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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttagggacaaatgtcaagacagttggctattcagaatttgaaataggtctgcacgatttctcagcacattataactctatgcaattttttgctgttttagGTCCTCAATGCTCTGTTCAATCTTTGCAAGATCAATAAAAGAAGACAGGAACAAGCAGCTGAAAATGGGATCATCCCTCACTTAATGAATTTTGTCATGT

Basic information

species Oryza sativa
transcript LOC_Os04g56530.1
intron # 21
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g56530.1 (Oryza sativa), 3'ss of exon 21
lower sequence: GRMZM2G017654_T01 (Zea mays), 3'ss of exon 21
-ttagggacaaatgtcaagacagttggctattcagaatttgaaataggtctgcacgattt-ctcagcacattat-aactctatgcaattttttgctgttttagGTCCTCAATGCTCTGTTCAATCTTTGCAAGATCAATAAAAGAAGACAGGAACAAGCAGCTGAAAATGGGATCATCCCTCACTTAATGAATTTTGTCATGT
  |      ||| |  ||   | ||  |     | || |||   |  || ||||| |||| || ||||||| ||  ||| | |     ||| || |  | |||||||| |||||| ||||||| |||||||| || |||||||||||||||||||||||||| |||||||| |||||||||||||| ||||| ||||||||||
gatgctactaaaagctaactaatttctcagcagacaacttgccttctgt-tgcactattttctgagcacataattgactgtctctgcctttctgtt--tctagGTCCTTAATGCTTTGTTCAACCTTTGCAAAATTAATAAAAGAAGACAGGAACAAGCAGCCGAAAATGGAATCATCCCTCACTTGATGAAATTTGTCATGT

upper sequence: LOC_Os04g56530.1 (Oryza sativa), 3'ss of exon 21
lower sequence: GRMZM2G084586_T01 (Zea mays), 3'ss of exon 7
ttagggacaaatgtcaaga--cagttggctattcag-aatttgaaataggtctgcacgattt-ctcagcacattataactctatgcaattttttgctgttttagGTCCTCAATGCTCTGTTCAATCTTTGCAAGATCAATAAAAGAAGACAGGAACAAGCAGCTGAAAATGGGATCATCCCTCACTTAATGAATTTTGTCATGT
 |      |||||  || |  || ||    |      |||||||  |  || ||||| |||| || ||||||   ||| |   |||   |   |     | ||||||||||||||| ||||||| ||||||||||| |||||||||||||||||||| |||||||||||||| ||||| |||||||| ||||||||||||||||
atgctattaaatgctaacaaccaatttatcagcagataatttgacttctgt-tgcactattttctgagcaca---taattgactgcctctgcctttgtctctagGTCCTCAATGCTTTGTTCAACCTTTGCAAGATTAATAAAAGAAGACAGGAACAGGCAGCTGAAAATGGAATCATTCCTCACTTGATGAATTTTGTCATGT

upper sequence: LOC_Os04g56530.1 (Oryza sativa), 3'ss of exon 21
lower sequence: Vv01s0011g02270.t01 (Vitis vinifera), 3'ss of exon 21
ttagggacaaatgtc--aagacagttggctattcagaatttgaaataggtctgcacgatttctcagcacattataa----ctctatgcaattttttgctgttttagGTCCTCAATGCTCTGTTCAATCTTTGCAAGATCAATAAAAGAAGACAGGAACAAGCAGCTGAAAATGGGATCATCCCTCACTTAATGAATTTTGTCATGT
        |||||||  ||||  | ||  | |||| | | |    | | |   |    |||     |||  | ||      ||     || |||    |  |  |||||||| ||||  | ||||| || |||||||| ||||| || || || |||||||||||||||||||| ||||| || ||||| ||| ||||| | ||||
------ttaaatgtctgaagatggctgattcttcacattgtactttggtttaactttttttgaggccacgatttagatgcttcctcataaatttcattttctgaagGTCCTCTATGCATTATTCAACCTCTGCAAGATAAATAAGAGGAGGCAAGAACAAGCAGCTGAAAATGGAATCATTCCACACTTGATGCATTTTATAATGT

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|88369578|gb|CI582773.1|CI582773
EST:     CGATTCTTGAACTTCATGATGGCCCTCTACTTTATCAAATACATAGTGAG                         GTCCTCAATGCTCTGTTCAATCTTTG
genomic: CGATTCTTGAACTTCATGATGGCCCTCTAGTTTATCAAATACATAGTGAGgtgggtagtt ... gctgttttagGTCCTCAATGCTCTGTTCAATCTTTG
EST: gi|218505517|gb|FG965290.1|FG965290
EST:     CTCTAGTTTATCAAATACATAGTGAG                         GTCCTCAATGCTCTGTTCAATCTTTGCAAGATCAATAAAAGAAGACAGGAA
genomic: CTCTAGTTTATCAAATACATAGTGAGgtgggtagtt ... gctgttttagGTCCTCAATGCTCTGTTCAATCTTTGCAAGATCAATAAAAGAAGACAGGAA
EST: gi|117220975|gb|CT845486.1|CT845486
EST:     CGATTCTTGAACTTCATGATGGCCCTCTAGTTTATCAAATACATAGTGAG                         GTCCTCAATGCTCTGTTCAATCTTTGCAAGATCAATAAAAGAAGACAGGAA
genomic: CGATTCTTGAACTTCATGATGGCCCTCTAGTTTATCAAATACATAGTGAGgtgggtagtt ... gctgttttagGTCCTCAATGCTCTGTTCAATCTTTGCAAGATCAATAAAAGAAGACAGGAA
EST: gi|33809579|gb|CF330675.1|CF330675
EST:     CGATTCTTGAACTTCATGATGGCCCTCTAGTTTATCAAATACATAGTGAG                         GTCCTCAATGCTCTGTTCAATCTTTGCAAGATCAATAAAAGAAGACAGGAA
genomic: CGATTCTTGAACTTCATGATGGCCCTCTAGTTTATCAAATACATAGTGAGgtgggtagtt ... gctgttttagGTCCTCAATGCTCTGTTCAATCTTTGCAAGATCAATAAAAGAAGACAGGAA

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: 50 (upstream exon), 21 (downstream exon)
Score: 19

TAATTGTCTCGAGACACTCCAGCGCACAGATGCAATCAAGCATCTGATACCGATTCTTGAACTTCATGATGGCCCTCTAGTTTATCAAATACATAGTGAGgtgggtagtt ... gctgttttagGTCCTCAATGCTCTGTTCAATCTTTGCAAGATCAATAAAAGAAGACAGGAACAAGCAGCTGAAAATGGGATCATCCCTCACTTAATGAATTTTGTCATGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtctgcacgatttctcagcacattataactctatgcaattttttgctgttttagGTCCTCAATGCTCTGTTCAATCTTTGCAAGATCAATAAAAGAAGACAGGAACAAGCAGCTGAAAATGGGATCATCCCTCACTTAATGAATTTTGTCATGT
                       ttataac  putative branch site (score: 19)
                                       ttttttgctgtttt  putative PPT
                                     aatttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttagggacaaatgtcaagacagttggctattcagaatttgaaataggtctgcacgatttctcagcacattataactctatgcaattttttgctgttttagGTCCTCAATGCTCTGTTCAATCTTTGCAAGATCAATAAAAGAAGACAGGAACAAGCAGCTGAAAATGGGATCATCCCTCACTTAATGAATTTTGTCATGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - ggacaaa
- - - - - - - - - - - - - - - - - - - - - - - -tctgcac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcacatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctatgca