAGA----------------
           || |    ||     | |  |||| |      || ||    | |  ||  | ||  | |  ||   |   | |   | || | |  |  ||||||||| || ||||| || || ||||| ||| ||||||||||||||||| | |||||  ||||||| || |||||  ||     |                
caaaaaggaaaatctgaggttcaccatccattttgtgaaacgttttac----tgtaaatcatgaatttgcgcaagatatctaatgtgagtttgctcatttacagATGCCCCTCCATACGATAATAGAGATACAATTGGGAGTTACTGGTGTTGAAGAGAAAAGATACAAACTAATGGACTGAAATGAACTGAAGGGAAAGAATA

upper sequence: PP1S242_66V6.1 (Physcomitrella patens), 3'ss of exon 23
lower sequence: AT1G07110.1 (Arabidopsis thaliana), 3'ss of exon 22
-----------tttccttgatatcgaattgtttctgc-tatttgcggtct---tgttcacgccgtttgcattttca---acatacataactaactcattcacaattcgatttgcacagATGCCACTGCATACTATTATTGAGATTCAAATGGGAGTTACTGGTGTTCAGGAGAAGCGATACAAGCTCATGGA---GACCCAGA---------------
            ||     |||    | | | |  |     ||| | | |     ||||    || |    |   |   ||| |||||| ||||  |||    ||    |||  |||||||||||| || ||||| || ||||| || ||||||||| ||||||| || ||||| || ||||| ||||||||    |  || |               
gtaaaatctgaattagaaaatacgagactatcttagaacgattgagctataagctttcagagagtcttggctgcaagccacacacataa-taacatattttggat---gtttcaacagATGCCACTTCACACTATAATAGAGATACAGATGGGAGTTTCTGGTGTGCAAGAGAAACGCTACAAACTCATGGACTGAATTCAAACAACTATTACCACAA

upper sequence: PP1S242_66V6.1 (Physcomitrella patens), 3'ss of exon 23
lower sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 22
tttccttgatatcgaattgtttctgctatttgcggtcttgttcacgccgtttgcattt--tcaacatacataactaactca-ttcacaattcgatttgcacagATGCCACTGCATACTATTATTGAGATTCAAATGGGAGTTACTGGTGTTCAGGAGAAGCGATACAAGCTCATGGA--GACCCAGA----------------
|| ||     ||   ||   |       ||| |          |  |  |    | ||   |||  ||||   || ||  | || |  ||||  ||| ||  | | || || |||||||| || ||||| |||||||||||||||||||| || |||||  ||||||||||||||||  |||   |                 
ttaccacatcattttatgaataaattccttttctaggagaagaaaacaatccaaagttggccaagttacacc-ctgacaaacttaatgattcacttttca--gGTACCGCTTCATACTATAATAGAGATACAAATGGGAGTTACTGGTGTCCAAGAGAAAAGATACAAGCTCATGGACTGACTTCGCTTCACAGAATCTTTTG

upper sequence: PP1S242_66V6.1 (Physcomitrella patens), 3'ss of exon 23
lower sequence: EFJ11749 (Selaginella moellendorffii), 3'ss of exon 17
tttccttgatatcgaattgtttctgctatttgcggtcttgttcacgccgtttgcattttcaacatacataactaactcattcacaattcgatttgcacagATGCCACTGCATACTATTATTGAGATTCAAATGGGAGTTACTGGTGTTCAGGAGAAGCGATACAAGCTCATGGAGACCCAGA
                  ||   ||  ||||    ||| ||  |     | ||      |||  | | |   |||     |      |   | ||| |||||||| || || ||||| |||||||| || ||||||||  | ||||| || |||||||||||||||||| |  |        
--------------gtgagtgagtggaattta---tctagtcaatatgatctgg----ccaagttccttctttaagcttctgcttcctttgtgtgc-cagATGCCTCTTCACACTATCATTGAGATCCAGATGGGAGTCGCAGGTGTACAAGAGAAGCGATACAAGCTCTTATAA-------

upper sequence: PP1S242_66V6.1 (Physcomitrella patens), 3'ss of exon 23
lower sequence: EFJ22544 (Selaginella moellendorffii), 3'ss of exon 17
tttccttgatatcgaattgtttctgctatttgcggtcttgttcacgccgtttgcattttcaacatacataactaactcattcacaattcgatttgcacagATGCCACTGCATACTATTATTGAGATTCAAATGGGAGTTACTGGTGTTCAGGAGAAGCGATACAAGCTCATGGAGACCCAGA
                  ||   ||  ||||    ||| ||  |     | ||      |||  | | |   |||     |      |   | ||| |||||||| || || ||||| |||||||| || ||||||||  | ||||| || |||||||||||||||||| |  |        
--------------gtgagtgagtggaattta---tctagtcaatatgatctgg----ccaagttccttctttaagcttctgcttcctttgtgtgc-cagATGCCTCTTCACACTATCATTGAGATCCAGATGGGAGTCCCAGGTGTACAAGAGAAGCGATACAAGCTCTTATAA-------

