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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttatttttgactgtttcttccatacagggtacagattcctcctaattcccttagttattcttaagcagtttgcacataattctggcatcttcttttgcagGTGTCATGATTGCTTGGACTGGTATTGAGCATTTCATTGCAGGCAGATTTGATGATCCTCCTGCTGTTGATGAGCCTGATGATATGCAG

Basic information

species Oryza sativa
transcript LOC_Os12g29990.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g29990.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G420055_T01 (Zea mays), 3'ss of exon 8
--ttatttttgactgtttcttccatacagggtacagattcctcctaattcccttagttattcttaagcagtttgc-acataattctggcatcttcttttgcagGTGTCATGATTGCTTGGACTGGTATTGAGCATTTCATTGCAGGCAGATTTGATGATCCTCCTGCTGTTGATGAGCCTGATGATATGCAG
|| || || | || | | | | || |||| | || || ||| || | | | | | | || || | | |||||||||||||||||||||||| ||||||||||| |||| || || ||||| || || ||||||| ||||||| ||||||||||||||
acctaattatggtagctttctttaca-atagtctttattctttgtataattctgagtaatgaacatataatcagttatactatgttgctgcatc--tgcatagGTGTCATGATTGCTTGGACTGGGATTGAGCATTTTGTTGCCGGGAGGTTTGAGGACCCACCTGCTGCTGATGAGTCTGATGATATGCAG

upper sequence: LOC_Os12g29990.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA03G03250.1 (Glycine max), 3'ss of exon 11
ttatttttgactgtttcttcc-atacagggtacagatt-cctcctaattcccttagttattcttaagcagtttg-cacataattctggcatcttcttttgcagGTGTCATGATTGCTTGGACTGGTATTGAGCATTTCATTGCAGGCAGATTTGATGATCCTCCTGCTGTTGATGAGCCTGATGATATGCAG
||| || | | | || || || | | | || | | || | || ||| ||| | | || | || | | |||||| |||||||||||||||||||||||||| ||| || |||| ||| ||||||| ||| || || ||||| || | |
---cgtttatctatctttcttgatccattgtttaaaataccagattaggatggtactattttttatgcaacatatcttattagcttgcttttgaactgaatagGTGTAATGATTGCTTGGACTGGTATTGAGCACTTCCGCATGGGAAGATATGACCCTCCTCCTCCTGCAGAAGAACCTGAAGACTTTGTG
















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|86890175|gb|CI321352.1|CI321352
EST:     GAATGGCCTACAGCTCGTATGCCCTCCCCCAAAGCTTTGCACTGACAATG                         GTGTCATGATTGCTTGGACTGGTATTGAGCATTTCATTGCAGGCAGATTTG
genomic: GAATGGCCTACAGCTCGTATGCCCTCCCCCAAAGCTTTGCACTGACAATGgtaaaaagtt ... tcttttgcagGTGTCATGATTGCTTGGACTGGTATTGAGCATTTCATTGCAGGCAGATTTG
EST: gi|89198378|gb|CI007438.1|CI007438
EST:     CCTCCCCCAAAGCTTTGCACTGACAATG                         GTGTCATGATTGCTTGGACTGGTATTGAGCATTTCATTGCAGGCAGATTTG
genomic: CCTCCCCCAAAGCTTTGCACTGACAATGgtaaaaagtt ... tcttttgcagGTGTCATGATTGCTTGGACTGGTATTGAGCATTTCATTGCAGGCAGATTTG
EST: gi|29684472|gb|CB680747.1|CB680747
EST:     GAATGGCCTACAGTTCGTATGCCCTCCCCCAAAGCTTTGCACTGACAATG                         GTGTCATGATTGCTTGGACTGGTATTGAGCATTTCATTGCAGGCAGATTTG
genomic: GAATGGCCTACAGCTCGTATGCCCTCCCCCAAAGCTTTGCACTGACAATGgtaaaaagtt ... tcttttgcagGTGTCATGATTGCTTGGACTGGTATTGAGCATTTCATTGCAGGCAGATTTG
EST: gi|29616288|gb|CB621300.1|CB621300
EST:     GAATGGCCTACAGCTCGTATGCCCTCCCCCAAAGCTTTGCACTGACAATG                         GTGTCATGATTGCTTGGACTGGTATTGAGCATTTCATTGCAGGCAGATTTG
genomic: GAATGGCCTACAGCTCGTATGCCCTCCCCCAAAGCTTTGCACTGACAATGgtaaaaagtt ... tcttttgcagGTGTCATGATTGCTTGGACTGGTATTGAGCATTTCATTGCAGGCAGATTTG
EST: gi|29637789|gb|CB642798.1|CB642798
EST:     GAATGGCCTACAGCTCGTATGCCCTCCCCCAAAGCTTTGCACTGACAATG                         GTGTCATGATTGCTTGGACTGGTATTGAGCATTTCATTGCAGGCAGATTTG
genomic: GAATGGCCTACAGCTCGTATGCCCTCCCCCAAAGCTTTGCACTGACAATGgtaaaaagtt ... tcttttgcagGTGTCATGATTGCTTGGACTGGTATTGAGCATTTCATTGCAGGCAGATTTG
EST: gi|87009957|gb|CI277458.1|CI277458
EST:     GAATGGCCTACAGCTCGTATGCCCTCCCCCAAAGCTTTGCACTGACAATG                         GTGTCATGATTGCTTGGACTGGTATTGAGCATTTCATTGCAGGCAGATTTG
genomic: GAATGGCCTACAGCTCGTATGCCCTCCCCCAAAGCTTTGCACTGACAATGgtaaaaagtt ... tcttttgcagGTGTCATGATTGCTTGGACTGGTATTGAGCATTTCATTGCAGGCAGATTTG
EST: gi|38481194|gb|CF965283.1|CF965283
EST:     GAATGGGCTACAGCTCGTATGCCCTCCCCCAAAGCTTTGGACTGACAATG                         GTGTCATGATT
genomic: GAATGGCCTACAGCTCGTATGCCCTCCCCCAAAGCTTTGCACTGACAATGgtaaaaagtt ... tcttttgcagGTGTCATGATT
EST: gi|29641596|gb|CB646603.1|CB646603
EST:     GAATGGCCTACAGCTCGTATGCCCTCCCCCAAAGCTTTGCACTGACAATG                         GTGTCATGATTGCTTGGACTGGTATTGAGCATTTCATTGCAGGCAGATTTG
genomic: GAATGGCCTACAGCTCGTATGCCCTCCCCCAAAGCTTTGCACTGACAATGgtaaaaagtt ... tcttttgcagGTGTCATGATTGCTTGGACTGGTATTGAGCATTTCATTGCAGGCAGATTTG
EST: gi|29664761|gb|CB661036.1|CB661036
EST:     GAATGGCCTACAGCTCGTATGCCCTCCCCCAAAGCTTTGCACTGACAATG                         GTGTCATGATTGCTTGGACTGGTATTGAGCATTTCATTGCAGGCAGATTTG
genomic: GAATGGCCTACAGCTCGTATGCCCTCCCCCAAAGCTTTGCACTGACAATGgtaaaaagtt ... tcttttgcagGTGTCATGATTGCTTGGACTGGTATTGAGCATTTCATTGCAGGCAGATTTG

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: 56 (upstream exon), 36 (downstream exon)
Score: 11

GTTGCATCAAACCAGTATGTCAGAACTCATTTGAATCAGATCGCTGAGAAGAATGGCCTACAGCTCGTATGCCCTCCCCCAAAGCTTTGCACTGACAATGgtaaaaagtt ... tcttttgcagGTGTCATGATTGCTTGGACTGGTATTGAGCATTTCATTGCAGGCAGATTTGATGATCCTCCTGCTGTTGATGAGCCTGATGATATGCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcccttagttattcttaagcagtttgcacataattctggcatcttcttttgcagGTGTCATGATTGCTTGGACTGGTATTGAGCATTTCATTGCAGGCAGATTTGATGATCCTCCTGCTGTTGATGAGCCTGATGATATGCAG
                                        catcttctttt  CT-rich tract
 ttagttattcttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttatttttgactgtttcttccatacagggtacagattcctcctaattcccttagttattcttaagcagtttgcacataattctggcatcttcttttgcagGTGTCATGATTGCTTGGACTGGTATTGAGCATTTCATTGCAGGCAGATTTGATGATCCTCCTGCTGTTGATGAGCCTGATGATATGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT