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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcttcatttgatcctttagccaagttgttaacaaccatgctactacctttgttttgtggaattattttgaacactatgtcaatattctgagaatttcttacagTTATACCGGTGAAGATGGGTTTGAAATCTCTGTTCCATCAGAGAATGCAGTTGATCTTGCAAAGGCCCTCCTGGAGAAATCTGAAGGCAAGGTGAGACTG

Basic information

species Oryza sativa
transcript LOC_Os04g53230.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g53230.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM5G876898_T01 (Zea mays), 3'ss of exon 2
gtatgcttcatttgatcctttagccaagttgttaacaaccatgctactacctttgttttgtggaattattttg--aacactatgtcaatattctgagaatttcttacagTTATACCGGTGAAGATGGGTTTGAAATCTCTGTTCCATCAGAGAATGCAGTTGATCTTGCAAAGGCCCTCCTGGAGAAATCTGAAGGCAAGGTGAGACTG
| ||| | || ||| | ||||||| | | | | || ||| | || || ||| || ||||| |||||||| ||||| ||||||||||| |||||||||||||| ||||||||| ||||| |||| |||| ||| |||||||||||| | |||
----------------------------------------gtatcacttcgattctttatcgccattatttgagcagtattgtaaggattgtcttatttcttatttcagCTACACCGGCGAAGATGGTTTTGAGATCTCTGTTCCGTCAGAGAATGCAGTGGATCTTGCAGAGGCCATCCTAGAGAGATCGGAAGGCAAGGTGCGGCTG

upper sequence: LOC_Os04g53230.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA17G01550.1 (Glycine max), 3'ss of exon 3
gtatgcttcatttgatcctttagccaagttgttaacaaccatgctactacctttgttttgtggaattattttgaacactatgtcaatattctgagaatttcttacagTTATACCGGTGAAGATGGGTTTGAAATCTCTGTTCCATCAGAGAATGCAGTTGATCTTGCAAAGGCCCTCCTGGAGAAATCTGAAGGCAAGGTGAGACTG
||| | |||| ||||| || || || | | | | | | | | || || | | || || | | | ||| ||| ||| ||||| || |||||||| ||||| ||||| ||||| |||||| ||| ||| |||||||| || || | ||||| ||||||||||| ||||| ||| ||
---tgcat-gtttgtgttattagctcagagtttctcagggacaccat--gcctaatctcattga-ttgtaccaagcataataaccttttcttgattgggactttcagGTATACTGGGGAAGATGGATTTGAGATCTCAGTTCCTTCAGAGCATGGAGTAGATCTTGCCAAAGCAATACTGGAAAAATCTGAAGGGAAGGTAAGATTG

upper sequence: LOC_Os04g53230.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA07G39190.1 (Glycine max), 3'ss of exon 3
----------------------------------------------------------------------gtatgcttcatttgatcctttagccaagttgtt-aacaaccatgctactacctttgttttgtggaattattttgaacactatgtcaatattctgagaatttcttacagTTATACCGGTGAAGATGGGTTTGAAATCTCTGTTCCATCAGAGAATGCAGTTGATCTTGCAAAGGCCCTCCTGGAGAAATCTGAAGGCAAGGTGAGACTG
| | || | | | ||||| || || || || || | || | || | || || || || | | ||| ||| ||| ||||| || |||||||| ||||| ||||| ||||| |||||| ||| | | |||||||| ||||| | ||||| ||||||||||| ||||| ||| ||
gtatgcttttattgtcattttctttcaccaacatcacctatttattcttcaaagttcatccgagttatgaaactccatcttgtattactttaatttcattattgaatgtttgtgttatgagctcagagtttcttagggataccatgcataataacactttcttgattgagactttcagGTATACTGGAGAAGATGGATTTGAGATCTCAGTTCCTTCAGAGCATGGACTAGATCTTGCCAAGGCAATACTGGAAAAATCTGAAGGGAAGGTAAGATTG

upper sequence: LOC_Os04g53230.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA15G11590.1 (Glycine max), 3'ss of exon 3
gtatgcttcatttgatcctttagccaagttgttaacaaccatgctactacctttgttttgtggaattattttgaacactatgtcaatattctgagaatttcttacagTTATACCGGTGAAGATGGGTTTGAAATCTCTGTTCCATCAGAGAATGCAGTTGATCTTGCAAAGGCCCTCCTGGAGAAATCTGAAGGCAAGGTGAGACTG
|| | | | | | | | || | | | | || | || | | | || | || | | || || | ||| || ||| ||| ||||| || |||||||| ||||| || || |||| ||||||| |||||| |||||||| ||||| | ||||| ||||||||||| ||| | ||||||
---tgatataacgagtgcaatttcataatttcagttagtctttttgtgttattagcttag--ggagtactgtgcataataacacactcttcactgag--actttcagGTATACTGGGGAAGATGGATTTGAGATATCAATTCCCTCAGAGAGTGCAGTGGATCTTGCCAAGGCAATTCTGGAAAAATCTGAAGGGAAGATAAGACTG

upper sequence: LOC_Os04g53230.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv10s0116g01540.t01 (Vitis vinifera), 3'ss of exon 2
gtatgcttcatttgatcctttagccaagttgttaacaaccatgctactacc-tttgttttgtggaattattttg---aacact--atgtcaatattctgagaatttcttacagTTATACCGGTGAAGATGGGTTTGAAATCTCTGTTCCATCAGAGAATGCAGTTGATCTTGCAAAGGCCCTCCTGGAGAAATCTGAAGGCAAGGTGAGACTG
| || ||||| || | || | || | || | || | || ||||| || | || ||| | || ||| || || ||||||||||| |||||||| || ||||| || ||||||||||| |||||||| || || || |||||||||||||||| ||||| || |
------------taatgatttagtcacaatccaaattgcaatatgatgactgtctgaatcaacaaaccccacaacaagacacttgatattttctttacacgaaaatttt-cagGTACACAGGTGAAGATGGATTTGAAATTTCAGTTCCTTCCGAGAATGCAGTAGATCTTGCCAAAGCAATCTTGGAGAAATCTGAAGGGAAGGTAAGGTTA

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|29614310|gb|CB619323.1|CB619323
EST:     TTCAAGATGATTGACATCAATGGATATGCTTGCTTTCTCACCAGAACTGG                         TTATACCGGTGAAGATGGGTTTGAAATCTCTGTTCCATCAGAGAATGCAGT
genomic: TTCAAGATGATTGACATCAATGGATATGCTTGCTTTCTCACCAGAACTGGgtatgcttca ... tttcttacagTTATACCGGTGAAGATGGGTTTGAAATCTCTGTTCCATCAGAGAATGCAGT
EST: gi|313084015|gb|HO213798.1|HO213798
EST:     TTCAAGATGATTGACATCAATGGATATGCTTGCTTTCTCACCAGAACTGG                         TTATACCGGTGAAGATGGGTTTGAAATCTCTGTTCCATCAGAGAATGCAGT
genomic: TTCAAGATGATTGACATCAATGGATATGCTTGCTTTCTCACCAGAACTGGgtatgcttca ... tttcttacagTTATACCGGTGAAGATGGGTTTGAAATCTCTGTTCCATCAGAGAATGCAGT
EST: gi|38473854|gb|CF957986.1|CF957986
EST:     TTCAAGATGATTGACATCAATGGATATGCTTGCTTTCTCACCAGAACTGG                         TTATACCGGTGAAGATGGGTTTGAAATCTCTGTTCCATCAGAGAATGCAGT
genomic: TTCAAGATGATTGACATCAATGGATATGCTTGCTTTCTCACCAGAACTGGgtatgcttca ... tttcttacagTTATACCGGTGAAGATGGGTTTGAAATCTCTGTTCCATCAGAGAATGCAGT

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: 74 (upstream exon), 75 (downstream exon)
Score: 76

CTCTCCAGTTGCTGACAAAAGAAGATTTAAGCAAAATGTATTTCAGTGACTTCAAGATGATTGACATCAATGGATATGCTTGCTTTCTCACCAGAACTGGgtatgcttca ... tttcttacagTTATACCGGTGAAGATGGGTTTGAAATCTCTGTTCCATCAGAGAATGCAGTTGATCTTGCAAAGGCCCTCCTGGAGAAATCTGAAGGCAAGGTGAGACTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgttttgtggaattattttgaacactatgtcaatattctgagaatttcttacagTTATACCGGTGAAGATGGGTTTGAAATCTCTGTTCCATCAGAGAATGCAGTTGATCTTGCAAAGGCCCTCCTGGAGAAATCTGAAGGCAAGGTGAGACTG
                                             tttcttac  CT-rich tract
 aattattttgaaca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcttcatttgatcctttagccaagttgttaacaaccatgctactacctttgttttgtggaattattttgaacactatgtcaatattctgagaatttcttacagTTATACCGGTGAAGATGGGTTTGAAATCTCTGTTCCATCAGAGAATGCAGTTGATCTTGCAAAGGCCCTCCTGGAGAAATCTGAAGGCAAGGTGAGACTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG