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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggaatcacgatcatttcttagtttccaacatgctattgaatttgagacaaattgacgcttcttcaaatagttaaaatgggatctaacaacttgatttcagCACATGCAGAGTAGAAGATATGAGCTTGTTGCAACCATCACGCATCTTGGGGCAAACCCGTCCAGGGGCCATTACACTGCCGATGCAAAGTCTGCCAGTG

Basic information

species Oryza sativa
transcript LOC_Os07g46660.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g46660.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G327635_T01 (Zea mays), 3'ss of exon 6
--ggaatcacgatcatttcttagtttccaacatgctattgaat--ttgagacaaattgacgcttcttcaa-atagttaaa--atgggatctaacaacttgatttcagCACATGCAGAGTAGAAGATATGAGCTTGTTGCAACCATCACGCATCTTGGGGCAAACCCGTCCAGGGGCCATTACACTGCCGATGCAAAGTCTGCCAGTG---------
  |  |    | |        |  |   ||  |  | || |    ||||||  |  | ||  ||  |    |    | ||  |   ||||||||   | |   |      || ||| |||||| |||||||||||||||||||||||| |||| ||||    |||| | ||| || || ||||||||  ||||||||  ||||   |         
gtgataatttgctggacatgcatctgtaaatgtttttttaacacattgagatgacataacagttgattggtactactgaatcacttgatctaaccgttcgtcgttgttgtatacagGGTAGAAAATATGAGCTTGTTGCAACCATCACTCATCATGGGAGGGACCCTTACAGAGGTCACTACACTGCTCATGCAAAGCATGCCGACGGGCAATGGC
















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|58654521|gb|CK043201.1|CK043201
EST:     CTCTTGAGCTGGTTCTTAGTCGTGATCTGCTGAGTTCGCCATCATCAGAG                         CACATGCAGAGTAGAAGATATGAGCTTGTTGCAACCATCACGCATCTTGGG
genomic: CTCTTGAGCTGGTTCTTAGTCGTGATCTGCTGAGTTCGCCATCATCAGAGgtgatagttt ... ttgatttcagCACATGCAGAGTAGAAGATATGAGCTTGTTGCAACCATCACGCATCTTGGG
EST: gi|218479637|gb|FG956050.1|FG956050
EST:     CTCTTGAGCTGGTTCTTAGTCGTGATCTGCTGAGTTCGCCATCATCAGAG                         CACATGCAGAGTAGAAGATATGAGCTTGTTGCAACCATCACGCATCTTGGG
genomic: CTCTTGAGCTGGTTCTTAGTCGTGATCTGCTGAGTTCGCCATCATCAGAGgtgatagttt ... ttgatttcagCACATGCAGAGTAGAAGATATGAGCTTGTTGCAACCATCACGCATCTTGGG
EST: gi|88843606|gb|CI372506.1|CI372506
EST:     TCTTGAGGCTGGTTCTTAGTCGTGATCTGCTGAGTTCGCCATCATCAGAG                         CACATGCAGATTAGAAGATATGAGCTTGTTGCAACCATCACGCATCTTGGG
genomic: TCTTGA-GCTGGTTCTTAGTCGTGATCTGCTGAGTTCGCCATCATCAGAGgtgatagttt ... ttgatttcagCACATGCAGAGTAGAAGATATGAGCTTGTTGCAACCATCACGCATCTTGGG
EST: gi|86598874|gb|CI355491.1|CI355491
EST:     CTCTTGAGCTGGTTCTTAGTCGTTATCTGCTGAGTTCGCCATCATCAGAG                         CACATGCAGAGTAGAAGATATGAGCTTGTTGCAACCATCACGCATCTTGGG
genomic: CTCTTGAGCTGGTTCTTAGTCGTGATCTGCTGAGTTCGCCATCATCAGAGgtgatagttt ... ttgatttcagCACATGCAGAGTAGAAGATATGAGCTTGTTGCAACCATCACGCATCTTGGG
EST: gi|88902318|gb|CI374926.1|CI374926
EST:     TGAGTTCGCCATCATCAGAG                         CACATGCAGAGTAGAAGATATGAGCTTGTTGCAACCATCACGCATCTTGGG
genomic: TGAGTTCGCCATCATCAGAGgtgatagttt ... ttgatttcagCACATGCAGAGTAGAAGATATGAGCTTGTTGCAACCATCACGCATCTTGGG
EST: gi|86512713|gb|CI155346.1|CI155346
EST:     CTCTTGAGCTGGTTCTTAGTCGTGATCTGCTGAGTTCGCCATCAT-----                         --CA-G-AGAGTAGAAGATATGAGCTTGTTGCAACCATCACGCATCTTGGG
genomic: CTCTTGAGCTGGTTCTTAGTCGTGATCTGCTGAGTTCGCCATCATCAGAGgtgatagttt ... ttgatttcagCACATGCAGAGTAGAAGATATGAGCTTGTTGCAACCATCACGCATCTTGGG
EST: gi|27554287|gb|CA998187.1|CA998187
EST:     CTCTTGAGCTGGTTCTTAGTCGTGATCTGCTGAGTTCGCCATCATCAGAG                         CACATGCAGAGTAGAAGATATGAGCTTGTTGCAACCATCACGCATCTTGGG
genomic: CTCTTGAGCTGGTTCTTAGTCGTGATCTGCTGAGTTCGCCATCATCAGAGgtgatagttt ... ttgatttcagCACATGCAGAGTAGAAGATATGAGCTTGTTGCAACCATCACGCATCTTGGG
EST: gi|29628666|gb|CB633677.1|CB633677
EST:     CTCTTGAGCTGGTTCTTAGTCGTGATCTGCTGAGTTCGCCATCAT-----                         --CA-G-AGAGTAGAAGATATGAGCTTGTTGCAACCATCACGCATCTTGGG
genomic: CTCTTGAGCTGGTTCTTAGTCGTGATCTGCTGAGTTCGCCATCATCAGAGgtgatagttt ... ttgatttcagCACATGCAGAGTAGAAGATATGAGCTTGTTGCAACCATCACGCATCTTGGG
EST: gi|14713804|gb|AU197768.1|AU197768
EST:     CTCTTGAGCTGGTTCTTAGTCGTGATCTGCTGAGTTCGCCATCATCAGAG                         CACATGCAGAGTAGAAGATATGAGCTTGTTGCAACCATCACGCATCTTGGG
genomic: CTCTTGAGCTGGTTCTTAGTCGTGATCTGCTGAGTTCGCCATCATCAGAGgtgatagttt ... ttgatttcagCACATGCAGAGTAGAAGATATGAGCTTGTTGCAACCATCACGCATCTTGGG
EST: gi|55431318|gb|CV728673.1|CV728673
EST:     TTAGTCGTGATTTGCTGCGTTCGCCATCATCAGAG                         CACATGCAGAGTAGAAGATATGAGCTTGTTGCAACCATCACGCATCTTGGG
genomic: TTAGTCGTGATCTGCTGAGTTCGCCATCATCAGAGgtgatagttt ... ttgatttcagCACATGCAGAGTAGAAGATATGAGCTTGTTGCAACCATCACGCATCTTGGG
EST: gi|25803696|gb|CA759657.1|CA759657
EST:     CTCTTGAGCTGGTTCTTAGTCGTGATCTGCTGAGTTCGCCATCATCAGAG                         CACATGCAGAGTAGAAGATATGAGCTTGTTGCAACCATCACGCATCTTGGG
genomic: CTCTTGAGCTGGTTCTTAGTCGTGATCTGCTGAGTTCGCCATCATCAGAGgtgatagttt ... ttgatttcagCACATGCAGAGTAGAAGATATGAGCTTGTTGCAACCATCACGCATCTTGGG
EST: gi|55431316|gb|CV728672.1|CV728672
EST:     CTCTTGAGCTGGTTCTTAGTCGTGATCTGCTGCGTTCGCCATCATCAGAG                         CACATGCAGAGTAGAAGATATGAGCTTGTTGCAACCATCACGCATCTTGGG
genomic: CTCTTGAGCTGGTTCTTAGTCGTGATCTGCTGAGTTCGCCATCATCAGAGgtgatagttt ... ttgatttcagCACATGCAGAGTAGAAGATATGAGCTTGTTGCAACCATCACGCATCTTGGG

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: 66 (upstream exon), 71 (downstream exon)
Score: 24

TAGTTATGGAAGTCATGGCTGCACGAAACTCTTCAAGCCAATTCACTTCCCTCTTGAGCTGGTTCTTAGTCGTGATCTGCTGAGTTCGCCATCATCAGAGgtgatagttt ... ttgatttcagCACATGCAGAGTAGAAGATATGAGCTTGTTGCAACCATCACGCATCTTGGGGCAAACCCGTCCAGGGGCCATTACACTGCCGATGCAAAGTCTGCCAGTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gacaaattgacgcttcttcaaatagttaaaatgggatctaacaacttgatttcagCACATGCAGAGTAGAAGATATGAGCTTGTTGCAACCATCACGCATCTTGGGGCAAACCCGTCCAGGGGCCATTACACTGCCGATGCAAAGTCTGCCAGTG
                ttcaaatagttaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggaatcacgatcatttcttagtttccaacatgctattgaatttgagacaaattgacgcttcttcaaatagttaaaatgggatctaacaacttgatttcagCACATGCAGAGTAGAAGATATGAGCTTGTTGCAACCATCACGCATCTTGGGGCAAACCCGTCCAGGGGCCATTACACTGCCGATGCAAAGTCTGCCAGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - catgcta
- - - - - - - - - - - - - - - - - - - - - - agacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -taacaac