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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagatgtgccatggacatgaagtatcacgcatcttggtgtctaccagcaactgatagtgttctttagcagGCATGGTGCTGGTTTAAGTTGATAGGTACCTGGCCCATCATAGAAATTTTGTTGCAGGATTAACTCCAACCAGATTGATCATAAAAGCAGTCTAATCTGC

Basic information

species Oryza sativa
transcript LOC_Os04g41100.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g41100.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G139038_T01 (Zea mays), 3'ss of exon 7
gtgagatgtgccatggacatgaagtatcacg-catcttggtgtctaccagcaactgatagtgttctttagcagGCATGGTGCTGGTTTAAGTTGATA-GGTACCT------GGCCCATCATAGAAATTTTGTTGCAGGATTAAC--TCCAACCAGATTGATCATAAAAGCAGTCTAATCTGC
  | || |||||||||||||||||||||||  | ||| |||||||| |||| ||||||||||||||||||||||| |||||| ||||| ||| |||| |||  ||      |||||||||||||||||||||||||||||||||  |||| ||||||||||||||||||||           
--gtgaggtgccatggacatgaagtatcacatcttctcggtgtctagcagcgactgatagtgttctttagcagGCTTGGTGCCGGTTTGAGTGGATAAGGTTTCTCCTTGTGGCCCATCATAGAAATTTTGTTGCAGGATTAACACTCCATCCAGATTGATCATAAAAGCAAA---------

upper sequence: LOC_Os04g41100.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G179097_T02 (Zea mays), 3'ss of exon 7
gtgagatgtgccatggacatgaagtatcacg-catcttggtgtctaccagcaactgatagtgttctttagcagGCATGGTGCTGGTTTAAGTTGATA-GGTACCT------GGCCCATCATAGAAATTTTGTTGCAGGATTAAC--TCCAACCAGATTGATCATAAAAGCAGTCTAATCTGC
  | || |||||||||||||||||||||||  | ||| |||||||| |||||||||||||||||||||||||||| |||| | ||||||| | |||| |||  ||      |||||||||||||||||||||||||||||||||  | || |||||| |||||||||||||           
--gtgaggtgccatggacatgaagtatcacatcttctcggtgtctagcagcaactgatagtgttctttagcagGCTTGGTACCGGTTTAAATGGATAAGGTTTCTCCTTGTGGCCCATCATAGAAATTTTGTTGCAGGATTAACGCTTCATCCAGATCGATCATAAAAGCAAA---------

upper sequence: LOC_Os04g41100.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G179097_T08 (Zea mays), 3'ss of exon 7
gtgagatgtgccatggacatgaagtatcacg-catcttggtgtctaccagcaactgatagtgttctttagcagGCATGGTGCTGGTTTAAGTTGATA-GGTACCT------GGCCCATCATAGAAATTTTGTTGCAGGATTAAC--TCCAACCAGATTGATCATAAAAGCAG-TCTAATCTGC-
  | || |||||||||||||||||||||||  | ||| |||||||| |||||||||||||||||||||||||||| |||| | ||||||| | |||| |||  ||      |||||||||||||||||||||||||||||||||  | || |||||| |||||||||||||  | |||||| | 
--gtgaggtgccatggacatgaagtatcacatcttctcggtgtctagcagcaactgatagtgttctttagcaggcttggtaccggtttaaatggataaggtttctccttgtggcccatcatagaaattttgttgcagGATTAACGCTTCATCCAGATCGATCATAAAAGCAAATATAATCTACC

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|29631272|gb|CB636281.1|CB636281
EST:     CCTGACTGTCATGCATCATTCTGAATCTATGAGGTCAGATACACTCTGAG                         GCATGGTGCTGGTTTAAGTTGATAGGTACCTGGCCCATCATAGAAATTTTG
genomic: CCTGACTGTCATGCATCATTCTGAATCTATGAGGTCAGATACACTCTGAGgtgagatgtg ... tctttagcagGCATGGTGCTGGTTTAAGTTGATAGGTACCTGGCCCATCATAGAAATTTTG
EST: gi|29631145|gb|CB636154.1|CB636154
EST:     CCTGACTGTCATGCATCATTCTGAATCTATGAGGTCAGATACACTCTGAG                         GCATGGTGCTGGTTTAAGTTGATAGGTACCTGGCCCATCATAGAAATTTTG
genomic: CCTGACTGTCATGCATCATTCTGAATCTATGAGGTCAGATACACTCTGAGgtgagatgtg ... tctttagcagGCATGGTGCTGGTTTAAGTTGATAGGTACCTGGCCCATCATAGAAATTTTG
EST: gi|88979130|gb|CI025633.1|CI025633
EST:     CCTGACTGTCATGCATCATTCTGAATCTATGAGGTCAGATACACTCTGAG                         GCATGGTGCTGGTTTAAGTTGATAGGTACCTGGCCCATCATAGAAATTTTG
genomic: CCTGACTGTCATGCATCATTCTGAATCTATGAGGTCAGATACACTCTGAGgtgagatgtg ... tctttagcagGCATGGTGCTGGTTTAAGTTGATAGGTACCTGGCCCATCATAGAAATTTTG
EST: gi|29626550|gb|CB631561.1|CB631561
EST:     CCTGACTGTCATGCATCATTCTGAATCTATGAGGTCAGATACACTCTGAGCAG                       
genomic: CCTGACTGTCATGCATCATTCTGAATCTATGAGGTCAGATACACTCT--G-AGgtgagatgtg ... tctttagc
EST: gi|44675738|gb|CR289172.1|CR289172
EST:     CCTGACTGTCATGCATCATTCTGAATCTATGAGGTCAGATACACTCTGAG                         C
genomic: CCTGACTGTCATGCATCATTCTGAATCTATGAGGTCAGATACACTCTGAGgtgagatgtg ... tctttagcag-
EST: gi|44675738|gb|CR289172.1|CR289172
EST:     CCTGACTGTCATGCATCATTCTGAATCTATGAGGTCAGATACACTCTGAG                         C
genomic: CCTGACTGTCATGCATCATTCTGAATCTATGAGGTCAGATACACTCTGAGgtgagatgtg ... tctttagcag-
EST: gi|44675738|gb|CR289172.1|CR289172
EST:     CCTGACTGTCATGCATCATTCTGAATCTATGAGGTCAGATACACTCTGAG                         C
genomic: CCTGACTGTCATGCATCATTCTGAATCTATGAGGTCAGATACACTCTGAGgtgagatgtg ... tctttagcag-
EST: gi|29631235|gb|CB636244.1|CB636244
EST:     CCTGACTGTCATGCATCATTCTGAATCTATGAGGTCAGATACACTCTGAG                         GCATGGTGCTGGTTTAAGTTGATAGGTACCTGGCCCATCATAGAAATTTTG
genomic: CCTGACTGTCATGCATCATTCTGAATCTATGAGGTCAGATACACTCTGAGgtgagatgtg ... tctttagcagGCATGGTGCTGGTTTAAGTTGATAGGTACCTGGCCCATCATAGAAATTTTG
EST: gi|15857726|gb|BI810538.1|BI810538
EST:     CCTGACTGTCATGCATCATTCTGAATCTATGAGGTCAGATACACTCTGAG                         GCATGGTGCTGGTTTAAGTTGATAGGTACCTGGCCCATCATAGAAATTTTG
genomic: CCTGACTGTCATGCATCATTCTGAATCTATGAGGTCAGATACACTCTGAGgtgagatgtg ... tctttagcagGCATGGTGCTGGTTTAAGTTGATAGGTACCTGGCCCATCATAGAAATTTTG

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: 70 (upstream exon), 61 (downstream exon)
Score: 16

CCGTGGTCTTTTTGGCTGAGCTATTAGCAACTTGTTTGGGCTCTATTGATCCTGACTGTCATGCATCATTCTGAATCTATGAGGTCAGATACACTCTGAGgtgagatgtg ... tctttagcagGCATGGTGCTGGTTTAAGTTGATAGGTACCTGGCCCATCATAGAAATTTTGTTGCAGGATTAACTCCAACCAGATTGATCATAAAAGCAGTCTAATCTGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgaagtatcacgcatcttggtgtctaccagcaactgatagtgttctttagcagGCATGGTGCTGGTTTAAGTTGATAGGTACCTGGCCCATCATAGAAATTTTGTTGCAGGATTAACTCCAACCAGATTGATCATAAAAGCAGTCTAATCTGC
                                 aactgat  putative branch site (score: 16)
                                          tgttcttt  putative PPT
                                            ttcttta  TA-rich tract