upper sequence: PP1S242_66V6.1 (Physcomitrella patens), 3'ss of exon 23
lower sequence: EFJ07831 (Selaginella moellendorffii), 3'ss of exon 18
tttccttgatatcgaattgtttctgctatttgcggtcttgttcacgccgtttgcattttcaacatacataactaactcattcacaattcgatttgcacagATGCCACTGCATACTATTATTGAGATTCAAATGGGAGTTACTGGTGTTCAGGAGAAGCGATACAAGCTCATGGAGACCCAGA--
                                                        |       |||  | ||   |   || |  || |      |||| | ||||| || ||| | |||||||| ||||||||||| |||||  | || ||||| ||||||||||| ||||||    |    
-------------------------------------------------------gtaatgctttacg-atcttgatttctcgcgtttagccgactacagGTACCACTCCACACTGTCATTGAGATCCAAATGGGAGTCACTGGGATCCAAGAGAAACGATACAAGCTAATGGAGGATAATTGA

upper sequence: PP1S242_66V6.1 (Physcomitrella patens), 3'ss of exon 23
lower sequence: EFJ07288 (Selaginella moellendorffii), 3'ss of exon 18
tttccttgatatcgaattgtttctgctatttgcggtcttgttcacgccgtttgcattttcaacatacataactaactcattcacaattcgatttgcacagATGCCACTGCATACTATTATTGAGATTCAAATGGGAGTTACTGGTGTTCAGGAGAAGCGATACAAGCTCATGGAGACCCAGA------------------
                                                        |   |   |||  | ||   |   || |  || |      |||| | ||||| || ||| | |||||||| ||||||||||| |||||  | || ||||| ||||||||||| ||||||    |                    
-------------------------------------------------------gtaatattttacg-atcttgatttctcgcgtttagccgactacagGTACCACTCCACACTGTCATTGAGATCCAAATGGGAGTCACTGGGATCCAAGAGAAACGATACAAGCTAATGGAGGATAATTGATAACCTCATTATAAAA

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|162190523|gb|FC366161.1|FC366161
EST:     TATATGCGTACTTTGCAGACAAACCTCTGAAAGAGGTACCGCATATTGAG                         ATGCCACTGCATACTATTATTGAGATTCAAATGGGAGTTACTGGTGTTCAG
genomic: TATATGCGTACTTTGCAGACAAACCTCTGAAAGAGGTACCGCATATTGAGgtactatcca ... atttgcacagATGCCACTGCATACTATTATTGAGATTCAAATGGGAGTTACTGGTGTTCAG
EST: gi|162256997|gb|FC432736.1|FC432736
EST:     TATATGCGTACTTTGCAGACAAACCTCTGAAAGAGGTACCGCATATTGAG                         ATGCCACTGCATACTATTATTGAGATTCAAATGGGAGTTACTGGTGTTCAG
genomic: TATATGCGTACTTTGCAGACAAACCTCTGAAAGAGGTACCGCATATTGAGgtactatcca ... atttgcacagATGCCACTGCATACTATTATTGAGATTCAAATGGGAGTTACTGGTGTTCAG
EST: gi|162230831|gb|FC406670.1|FC406670
EST:     TATATGCGTACTTTGCAGACNAACCTCTGAAAGAGGTACCGCATATTGAG                         ATGCCACTGCATACTATTATTGAG
genomic: TATATGCGTACTTTGCAGACAAACCTCTGAAAGAGGTACCGCATATTGAGgtactatcca ... atttgcacagATGCCACTGCATACTATTATTGAG
EST: gi|162230830|gb|FC406669.1|FC406669
EST:     TATATGCGTACTTTGCAGACAAACCTCTGAAAGAGGTACCGCATATTGAG                         ATGCCACTGCATACTATTATTGAGATTCAAATGGGAGTTACTGGTGTTCAG
genomic: TATATGCGTACTTTGCAGACAAACCTCTGAAAGAGGTACCGCATATTGAGgtactatcca ... atttgcacagATGCCACTGCATACTATTATTGAGATTCAAATGGGAGTTACTGGTGTTCAG
EST: gi|67693913|gb|BJ954146.1|BJ954146
EST:     TATATGCGTACTTTGCAGACAAACCTCTGAAAGAGGTACCGCATATTGAG                         ATGCCACTGCATACTATTATTGAGATTCAAATGGGAGTTACTGGTGTTCAG
genomic: TATATGCGTACTTTGCAGACAAACCTCTGAAAGAGGTACCGCATATTGAGgtactatcca ... atttgcacagATGCCACTGCATACTATTATTGAGATTCAAATGGGAGTTACTGGTGTTCAG

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: 11 (upstream exon), 32 (downstream exon)
Score: 3

GCAATTCTACGCTCTCTATATGCGTACTTTGCAGACAAACCTCTGAAAGAGGTACCGCATATTGAGgtactatcca ... atttgcacagATGCCACTGCATACTATTATTGAGATTCAAATGGGAGTTACTGGTGTTCAGGAGAAGCGATACAAGCTCATGGAGACCCAGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gccgtttgcattttcaacatacataactaactcattcacaattcgatttgcacagATGCCACTGCATACTATTATTGAGATTCAAATGGGAGTTACTGGTGTTCAGGAGAAGCGATACAAGCTCATGGAGACCCAGA
                        aactaac  putative branch site (score: 3)
         attttcaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttccttgatatcgaattgtttctgctatttgcggtcttgttcacgccgtttgcattttcaacatacataactaactcattcacaattcgatttgcacagATGCCACTGCATACTATTATTGAGATTCAAATGGGAGTTACTGGTGTTCAGGAGAAGCGATACAAGCTCATGGAGACCCAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA