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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtagtgtgataagtaataaccatattatttgtttctttatttttgggaatatgaatttatatctgcaaataataatggtaattttccttgattttctagGTTTGTATTTGATGCCATGCATGCTGTGACTGGTGCATATGCGGATCCTATTTTTGTTGAGAAACTTGGAGCTGATCCG

Basic information

species Oryza sativa
transcript LOC_Os10g11140.2
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g11140.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G025854_T02 (Zea mays), 3'ss of exon 10
tgtagtgtgataagtaataaccatattatttgtttctttatttttgggaatatgaatttatatct-----gcaaataataa--tggtaattttccttgattttctagGTTTGTATTTGATGCCATGCATGCTGTGACTGGTGCATATGCGGATCCTATTTTTGTTGAGAAACTTGGAGCTGATCCG
       ||   | |  || | | | | | |  ||  || || |||| |||||||   | |   |     ||| ||| |||  |    ||||  ||  |||||  |||||  |||||||||| ||||||||  | |||||||| ||||| |  || ||||||||||||||||||||||||||||||
-------tggctattcttagcaaaagtttctcattggttgttcttggtaatatgagcatgttattaaaaagcacatattaagttaaatatttggctcaattttacagGTTCATATTTGATGCAATGCATGCAATTACTGGTGCGTATGCCGGACCCATTTTTGTTGAGAAACTTGGAGCTGATCCG

upper sequence: LOC_Os10g11140.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA20G29230.1 (Glycine max), 3'ss of exon 10
tgtagtgtgataagtaataaccatattatttgtttctttatttttgggaatatgaatttat----atctgcaaataataatggtaattttccttgattttctagGTTTGTATTTGATGCCATGCATGCTGTGACTGGTGCATATGCGGATCCTATTTTTGTTGAGAAACTTGGAGCTGATCCG
 |   | |   || | |       ||   | |||    | |||  ||   |||||   |      ||||  ||||  | || | | ||||  ||  | || ||||||| ||||||||||||||||||| || |||||||| |||||  | || || || ||||| ||||| || |||  || |
-gggctatctcaactcaagggt-catggctggttataatgtttaaggttctatgagaatcccacaatctttaaat--ttattgcatttttttttattgttttagGTTTATATTTGATGCCATGCATGCAGTTACTGGTGCTTATGCTAAACCCATCTTGGTTGATAAACTCGGTGCTAGTCTG

upper sequence: LOC_Os10g11140.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA10G38590.1 (Glycine max), 3'ss of exon 10
tgtagtgtgataagtaataaccatattatttgtttctttatttttgggaatatgaatttatatctgcaaataataatggta-attttccttgattttctagGTTTGTATTTGATGCCATGCATGCTGTGACTGGTGCATATGCGGATCCTATTTTTGTTGAGAAACTTGGAGCTGATCCG
 |   | |   || | |       ||   | |||     ||||  ||   |||||   |    | |    |||   |  |  |||||  ||  | |   |||||| ||||||||||||||||||| || |||||||| |||||  | || || || ||||| ||||| || |||  || |
agggctatcccaactcaagggt-catggctagttataacatttaaggttctatgagaatcccacagtctctaaatttactgtattttttttattatgtcagGTTTATATTTGATGCCATGCATGCAGTTACTGGTGCTTATGCTAAACCCATCTTCGTTGATAAACTCGGTGCTAGTCTG

upper sequence: LOC_Os10g11140.2 (Oryza sativa), 3'ss of exon 10
lower sequence: AT5G51820.1 (Arabidopsis thaliana), 3'ss of exon 10
--------------------------------------------tgtagtgtgataagtaataaccatattatttgt---ttctttatttttgggaa--------------tatgaatttatatctgcaaataat--aatggtaattttccttg---attttc--------tagGTTTGTATTTGATGCCATGCATGCTGTGACTGGTGCATATGCGGATCCTATTTTTGTTGAGAAACTTGGAGCTGATCCG
                                            | |  || | |   | ||   | |||||||||    |||| | |  |||   |              || |||   | |   ||  || ||   ||| || ||||  |||   ||||||        ||||||  | |||||||||||||||||||| |||||||| |||||| | || |||||||| || || ||||||||  | |||
gtatgttcttacatctagagccaaataggctagaagcttttgtcttttttggggttt-tgatggtcctattatttgcgccttctgtctggttgcagagtcgctcaacatgctaagaaccgaaactagcctatgatttgatgatattttttgttgttcattttccttgcctttagGTTCATGTTTGATGCCATGCATGCTGTTACTGGTGCTTATGCGAAACCAATTTTTGTCGACAATCTTGGAGCCAAACCG

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|58691145|gb|CK079832.1|CK079832
EST:     GTGTTTGACTTCCAACTTATCAAGGGCTTGTTGTCTCGGCCAGATTTCAGG                         GTTTGTATTTGATGCCATGCATGCTGTGACTGGTGCATATGCGGATCCAT
genomic: GTGTTTGACTTCCAACTTATCAAGGGCTTGTTGTCTCGGCCAGATTTCA-Ggttctgtata ... gattttctagGTTTGTATTTGATGCCATGCATGCTGTGACTGGTGCATATGCGGATCC-T
EST: gi|58676489|gb|CK065176.1|CK065176
EST:     GTGTTTGACTTCCAACTTATCAAGGGCTTGTTGTCTCGGCCAGATTTCAG                         GTTTGTATTTGATGCCATGCATGCTGTGACTGGTGCATATGCGGATCCTAT
genomic: GTGTTTGACTTCCAACTTATCAAGGGCTTGTTGTCTCGGCCAGATTTCAGgttctgtata ... gattttctagGTTTGTATTTGATGCCATGCATGCTGTGACTGGTGCATATGCGGATCCTAT
EST: gi|58608460|gb|CK036493.1|CK036493
EST:     GTGTTTGACTTCCAACTTATCAAGGGCTTGTTGTCTCGGCCAGATTTCAG                         GTTTGTATTTGATGCCATGCATGCTGTGACTGGTGC
genomic: GTGTTTGACTTCCAACTTATCAAGGGCTTGTTGTCTCGGCCAGATTTCAGgttctgtata ... gattttctagGTTTGTATTTGATGCCATGCATGCTGTGACTGGTGC
EST: gi|33796171|gb|CF323951.1|CF323951
EST:     GTGTTTGACTTCCAACTTATCAAGGGCTTGTTGTCTCGGCCAGATTTCAG                         GTTTGTATTTGATGCCATGCATGCTGTGACTGGTGCATATGCGGATCCTAT
genomic: GTGTTTGACTTCCAACTTATCAAGGGCTTGTTGTCTCGGCCAGATTTCAGgttctgtata ... gattttctagGTTTGTATTTGATGCCATGCATGCTGTGACTGGTGCATATGCGGATCCTAT
EST: gi|29681950|gb|CB678225.1|CB678225
EST:     GTGTTTGACTTCCAACTTATCAAGGGCTTGTTGTCTCGGCCAGATTTCAG                         GTTTGTATTTGATGCCATGCATGCTGTGACTGGTGCATATGCGGATCCTAT
genomic: GTGTTTGACTTCCAACTTATCAAGGGCTTGTTGTCTCGGCCAGATTTCAGgttctgtata ... gattttctagGTTTGTATTTGATGCCATGCATGCTGTGACTGGTGCATATGCGGATCCTAT

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: 65 (upstream exon), 75 (downstream exon)
Score: 61

AATGTGTTTGACTTCCAACTTATCAAGGGCTTGTTGTCTCGGCCAGATTTCAGgttctgtata ... gattttctagGTTTGTATTTGATGCCATGCATGCTGTGACTGGTGCATATGCGGATCCTATTTTTGTTGAGAAACTTGGAGCTGATCCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gggaatatgaatttatatctgcaaataataatggtaattttccttgattttctagGTTTGTATTTGATGCCATGCATGCTGTGACTGGTGCATATGCGGATCCTATTTTTGTTGAGAAACTTGGAGCTGATCCG
                                         ccttgat  putative branch site (score: 61)
                                     ttttccttgattttct  CT-rich tract
     tatgaatttatatctg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtagtgtgataagtaataaccatattatttgtttctttatttttgggaatatgaatttatatctgcaaataataatggtaattttccttgattttctagGTTTGTATTTGATGCCATGCATGCTGTGACTGGTGCATATGCGGATCCTATTTTTGTTGAGAAACTTGGAGCTGATCCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - -tgtgata
- - - - - - - - - aaccata
- - - - - - - - - - - - - - - tgtttct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atctgca