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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtacaacttctgtaaacccatttatctgaagatatgtcagaattgtctattcatctttgcctgaagagaactccaaaaaaacaagtgttgtctgaacaaagtgcatgaactgttgcagGTCAAGAAACCCGGACTAGAAATGGCAACCGAACAAAGCGAGCTGGATCTGTCATATGGGCTACGCTACCAAGACGTGAAGATCCCAGAAGCGTATGAAC

Basic information

species Oryza sativa
transcript LOC_Os02g38840.2
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g38840.2 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G031107_T02 (Zea mays), 3'ss of exon 13
gtatgtacaacttctgtaaacccatttatctgaagatatgtcagaatt-gtctattcatctttgcctgaagagaactccaaaaaa---acaagtgttgtctgaacaaagtgcatgaactgttgcagGTCAAGAAACCCGGACTAGAAATGGCAACCGAACAAAGCGAGCTGGATCTGTCATATGGGCTACGCTACCAAGACGTGAAGATCCCAGAAGCGTATGAAC
||| | |||||| || | | || || | | | | ||||| | ||| | |||| | || |||| || |||| | ||||| ||||||||||| ||||||||||| ||||||||||||||||||||||| |||||||| || |||||| | || ||| | | ||| || ||||||||||| || || |
---------------gtacatacatttacctctgtaaactctagcctttgaatttcccgctttgtttaaaggagagaaaaaaagatgcggcagaattgtatgtctaaag--aacgaacttttgcagGTCAAAAAACCCGGACTGGAAATGGCAACCGAACAAAGCGAACTGGATCTATCGTATGGGATGCGGTACAATGGCGTCAAAATCCCAGAAGCATACGAGC
















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|88219092|gb|CI220365.1|CI220365
EST:     ATATGAAATTAACT                         GTCAAGAAACCCGGACTAGAAATGGCAACCGAACGAAGCGAGCTGGATCTG
genomic: ATATGAAATTAACTgtatgtacaa ... actgttgcagGTCAAGAAACCCGGACTAGAAATGGCAACCGAACAAAGCGAGCTGGATCTG
EST: gi|89176067|gb|CI043088.1|CI043088
EST:     AATTCGTTATACGGTTGCAGCCATCGGAAGCCATGTATATGAAATTAACT                         GTCAAGAAACCCGGACTAGAAATGGCAACCGAACAAAGCGAGCTGGATCTG
genomic: AATTCGTTATACGGTTGCAGCCATCGGAAGCCATGTATATGAAATTAACTgtatgtacaa ... actgttgcagGTCAAGAAACCCGGACTAGAAATGGCAACCGAACAAAGCGAGCTGGATCTG
EST: gi|89180521|gb|CI044800.1|CI044800
EST:     AATTCGTTATACGGTTGCAGCCATCGGAAGCCATGTATATGAAATTAACT                         GTCAAGAAACCCGGACTAGAAATGGCAACCGAACAAAGCGAGCTGGATCTG
genomic: AATTCGTTATACGGTTGCAGCCATCGGAAGCCATGTATATGAAATTAACTgtatgtacaa ... actgttgcagGTCAAGAAACCCGGACTAGAAATGGCAACCGAACAAAGCGAGCTGGATCTG
EST: gi|88262014|gb|CI365590.1|CI365590
EST:     CATGTATATGAAATTAACT                         GTCAAGAAACCCGGACTAGAAATGGCAACCGAACAAAGCGAGCTGGATCTG
genomic: CATGTATATGAAATTAACTgtatgtacaa ... actgttgcagGTCAAGAAACCCGGACTAGAAATGGCAACCGAACAAAGCGAGCTGGATCTG
EST: gi|89192387|gb|CI049848.1|CI049848
EST:     CCATCGGAAGCCATGTATATGAAATTAACT                         GTCAAGAAACCCGGACTAGAAATGGCAACCGAACAAAGCGAGCTGGATCTG
genomic: CCATCGGAAGCCATGTATATGAAATTAACTgtatgtacaa ... actgttgcagGTCAAGAAACCCGGACTAGAAATGGCAACCGAACAAAGCGAGCTGGATCTG
EST: gi|29616737|gb|CB621749.1|CB621749
EST:     AATTCGTTATACGGTTGCAGCCATCGGAAGCCATGTATATGAAATTAACT                         GTCAAGAAACCCGGACTAGAAATGGCAACCGAACAAAGCGAGCTGGATCTG
genomic: AATTCGTTATACGGTTGCAGCCATCGGAAGCCATGTATATGAAATTAACTgtatgtacaa ... actgttgcagGTCAAGAAACCCGGACTAGAAATGGCAACCGAACAAAGCGAGCTGGATCTG
EST: gi|88845594|gb|CI084519.1|CI084519
EST:     CAGCCATCGGAAGCCATGTATATGAAATTAACT                         GTCAAGAAACCCGGACTAGAAATGGCAACCGAACAAAGCGAGCTGGATCTG
genomic: CAGCCATCGGAAGCCATGTATATGAAATTAACTgtatgtacaa ... actgttgcagGTCAAGAAACCCGGACTAGAAATGGCAACCGAACAAAGCGAGCTGGATCTG
EST: gi|218492006|gb|FG967745.1|FG967745
EST:     AATTCGTTATACGGTTGCAGCCATCGGAAGCCATGTATATGAAATTAACT                         GTCAAGAAACCCGGACTAGAAATGGCAACCGAACAAAGCGAGCTGGATCTG
genomic: AATTCGTTATACGGTTGCAGCCATCGGAAGCCATGTATATGAAATTAACTgtatgtacaa ... actgttgcagGTCAAGAAACCCGGACTAGAAATGGCAACCGAACAAAGCGAGCTGGATCTG
EST: gi|89177186|gb|CI043689.1|CI043689
EST:     AATTCGTTATACGGTTGCAGCCATCGGAAGCCATGTATATGAAATTAACT                         GTCAAGAAACCCGGACTAGAAATGGCAACCGAACAAAGCGAGCTGGATCTG
genomic: AATTCGTTATACGGTTGCAGCCATCGGAAGCCATGTATATGAAATTAACTgtatgtacaa ... actgttgcagGTCAAGAAACCCGGACTAGAAATGGCAACCGAACAAAGCGAGCTGGATCTG
EST: gi|88242908|gb|CI240759.1|CI240759
EST:     TGAAATTAACT                         GTCAAGAAACCCGGACTAGAAATGGCAACCGAACAAAGCGAGCTGGATCTG
genomic: TGAAATTAACTgtatgtacaa ... actgttgcagGTCAAGAAACCCGGACTAGAAATGGCAACCGAACAAAGCGAGCTGGATCTG

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: 53 (upstream exon), 64 (downstream exon)
Score: 19

GCAAGAAGCAAGGAAGGAATGAATTCGTTATACGGTTGCAGCCATCGGAAGCCATGTATATGAAATTAACTgtatgtacaa ... actgttgcagGTCAAGAAACCCGGACTAGAAATGGCAACCGAACAAAGCGAGCTGGATCTGTCATATGGGCTACGCTACCAAGACGTGAAGATCCCAGAAGCGTATGAAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagagaactccaaaaaaacaagtgttgtctgaacaaagtgcatgaactgttgcagGTCAAGAAACCCGGACTAGAAATGGCAACCGAACAAAGCGAGCTGGATCTGTCATATGGGCTACGCTACCAAGACGTGAAGATCCCAGAAGCGTATGAAC
           aaaaaaacaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtacaacttctgtaaacccatttatctgaagatatgtcagaattgtctattcatctttgcctgaagagaactccaaaaaaacaagtgttgtctgaacaaagtgcatgaactgttgcagGTCAAGAAACCCGGACTAGAAATGGCAACCGAACAAAGCGAGCTGGATCTGTCATATGGGCTACGCTACCAAGACGTGAAGATCCCAGAAGCGTATGAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC