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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGATGGACCGAAGTTGGTGCGAGAGCTATTTCGGGTGGCTGATGAACTGTCTCCTACCATTGTTTTTATCGATGAAATTGATGCTGTCGGTACAAAAAGgtaattctggcctgcttctcattatttttatttgcggtgtttctcataatgtttcgattcttgcaaccacactctcaaggttgccactgcactcttatct...

Basic information

species Physcomitrella patens
transcript PP1S4_277V6.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S4_277V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GRMZM2G104373_T01 (Zea mays), 5'ss of exon 3
GAGATGGACCGAAGTTGGTGCGAGAGCTATTTCGGGTGGCTGATGAACTGTCTCCTACCATTGTTTTTATCGATGAAATTGATGCTGTCGGTACAAAAAGgtaattctggcctgcttctcatta-tttttatttgcggtgtttctcataatgtttcgattcttgcaaccacactctcaaggttgccactgcactcttatct--
| ||||| || ||| | ||  ||||  | ||  ||||||||||||| || |||||| | ||||| ||||| ||||| ||||||||||| || ||||| |||||  || | | ||    | |  |    |||||| |  || || | | ||      | |    |   |   |  ||   ||||   |  | | ||| |     
GTGATGGTCCCAAGCTTGTTAGAGAATTGTTCAGGGTGGCTGATGATCTTTCTCCTTCAATTGTCTTTATTGATGAGATTGATGCTGTTGGGACAAAGAGgtatatcagacatgaaagttaacagcagttattttctttggttatgaaaaaaagctggtgaaagggcctctagcctagtggtt---aaaggattctgagtagc

upper sequence: PP1S4_277V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA13G19280.1 (Glycine max), 5'ss of exon 3
GAGATGGACCGAAGTTGGTGCGAGAGCTATTTCGGGTGGCTGATGAACTGTCTCCTACCATTGTTTTTATCGATGAAATTGATGCTGTCGGTACAAAAAGgtaattctggcctgcttctc-attattttt--atttgcggtgtttctcataatgtttcgattcttgcaaccaca----ctctcaaggttgccactgcactcttatct--------------------------
||||||| || ||  | ||  |||| || ||  | || |||||||| || |||||| | ||||| || || |||||||||||||| || ||||||||||||||||| |  ||| |  ||  | ||||  |  |  |  ||||    |   |  ||   |  |  |   ||   |    |||| | | ||        ||  | ||                            
GAGATGGCCCAAAACTTGTAAGAGAACTTTTCAGAGTTGCTGATGATCTTTCTCCTTCTATTGTATTCATTGATGAAATTGATGCAGTTGGTACAAAAAGgtaattttaacctccaactttagtattcatgaaggtagggtggggttggaagagtgatgtcttgtatcactctatgagctcttaggattcttttcctacattcatgagcttactaataaatatgtatttacag

upper sequence: PP1S4_277V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA10G04920.1 (Glycine max), 5'ss of exon 3
GAGATGGACCGAAGTTGGTGCGAGAGCTATTTCGGGTGGCTGATGAACTGTCTCCTACCATTGTTTTTATCGATGAAATTGATGCTGTCGGTACAAAAAGgtaattctggcctgcttctcattatttttatttgcggtgtttctcataatgtttcgattcttgcaaccacactctcaagg-ttgccactgcactcttatct--------------------------------
||||||| || ||  | ||| |||| || ||  | || || ||||| || |||||| | ||||| || || |||||||| ||||| || ||||||||||||||||| |  ||  |  ||  |||  | |  |   |||       ||        ||| | |   | ||| || | |    |||  | |    || ||  |                                
GAGATGGCCCAAAACTTGTGAGAGAACTTTTCAGAGTTGCCGATGATCTTTCTCCTTCTATTGTATTCATTGATGAAATCGATGCAGTTGGTACAAAAAGgtaattttaacccccaact--ttagctgtcatgaaggtaccggggatggaagagtgatgccttgtatcactctatgagctcttgggattcttttcctacattcatgagcttaccagtaaatatgtatttacag

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|162268182|gb|FC443860.1|FC443860
EST:     TCTCCTACCATTGTTTTTATCGATGAAATTGATGCTGTCGGTACAAAAAG                         ATATGATGCCCATTCCGGTGGAGAGCGAGAAATTCAAAGGACTATGTTGGA
genomic: TCTCCTACCATTGTTTTTATCGATGAAATTGATGCTGTCGGTACAAAAAGgtaattctgg ... tttactgcagATATGATGCCCATTCCGGTGGAGAGCGAGAAATTCAAAGGACTATGTTGGA
EST: gi|37841464|gb|BJ599472.1|BJ599472
EST:     TCTCCTACCATTGTTTTTATCGATGAAATTGATGCTGTCGGTACAAAAAG                         ATATGATGCCCATTCCGGTGGAGAGCGAGAAATTCAAAGGACTATGTTGGA
genomic: TCTCCTACCATTGTTTTTATCGATGAAATTGATGCTGTCGGTACAAAAAGgtaattctgg ... tttactgcagATATGATGCCCATTCCGGTGGAGAGCGAGAAATTCAAAGGACTATGTTGGA
EST: gi|162171249|gb|FC346394.1|FC346394
EST:     TCTCCTACCATTGTTTTTATCGATGAAATTGATGCTGTCGGTACAAAAAG                         ATATGATGCCCATTCCGGTGGAGAGCGAGAAATTCAAAGGACTATGTTGGA
genomic: TCTCCTACCATTGTTTTTATCGATGAAATTGATGCTGTCGGTACAAAAAGgtaattctgg ... tttactgcagATATGATGCCCATTCCGGTGGAGAGCGAGAAATTCAAAGGACTATGTTGGA
EST: gi|22131707|gb|BQ826756.1|BQ826756
EST:     CCATTGTTTTTATCGATGAAATTGATGCTGTGGGGTNA-AAAAAG                         ATATGATGCCCATTCCGGTGGAGAGCGAGAAATTCAAAGGACTATGTGGG
genomic: CCATTGTTTTTATCGATGAAATTGATGCTGT-CGGT-ACAAAAAGgtaattctgg ... tttactgcagATATGATGCCCATTCCGGTGGAGAGCGAGAAATTCAAAGGACTATGTTGG
EST: gi|162224576|gb|FC400472.1|FC400472
EST:     TCTCCTACCATTGTTTTTATCGATGAAATTGATGCTGTCGGTACAAAAAG                         ATATGATGCCCATTCCGGTGGAGAGCGAGAAATTCAAAGGACTATGTTGGA
genomic: TCTCCTACCATTGTTTTTATCGATGAAATTGATGCTGTCGGTACAAAAAGgtaattctgg ... tttactgcagATATGATGCCCATTCCGGTGGAGAGCGAGAAATTCAAAGGACTATGTTGGA
EST: gi|162258957|gb|FC435900.1|FC435900
EST:     TCTCCTACCATTGTTTTTATCGATGAAATTGATGCTGTCGGTACAAAAAG                         ATATGATGCCCATTCCGGTGGAGAGCGAGAAATTCAAAGGACTATGTTGGA
genomic: TCTCCTACCATTGTTTTTATCGATGAAATTGATGCTGTCGGTACAAAAAGgtaattctgg ... tttactgcagATATGATGCCCATTCCGGTGGAGAGCGAGAAATTCAAAGGACTATGTTGGA
EST: gi|37840238|gb|BJ598246.1|BJ598246
EST:     TCTCCTACCATTGTTTTTATCGATGAAATTGATGCTGTCGGTACAAAAAG                         ATATGATGCCCATTCCGGTGGAGAGCGAGAAATTCAAAGGACTATGTTGGA
genomic: TCTCCTACCATTGTTTTTATCGATGAAATTGATGCTGTCGGTACAAAAAGgtaattctgg ... tttactgcagATATGATGCCCATTCCGGTGGAGAGCGAGAAATTCAAAGGACTATGTTGGA
EST: gi|162216154|gb|FC392987.1|FC392987
EST:     TCTCCTACCATTGTTTTTATCGATGAAATTGATGCTGTCGGTACAAAAAG                         ATATGATGCCCATTCCGGTGGAGAGCGAGAAATTCAAAGGACTATGTTGGA
genomic: TCTCCTACCATTGTTTTTATCGATGAAATTGATGCTGTCGGTACAAAAAGgtaattctgg ... tttactgcagATATGATGCCCATTCCGGTGGAGAGCGAGAAATTCAAAGGACTATGTTGGA
EST: gi|37838576|gb|BJ596584.1|BJ596584
EST:     TCTCCTACCATTGTTTTTATCGATGAAATTGATGCTGTCGGTACAAAAAG                         ATATGATGCCCATTCCGGTGGAGAGCGAGAAATTCAAAGGACTATGTTGGA
genomic: TCTCCTACCATTGTTTTTATCGATGAAATTGATGCTGTCGGTACAAAAAGgtaattctgg ... tttactgcagATATGATGCCCATTCCGGTGGAGAGCGAGAAATTCAAAGGACTATGTTGGA
EST: gi|67578692|gb|BJ950859.1|BJ950859
EST:     TCTCCTACCATTGTTTTTATCGATGAAATTGATGCTGTCGGTACAAAAAG                         ATATGATGCCCATTCCGGTGGAGAGCGAGAAATTCAAAGGACTATGTTGGA
genomic: TCTCCTACCATTGTTTTTATCGATGAAATTGATGCTGTCGGTACAAAAAGgtaattctgg ... tttactgcagATATGATGCCCATTCCGGTGGAGAGCGAGAAATTCAAAGGACTATGTTGGA
EST: gi|162224575|gb|FC400471.1|FC400471
EST:     TCTCCTACCATTGTTTTTATCGATGAAATTGATGCTGTCGGTACAAAAAG                         ATATGATGCCCATTCCGGTGGAGAGCGAGAAATTCAAAGGACTATGTTGGA
genomic: TCTCCTACCATTGTTTTTATCGATGAAATTGATGCTGTCGGTACAAAAAGgtaattctgg ... tttactgcagATATGATGCCCATTCCGGTGGAGAGCGAGAAATTCAAAGGACTATGTTGGA
EST: gi|37853193|gb|BJ611201.1|BJ611201
EST:     TCTCCTACCATTGTTTTTATCGATGAAATTGATGCTGTCGGTACAAAAAG                         ATATGATGCCCATTCCGGTGGAGAGCGAGAAATTCAAAGGACTATGTTGGA
genomic: TCTCCTACCATTGTTTTTATCGATGAAATTGATGCTGTCGGTACAAAAAGgtaattctgg ... tttactgcagATATGATGCCCATTCCGGTGGAGAGCGAGAAATTCAAAGGACTATGTTGGA
EST: gi|162243828|gb|FC423145.1|FC423145
EST:     TCTCCTACCATTGTTTTTATCGATGAAATTGATGCTGTCGGTACAAAAAG                         ATATGATGCCCATTCCGGTGGAGAGCGAGAAATTCAAAGGACTATGTTGGA
genomic: TCTCCTACCATTGTTTTTATCGATGAAATTGATGCTGTCGGTACAAAAAGgtaattctgg ... tttactgcagATATGATGCCCATTCCGGTGGAGAGCGAGAAATTCAAAGGACTATGTTGGA
EST: gi|18338331|gb|BJ170355.1|BJ170355
EST:     TCTCCTACCATTGTTTTTATCGATGAAATTGATGCTGTCGGTACAAAAAG                         ATATGATGCCCATTCCGGTGGAGAGCGAGAAATTCAAAGGACTATGTTGGA
genomic: TCTCCTACCATTGTTTTTATCGATGAAATTGATGCTGTCGGTACAAAAAGgtaattctgg ... tttactgcagATATGATGCCCATTCCGGTGGAGAGCGAGAAATTCAAAGGACTATGTTGGA
EST: gi|67724880|gb|BJ975139.1|BJ975139
EST:     TCTCCTACCATTGTTTTTATCGATGAAATTGATGCTGTCGGTACAAAAAG                         ATATGATGCCCATTCCGGTGGAGAGCGAGAAATTCAAAGGACTATGTTGGA
genomic: TCTCCTACCATTGTTTTTATCGATGAAATTGATGCTGTCGGTACAAAAAGgtaattctgg ... tttactgcagATATGATGCCCATTCCGGTGGAGAGCGAGAAATTCAAAGGACTATGTTGGA
EST: gi|37847407|gb|BJ605415.1|BJ605415
EST:     CATTGTTTTTATCGATGAAATTGATGCTGTCGGTACAAAAAG                         ATATGATGCCCATTCCGGTGGAGAGCGAGAAATTCAAAGGACTATGTTGGA
genomic: CATTGTTTTTATCGATGAAATTGATGCTGTCGGTACAAAAAGgtaattctgg ... tttactgcagATATGATGCCCATTCCGGTGGAGAGCGAGAAATTCAAAGGACTATGTTGGA
EST: gi|162171248|gb|FC346393.1|FC346393
EST:     TCTCCTACCATTGTTTTTATCGATGAAATTGATGCTGTCGGTACAAAAAG                         ATATGATGCCCATTCCGGTGGAGAGCGAGAAATTCAAAGGACTATGTTGGA
genomic: TCTCCTACCATTGTTTTTATCGATGAAATTGATGCTGTCGGTACAAAAAGgtaattctgg ... tttactgcagATATGATGCCCATTCCGGTGGAGAGCGAGAAATTCAAAGGACTATGTTGGA

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: 25 (upstream exon), 23 (downstream exon)
Score: 6

GAGATGGACCGAAGTTGGTGCGAGAGCTATTTCGGGTGGCTGATGAACTGTCTCCTACCATTGTTTTTATCGATGAAATTGATGCTGTCGGTACAAAAAGgtaattctgg ... tttactgcagATATGATGCCCATTCCGGTGGAGAGCGAGAAATTCAAAGGACTATGTTGGAGTTGCTGAATCAGTTGGATGGTTTTGATGCTCGTGGTGATGTTAAGGTT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGATGGACCGAAGTTGGTGCGAGAGCTATTTCGGGTGGCTGATGAACTGTCTCCTACCATTGTTTTTATCGATGAAATTGATGCTGTCGGTACAAAAAGgtaattctggcctgcttctcattatttttatttgcggtgtttctcataatgtttcgattcttgcaaccacactctcaaggttgccactgcactcttatct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG