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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtctgataatgtattttttgtggtcattttgaggatatgacttgctgttctatttgttctcttgctgcaagatctgactccttgaatatgtccctacagGATGGCTCCTTCCAGAATTCATGTAACATGTGCGTTAGTTTATGGACCTACACCAACGGGAAGGATTCACCAAGGAGTTTGTTCGACATGGATGAAG

Basic information

species Oryza sativa
transcript LOC_Os04g55960.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g55960.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G086489_T02 (Zea mays), 3'ss of exon 12
tgtctgataatgtattttttgtggtcattttg-aggatatgacttgctgttctatttgttctcttgctgcaagatctgactccttgaa----tatgtccctacagGATGGCTCCTTCCAGAATTCATGTAACATGTGCGTTAGTTTATGGACCTACACCAACGGGAAGGATTCACCAAGGAGTTTGTTCGACATGGATGAAG
|||  ||   | |  ||  | | |   |     |  ||    ||||  ||  |  |   |  ||| |   | |    | |  |||||     |||||| |  |||||||||||| ||||||||||||||||||||||||||||||||||| ||| ||||||| |||||||| ||||||||||||||||| ||||||||||||
tgttggactgtcttgttcatatcggtgtgccatatcattatgcttgaggtggtggtatgtaccttccattaggga--ggcctcttgacaacttatgtctcagCAGGATGGCTCCCTCCAGAATTCATGTAACATGTGCGTTAGTTTATGGGCCTTCACCAACAGGAAGGATCCACCAAGGAGTTTGTTCAACATGGATGAAG

upper sequence: LOC_Os04g55960.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G086489_T01 (Zea mays), 3'ss of exon 12
tgtctgataatgtattttttgtggt-cattttgaggatatgacttgctgttctatttgttctcttgctgcaagatctgactccttgaatatgtccctacagGATGGCTCCTTCCAGAATTCATGTAACATGTGCGTTAGTTTATGGACCTACACCAACGGGAAGGATTCACCAAGGAGTTTGTTCGACATGGATGAAG
||     |  |||   | | |  || |  | | |  ||       |  ||  ||| |    ||     |  ||  ||   |       |||||| |  |||||||||||| ||||||||||||||||||||||||||||||||||| ||| ||||||| |||||||| ||||||||||||||||| ||||||||||||
tggactgtcttgttcatatcggtgtgccatatcattatgcttgaggtggtggtatgtaccttccattagggaggcctc-ttgacaacttatgtctcagcagGATGGCTCCCTCCAGAATTCATGTAACATGTGCGTTAGTTTATGGGCCTTCACCAACAGGAAGGATCCACCAAGGAGTTTGTTCAACATGGATGAAG

upper sequence: LOC_Os04g55960.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G104294_T02 (Zea mays), 3'ss of exon 6
tgtctgataatgtattttttgtggtcattttgaggatatgacttgctgttctatttgttctcttgctgcaagatc--tgactccttgaatatgtccctacagGATGGCTCCTTCCAGAATTCATGTAACATGTGCGTTAGTTTATGGACCTACACCAACGGGAAGGATTCACCAAGGAGTTTGTTCGACATGGATGAAG
      |  | | |  | |  ||   |||      | |  |  || || | | |   |||  ||   | | |     ||||  |||  |  |||| || |||||||||||| ||||||||||||||||||||||| ||||||||||| ||| ||||||| |||||||| ||||||||||||||||| ||||||||||||
--caaaaatacgcagatctcctgcgtattcaagaaaaaaaaggtggtggtatgtaccttccattaggggatgcctcttgacaacttataagtgtctctgcagGATGGCTCCCTCCAGAATTCATGTAACATGTGCATTAGTTTATGGGCCTTCACCAACAGGAAGGATCCACCAAGGAGTTTGTTCAACATGGATGAAG

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|27577335|gb|CB000030.1|CB000030
EST:     T-C-CCTTTCGCCTACAACCGCGTTACTACTCCATATCATCATCTCCAAA                         GATGGCTCCTTCCAGAATTCATGTAACATGTGCGTTAGTTTATGGACCTAC
genomic: TGCACC--TCGCCTACAACCGCGTTACTACTCCATATCATCATCTCCAAAgtaagtatat ... gtccctacagGATGGCTCCTTCCAGAATTCATGTAACATGTGCGTTAGTTTATGGACCTAC
EST: gi|58666486|gb|CK055172.1|CK055172
EST:     GTTGCACCTCGCCTACAACCGCGTTACTACTCCATATCATCATCTCCAAA                         GATGGCTCCTTCCAGAATTCATGTAACATGTGCGTTAGTTTATGGACCTAC
genomic: GTTGCACCTCGCCTACAACCGCGTTACTACTCCATATCATCATCTCCAAAgtaagtatat ... gtccctacagGATGGCTCCTTCCAGAATTCATGTAACATGTGCGTTAGTTTATGGACCTAC
EST: gi|58676313|gb|CK065000.1|CK065000
EST:     GTTGCACCTCGCCTACAACCGCGTTACTACTCCATATCATCATCTCCAAA                         GATGGCTCCTTCC
genomic: GTTGCACCTCGCCTACAACCGCGTTACTACTCCATATCATCATCTCCAAAgtaagtatat ... gtccctacagGATGGCTCCTTCC
EST: gi|163926612|gb|EG713628.1|EG713628
EST:     CCGCGTTACTACTCCATATCATCATCTCCAAA                         GATGGCTCCTTCCAGAATTCATGTAACATGTGCGTTAGTTTATGGACCTAC
genomic: CCGCGTTACTACTCCATATCATCATCTCCAAAgtaagtatat ... gtccctacagGATGGCTCCTTCCAGAATTCATGTAACATGTGCGTTAGTTTATGGACCTAC
EST: gi|29674048|gb|CB670323.1|CB670323
EST:     GTTGCACCTCGCCTACAACCGCGTTACTACTCCATATCATCATCTCCAAA                         GATGGCTCCTTCCAGAATTCATGTAACATGTGCGTTAGTTTATGGACCTAC
genomic: GTTGCACCTCGCCTACAACCGCGTTACTACTCCATATCATCATCTCCAAAgtaagtatat ... gtccctacagGATGGCTCCTTCCAGAATTCATGTAACATGTGCGTTAGTTTATGGACCTAC
EST: gi|58661320|gb|CK050000.1|CK050000
EST:     GTTGCACCTCGCCTACAAGCGCGTTACTACTCCATATCATCATCTCCAAA                         GATGGCTCCTTCCAGAATTCAT
genomic: GTTGCACCTCGCCTACAACCGCGTTACTACTCCATATCATCATCTCCAAAgtaagtatat ... gtccctacagGATGGCTCCTTCCAGAATTCAT
EST: gi|33676427|gb|CF304666.1|CF304666
EST:     GTTGCACCTCGCCTACAACCGCGTTACTACTCCATATCATCATCTCCAAA                         GATGGCTCCTTCCAGAATTCATGTAACATGTGCGTTAGTTTATGGACCTAC
genomic: GTTGCACCTCGCCTACAACCGCGTTACTACTCCATATCATCATCTCCAAAgtaagtatat ... gtccctacagGATGGCTCCTTCCAGAATTCATGTAACATGTGCGTTAGTTTATGGACCTAC
EST: gi|58681936|gb|CK070623.1|CK070623
EST:     GTTGCACCTCGCCTACAACCGCGTTACTACTCCATATCATCATCTCCAAA                         GATGGCTCCTTCCAGAATTCATGTAACATGTGCGTTAGTTTATGGACCTAC
genomic: GTTGCACCTCGCCTACAACCGCGTTACTACTCCATATCATCATCTCCAAAgtaagtatat ... gtccctacagGATGGCTCCTTCCAGAATTCATGTAACATGTGCGTTAGTTTATGGACCTAC
EST: gi|58655931|gb|CK044611.1|CK044611
EST:     GTTGCACCTCGCCTACAACCGCGTTACTACTCCATATCATCATCTCCAAA                         GATGGCTCCTTCCAGAATTCATGTAACATGTGCGTTAGTT
genomic: GTTGCACCTCGCCTACAACCGCGTTACTACTCCATATCATCATCTCCAAAgtaagtatat ... gtccctacagGATGGCTCCTTCCAGAATTCATGTAACATGTGCGTTAGTT
EST: gi|58654591|gb|CK043271.1|CK043271
EST:     GTTGCACCTCGCCTACAACCGCGTTACTACTCCATATCATCATCTCCAAA                         GATGGCTCCTTCCAGAATTCATGTAACATGTGCGTTAGTTTATGGACCTAC
genomic: GTTGCACCTCGCCTACAACCGCGTTACTACTCCATATCATCATCTCCAAAgtaagtatat ... gtccctacagGATGGCTCCTTCCAGAATTCATGTAACATGTGCGTTAGTTTATGGACCTAC
EST: gi|27576047|gb|CA998741.1|CA998741
EST:     GTTGCACCTCTCCTCCAACCGCGTTACTACTCCATATCATCATCTCCAAA                         GATGGCTCCTTCCAGAATTCATGTAACATGTGCGTTAGTTTATGGACCTAC
genomic: GTTGCACCTCGCCTACAACCGCGTTACTACTCCATATCATCATCTCCAAAgtaagtatat ... gtccctacagGATGGCTCCTTCCAGAATTCATGTAACATGTGCGTTAGTTTATGGACCTAC

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: 69 (upstream exon), 75 (downstream exon)
Score: 96

TGGCTGCATTCCCTTCAGCTAAGCCCCCACTGGGAGTATTCTTTGCAGCTGTTGCACCTCGCCTACAACCGCGTTACTACTCCATATCATCATCTCCAAAgtaagtatat ... gtccctacagGATGGCTCCTTCCAGAATTCATGTAACATGTGCGTTAGTTTATGGACCTACACCAACGGGAAGGATTCACCAAGGAGTTTGTTCGACATGGATGAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgttctatttgttctcttgctgcaagatctgactccttgaatatgtccctacagGATGGCTCCTTCCAGAATTCATGTAACATGTGCGTTAGTTTATGGACCTACACCAACGGGAAGGATTCACCAAGGAGTTTGTTCGACATGGATGAAG
                           atctgac  putative branch site (score: 96)
                                            tgtccct  putative PPT
      tatttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtctgataatgtattttttgtggtcattttgaggatatgacttgctgttctatttgttctcttgctgcaagatctgactccttgaatatgtccctacagGATGGCTCCTTCCAGAATTCATGTAACATGTGCGTTAGTTTATGGACCTACACCAACGGGAAGGATTCACCAAGGAGTTTGTTCGACATGGATGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - -cttgctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgcaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctccttg