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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttatatgcatgttcgtaagctgataagcatgtccaagtaaacacatgttttcaatgtacgaatgtacgattgtagtattgatttttttttcactatacagTGCAGCACACAAGCGCTTCCCTAACCATCAATGAGAACTATGACTCCGATGTACAAGCTGACACCGAAACTTTCCTTAACCGAATTGTACCAGAG

Basic information

species Oryza sativa
transcript LOC_Os02g09460.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g09460.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G092988_T02 (Zea mays), 3'ss of exon 2
---------tta--tatgcatgttcgtaagctgataagcatgtccaagtaaacacatgttttcaatgtacgaatgtacgattgtagtattgatttttttttcactatacagTGCAGCACACAAGCGCTTCCCTAACCATCAATGAGAACTATGACTCCGATGTACAAGCTGACACCGAAACTTTCCTTAACCGAATTGTACCAGAG-----
         ||    |   || ||| | |||||| ||||||||  |  |||  || | ||  |    |   | |||   |||   ||       |||||||   | | |||| |||||||||||||| || || |||||||| |||||||||||||| ||||| || |||||||| || ||||| |||||| ||||||| ||||||     
tggccttttttggtcacatatattcatgagctgacaagcatgt--agataagaac-tattccctgcattttagtgt-taattaatgt-------tttttttggttttgcagTTCAGCACACAAGCGCATCGCTGACCATCAACGAGAACTATGACTCTGATGTGCAGGCTGACACTGAGACTTTTCTTAACAGAATTGTTCCAGAGGTCAG

upper sequence: LOC_Os02g09460.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G092988_T04 (Zea mays), 3'ss of exon 1
---------tta--tatgcatgttcgtaagctgataagcatgtccaagtaaacacatgttttcaatgtacgaatgtacgattgtagtattgatttttttttcactatacagTGCAGCACACAAGCGCTTCCCTAACCATCAATGAGAACTATGACTCCGATGTACAAGCTGACACCGAAACTTTCCTTAACCGAATTGTACCAGAG
         ||    |   || ||| | |||||| ||||||||  |  |||  || | ||  |    |   | |||   |||   ||       |||||||   | | |||| |||||||||||||| || || |||||||| |||||||||||||| ||||| || |||||||| || ||||| |||||| ||||||| ||||||
tggccttttttggtcacatatattcatgagctgacaagcatgt--agataagaac-tattccctgcattttagtgt-taattaatgt-------tttttttggttttgcagTTCAGCACACAAGCGCATCGCTGACCATCAACGAGAACTATGACTCTGATGTGCAGGCTGACACTGAGACTTTTCTTAACAGAATTGTTCCAGAG

upper sequence: LOC_Os02g09460.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G092988_T01 (Zea mays), 3'ss of exon 1
----tta--tatgcatgttcgtaagctgataagcatgtccaagtaaacacatgttttcaatgtacgaatgtacgattgtagtattgatttttttttcactatacagTGCAGCACACAAGCGCTTCCCTAACCATCAATGAGAACTATGACTCCGATGTACAAGCTGACACCGAAACTTTCCTTAACCGAATTGTACCAGAG
    ||    |   || ||| | |||||| ||||||||  |  |||  || | ||  |    |   | |||   |||   ||       |||||||   | | |||| |||||||||||||| || || |||||||| |||||||||||||| ||||| || |||||||| || ||||| |||||| ||||||| ||||||
ttttttggtcacatatattcatgagctgacaagcatgt--agataagaac-tattccctgcattttagtgt-taattaatgt-------tttttttggttttgcagttcagCACACAAGCGCATCGCTGACCATCAACGAGAACTATGACTCTGATGTGCAGGCTGACACTGAGACTTTTCTTAACAGAATTGTTCCAGAG

upper sequence: LOC_Os02g09460.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA07G34680.2 (Glycine max), 3'ss of exon 2
---ttatatgcatgttcgtaagctgataagcatgtccaagtaaacacat-gttttcaatgtacgaatgtacgattgtagtattgatttttttttcactatacagTGCAGCACACAAGCGCTTCCCTAACCATCAATGAGAACTATGACTCCGATGTACAAGCTGACACCGAAACTTTCCTTAACCGAATTGTACCAGAG
       ||     ||   || |    |    |     | |||  |  | |||||||||  |   |  |    | | | |  |||| |    || |    |||||||||||||| || ||||| || |||||||||||||| |||||||| ||||| |  |  || |||||||| ||||| || || || || || |||
gaccgcaatagcaatttaaaaccatgcataggtacatgaataattaagttgttttcaattcattgaact----tggaaattgtgatgtgaaattaaaacgacagTGCAGCACACCAGTGCTTCTCTTACCATCAATGAGAATTATGACTCAGATGTTCGCGAGGATACCGAAACCTTCCTCAATCGGATAGTTCCCGAG

upper sequence: LOC_Os02g09460.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA15G17340.1 (Glycine max), 3'ss of exon 2
ttatatgcatgttcgtaagctgataagcatgtccaagtaaacacatgtttt-caatgtacg---aatgtacgatt-gtagtattgatttttttttcactatacagTGCAGCACACAAGCGCTTCCCTAACCATCAATGAGAACTATGACTCCGATGTACAAGCTGACACCGAAACTTTCCTTAACCGAATTGTACCAGAG
     |   | |   ||   |  |||    ||||   | |      |||||   ||||      ||| |  | ||  ||| ||  | || |  |     ||| |||||| |||||||| ||||| || |||||||||||||| |||||||  ||||| |  | ||| || ||||| ||||| ||  | || || ||||||
----gtaagtatatatattttattaattgggtcctctttattgttagttttgttatgtcaattcaatttgggcttcatagaatgaacttctaatgagaaatatagTGCATCACACAAGTGCTTCTCTTACCATCAATGAGAATTATGACTATGATGTTCGGGATGATACAGAAACCTTCCTCAATGGGATAGTTCCAGAG

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|88211486|gb|CI211126.1|CI211126
EST:     CCTGTCCGGGTTCAAGTGCGGCTTGGCGCATCTGTTCT                         TGCAGCACACAAGCGCTTCCCTAACCATCAATGAGAACTATGACTCCGATG
genomic: CCTGTCCGGGTTCAAGTGCGGCTTGGCGCATCTGTTCTgtatgtagat ... cactatacagTGCAGCACACAAGCGCTTCCCTAACCATCAATGAGAACTATGACTCCGATG
EST: gi|9866191|gb|AU101941.1|AU101941
EST:     GATTGAGGGCGACCTGTCCGGGTTCAAGTGCGGCTTGGCGCATCTGTTCT                         TGCAGCACACAAGCGCTTCCCTNNCCATCAATGAGNACTATGACTCCGATG
genomic: GATTGAGGGCGACCTGTCCGGGTTCAAGTGCGGCTTGGCGCATCTGTTCTgtatgtagat ... cactatacagTGCAGCACACAAGCGCTTCCCTAACCATCAATGAGAACTATGACTCCGATG
EST: gi|86595369|gb|CI262607.1|CI262607
EST:     GATTGAGGGCGACCTGTCCGGGTTCAAGTGCGGCTTGGCGCATCTGTTCT                         TGCAGCACACAAGCGCTTCCCTAACCATCAATGAGAACTATGACTCCGATG
genomic: GATTGAGGGCGACCTGTCCGGGTTCAAGTGCGGCTTGGCGCATCTGTTCTgtatgtagat ... cactatacagTGCAGCACACAAGCGCTTCCCTAACCATCAATGAGAACTATGACTCCGATG
EST: gi|40493973|gb|BX901795.1|BX901795
EST:     GATTGAGGGCGACCTGTCCGGGTTCAAGTGCGGCTTGGCGCATTTGTTCT                         TGCAGCACACAAGCGCTTCCCTAACCATCAATGAGAACTATGACTCCGATG
genomic: GATTGAGGGCGACCTGTCCGGGTTCAAGTGCGGCTTGGCGCATCTGTTCTgtatgtagat ... cactatacagTGCAGCACACAAGCGCTTCCCTAACCATCAATGAGAACTATGACTCCGATG
EST: gi|86414523|gb|CI068926.1|CI068926
EST:     TGCGGCTTGGCGCATCTGTTCT                         TGCAGCACACAAGCGCTTCCCTAACCATCAATGAGAACTATGACTCCGATG
genomic: TGCGGCTTGGCGCATCTGTTCTgtatgtagat ... cactatacagTGCAGCACACAAGCGCTTCCCTAACCATCAATGAGAACTATGACTCCGATG
EST: gi|88244910|gb|CI242761.1|CI242761
EST:     GCGCATCTGTTCT                         TGCAGCACACAAGCGCTTCCCTAACCATCAATGAGAACTATGACTCCGATG
genomic: GCGCATCTGTTCTgtatgtagat ... cactatacagTGCAGCACACAAGCGCTTCCCTAACCATCAATGAGAACTATGACTCCGATG
EST: gi|88979867|gb|CI026167.1|CI026167
EST:     GATTGAGGGCGACCTGTCCGGGTTCAAGTGCGGCTTGGCGCATCTGTTCT                         TGCAGCACACAAGCGCTTCCCTAACCATCAATGAGAACTATGACTCCGATG
genomic: GATTGAGGGCGACCTGTCCGGGTTCAAGTGCGGCTTGGCGCATCTGTTCTgtatgtagat ... cactatacagTGCAGCACACAAGCGCTTCCCTAACCATCAATGAGAACTATGACTCCGATG
EST: gi|88239487|gb|CI239964.1|CI239964
EST:     TTGGCGCATCTGTTCT                         TGCAGCACACAAGCGCTTCCCTAACCATCAATGAGAACTATGACTCCGATG
genomic: TTGGCGCATCTGTTCTgtatgtagat ... cactatacagTGCAGCACACAAGCGCTTCCCTAACCATCAATGAGAACTATGACTCCGATG
EST: gi|88214348|gb|CI214197.1|CI214197
EST:     AGGGCGACCTGTCCGGGTTCAAGTGCGGCTTGGCGCATCTGTTCT                         TGCAGCACACAAGCGCTTCCCTAACCATCAATGAGAACTATGACTCCGATG
genomic: AGGGCGACCTGTCCGGGTTCAAGTGCGGCTTGGCGCATCTGTTCTgtatgtagat ... cactatacagTGCAGCACACAAGCGCTTCCCTAACCATCAATGAGAACTATGACTCCGATG
EST: gi|88243875|gb|CI242997.1|CI242997
EST:     GATTGAGGGCGACCTGTCCGGGTTCAAGTGCGGCTTGGCGCATCTGTTCT                         TGCAGCACACAAGCGCTTCCCTAACCATCAATGAGAACTATGACTCCGATG
genomic: GATTGAGGGCGACCTGTCCGGGTTCAAGTGCGGCTTGGCGCATCTGTTCTgtatgtagat ... cactatacagTGCAGCACACAAGCGCTTCCCTAACCATCAATGAGAACTATGACTCCGATG
EST: gi|88213410|gb|CI213259.1|CI213259
EST:     TTGGCGCATCTGTTCT                         TGCAGCACACAAGCGCTTCCCTAACCATCAATGAGAACTATGACTCCGATG
genomic: TTGGCGCATCTGTTCTgtatgtagat ... cactatacagTGCAGCACACAAGCGCTTCCCTAACCATCAATGAGAACTATGACTCCGATG

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: 43 (upstream exon), 55 (downstream exon)
Score: 52

ATTCTGAGGGAGATTGAGGGCGACCTGTCCGGGTTCAAGTGCGGCTTGGCGCATCTGTTCTgtatgtagat ... cactatacagTGCAGCACACAAGCGCTTCCCTAACCATCAATGAGAACTATGACTCCGATGTACAAGCTGACACCGAAACTTTCCTTAACCGAATTGTACCAGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttttcaatgtacgaatgtacgattgtagtattgatttttttttcactatacagTGCAGCACACAAGCGCTTCCCTAACCATCAATGAGAACTATGACTCCGATGTACAAGCTGACACCGAAACTTTCCTTAACCGAATTGTACCAGAG
                              tattgat  putative branch site (score: 52)
                                    tttttttttcactat  CT-rich tract
                       attgtagtattgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttatatgcatgttcgtaagctgataagcatgtccaagtaaacacatgttttcaatgtacgaatgtacgattgtagtattgatttttttttcactatacagTGCAGCACACAAGCGCTTCCCTAACCATCAATGAGAACTATGACTCCGATGTACAAGCTGACACCGAAACTTTCCTTAACCGAATTGTACCAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - -tgcatgt
- - - - - - - - - gctgata
- - - - - - - - - - - - - -catgtcc
- - - - - - - - - - - - - - - - - aagtaaac
- - - - - - - - - - - - - - - - - - - - - acatgtt