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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatcatatgcagttttcaagagcagtcaattgtggtagtaaagtcgcattaattcaaaaaatatgatttgtgcagGTTCAAGATATAACTCACTTGCCTTTTGCTGAAAGAGAACTTATGCTTATCAAGGTTTCTGTGAACACTGCTGCTCGGAGAGACATACTAGATATTGCTG

Basic information

species Oryza sativa
transcript LOC_Os02g39570.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g39570.5 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G407044_T01 (Zea mays), 3'ss of exon 9
gtaaatcatatgcagtttt-caagagcagtcaattgtggtagtaaagtcgcattaattcaaaaaa---tatgatttgtgcagGTTCAAGATATAACTCACTTGCCTTTTGCTGAAAGAGAACTTATGCTTATCAAGGTTTCTGTGAACACTGCTGCTCGGAGAGACATACTAGATATTGCTG
||||     |   | || |   | |   ||   |  | | | |    |    |||  | | ||||   | |||||  |||||||||| || || || ||||  |||||||||||||| |||||||||||||| ||||||||||| ||||||||||||||||  || || |||||||||||||
gtaagctgcaaaaacttctgtcaaaatcgtttgtgattgcaattttattatgttagctaacaaaagcatgtgattcctgcagGTTCATGACATTACCCACTCACCTTTTGCTGAAAGGGAACTTATGCTTATTAAGGTTTCTGTCAACACTGCTGCTCGGAAGGAAATCCTAGATATTGCTG

upper sequence: LOC_Os02g39570.5 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G007647_T01 (Zea mays), 3'ss of exon 9
gtaaatcatatgcagttttcaagagcagtcaattgtggtagtaaa---gtcgcattaattcaaaaaatatgatttgtgc--agGTTCAAGATATAACTCACTTGCCTTTTGCTGAAAGAGAACTTATGCTTATCAAGGTTTCTGTGAACACTGCTGCTCGGAGAGACATACTAGATATTGCTG
||||     ||| |  ||  |   | | ||| ||||||| | |||    |     |||   |||| ||  ||| |   |  ||||||| || || || ||||  |||||||||||||| || || |||||||| ||||||||||| ||||||||||||||||| || || |||||||||||||
gtaagctgcatgtaacttctatc-gaaatcatttgtggttgcaaatttattatgctaacaaaaaacatgcgatcttccctcagGTTCATGACATTACCCACTCACCTTTTGCTGAAAGGGAGCTGATGCTTATTAAGGTTTCTGTAAACACTGCTGCTCGGAGGGAAATTCTAGATATTGCTG
















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|29676546|gb|CB672821.1|CB672821
EST:     CCATTGAGAAGTTAGTTCAGCAGCTTAACAAACTTGTTGATGTGCATGAG                         GTTCAAGATATAACTCACTTGCCTTTTGCTGAAAGAGAACTTATGCTTATC
genomic: CCATTGAGAAGTTAGTTCAGCAGCTTAACAAACTTGTTGATGTGCATGAGgtaaatcata ... atttgtgcagGTTCAAGATATAACTCACTTGCCTTTTGCTGAAAGAGAACTTATGCTTATC
EST: gi|29656805|gb|CB653080.1|CB653080
EST:     CCATTGAGAAGTTAGTTCAGCAGCTTAACAAACTTGTTGATGTGCATGAG                         GTTCAAGATATAACTCACTTGCCTTTTGCTGAAAGAGAACTTATGCTTATC
genomic: CCATTGAGAAGTTAGTTCAGCAGCTTAACAAACTTGTTGATGTGCATGAGgtaaatcata ... atttgtgcagGTTCAAGATATAACTCACTTGCCTTTTGCTGAAAGAGAACTTATGCTTATC
EST: gi|15853702|gb|BI806498.1|BI806498
EST:     CCATTGAGAAGTTAGTTCAGCAGCTTAACAAACTTGTTGATGTGCATGAG                         GTTCAAGATATAACTCAC-TGCCTTTTGCTGAAAGAGAACTTATGCTTATC
genomic: CCATTGAGAAGTTAGTTCAGCAGCTTAACAAACTTGTTGATGTGCATGAGgtaaatcata ... atttgtgcagGTTCAAGATATAACTCACTTGCCTTTTGCTGAAAGAGAACTTATGCTTATC
EST: gi|32948291|gb|BP184863.1|BP184863
EST:     CCATTGAGAAGTTAGTTCAGCAGCTTAACAAACTTGTTGATGTGCATGAG                         GTTCAAGATATAACTCACTTGCCTTTTGCTGAAAGAGAACTTATGCTTATC
genomic: CCATTGAGAAGTTAGTTCAGCAGCTTAACAAACTTGTTGATGTGCATGAGgtaaatcata ... atttgtgcagGTTCAAGATATAACTCACTTGCCTTTTGCTGAAAGAGAACTTATGCTTATC
EST: gi|32948361|gb|BP184933.1|BP184933
EST:     CCATTGAGAAGTTAGTTCAGCAGCTTAACAAACTTGTTGATGTGCATGAG                         GTTCAAGATATAACTCACTTGCCTTTTGCTGAAAGAGAACTTATGCTTATC
genomic: CCATTGAGAAGTTAGTTCAGCAGCTTAACAAACTTGTTGATGTGCATGAGgtaaatcata ... atttgtgcagGTTCAAGATATAACTCACTTGCCTTTTGCTGAAAGAGAACTTATGCTTATC
EST: gi|86522997|gb|CI163203.1|CI163203
EST:     CCATTGAGAAGTTAGTTCAGCAGCTTAACAAACTTGTTGATGTGCATGAG                         GTTCAAGACATAACTCACTTGCCTTTTGCTGAAAGAGAACTTATGCTTATC
genomic: CCATTGAGAAGTTAGTTCAGCAGCTTAACAAACTTGTTGATGTGCATGAGgtaaatcata ... atttgtgcagGTTCAAGATATAACTCACTTGCCTTTTGCTGAAAGAGAACTTATGCTTATC
EST: gi|33682201|gb|CF310440.1|CF310440
EST:     CCATTGAGAAGTTAGTTCAGCAGCTTAACAAACTTGTTGATGTGCATGAG                         GTTCAAGATATAACTCACTTGCCTTTTGCTGAAAGAGAACTTATGCTTATC
genomic: CCATTGAGAAGTTAGTTCAGCAGCTTAACAAACTTGTTGATGTGCATGAGgtaaatcata ... atttgtgcagGTTCAAGATATAACTCACTTGCCTTTTGCTGAAAGAGAACTTATGCTTATC
EST: gi|33682200|gb|CF310439.1|CF310439
EST:     CATTGAGAAGTTAGTTCAGCAGCTTAACAAACTNTGTTGATGTGCATGAG                         GTTCAAGATATAACTCACTTGCCTTTTGCTGAAAGAGAACTTATGCTTATC
genomic: CATTGAGAAGTTAGTTCAGCAGCTTAACAAACT-TGTTGATGTGCATGAGgtaaatcata ... atttgtgcagGTTCAAGATATAACTCACTTGCCTTTTGCTGAAAGAGAACTTATGCTTATC

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: 75 (upstream exon), 74 (downstream exon)
Score: 85

AAAGTCAGGCCTTTCGCGTATTACAACAGTTGCTCCTGGAACAGATGAATCCATTGAGAAGTTAGTTCAGCAGCTTAACAAACTTGTTGATGTGCATGAGgtaaatcata ... atttgtgcagGTTCAAGATATAACTCACTTGCCTTTTGCTGAAAGAGAACTTATGCTTATCAAGGTTTCTGTGAACACTGCTGCTCGGAGAGACATACTAGATATTGCTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agcagtcaattgtggtagtaaagtcgcattaattcaaaaaatatgatttgtgcagGTTCAAGATATAACTCACTTGCCTTTTGCTGAAAGAGAACTTATGCTTATCAAGGTTTCTGTGAACACTGCTGCTCGGAGAGACATACTAGATATTGCTG
                          cattaat  putative branch site (score: 85)
                           attaattcaaaaaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatcatatgcagttttcaagagcagtcaattgtggtagtaaagtcgcattaattcaaaaaatatgatttgtgcagGTTCAAGATATAACTCACTTGCCTTTTGCTGAAAGAGAACTTATGCTTATCAAGGTTTCTGTGAACACTGCTGCTCGGAGAGACATACTAGATATTGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT