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'   		10  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaattgtttttctaacagtaaacctttatataccgtatttatcatcatctttatatgattctgaattctcctaatgattgtaacatgcagGTTATAATGAACGGTAGAGGTTACCATCTACCAGTTGACATTTGGAGTTTGGGATGTACTATTATTGAAATGGCAACGGCAAAACCTCCTTGGCATAAAT

Basic information

species Oryza sativa
transcript LOC_Os04g35700.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g35700.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G064773_T01 (Zea mays), 3'ss of exon 3
gtaaattgtttttctaacagtaaacctttatataccgtatttatcatcatct-ttatatgattctgaat----tctcctaatgatt--gtaacatgcagGTTATAATGAACGGTAGAGGTTACCATCTACCAGTTGACATTTGGAGTTTGGGATGTACTATTATTGAAATGGCAACGGCAAAACCTCCTTGGCATAAAT
|| |  | || |   || | | ||| |    |     | ||| || | ||||  ||   |  ||| |||    |   || || |||  | ||| | ||||||||||||||| ||  | | |||  | || |||| |||||||||||| |||| ||||| |||||||||||||| ||| ||| ||||||||||||  |||
gtgagctattgt---aataatgaactt---cactggttgtttgtcgtaatctgctacgcgtctcttaatgaagttctctcatcattaggaaaccttcagGTTATAATGAACAGTGCAAGCTACAGTTTATCAGTGGACATTTGGAGTCTGGGTTGTACCATTATTGAAATGGCGACGACAAGACCTCCTTGGCACCAAT

upper sequence: LOC_Os04g35700.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G140726_T01 (Zea mays), 3'ss of exon 7
gtaaattgtttttctaacagtaaacctttatataccgtatttatcatcatct-ttatatgattctgaat----tctcctaatgattgt--aacatgcagGTTATAATGAACGGTAGAGGTTACCATCTACCAGTTGACATTTGGAGTTTGGGATGTACTATTATTGAAATGGCAACGGCAAAACCTCCTTGGCATAAAT
|| |  | ||||  || |      |||| ||      ||||| |||| ||||  | |  |  |||||||    |   |  || ||||   ||| | ||||||||||||||| ||| ||| |||  | || |||| ||||| |||||| |||| ||||| |||||||||||||| ||||||| ||||||||||||  |||
gtgagctattttaataccgaacttccttgat------tatttgtcataatctgctgtgcgtctctgaatgaagttctcccatcattgggaaaccttcagGTTATAATGAACTGTAAAGGCTACAGTTTATCAGTGGACATATGGAGTCTGGGCTGTACCATTATTGAAATGGCGACGGCAAGACCTCCTTGGCACCAAT

upper sequence: LOC_Os04g35700.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA08G16670.2 (Glycine max), 3'ss of exon 7
-----------------------------gtaaattgtttttctaacagtaaacctttatataccgtatttatcatcatctttatatgattctgaattctcctaatgattgtaacatgcagGTTATAATGAACGGTAGAGGTTACCATCTACCAGTTGACATTTGGAGTTTGGGATGTACTATTATTGAAATGGCAACGGCAAAACCTCCTTGGCATAAAT
                              |  |   || || ||| ||| | | | |   | ||   | |  ||     ||   |  ||  | | |          ||| |    |  ||||| |||||||    |  || ||   ||| |||||||| || ||||| ||||| || || |||||||||||||||||  |||||||||| ||| || | |
gtaaattgttttttctattattctgcaatattgaaatttcttttaaaagtgagcatattcttccctcctcttccacttctttctcaccatagttactggataatgatattctcttttttagGTTGTAATGAATACAAATGGCTATAGTCTTCCAGTTGATATATGGAGCTTGGGGTGCACAATTATTGAAATGGCAACATCAAAACCTCCCTGGAATCAGT

upper sequence: LOC_Os04g35700.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA05G32510.1 (Glycine max), 3'ss of exon 7
-----------------------------gtaaattgtttttctaacagtaaacctttatataccgtatttatcatcatctttatatgattctgaattctcctaatgattgtaacatgcagGTTATAATGAACGGTAGAGGTTACCATCTACCAGTTGACATTTGGAGTTTGGGATGTACTATTATTGAAATGGCAACGGCAAAACCTCCTTGGCATAAAT
                              |  |   || || ||| ||| | | | | | |      | |  ||     ||   |  ||  | | |          ||| |    |  ||||| |||||||    |  || ||   ||| |||||||| || ||||| |||||||| || |||||||||||||||||  |||||||||| ||| || | |
gtaaaaaaaattttcttttcttctgcaatattgaaatttcttttaaaagtgagcatatttttctttcctcttccacttctttctcaccataattactggataatgatattctcttttttagGTTGTAATGAATACAAATGGCTATAGTCTTCCAGTTGATATATGGAGCTTGGGATGCACAATTATTGAAATGGCAACATCAAAACCTCCATGGAATCAGT

upper sequence: LOC_Os04g35700.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA06G15870.1 (Glycine max), 3'ss of exon 8
----------gtaaattgtttttctaaca----gtaa--acctttatataccgtatttatcatcatcttta-tatgattctgaat-tctcctaatgattgtaacatgcagGTTATAATGAACGGTAGAGGTTACCATCTACCAGTTGACATTTGGAGTTTGGGATGTACTATTATTGAAATGGCAACGGCAAAACCTCCTTGGCATAAAT
           |    | | ||| | |||    ||||  || |||  | |      |  | |||   |  | | | | | | ||| | |||  | | |||     |  ||||| |||||||    |  || ||   ||| || ||||| || |||||||||||||| || ||| |||||||||||||  |||| ||||||||| || | |
gtaaagtattttttcctttctttttcacatcttgtaattacttttgaacaagaacatccttatctcttccactgtaagttttaatgtatcccgacgtttgctttct-tagGTTGTAATGAATACAAATGGCTATAGTCTTCCTGTTGATATATGGAGTTTGGGATGCACAATTCTTGAAATGGCAACATCAAAGCCTCCTTGGAATCAGT

upper sequence: LOC_Os04g35700.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv04s0044g01290.t01 (Vitis vinifera), 3'ss of exon 7
--------------------------------------------------------------------------------------------------------gtaaattgtttttctaacagtaaacctttatataccgtattt-atcatcatctttatatgattctgaattctcctaatgattgtaacatg---cagGTTATAATGAACGGTAGAGGTTACCATCTACCAGTTGACATTTGGAGTTTGGGATGTACTATTATTGAAATGGCAACGGCAAAACCTCCTTGGCATAAAT
                                                                                                         |  |   |   |  |    |   | |||   | || |  || |   |  | | |   |||     || | ||||  || ||||  |      |||||| |||||||    |  || |||   ||  | || || |||||||| || |||||||| ||| |||||||||||||  ||||||| ||||||  | |||
gtatttacatacaacaccccacaccccacaccccaacaccccttctctctctctctctcacacacacacacatacacacaaaacaagtaaacacacagataaacatgcacactagcttcagttatgttctttttatttccttgcttcaatgttttttctccgtgaacaccaagtttccttgtgtttgtgtccaatctcagGTTGTAATGAATACAAATGGCTACAGCCTTGCGGTGGATATTTGGAGCTTAGGATGTACAATTCTTGAAATGGCAACATCAAAACCACCTTGGAGTCAAT

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|33684300|gb|CF312539.1|CF312539
EST:     TTGCTGAAATACGCTCTTTCAAAGGAAGTCCTTACTGGATGGCTCCTGAG                         GTTATAATGAACGGTAGAGGTTACCATCTACCAGTTGACATTTGGAGTTTN
genomic: TTGCTGAAATACGCTCTTTCAAAGGAAGTCCTTACTGGATGGCTCCTGAGgtaaattgtt ... taacatgcagGTTATAATGAACGGTAGAGGTTACCATCTACCAGTTGACATTTGGAGTTT-
EST: gi|29666845|gb|CB663120.1|CB663120
EST:     TTGCTGAAATACGCTCTTTCAAAGGAAGTCCTTACTGGATGGCTCCTGAG                         GTTATAATGAACGGTAGAGGTTACCATCTACCAGTTGACATTTGGAGTTTG
genomic: TTGCTGAAATACGCTCTTTCAAAGGAAGTCCTTACTGGATGGCTCCTGAGgtaaattgtt ... taacatgcagGTTATAATGAACGGTAGAGGTTACCATCTACCAGTTGACATTTGGAGTTTG
EST: gi|29629684|gb|CB634693.1|CB634693
EST:     TTGCTGAAATACGCTCTTTCAAAGGAAGTCCTTACTGGATGGCTCCTGAG                         GTTATAATGAACGGTAGAGGTTACCATCTACCAGTTGACATTTGGAGTTTG
genomic: TTGCTGAAATACGCTCTTTCAAAGGAAGTCCTTACTGGATGGCTCCTGAGgtaaattgtt ... taacatgcagGTTATAATGAACGGTAGAGGTTACCATCTACCAGTTGACATTTGGAGTTTG

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: 69 (upstream exon), 63 (downstream exon)
Score: 19

ATATCATCTTTTGCTGAAATACGCTCTTTCAAAGGAAGTCCTTACTGGATGGCTCCTGAGgtaaattgtt ... taacatgcagGTTATAATGAACGGTAGAGGTTACCATCTACCAGTTGACATTTGGAGTTTGGGATGTACTATTATTGAAATGGCAACGGCAAAACCTCCTTGGCATAAAT




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatttatcatcatctttatatgattctgaattctcctaatgattgtaacatgcagGTTATAATGAACGGTAGAGGTTACCATCTACCAGTTGACATTTGGAGTTTGGGATGTACTATTATTGAAATGGCAACGGCAAAACCTCCTTGGCATAAAT
                                          ttgtaac  putative branch site (score: 19)
           atctttatatgatt  TA-rich tract