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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTGATGAACGCTTACTGTGACCGCCAGTCTGTGGATCCTTCCTCTATTGCATTCCTCTTTGACGGCCGTCGTCTTCGAGCTGAACAGACACCTGCTGAGgtattcccttcaaagctttgttttgcattcgccaaaacagaaataaaaagaacattacctttaaaacggttcttcagctgaaattcctgaagacatcaac...

Basic information

species Physcomitrella patens
transcript PP1S61_57V6.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S61_57V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: LOC_Os01g68950.1 (Oryza sativa), 5'ss of exon 2
GCTGATGAACGCTTACTGTGACCGCCAGTCTGTGGATCCTTCCTCTATTGCATTCCTCTTTGACGGCCGTCGTCTTCGAGCTGAACAGACACCTGCTGAGgtatt---cccttcaaagctttgttttgcattcgccaaa-acagaaataaaaagaacattacc--tttaaaacggttcttcagctgaaattcctgaagacatcaac
|||||||||||| || |||||||| ||||||||||||       ||||||||||||| ||||| || ||| | || || |  || ||||| ||||  |||||      |   ||    |||  |  |  ||||   |    | ||    |  | | ||| |||  |  |  || | |   ||    ||| |  |  ||        
GCTGATGAACGCCTATTGTGACCGTCAGTCTGTGGATATGAATGCTATTGCATTCCTATTTGATGGTCGTAGGCTCCGTGGCGAGCAGACCCCTGACGAGgtgcgtagcttatcttctcttcatactcaattcagtatttgcggagcctagcaaatcatcaccaatccattactgatgaccattgcaaacttgttcag--------

upper sequence: PP1S61_57V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: LOC_Os01g68940.1 (Oryza sativa), 5'ss of exon 2
GCTGATGAACGCTTACTGTGACCGCCAGTCTGTGGATCCTTCCTCTATTGCATTCCTCTTTGACGGCCGTCGTCTTCGAGCTGAACAGACACCTGCTGAGgtattcccttcaaagctttgttttgcattcgcca-aaacagaaataaaaagaacattacctttaaaacggttcttcagctga-aattcctgaagacatcaac--------------
|||||||||||| |||||||| |||||||| ||||||      |||||||| ||||| ||||| || ||| | ||    ||||| ||||| ||||   ||||      |  |      ||  ||   |   | |  | | ||   ||| |   | || |||  ||  | || ||  ||||||   ||  | |  ||  |||               
GCTGATGAACGCCTACTGTGATCGCCAGTCCGTGGATATCAAATCTATTGCCTTCCTGTTTGATGGTCGTAGGCTCAATGCTGAGCAGACCCCTGACCAGgtgcgtgatataccatactgccttctctaaacaatgagctgatgcaaatactgccttccctaaaacccagtgctatagctgatgcttttttaccactgcaaactgtttgatttcag

upper sequence: PP1S61_57V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GRMZM2G082390_T01 (Zea mays), 5'ss of exon 2
GCTGATGAACGCTTACTGTGACCGCCAGTCTGTGGATCCTTCCTCTATTGCATTCCTCTTTGACGGCCGTCGTCTTCGAGCTGAACAGACACCTGCTGAGgtattcccttcaaagctttgttttgcattcgccaaaacagaaataaaaagaacattacctttaaaacggttcttcagctgaaattcctgaagacatcaac
||||||||||||||| ||||||||||||||||||||        | ||||| ||||| ||||| |||||  | ||||| |  || ||||| |||| ||||||   ||      |  |  | |||  || |       ||| | | |   ||| | |   |  | |    || | |   || |                  
GCTGATGAACGCTTATTGTGACCGCCAGTCTGTGGACATGAATGCCATTGCGTTCCTGTTTGATGGCCGCAGGCTTCGCGGCGAGCAGACCCCTGATGAGgtgaccc------aattcggctttagatcc-------cagcattgagtggaatacttgatcgatagatcttttgcctgtgcag-----------------

upper sequence: PP1S61_57V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: AT5G55160.2 (Arabidopsis thaliana), 5'ss of exon 3
GCTGATGAACGCTTACTGTGACCGCCAGTCTGTGGATCCTTCCTCTATTGCATTCCTCTTTGACGGCCGTCGTCTTCGAGCTGAACAGACACCTGCTGAGgtattcccttcaaagctttgttttgcattcgccaaaacagaaataaaaagaacattacctttaaaacggttcttcagctgaaattcctgaagacatcaac
 |||||||| |||||||||||||| ||||||||||||     ||| ||||| ||| | ||||| || ||||||||||| || || ||||| || | |||||||    |       || |||    ||||| |    || |   |     |    | |   ||  |    ||| | | | || | || | ||     ||  
ACTGATGAATGCTTACTGTGACCGTCAGTCTGTGGATTTCAACTCAATTGCTTTCTTGTTTGATGGTCGTCGTCTTCGTGCCGAGCAGACTCCAGATGAGgtaacatcact----ctctgtaccccattctcttttactgttttcc---gtttttcaaagttgtatgatttccttaaccgagaatcttcaattttacag-

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|162272448|gb|FC448255.1|FC448255
EST:     CATTCCTCTTTGACGGCCGTCGTCTTCGAGCTGAACAGACACCTGCTGAG                         CTCGACATGGAAGATGGTGACGAGATTGATGCCATGCTCCATCAAACAGGC
genomic: CATTCCTCTTTGACGGCCGTCGTCTTCGAGCTGAACAGACACCTGCTGAGgtattccctt ... taccctgcagCTCGACATGGAAGATGGTGACGAGATTGATGCCATGCTCCATCAAACAGGC
EST: gi|162253843|gb|FC430152.1|FC430152
EST:     CATTCCTCTTTGACGGCCGTCGTCTTCGAGCTGAACAGACACCTGCTGAG                         CTCGACATGGAAGATGGTGACGAGATTGATGCCATGCTCCATCAAACAGGC
genomic: CATTCCTCTTTGACGGCCGTCGTCTTCGAGCTGAACAGACACCTGCTGAGgtattccctt ... taccctgcagCTCGACATGGAAGATGGTGACGAGATTGATGCCATGCTCCATCAAACAGGC
EST: gi|162238524|gb|FC414610.1|FC414610
EST:     CATTCCTCTTTGACGGCCGTCGTCTTCGAGCTGAACAGACACCTGCTGAG                         CTCGACATGGAAGATGGTGACGAGATTGATGCCATGCTCCATCAAACAGGC
genomic: CATTCCTCTTTGACGGCCGTCGTCTTCGAGCTGAACAGACACCTGCTGAGgtattccctt ... taccctgcagCTCGACATGGAAGATGGTGACGAGATTGATGCCATGCTCCATCAAACAGGC
EST: gi|15728725|gb|BI740940.1|BI740940
EST:     CATTCCTCTTTGACGGCCGTCGTCTTCGAGCTGAACAGACACCTGCTGAG                         CTCGACATGGAAGATGGTGACGAGATTGATGCCATGCTCCATCAAACAGGC
genomic: CATTCCTCTTTGACGGCCGTCGTCTTCGAGCTGAACAGACACCTGCTGAGgtattccctt ... taccctgcagCTCGACATGGAAGATGGTGACGAGATTGATGCCATGCTCCATCAAACAGGC
EST: gi|18328994|gb|BJ161000.1|BJ161000
EST:     CATTCCTCTTTGACGGCCGTCGTCTTCGAGCTGAACAGACACCTGCTGAG                         CTCGACATGGAAGATGGTGACGAGATTGATGCCATGCTCCATCAAACAGGC
genomic: CATTCCTCTTTGACGGCCGTCGTCTTCGAGCTGAACAGACACCTGCTGAGgtattccctt ... taccctgcagCTCGACATGGAAGATGGTGACGAGATTGATGCCATGCTCCATCAAACAGGC
EST: gi|67692582|gb|BJ952815.1|BJ952815
EST:     CATTCCTCTTTGACGGCCGTCGTCTTCGAGCTGAACAGACACCTGCTGAG                         CTCGACATGGAAGATGGTGACGAGATTGATGCCATGCTCCATCAAACAGGC
genomic: CATTCCTCTTTGACGGCCGTCGTCTTCGAGCTGAACAGACACCTGCTGAGgtattccctt ... taccctgcagCTCGACATGGAAGATGGTGACGAGATTGATGCCATGCTCCATCAAACAGGC
EST: gi|162201142|gb|FC377649.1|FC377649
EST:     CATTCCTCTTTGACGGCCGTCGTCTTCGAGCTGAACAGACACCTGCTGAG                         CTCGACATGGAAGATGGTGACGAGATTGATGCCATGCTCCATCAAACAGGC
genomic: CATTCCTCTTTGACGGCCGTCGTCTTCGAGCTGAACAGACACCTGCTGAGgtattccctt ... taccctgcagCTCGACATGGAAGATGGTGACGAGATTGATGCCATGCTCCATCAAACAGGC
EST: gi|162167757|gb|FC344071.1|FC344071
EST:     TCGAGCTGAACAGACACCTGCTGAG                         CTCGACATGGAAGATGGTGACGAGATTGATGCCATGCTCCATCAAACAGGC
genomic: TCGAGCTGAACAGACACCTGCTGAGgtattccctt ... taccctgcagCTCGACATGGAAGATGGTGACGAGATTGATGCCATGCTCCATCAAACAGGC
EST: gi|37838985|gb|BJ596993.1|BJ596993
EST:     TTCGAGCTGAACAGACACCTGCTGAG                         CTCGACATGGAAGATGGTGACGAGATTGATGCCATGCTCCATCAAACAGGC
genomic: TTCGAGCTGAACAGACACCTGCTGAGgtattccctt ... taccctgcagCTCGACATGGAAGATGGTGACGAGATTGATGCCATGCTCCATCAAACAGGC
EST: gi|162167758|gb|FC344072.1|FC344072
EST:     CATTCCTCTTTGACGGCCGTCGTCTTCGAGCTGAACAGACACCTGCTGAG                         CTCGACATGGAAGATGGTGACGAGATTGATGCCATGCTCCATCAAACAGGC
genomic: CATTCCTCTTTGACGGCCGTCGTCTTCGAGCTGAACAGACACCTGCTGAGgtattccctt ... taccctgcagCTCGACATGGAAGATGGTGACGAGATTGATGCCATGCTCCATCAAACAGGC
EST: gi|67569322|gb|BJ942146.1|BJ942146
EST:     CATTCCTCTTTGACGGCCGTCGTCTTCGAGCTGAACAGACACCTGCTGAG                         CTCGACATGGAAGATGGTGACGAGATTGATGCCATGCTCCATCAAACAGGC
genomic: CATTCCTCTTTGACGGCCGTCGTCTTCGAGCTGAACAGACACCTGCTGAGgtattccctt ... taccctgcagCTCGACATGGAAGATGGTGACGAGATTGATGCCATGCTCCATCAAACAGGC
EST: gi|208371829|gb|DC951835.1|DC951835
EST:     ATTCCTCTTTGACGGGCCGTCGTCTTCGAGCTGAACAGACACCTGCTGAG                         CTCGACATGGAAGATGGTGACGAGATTGATGCCATGCTCCATCAAACAGGC
genomic: ATTCCTCTTTGAC-GGCCGTCGTCTTCGAGCTGAACAGACACCTGCTGAGgtattccctt ... taccctgcagCTCGACATGGAAGATGGTGACGAGATTGATGCCATGCTCCATCAAACAGGC
EST: gi|162168724|gb|FC344714.1|FC344714
EST:     CATTCCTCTTTGACGGCCGTCGTCTTCGAGCTGAACAGACACCTGCTGAG                         CTCGACATGGAAGATGGTGACGAGATTGATGCCATGCTCCATCAAACAGGC
genomic: CATTCCTCTTTGACGGCCGTCGTCTTCGAGCTGAACAGACACCTGCTGAGgtattccctt ... taccctgcagCTCGACATGGAAGATGGTGACGAGATTGATGCCATGCTCCATCAAACAGGC
EST: gi|18356302|gb|BJ188361.1|BJ188361
EST:     CATTCCTCTTTGACGGCCGTCGTCTTCGAGCTGAACAGACACCTGCTGAG                         CTCGACATGGAAGATGGTGACGAGATTGATGCCATGCTCCGTCAAACAGGC
genomic: CATTCCTCTTTGACGGCCGTCGTCTTCGAGCTGAACAGACACCTGCTGAGgtattccctt ... taccctgcagCTCGACATGGAAGATGGTGACGAGATTGATGCCATGCTCCATCAAACAGGC
EST: gi|162273907|gb|FC450046.1|FC450046
EST:     CATTCCTCTTTGACGGCCGTCGTCTTCGAGCTGAACAGACACCTGCTGAG                         CTCGACATGGAAGATGGTGACGAGATTGATGCCATGCTCCATCAAACAGGC
genomic: CATTCCTCTTTGACGGCCGTCGTCTTCGAGCTGAACAGACACCTGCTGAGgtattccctt ... taccctgcagCTCGACATGGAAGATGGTGACGAGATTGATGCCATGCTCCATCAAACAGGC
EST: gi|162267422|gb|FC443965.1|FC443965
EST:     CATTCCTCTTTGACGGCCGTCGTCTTCGAGCTGAACAGACACCTGCTGAG                         CTCGACATGGAAGATGGTGACGAGATTGATGCCATGCTCCATCAAACAGGC
genomic: CATTCCTCTTTGACGGCCGTCGTCTTCGAGCTGAACAGACACCTGCTGAGgtattccctt ... taccctgcagCTCGACATGGAAGATGGTGACGAGATTGATGCCATGCTCCATCAAACAGGC
EST: gi|100413413|gb|BY956659.1|BY956659
EST:     CATTCCTCTTTGACGGCCGTCGTCTTCGAGCTGAACAGACACCTGCTGAG                         CTCGACATGGAAGATGGTGACGAGATTGATGCCATGCTCCATCAAACAGGC
genomic: CATTCCTCTTTGACGGCCGTCGTCTTCGAGCTGAACAGACACCTGCTGAGgtattccctt ... taccctgcagCTCGACATGGAAGATGGTGACGAGATTGATGCCATGCTCCATCAAACAGGC
EST: gi|162270077|gb|FC446777.1|FC446777
EST:     CATTCCTCTTTGACGGCCGTCGTCTTCGAGCTGAACAGACACCTGCTGAG                         CTCGACATGGAAGATGGTGACGAGATTGATGCCATGCTCCATCAAACAGGC
genomic: CATTCCTCTTTGACGGCCGTCGTCTTCGAGCTGAACAGACACCTGCTGAGgtattccctt ... taccctgcagCTCGACATGGAAGATGGTGACGAGATTGATGCCATGCTCCATCAAACAGGC
EST: gi|208355471|gb|DC938816.1|DC938816
EST:     CATTCCTCTTTGACGGCCGTCGTCTTCGAGCTGAACAGACACCTGCTGAG                         CTCGACATGGAAGATGGTGACGAGATTGATGCCATGCTCCATCAAACAGGC
genomic: CATTCCTCTTTGACGGCCGTCGTCTTCGAGCTGAACAGACACCTGCTGAGgtattccctt ... taccctgcagCTCGACATGGAAGATGGTGACGAGATTGATGCCATGCTCCATCAAACAGGC
EST: gi|162238525|gb|FC414611.1|FC414611
EST:     CATTCCTCTTTGACGGCCGTCGTCTTCGAGCTGAACAGACACCTGCTGAG                         CTCGACATGGAAGATGGTGACGAGATTGATGCCATGCTCCATCAAACAGGC
genomic: CATTCCTCTTTGACGGCCGTCGTCTTCGAGCTGAACAGACACCTGCTGAGgtattccctt ... taccctgcagCTCGACATGGAAGATGGTGACGAGATTGATGCCATGCTCCATCAAACAGGC
EST: gi|37833234|gb|BJ591246.1|BJ591246
EST:     CATTCCTCTTTGACGGCCGTCGTCTTCGAGCTGAACAGACACCTGCTGAG                         CTCGACATGGAAGATGGTGACGAGATTGATGCCATGCTCCGTCAAACAGGC
genomic: CATTCCTCTTTGACGGCCGTCGTCTTCGAGCTGAACAGACACCTGCTGAGgtattccctt ... taccctgcagCTCGACATGGAAGATGGTGACGAGATTGATGCCATGCTCCATCAAACAGGC
EST: gi|208344666|gb|DC905115.1|DC905115
EST:     CATTCCTCTTTGACGGCCGTCGTCTTCGAGCTGAACAGACACCTGCTGAG                         CTCGACATGGAAGATGGTGACGAGATTGATGCCATGCTCCATCAAACAAGC
genomic: CATTCCTCTTTGACGGCCGTCGTCTTCGAGCTGAACAGACACCTGCTGAGgtattccctt ... taccctgcagCTCGACATGGAAGATGGTGACGAGATTGATGCCATGCTCCATCAAACAGGC
EST: gi|162216231|gb|FC392648.1|FC392648
EST:     CATTCCTCTTTGACGGCCGTCGTCTTCGAGCTGAACAGACACCTGCTGAG                         CTCGACATGGAAGATGGTGACGAGATTGATGCCATGCTCCATCAAACAGGG
genomic: CATTCCTCTTTGACGGCCGTCGTCTTCGAGCTGAACAGACACCTGCTGAGgtattccctt ... taccctgcagCTCGACATGGAAGATGGTGACGAGATTGATGCCATGCTCCATCAAACAGGC
EST: gi|18361093|gb|BJ193157.1|BJ193157
EST:     CATTCCTCTTTGACGGCCGTCGTCTTCGAGCTGAACAGACACCTGCTGAG                         CTCGACATGGAAGATGGTGACGAGATTGATGCCATGCTCCATCAAACAGGC
genomic: CATTCCTCTTTGACGGCCGTCGTCTTCGAGCTGAACAGACACCTGCTGAGgtattccctt ... taccctgcagCTCGACATGGAAGATGGTGACGAGATTGATGCCATGCTCCATCAAACAGGC
EST: gi|162267423|gb|FC443966.1|FC443966
EST:     CATTCCTCTTTGACGGCCGTCGTCTTCGAGCTGAACAGACACCTGCTGAG                         CTCGACATGGAAGATGGTGACGAGATTGATGCCATGCTCCATCAAACAGGC
genomic: CATTCCTCTTTGACGGCCGTCGTCTTCGAGCTGAACAGACACCTGCTGAGgtattccctt ... taccctgcagCTCGACATGGAAGATGGTGACGAGATTGATGCCATGCTCCATCAAACAGGC
EST: gi|18337202|gb|BJ169226.1|BJ169226
EST:     CATTCCTCTTTGACGGCCGTCGTCTTCGAGCTGAACAGACACCTGCTGAG                         CTCGACATGGAAGATGGTGACGAGATTGATGCCATGCTCCATCAAACAGGC
genomic: CATTCCTCTTTGACGGCCGTCGTCTTCGAGCTGAACAGACACCTGCTGAGgtattccctt ... taccctgcagCTCGACATGGAAGATGGTGACGAGATTGATGCCATGCTCCATCAAACAGGC
EST: gi|162270076|gb|FC446776.1|FC446776
EST:     CGAGCTGAACAGACACCTGCTGAG                         CTCGACATGGAAGATGGTGACGAGATTGATGCCATGCTCCATCAAACAGGC
genomic: CGAGCTGAACAGACACCTGCTGAGgtattccctt ... taccctgcagCTCGACATGGAAGATGGTGACGAGATTGATGCCATGCTCCATCAAACAGGC
EST: gi|67699199|gb|BJ959432.1|BJ959432
EST:     CATTCCTCTTTGACGGCCGTCGTCTTCGAGCTGAACAGACACCTGCTGAG                         CTCGACATGGAAGATGGTGACGAGATTGATGCCATGCTCCATCAAACAGGC
genomic: CATTCCTCTTTGACGGCCGTCGTCTTCGAGCTGAACAGACACCTGCTGAGgtattccctt ... taccctgcagCTCGACATGGAAGATGGTGACGAGATTGATGCCATGCTCCATCAAACAGGC
EST: gi|162216232|gb|FC392649.1|FC392649
EST:     CATTCCTCTTTGACGGCCGTCGTCTTCGAGCTGAACAGACACCTGCTGAG                         CTCGACATGGAAGATGGTGACGAGATTGATGCCATGCTCCATCAAACAGGC
genomic: CATTCCTCTTTGACGGCCGTCGTCTTCGAGCTGAACAGACACCTGCTGAGgtattccctt ... taccctgcagCTCGACATGGAAGATGGTGACGAGATTGATGCCATGCTCCATCAAACAGGC

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: 35 (upstream exon), 35 (downstream exon)
Score: 27

GCTGATGAACGCTTACTGTGACCGCCAGTCTGTGGATCCTTCCTCTATTGCATTCCTCTTTGACGGCCGTCGTCTTCGAGCTGAACAGACACCTGCTGAGgtattccctt ... taccctgcagCTCGACATGGAAGATGGTGACGAGATTGATGCCATGCTCCATCAAACAGGCGGAGCCTCTTCCTGATATGAATATGCCGTCTCAGGCAGTGTGGTCCTGA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTGATGAACGCTTACTGTGACCGCCAGTCTGTGGATCCTTCCTCTATTGCATTCCTCTTTGACGGCCGTCGTCTTCGAGCTGAACAGACACCTGCTGAGgtattcccttcaaagctttgttttgcattcgccaaaacagaaataaaaagaacattacctttaaaacggttcttcagctgaaattcctgaagacatcaac

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aacagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaagaa