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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggtatcctttcggtttttttttaagtttttacaaataaatctttcaagcatagcttaatgacttgttaaccgtccttttctttacttgtgtgtatcagACAACCTATGAGAACTTTAGGTATCGGTACGATCGGCGGGCTAACCCATATAACAGAGGTATGGTGAACAACTTTCTGGAGATCTTCTGCACTGCAATTC

Basic information

species Oryza sativa
transcript LOC_Os09g33450.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g33450.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G179002_T03 (Zea mays), 3'ss of exon 4
-----------------------------------------------------gttggtatcctttcggtttttttttaagttt-ttacaaataaatctt--tcaagcatagcttaatgact-tgttaaccgtccttttctttacttgtgtgtatcagACAACCTATGAGAACTTTAGGTATCGGTACGATCGGCGGGCTAACCCATATAACAGAGGTATGGTGAACAACTTTCTGGAGATCTTCTGCACTGCAATTC
                                                     | || ||     |  ||||  |  ||||  | || | |  || |  |  | |  |  |  |    | || ||  |   |  ||   |||| | | |   |  |||||||||||||||||||| || || || || ||||||||||  || || || |||||||| |  |||||||||||  ||||||| ||||||||  || |  
gttggtaccctgtcaacttttttaatatagttggttttacccgtaagcatattgctgataattggttagtttactcgtaagcatattgctaggaatttgtaattactctcatgtgggagcctctggcattgggtctgcccttttcctatcctttgcagACAACCTATGAGAACTTCAGATACCGCTATGATCGGCGGGACAATCCGTACAACAGAGGGACCGTGAACAACTTCATGGAGATATTCTGCACCTCAGTCG

upper sequence: LOC_Os09g33450.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM5G868588_T01 (Zea mays), 3'ss of exon 4
gttggtatcctttcggtttttttttaagtttttacaaataaatctttcaagcatagcttaatgacttgttaaccgtccttttctttacttgtgtgtatcagACAACCTATGAGAACTTTAGGTATCGGTACGATCGGCGGGCTAACCCATATAACAGAGGTATGGTGAACAACTTTCTGGAGATCTTCTGCACTGCAATTC
||||| | ||| ||   |||||  ||   ||       |    | |  |||||||     | || ||  ||| |  | ||| || ||||   |     |||||||||||||||||||| || ||||| || ||||||||||| ||||| || |||| ||| ||  ||||||||||  ||||||| |||||||| ||| | |
gttggcaccctgtcaactttttaatataatt-----ggttttacctgtaagcatattgctaggaatttgtaatca-cttttcctatact-acg-----cagACAACCTATGAGAACTTCAGATATCGCTATGATCGGCGGGCCAACCCGTACAACATAGGGATCTTGAACAACTTCATGGAGATATTCTGCACCGCAGTCC
















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|58661979|gb|CK050659.1|CK050659
EST:     TCGTTGGTGGTCTGTCTGTCTTTCATTTCTAGCGGATGAGCACCAATCAG                         ACAACCTATGAGAACTTTAGGTATCGGTACGATCGGCGGGCTAACCCATAT
genomic: TCGTTGGTGGTCTGTCTGTCTTTCATTTCTACCTGATGAGCACCAATCAGgttggtatcc ... tgtgtatcagACAACCTATGAGAACTTTAGGTATCGGTACGATCGGCGGGCTAACCCATAT
EST: gi|218488991|gb|FG968334.1|FG968334
EST:     TCGTTGGTGGTCTGTCTGTCTTTCATTTCTACCTGATGAGCACCAATCAG                         ACAACCTATGAGAACTTTAGGTATCGGTACGATCGGCGGGCTAACCCATAT
genomic: TCGTTGGTGGTCTGTCTGTCTTTCATTTCTACCTGATGAGCACCAATCAGgttggtatcc ... tgtgtatcagACAACCTATGAGAACTTTAGGTATCGGTACGATCGGCGGGCTAACCCATAT
EST: gi|29683946|gb|CB680221.1|CB680221
EST:     TCGTTGGTGGTCTGTCTGTCTTTCATTTCTACCTGATGAGCACCAATCAG                         ACAACCTATGAGAACTTTAGGTATCGGTACGATCGGCGGGCTAACCCATAT
genomic: TCGTTGGTGGTCTGTCTGTCTTTCATTTCTACCTGATGAGCACCAATCAGgttggtatcc ... tgtgtatcagACAACCTATGAGAACTTTAGGTATCGGTACGATCGGCGGGCTAACCCATAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaagcatagcttaatgacttgttaaccgtccttttctttacttgtgtgtatcagACAACCTATGAGAACTTTAGGTATCGGTACGATCGGCGGGCTAACCCATATAACAGAGGTATGGTGAACAACTTTCTGGAGATCTTCTGCACTGCAATTC
                    tgttaac  putative branch site (score: 2)
                             tccttttctttacttg  putative PPT
                                ttttcttta  TA-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggtatcctttcggtttttttttaagtttttacaaataaatctttcaagcatagcttaatgacttgttaaccgtccttttctttacttgtgtgtatcagACAACCTATGAGAACTTTAGGTATCGGTACGATCGGCGGGCTAACCCATATAACAGAGGTATGGTGAACAACTTTCTGGAGATCTTCTGCACTGCAATTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC