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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aataaatctttgtacacgtcctgtaccagatattatgtttttcctaagctaattgcactgtggctgttcaggatatgataaaattttctttttcgtgcagGAATTAACTCCAGCCCCTGTATTTCCTCTTATTGTCGGAGTTTCCGTGATTGCATTGGTCATCAGCATGCCAAG

Basic information

species Oryza sativa
transcript LOC_Os01g19470.1
intron # 25
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g19470.1 (Oryza sativa), 3'ss of exon 25
lower sequence: Vv07s0005g01650.t01 (Vitis vinifera), 3'ss of exon 25
------------------------------------------------------------------------------aataaatctttgtacacgtcctgtaccagatattatgtttttcctaagctaat---tgcactgtggctgttcaggatatgataaaattttctttt--------tcgtgcagGAATTAACTCCAGCCCCTGTATTTCCTCTTATTGTCGGAGTTTCCGTGATTGCATTGGTCATCAGCATGCCAAG
                                                                               |  | | || | ||   || | | |||   |  |  ||      || | | |   |  |   ||  |   ||  |  | |  |  || |  |          || | ||||||||||||||||| || || |||||||| || || |||||||| ||||||||  |  | ||||| ||||||||
gtctgtttcactttcttcaaacaaataattcttttcatgattagttatcaccaactatgcatattgctcacctacccacactactattggaactgctcttctgccatccaa-accttccaaacaatccagtgaatttagaatgatttaacaaaacttaaccatgttcttctccctaccatgtcctacagGAATTAACTCCAGCACCCGTGTTTCCTCTCATCGTTGGAGTTTCAGTGATTGCTCTTTTTATCAGTATGCCAAG
















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|87016323|gb|CI271734.1|CI271734
EST:     TTCATGTTGGTCCTCTTAAATATAAAACCGAAGAGCGACATCACAAACAG                         GAATTAACTCCAGCCCCTGTATTTCCTCTTATTGTCGGAGTTTCCGTGATT
genomic: TTCATGTTGGTCCTCTTAAATATAAAACCGAAGAGCGACATCACAAACAGgtaatttctt ... tttcgtgcagGAATTAACTCCAGCCCCTGTATTTCCTCTTATTGTCGGAGTTTCCGTGATT
EST: gi|4715027|gb|AU056144.1|AU056144
EST:     CCATGTTGGTCCTCTTAAATATAAACCCGAAGANCGACATCACAAACCAG                         GAATTAACTCCAGCCCCTGTATTTCCTCTTATTGTCGGAGTTNCCGTGAT
genomic: -CATGTTGGTCCTCTTAAATATAAAACCGAAGAGCGACATCACAAA-CAGgtaatttctt ... tttcgtgcagGAATTAACTCCAGCCCCTGTATTTCCTCTTATTGTCGGAGTTTCCGTGAT
EST: gi|88995505|gb|CI022828.1|CI022828
EST:     TTCATGTTGGTCCTCTTAAATATAAAACCGAAGAGCGACATCACAAACAG                         GAATTAACTCCAGCCCCTGTATTTCCTCTTATTGTCGGAGTTTCCGTGATT
genomic: TTCATGTTGGTCCTCTTAAATATAAAACCGAAGAGCGACATCACAAACAGgtaatttctt ... tttcgtgcagGAATTAACTCCAGCCCCTGTATTTCCTCTTATTGTCGGAGTTTCCGTGATT
EST: gi|89183106|gb|CI003170.1|CI003170
EST:     AAAACCGAAGAGCGACATCACAAACAG                         GAATTAACTCCAGCCCCTGTATTTCCTCTTATTGTCGGAGTTTCCGTGATT
genomic: AAAACCGAAGAGCGACATCACAAACAGgtaatttctt ... tttcgtgcagGAATTAACTCCAGCCCCTGTATTTCCTCTTATTGTCGGAGTTTCCGTGATT
EST: gi|86480905|gb|CI123538.1|CI123538
EST:     TTCATGTTGGTCCTCTTAAATATAAAACCGAAGAGCGACATCACAAACAG                         GAATTAACTCCAGCCCCTGTATTTCCTCTTATTGTCGGAGTTTCCGTGATT
genomic: TTCATGTTGGTCCTCTTAAATATAAAACCGAAGAGCGACATCACAAACAGgtaatttctt ... tttcgtgcagGAATTAACTCCAGCCCCTGTATTTCCTCTTATTGTCGGAGTTTCCGTGATT
EST: gi|27547001|gb|CA765154.2|CA765154
EST:     TTCATGTTGCTCCTCTTAAATATAAAACCGAAGAGCGACATCACAAACAG                         GAATTAACTCCAGCCCCTGTATTTCCTCTTATTGTCGGAGTTTCTGTGATT
genomic: TTCATGTTGGTCCTCTTAAATATAAAACCGAAGAGCGACATCACAAACAGgtaatttctt ... tttcgtgcagGAATTAACTCCAGCCCCTGTATTTCCTCTTATTGTCGGAGTTTCCGTGATT
EST: gi|88508413|gb|CI435919.1|CI435919
EST:     TCATGTTGGTCCTCTTAGATATAAAACCGAAGAGGCGACATCACAGACAG                         GAATTAACTCCAGCCCCTGTATTTCCTCTTATTGTCGGAGGTTTCCGTGAT
genomic: TCATGTTGGTCCTCTTAAATATAAAACCGAAGA-GCGACATCACAAACAGgtaatttctt ... tttcgtgcagGAATTAACTCCAGCCCCTGTATTTCCTCTTATTGTCGGA-GTTTCCGTGAT
EST: gi|88490324|gb|CI427596.1|CI427596
EST:     CGAAGAGCGACATCACAAACAG                         GAATTAACTCCAGCCCCTGTATTTCCTCTTATTGTCGGAGTTTCCGTGATT
genomic: CGAAGAGCGACATCACAAACAGgtaatttctt ... tttcgtgcagGAATTAACTCCAGCCCCTGTATTTCCTCTTATTGTCGGAGTTTCCGTGATT
EST: gi|38482233|gb|CF966283.1|CF966283
EST:     TTCATGTTGGTCCTCTTAAATATAAAACCGAAGAGCGACATCACAAACAG                         GAATTAACTCCAGCCCCTGTATTTCCTCTTATTGTCGGAGTTTCTGTGATT
genomic: TTCATGTTGGTCCTCTTAAATATAAAACCGAAGAGCGACATCACAAACAGgtaatttctt ... tttcgtgcagGAATTAACTCCAGCCCCTGTATTTCCTCTTATTGTCGGAGTTTCCGTGATT
EST: gi|86250806|gb|CI007669.1|CI007669
EST:     CGACATCACAAACAG                         GAATTAACTCCAGCCCCTGTATTTCCTCTTATTGTCGGAGTTTCCGTGATT
genomic: CGACATCACAAACAGgtaatttctt ... tttcgtgcagGAATTAACTCCAGCCCCTGTATTTCCTCTTATTGTCGGAGTTTCCGTGATT
EST: gi|88725754|gb|CI749013.1|CI749013
EST:     GAAGAGCGACATCACAAACAG                         GAATTAACTCCAGCCCCTGTATTTCCTCTTATTGTCGGAGTTTCCGTGATT
genomic: GAAGAGCGACATCACAAACAGgtaatttctt ... tttcgtgcagGAATTAACTCCAGCCCCTGTATTTCCTCTTATTGTCGGAGTTTCCGTGATT

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: 73 (upstream exon), 66 (downstream exon)
Score: 7

TAGATTTGAGTCAGAGATAGTTGAAGTTGACTTGGACAAGCAACCTCAGATTCATGTTGGTCCTCTTAAATATAAAACCGAAGAGCGACATCACAAACAGgtaatttctt ... tttcgtgcagGAATTAACTCCAGCCCCTGTATTTCCTCTTATTGTCGGAGTTTCCGTGATTGCATTGGTCATCAGCATGCCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagctaattgcactgtggctgttcaggatatgataaaattttctttttcgtgcagGAATTAACTCCAGCCCCTGTATTTCCTCTTATTGTCGGAGTTTCCGTGATTGCATTGGTCATCAGCATGCCAAG
 agctaat  putative branch site (score: 7)
                                      ttttctttttcgtgc  putative PPT
                           atatgataaaattttc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aataaatctttgtacacgtcctgtaccagatattatgtttttcctaagctaattgcactgtggctgttcaggatatgataaaattttctttttcgtgcagGAATTAACTCCAGCCCCTGTATTTCCTCTTATTGTCGGAGTTTCCGTGATTGCATTGGTCATCAGCATGCCAAG

- - - - - tgtacac
- - - - - - - - - -cctgtac
- - - - - - - - - - - - - - - - ttatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - aattgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtggctg