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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAAAATGCACCTGATGTGAAGGCCAAATTTATAATTGAAGCTGCTAATCATCCAACTGATCCAGAAGCTGACGAGgtaaccacagaacaaaacattgtaccctaactttgtctttgagaaacatcagaaatgttgccaattttggcagttctgattgatgctgtatgcactacag

Basic information

species Oryza sativa
transcript LOC_Os04g45970.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g45970.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G427097_T01 (Zea mays), 5'ss of exon 7
GGAAAATGCACCTGATGTGAAGGCCAAATTTATAATTGAAGCTGCTAATCATCCAACTGATCCAGAAGCTGACGAGgta--accacagaacaaaacattgtaccctaactttgtct--ttgagaaacatcagaaatgttgccaattttggcagttctgattgatgctgtatgcactacag
||| |||||||| || ||||||||||||||| |||| ||||||||||| ||||||||||||||||| || |||||||||  ||||   |   ||   | ||| |   |      |   ||  | ||| |      | ||   | ||||   || |        |  || ||    |  ||
GGATAATGCACCAGACGTGAAGGCCAAATTTGTAATCGAAGCTGCTAACCATCCAACTGATCCAGAGGCAGACGAGgtagaaccatctattgaacagtagtatcaggaacacaaccaattttgcaacctt-----ttttattatttttctgagcttctgcc--tcttgcatatgttgtag

upper sequence: LOC_Os04g45970.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA01G41310.1 (Glycine max), 5'ss of exon 7
GGAAAATGCACCTGATGTGAAGGCCAAATTTATAATTGAAGCTGCTAATCATCCAACTGATCCAGAAGCTGACGAGgtaaccacagaacaaaacattgtaccctaactttgtctttgagaaacatcagaaatgttgccaattttggcagttctgattgatgctgtatgcactacag
|||||||||  |||||||||| || ||||||||||| |||||||| |||||||||||||| || || ||||| |||||||     |   |   | ||||    |  | |    |  || |  |   |   || ||    | | |    |   |||||        ||  | |  ||
GGAAAATGCTGCTGATGTGAAAGCGAAATTTATAATAGAAGCTGCAAATCATCCAACTGACCCTGATGCTGATGAGgtaa-----ggttattgctttgttgttttgcatgagatgagatatgctgaattgatattagagaatataatggaagtgattt------catttattgtag

upper sequence: LOC_Os04g45970.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA17G15740.1 (Glycine max), 5'ss of exon 8
GGAAAATGCACCTGATGTGAAGGCCAAATTTATAATTGAAGCTGCTAATCATCCAACTGATCCAGAAGCTGACGAGgtaaccacagaacaaaacattgtaccctaactttgtctttgagaaacatcagaaatgttgccaattttggcagttc-tgattgatgctgtatgcactacag
|||||||||  ||||||||||||| ||||||||||| ||||| || ||||| || ||||| || || || || | |||||     |   |     |||   |    |  | |  ||| |||| ||     || |    || ||   || | | | ||  | ||  |      | |||
GGAAAATGCTGCTGATGTGAAGGCAAAATTTATAATAGAAGCAGCAAATCACCCCACTGACCCTGATGCGGATGGGgtaa-----gtttactgacttgcggctatgccat-ttgttgtgaaatat-----atatcctgaactt--acattacataatgaaagcgattctttttgcag

upper sequence: LOC_Os04g45970.1 (Oryza sativa), 5'ss of exon 7
lower sequence: AT5G07440.1 (Arabidopsis thaliana), 5'ss of exon 6
GGAAAATGCACCTGATGTGAAGGCCAAATTTATAATTGAAGCTGCTAATCATCCAACTGATCCAGAAGCTGACGAGgtaaccacagaacaaaacattgtaccctaactttgtctttgagaa--acatcagaaatgttgccaattttggcagttctgattgatgctgtatgcactacag
|||||||||    ||||||||||| || |||||| | || || ||||| |||||||| |||||||| ||||| |||||||       | || |||      | |  ||    ||  || ||  | |     ||| |      |||||||||                           
GGAAAATGCTGGAGATGTGAAGGCAAAGTTTATAGTAGAGGCAGCTAACCATCCAACAGATCCAGATGCTGATGAGgtaatgcatcgataacacaagaactcatccctgaaactccgaaaataaaaatcctaatctgtttggttttggcag---------------------------

upper sequence: LOC_Os04g45970.1 (Oryza sativa), 5'ss of exon 7
lower sequence: Vv16s0039g02720.t01 (Vitis vinifera), 5'ss of exon 7
GGAAAATGCACCTGATGTGAAGGCCAAATTTATAATTGAAGCTGCTAATCATCCAACTGATCCAGAAGCTGACGAGgtaaccacagaacaaaacattgtaccctaactttgtctttgagaaacatcagaaatgttgccaattttggcagttctgattgatgctgtatgcactacag
 ||||||||  | ||||| ||||| || || ||||| ||||| || |||||||| ||||||||||||||||| ||||||||     |       || ||||    ||||           ||      | | |||| || |  ||  |  ||||                      
AGAAAATGCTGCGGATGTTAAGGCAAAGTTCATAATAGAAGCAGCAAATCATCCTACTGATCCAGAAGCTGATGAGgtaacatagtatttgtgtatggtacat--acttaaataccatagaa----gaagaagttggcattgatgatatctctgcag-------------------

upper sequence: LOC_Os04g45970.1 (Oryza sativa), 5'ss of exon 7
lower sequence: Vv00s0204g00160.t01 (Vitis vinifera), 5'ss of exon 1
-----------------------GGAAAATGCACCTGATGTGAAGGCCAAATTTATAATTGAAGCTGCTAATCATCCAACTGATCCAGAAGCTGACGAGgtaaccacagaacaaaacattgtaccctaactttgtctttgagaaacatcagaaatgttgccaattttggcagttctgattgatgctgtatgcactacag------
                       ||| |||||  || |||| || || ||||||||||| |||||||| |||||||| ||||||||||| |||||||||||||  |        |   || || |  ||| | |||   |    |  |     |  |  | ||  |   || ||   ||   |||||||     |          
ATGGTTTACACATTTTCTCAAAGGGATAATGCTGCTCATGTTAAAGCAAAATTTATAATAGAAGCTGCAAATCATCCCACTGATCCAGAGGCTGACGAGgtaaatattttgactatggttctatc--aacatggtcaggggctcaattttctgaactcacaaacct--acaatt--aatccttgctgtagatcttgtccaagaaa

upper sequence: LOC_Os04g45970.1 (Oryza sativa), 5'ss of exon 7
lower sequence: Vv00s1491g00010.t01 (Vitis vinifera), 5'ss of exon 5
GGAAAATGCACCTGATGTGAAGGCCAAATTTATAATTGAAGCTGCTAATCATCCAACTGATCCAGAAGCTGACGAGgtaaccacagaacaaaacattgtaccctaactttgtctttgagaaacatcagaaatgttgccaattttggcagttctgattgatgctgtatgcactacag------
||| |||||  || |||| || || ||||||||||| |||||||| |||||||| ||||||||||| |||||||||||||  |            || || |  ||| | |||   |    |  |     |  |  | ||  |   || ||   ||   |||||||     |          
GGATAATGCTGCTCATGTTAAAGCAAAATTTATAATAGAAGCTGCAAATCATCCCACTGATCCAGAGGCTGACGAGgtaaatattttgactgtggttctatc--aacatggtcgggggcttaattttctgaactcacaaacct--acaatt--aatccttgctgtagatcttgtccaagaaa

upper sequence: LOC_Os04g45970.1 (Oryza sativa), 5'ss of exon 7
lower sequence: Vv16s0039g02750.t01 (Vitis vinifera), 5'ss of exon 7
GGAAAATGCACCTGATGTGAAGGCCAAATTTATAATTGAAGCTGCTAATCATCCAACTGATCCAGAAGCTGACGAGgtaaccacagaacaaaacat-tgtaccctaactttgtctttgagaaacatcagaaatgttgccaattttggcagttctgattgatgctgtatgcactacag
 ||||||||  | ||||| ||||| || || ||||| ||||| || |||||||| ||||||||||||||||| |||||||| | ||     |   |   |||   ||     |    || | |  |  | | || ||  | | ||| |  | | |                      
AGAAAATGCTGCGGATGTTAAGGCAAAGTTCATAATAGAAGCAGCAAATCATCCTACTGATCCAGAAGCTGATGAGgtaac-atagtgtttatggtgcatacttaaatgccatagaggaaagaagttggcattgatgata-tattgtctctgcag----------------------

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|86432770|gb|CI086381.1|CI086381
EST:     TCCAACTGATCCAGAAGCTGACGAG                         ATTCTTGCCAAGAAGGGAGTGACCATATTACCTGACATTTACGCCAACTCC
genomic: TCCAACTGATCCAGAAGCTGACGAGgtaaccacag ... tgcactacagATTCTTGCCAAGAAGGGAGTGACCATATTACCTGACATTTACGCCAACTCC
EST: gi|38473890|gb|CF958022.1|CF958022
EST:     AATTTATAATTGAAGCTGCTAATCATCCAACTGATCCAGAAGCTGACGAG                         ATTCTTGCCAAGAAGGGAGTGACCATATTACCTGACATTTACGCCAACTCC
genomic: AATTTATAATTGAAGCTGCTAATCATCCAACTGATCCAGAAGCTGACGAGgtaaccacag ... tgcactacagATTCTTGCCAAGAAGGGAGTGACCATATTACCTGACATTTACGCCAACTCC
EST: gi|29639773|gb|CB644782.1|CB644782
EST:     AATTTATAATTGAAGCTGCTAATCATCCAACTGATCCAGAAGCTGACGAG                         ATTCTTGCCAAGAAGGGAGTGACCATATTACCTGACATTTACGCCAACTCC
genomic: AATTTATAATTGAAGCTGCTAATCATCCAACTGATCCAGAAGCTGACGAGgtaaccacag ... tgcactacagATTCTTGCCAAGAAGGGAGTGACCATATTACCTGACATTTACGCCAACTCC
EST: gi|86499922|gb|CI142555.1|CI142555
EST:     TCCAGAAGCTGACGAG                         ATTCTTGCCAAGAAGGGAGTGACCATATTACCTGACATTTACGCCAACTCC
genomic: TCCAGAAGCTGACGAGgtaaccacag ... tgcactacagATTCTTGCCAAGAAGGGAGTGACCATATTACCTGACATTTACGCCAACTCC
EST: gi|88967853|gb|CI098095.1|CI098095
EST:     AAGCTGCTAATCATCCAACTGATCCAGAAGCTGACGAG                         ATTCTTGCCAAGAAGGGAGTGACCATATTACCTGACATTTACGCCAACTCC
genomic: AAGCTGCTAATCATCCAACTGATCCAGAAGCTGACGAGgtaaccacag ... tgcactacagATTCTTGCCAAGAAGGGAGTGACCATATTACCTGACATTTACGCCAACTCC
EST: gi|86260911|gb|CI066586.1|CI066586
EST:     TGATCCAGAAGCTGACGAG                         ATTCTTGCCAAGAAGGGAGTGACCATATTACCTGACATGTACGCCAACTCC
genomic: TGATCCAGAAGCTGACGAGgtaaccacag ... tgcactacagATTCTTGCCAAGAAGGGAGTGACCATATTACCTGACATTTACGCCAACTCC
EST: gi|29643302|gb|CB648309.1|CB648309
EST:     AATTTATAATTGAAGCTGCTAATCATCCAACTGATCCAGAAGCTGACGAG                         ATTCTTGCCAAGAAGGGAGTGACCATATTACCTGACATTTACGCCAACTCC
genomic: AATTTATAATTGAAGCTGCTAATCATCCAACTGATCCAGAAGCTGACGAGgtaaccacag ... tgcactacagATTCTTGCCAAGAAGGGAGTGACCATATTACCTGACATTTACGCCAACTCC
EST: gi|25804045|gb|CA760006.1|CA760006
EST:     AATTTATAATTGAAGCTGCTAATCATCCAACTGATCCAGAAGCTGACGAG                         ATTCTTGCCAAGAAGGGAGTGACCATATTACCTGACATTTACGCCAACTCC
genomic: AATTTATAATTGAAGCTGCTAATCATCCAACTGATCCAGAAGCTGACGAGgtaaccacag ... tgcactacagATTCTTGCCAAGAAGGGAGTGACCATATTACCTGACATTTACGCCAACTCC
EST: gi|29669247|gb|CB665522.1|CB665522
EST:     AATTTATAATTGAAGCTGCTAATCATCCAACTGATCCAGAAGCTGACGAG                         ATTCTTGCCAAGAAGGGAGTGACCATATTACCTGACATTTACGCCAACTCC
genomic: AATTTATAATTGAAGCTGCTAATCATCCAACTGATCCAGAAGCTGACGAGgtaaccacag ... tgcactacagATTCTTGCCAAGAAGGGAGTGACCATATTACCTGACATTTACGCCAACTCC
EST: gi|29678533|gb|CB674808.1|CB674808
EST:     AATTTATAATTGAAGCTGCTAATCATCCAACTGATCCAGAAGCTGACGAG                         ATTCTTGCCAAGAAGGGAGTGACCATATTACCTGACATTTACGCCAACTCC
genomic: AATTTATAATTGAAGCTGCTAATCATCCAACTGATCCAGAAGCTGACGAGgtaaccacag ... tgcactacagATTCTTGCCAAGAAGGGAGTGACCATATTACCTGACATTTACGCCAACTCC

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: 75 (upstream exon), 72 (downstream exon)
Score: 52

GGAAAATGCACCTGATGTGAAGGCCAAATTTATAATTGAAGCTGCTAATCATCCAACTGATCCAGAAGCTGACGAGgtaaccacag ... tgcactacagATTCTTGCCAAGAAGGGAGTGACCATATTACCTGACATTTACGCCAACTCCGGTGGTGTGATCGTTAGCTATTTTGAGTGGGTTCAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAAAATGCACCTGATGTGAAGGCCAAATTTATAATTGAAGCTGCTAATCATCCAACTGATCCAGAAGCTGACGAGgtaaccacagaacaaaacattgtaccctaactttgtctttgagaaacatcagaaatgttgccaattttggcagttctgattgatgctgtatgcactacag

- - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA