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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_Os04g41100.2
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|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|29623101|gb|CB628112.1|CB628112
EST:     CCTGACTGTCATGCATCATTCTGAATCTATGAGGTCAGATACACTCTGAG                         GCATGGTGCTGGTTTAAGTTGATAGGTACCTGGCCCATCATAGAAATTTTG
genomic: CCTGACTGTCATGCATCATTCTGAATCTATGAGGTCAGATACACTCTGAGgtgagatgtg ... tctttagcagGCATGGTGCTGGTTTAAGTTGATAGGTACCTGGCCCATCATAGAAATTTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgaagtatcacgcatcttggtgtctaccagcaactgatagtgttctttagcagGCATGGTGCTGGTTTAAGTTGATAGGTACCTGGCCCATCATAGAAATTTTGTTGCAGGATTAACTCCAACCAGATTGATCATAAAAGCAGTCTAATCTGC
                                 aactgat  putative branch site (score: 3)
                                          tgttcttt  putative PPT
                                            ttcttta  TA-rich tract