Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgccacgttttgctgttcagcactccattttttttattattttttatttttgcgaaagtcacatgtgcagcaatagtcacctgttgttgtctctcttgccgccagTTTCATCAAGGAAAGGCAGGAGAAAGAACAGATTGATGTTGCCGTCGCAACAAAGTTTGCTGCACTTCCATGGAGATTTGGCCGAGGAAGTGTTCTTTCC

Basic information

species Oryza sativa
transcript LOC_Os07g04990.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g04990.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G111954_T03 (Zea mays), 3'ss of exon 3
gtatgccacgttttgctgttcagcactccattttttttattattttttatttttgcgaaagtcacatgtg-cagcaat--------agtcacctgttgttgtctctcttgccgccagTTTCATCAAGGAAAGGCAGGAGAAAGAACAGATTGATGTTGCCGTCGCAACAAAGTTTGCTGCACTTCCATGGAGATTTGGCCGAGGAAGTGTTCTTTCC
|||    || || | |||||      |   ||  ||| |  | |||  |     |  |||   | ||||  ||| |||        || |  |   || ||  |  ||||||  ||| |||||||||||||||||  |||| || ||||| || ||  |||| ||||||||||| ||||| ||||| |||||||||||  | || || |||||||| 
gtaatatactttcttctgttt-----tttgttactttaacaaatttacaaaaaagaaaaaaaaatatgtaacagtaatcttgatcaagacgtcaagtgatgcatgccttgccatcagATTCATCAAGGAAAGGCAACAGAAGGACCAGATCGAGGTGTCCGTTGCAACAAAGTTCGCTGCCCTTCCTTGGAGATTTGGAAGGGGTAGCGTTCTTTCG

upper sequence: LOC_Os07g04990.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA18G14510.1 (Glycine max), 3'ss of exon 3
gtatgccacgttttgctgttcagcactccattttttttat-tattttttatttttgcgaaagtcacatgtgcagcaatagtcacctgttgttgtctctcttgccgccagTTTCATCAAGGAAAGGCAGGAGAAAGAAC---AGATTGATGTTGCCGTCGCAACAAAGTTTGCTGCACTTCCATGGAGATTTGGCCGAGGAAGTGTTCTTTCC
                 ||       |  ||  |||| || |    ||| |  ||  |||||     |   ||   ||  |  | | |  ||||      |  |  ||| |  || ||||||||  | || || || |   || ||||  |||  || ||||| |||||||||||||| || ||||||||||||||   |||||||||    
-----------------gtatgagcttagatgattttcatatgcagtttgtagttaagaaag----gttcacattgatgcttccatatgtttgt------tatctgcagATATATTAAGGAAAGAAAAGAAAAGGATCCAGAGGTTGAGATTGAAGTAGCAACCAAGTTTGCTGCACTGCCGTGGAGATTTGGCCGTCAAAGTGTTCTC---

upper sequence: LOC_Os07g04990.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA08G41630.1 (Glycine max), 3'ss of exon 3
gtatgccacgttttgctgttcagcactccattttttttat-tattttttatttttgcgaaagtcacatgtgcagcaatagtcacctgttgttgtctctcttgccgccagTTTCATCAAGGAAAGGCAGGAGAAAGAAC---AGATTGATGTTGCCGTCGCAACAAAGTTTGCTGCACTTCCATGGAGATTTGGCCGAGGAAGTGTTCTTTCC
                 ||       | |||  |||| ||  |   ||| |  ||  ||| ||  ||  |   |   |   ||  ||||||| |||           || |  || ||||||||  | || || || |   |  ||||  |||  || ||||| |||||||||||||| || ||||||||||||||   |||||||||    
-----------------gtatgagcttacatgattttcatacacagtttgtaattaagaaggtt-cacat-tggtgctt-ccatatgttgttatct---------gaagATATATTAAGGAAAGAAAAGAAAAGGATCCAGACGTTGAGATTGAAGTAGCAACCAAGTTTGCTGCACTACCGTGGAGATTTGGCCGTCAAAGTGTTCTC---

upper sequence: LOC_Os07g04990.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ32160 (Selaginella moellendorffii), 3'ss of exon 4
gtatgccacgttttgctgttcagcactccattttttttattattttttatttttgcgaaagtcacatgtgcagcaatagtcacctgttgttgtctctcttgccgccagTTTCATCAAGGAAAGGCAGGAGAAAGAACAGATTGATGTTGCCGTCGCAACAAAGTTTGCTGCACTTCCATGGAGATTTGGCCGAGGAAGTGTTCTTTCC
                                                         |||    | |||     | |  |||   ||| |  ||| |||| |||| || || |||||||| |   |  |  |||| ||   | |  |||  || ||||| |||||||||||||| |||||||| ||||||||||| || ||| |    
-------------------------------------------------------gtaaacaagcttgtcttctatttttca--agttttcctctttcttcccgc-agGTTTATCAAGGAGATCAAACAAGAAGAGCAATCTAAGATTGTAGTGGCAACGAAGTTTGCTGCACTGCCATGGAGGTTTGGCCGAGGGAGCGTTGTCAAA

upper sequence: LOC_Os07g04990.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ16831 (Selaginella moellendorffii), 3'ss of exon 5
gtatgccacgttttgctgttcagcactccattttttttattattttttatttttgcgaaagtcacatgtgcagcaatagtcacctgttgttgtctctcttgccgccagTTTCATCAAGGAAAGGCAGGAGAAAGAACAGATTGATGTTGCCGTCGCAACAAAGTTTGCTGCACTTCCATGGAGATTTGGCCGAGGAAGTGTTCTTTCC
                                                         |||    | |||     | |  |||   ||| |  ||| |||| |||| || || |||||||| |   |  |  |||||||   | |  |||  || ||||| |||||||||||||| |||||||| ||||||||||| || ||| |    
-------------------------------------------------------gtaaacaagcttgtcttctatttttca--agttttcctctttcttcccgc-agGTTTATCAAGGAGATCAAACAAGAAGAACAATCTAAGATTGTAGTGGCAACGAAGTTTGCTGCACTGCCATGGAGGTTTGGCCGAGGGAGCGTTGTCAAA

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|38478740|gb|CF962873.1|CF962873
EST:     CTGATGGGAGCAGTAAATTCTGAAAGTTTACTCGGAGG                         TTTCAGTCAAGGAAAGGCAGGAGAAAGAACAGATTGATGTTGCCGTCGCAA
genomic: CTGATGGGAGCAGTAAATTCTGAAAGTTTACTCGGAGGgtatgccacg ... ttgccgccagTTTCA-TCAAGGAAAGGCAGGAGAAAGAACAGATTGATGTTGCCGTCGCAA
EST: gi|38477681|gb|CF961814.1|CF961814
EST:     CTGATGGGAGCAGTAAATTCTGAAAGTTTACTCGGAGG                         TTTCATCAAGGAAAGGCAGGAGAAAGAACAGATTGATGTTGCCGTCGCAAC
genomic: CTGATGGGAGCAGTAAATTCTGAAAGTTTACTCGGAGGgtatgccacg ... ttgccgccagTTTCATCAAGGAAAGGCAGGAGAAAGAACAGATTGATGTTGCCGTCGCAAC
EST: gi|313083769|gb|HO213899.1|HO213899
EST:     ACAGCGCTGATGGGAGCAGTAAATTCTGAAAGTTTACTCGGAGG                         TTTCATCAAGGAAAGGCAGGAGAAAGAACAGATTGATGTTGCCGTCGCAAC
genomic: ACAGCGCTGATGGGAGCAGTAAATTCTGAAAGTTTACTCGGAGGgtatgccacg ... ttgccgccagTTTCATCAAGGAAAGGCAGGAGAAAGAACAGATTGATGTTGCCGTCGCAAC
EST: gi|58586534|gb|CF984842.1|CF984842
EST:     CTGATGGGAGCAGTAAATTCTGAAAGTTTACTCGGAGG                         TTTCATCAAGGAAAGGCAGGAGAAAGAACAGATTGATGTTGCCGTCGGGAA
genomic: CTGATGGGAGCAGTAAATTCTGAAAGTTTACTCGGAGGgtatgccacg ... ttgccgccagTTTCATCAAGGAAAGGCAGGAGAAAGAACAGATTGATGTTGCCGTC-GCAA
EST: gi|58605103|gb|CK033136.1|CK033136
EST:     CTGATGGGAGCAGTAAATTCTGAAAGTTTACTCGGAGG                         TTTCATCAAGGAAAGGCAGGAGAAAGAACAGATTGATGTTGCCGTCGCAAC
genomic: CTGATGGGAGCAGTAAATTCTGAAAGTTTACTCGGAGGgtatgccacg ... ttgccgccagTTTCATCAAGGAAAGGCAGGAGAAAGAACAGATTGATGTTGCCGTCGCAAC
EST: gi|58590950|gb|CF989258.1|CF989258
EST:     CTGATGGGAGCAGTAAATTCTGGGAAGTTTACTCGGAGG                         TTTCATCAAGGAAAGGCAGGAGAAAGAACAGATTGATGTTGCCGTCGCAAC
genomic: CTGATGGGAGCAGTAAATTCT-GAAAGTTTACTCGGAGGgtatgccacg ... ttgccgccagTTTCATCAAGGAAAGGCAGGAGAAAGAACAGATTGATGTTGCCGTCGCAAC
EST: gi|58592358|gb|CF990666.1|CF990666
EST:     CTGATGGGAGCAGTAAATTCTGAAAGTTTACTCGGAGG                         TTTCATCAAGGAAAGGCAGGAGAAAGAACAGATTGATGTTGCCGTCGCAAC
genomic: CTGATGGGAGCAGTAAATTCTGAAAGTTTACTCGGAGGgtatgccacg ... ttgccgccagTTTCATCAAGGAAAGGCAGGAGAAAGAACAGATTGATGTTGCCGTCGCAAC
EST: gi|313080415|gb|HO213423.1|HO213423
EST:     ACAGCGCTGATGGGAGCAGTAAATTCTGAAAGTTTACTCGGAGG                         TTTCATCAAGGAAAGGCAGGAGAAAGAACAGATTGATGTTGCCGTCGCAAC
genomic: ACAGCGCTGATGGGAGCAGTAAATTCTGAAAGTTTACTCGGAGGgtatgccacg ... ttgccgccagTTTCATCAAGGAAAGGCAGGAGAAAGAACAGATTGATGTTGCCGTCGCAAC
EST: gi|29685611|gb|CB681886.1|CB681886
EST:     CTGATGGGAGCAGTAAATTCTGAAAGTTTACTCGGAGG                         TTTCATCAAGGAAAGGCAGGAGAAAGAACAGATTGATGTTGCCGTCGCAAC
genomic: CTGATGGGAGCAGTAAATTCTGAAAGTTTACTCGGAGGgtatgccacg ... ttgccgccagTTTCATCAAGGAAAGGCAGGAGAAAGAACAGATTGATGTTGCCGTCGCAAC
EST: gi|38469835|gb|CF953966.1|CF953966
EST:     CTGATGGGAGCAGTAAATTCTGAAAGTTTACTCGGAGG                         TTTCATCAAGGAAAGGCAGGAGAAAGAACAGATTGATGTTGCCGTCGCAAC
genomic: CTGATGGGAGCAGTAAATTCTGAAAGTTTACTCGGAGGgtatgccacg ... ttgccgccagTTTCATCAAGGAAAGGCAGGAGAAAGAACAGATTGATGTTGCCGTCGCAAC
EST: gi|38483088|gb|CF966890.1|CF966890
EST:     CTGAT-GGAGCAGTAAATTCTGAAAGTTTACTCGGAGG                         TTTCATCAAGGAAAGGCAGGAGAAAGAACAGATTGATGTTGCCGTCGCAAC
genomic: CTGATGGGAGCAGTAAATTCTGAAAGTTTACTCGGAGGgtatgccacg ... ttgccgccagTTTCATCAAGGAAAGGCAGGAGAAAGAACAGATTGATGTTGCCGTCGCAAC
EST: gi|58589665|gb|CF987973.1|CF987973
EST:     CTGATGGGAGCAGTAAATTCTGAAAGTGGACTCGGAGG                         TTTCATCAAGTGAAAGGCAGGAGAAAGAACAGATTGATGTTGCCGTCGCAA
genomic: CTGATGGGAGCAGTAAATTCTGAAAGTTTACTCGGAGGgtatgccacg ... ttgccgccagTTTCATCAAG-GAAAGGCAGGAGAAAGAACAGATTGATGTTGCCGTCGCAA
EST: gi|38480259|gb|CF964348.1|CF964348
EST:     CTGATGGGAGCAGTAAATTCTGAAAGTTTACTCGGGGG                         TTTCATCAAGGAAAGGCAGGAGAAAGAACAGATTGATGTTGCCGTCGCAAC
genomic: CTGATGGGAGCAGTAAATTCTGAAAGTTTACTCGGAGGgtatgccacg ... ttgccgccagTTTCATCAAGGAAAGGCAGGAGAAAGAACAGATTGATGTTGCCGTCGCAAC

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: 50 (upstream exon), 60 (downstream exon)
Score: 71

CTGATGGGAGCAGTAAATTCTGAAAGTTTACTCGGAGGgtatgccacg ... ttgccgccagTTTCATCAAGGAAAGGCAGGAGAAAGAACAGATTGATGTTGCCGTCGCAACAAAGTTTGCTGCACTTCCATGGAGATTTGGCCGAGGAAGTGTTCTTTCC




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcgaaagtcacatgtgcagcaatagtcacctgttgttgtctctcttgccgccagTTTCATCAAGGAAAGGCAGGAGAAAGAACAGATTGATGTTGCCGTCGCAACAAAGTTTGCTGCACTTCCATGGAGATTTGGCCGAGGAAGTGTTCTTTCC
                                 ttgttgtctctctt  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgccacgttttgctgttcagcactccattttttttattattttttatttttgcgaaagtcacatgtgcagcaatagtcacctgttgttgtctctcttgccgccagTTTCATCAAGGAAAGGCAGGAGAAAGAACAGATTGATGTTGCCGTCGCAACAAAGTTTGCTGCACTTCCATGGAGATTTGGCCGAGGAAGTGTTCTTTCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT