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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgtgccatcttttatgcatgcagttcaagtatggctttaaacatatattaaacattgtcatcctgagtttgaaacttttactaacctattccagTGTATCGGGCAAGCATATGAGGACATACAGGCACAAAACCAACAATTGCTACAGCAGATTATTGAAAGAGATGATGATAATACCAAG

Basic information

species Oryza sativa
transcript LOC_Os04g46450.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g46450.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM5G854499_T01 (Zea mays), 3'ss of exon 17
gtgtgtgccatcttttatgcatgcagttcaagtatggctttaaacatatattaaacattgtcatcctgagtttgaaacttttactaacctattccagTGTATCGGGCAAGCATATGAGGACATACAGGCACAAAACCAACAATTGCTACAGCAGATTATTGAAAGAGATGATGATAATACCAAG
|||||  | |||||  || | |    ||  |  || | | | ||          | ||| |||      |  | ||| ||||| |   ||||| ||| | || || || || ||||| ||||||  | ||||||| |||||||||||||||||||||||||||||||||||| |||||||||||
gtgtggacaatcttccatacct----tttgaccatagttatcaatgct------atattttca-----ggcctcaaaattttattc-tctattacagAGCATTGGCCATGCCTATGAAGACATAATGTCACAAAATCAACAATTGCTACAGCAGATTATTGAAAGAGATGATCATAATACCAAG

upper sequence: LOC_Os04g46450.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM2G162184_T01 (Zea mays), 3'ss of exon 16
gtgtgtgccatcttttatgcatgcagttcaagtatggctttaaacatatattaaacattgtcatcctgagtttgaaacttttactaacctattccagTGTATCGGGCAAGCATATGAGGACATACAGGCACAAAACCAACAATTGCTACAGCAGATTATTGAAAGAGATGATGATAATACCAAG
|||||  | |||||  ||  || |  | |||  |||  ||||         |  |  || |  |     |  | ||| | ||| |   ||||  ||| | || || || || ||||| || |||  | ||||||| |||||||||||||||||||||||||||||||||||| |||||||||||
gtgtggacaatcttccatctataccttccaaccatg--ttta---------tcgatgttatattttcaggcctcaaaatgttattt-tctatgacagAGCATTGGCCATGCCTATGAAGATATAATGTCACAAAATCAACAATTGCTACAGCAGATTATTGAAAGAGATGATCATAATACCAAG

upper sequence: LOC_Os04g46450.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GLYMA01G13430.1 (Glycine max), 3'ss of exon 9
------------------gtgtg-tgccatctttta-tgcatgcagt--tcaagtatggctttaaacatatattaaacattgtcatcctgagtttgaaacttttactaac---------ctattccagTGTATCGGGCAAGCATATGAGGACATACAGGCACAAAACCAACAATTGCTACAGCAGATTATTGAAAGAGATGATGATAATACCAAG
                   || | ||  ||  |||  |||||   |   |    ||  | ||    ||| | | |    ||  || | | | |||    || || | |            |  | ||| |||| || ||||||||||| ||||| ||  | |||||||||||  || | |||||||||| ||||||||||||| ||||||  |||
gtttgatttcttatctgaatgggatgtaattctttgctgcataatgccattttttactgattattccatttgtaatggttttacaacattaattttcgtctgttgccattgggttgattttcctgcagAGTATTGGACAAGCATATGACGACATGCAAACTCAAAACCAACATCTGTTGCAGCAGATTACTGAAAGAGATGATTATAATATTAAG

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|58654134|gb|CK042814.1|CK042814
EST:     TGCTGAAGTCTAAACAGGAAGAATGTGAAGCTTACAGAGTGGAGGTCGAG                         TGTATCGGGCAAGCATATGAGGACATACAGGCACAAAACCAACAATTGCTA
genomic: TGCTGAAGTCTAAACAGGAAGAATGTGAAGCTTACAGAGTGGAGGTCGAGgtgtgtgcca ... cctattccagTGTATCGGGCAAGCATATGAGGACATACAGGCACAAAACCAACAATTGCTA
EST: gi|58658167|gb|CK046847.1|CK046847
EST:     TGCTGAAGTCTAAACAGGAAGAATGTGAAGCTTACAGAGTGGAGGTCGAG                         TGTATCGGGCAAGCATATGAGGACATACAGGCACAAAACCAACAATTGCTA
genomic: TGCTGAAGTCTAAACAGGAAGAATGTGAAGCTTACAGAGTGGAGGTCGAGgtgtgtgcca ... cctattccagTGTATCGGGCAAGCATATGAGGACATACAGGCACAAAACCAACAATTGCTA
EST: gi|88360993|gb|CI625299.1|CI625299
EST:     TGCTGAAGTCTAAACAGGAAGAATGTGAAGCTTACAGAGTGGAGGTCGAG                         TGTATCGGGCAAGCATATGAGGACATACAGGCACCAAAC-AACAATTGCTA
genomic: TGCTGAAGTCTAAACAGGAAGAATGTGAAGCTTACAGAGTGGAGGTCGAGgtgtgtgcca ... cctattccagTGTATCGGGCAAGCATATGAGGACATACAGGCACAAAACCAACAATTGCTA
EST: gi|58659385|gb|CK048065.1|CK048065
EST:     TGCTGAAGTCTAAACAGGAAGAATGTGAAGCTTACAGAGTGGAGGTCGAG                         TGTATCGGGCAAGCATATGAGGACATACAGGCACAAAACCAACAATTGCTA
genomic: TGCTGAAGTCTAAACAGGAAGAATGTGAAGCTTACAGAGTGGAGGTCGAGgtgtgtgcca ... cctattccagTGTATCGGGCAAGCATATGAGGACATACAGGCACAAAACCAACAATTGCTA
EST: gi|25777950|gb|CA752700.1|CA752700
EST:     TGCTGAAGTCTAAACAGGAAGAATGTGAAGCTTACAGAGTGGAGGTCGAG                         TGTATCGGGCAAGCATATGAGGACATACAGGCACAAAACCAACAATTGCTA
genomic: TGCTGAAGTCTAAACAGGAAGAATGTGAAGCTTACAGAGTGGAGGTCGAGgtgtgtgcca ... cctattccagTGTATCGGGCAAGCATATGAGGACATACAGGCACAAAACCAACAATTGCTA
EST: gi|218487991|gb|FG954428.1|FG954428
EST:     TGCTGAAGTCTAAACAGGAAGAATGTGAAGCTTACAGAGTGGAGGTCGAG                         TGTATCGGGCAAGCATATGAGGACATACAGGCACAAAACCAACAATTGCTA
genomic: TGCTGAAGTCTAAACAGGAAGAATGTGAAGCTTACAGAGTGGAGGTCGAGgtgtgtgcca ... cctattccagTGTATCGGGCAAGCATATGAGGACATACAGGCACAAAACCAACAATTGCTA

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: 72 (upstream exon), 74 (downstream exon)
Score: 14

GGATCTAGTCAGTTTATCCCATATGCTGAAGTCTAAACAGGAAGAATGTGAAGCTTACAGAGTGGAGGTCGAGgtgtgtgcca ... cctattccagTGTATCGGGCAAGCATATGAGGACATACAGGCACAAAACCAACAATTGCTACAGCAGATTATTGAAAGAGATGATGATAATACCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacatatattaaacattgtcatcctgagtttgaaacttttactaacctattccagTGTATCGGGCAAGCATATGAGGACATACAGGCACAAAACCAACAATTGCTACAGCAGATTATTGAAAGAGATGATGATAATACCAAG
                                       tactaac  putative branch site (score: 14)
                                             cctattcc  CT-rich tract
     atattaaacattgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgtgccatcttttatgcatgcagttcaagtatggctttaaacatatattaaacattgtcatcctgagtttgaaacttttactaacctattccagTGTATCGGGCAAGCATATGAGGACATACAGGCACAAAACCAACAATTGCTACAGCAGATTATTGAAAGAGATGATGATAATACCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG