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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggactggagcctgattgctgttaactggttaattgattgaaacatttcttaactagttaattatatctttgttgcagATTGGCTGGATCTACGGATCAGTTACAGAAGATATTCTAACTGGTTTTAAGATGCACTGCCATGGTTGGCGGTCAATTTACTGCATACCTAAACTACCTG

Basic information

species Oryza sativa
transcript LOC_Os07g24190.3
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g24190.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G025231_T02 (Zea mays), 3'ss of exon 12
gtaaggactggagcctgattgctgttaactggttaattgattgaaacatttcttaactagttaattatatctt------tgttgcagATTGGCTGGATCTACGGATCAGTTACAGAAGATATTCTAACTGGTTTTAAGATGCACTGCCATGGTTGGCGGTCAATTTACTGCATACCTAAACTACCTG
|| | | || |||| ||     || | | || || ||   |  |||||| | |||  |||| ||| |||| |         || ||||||||||||||||| |||||||||||||||||||||||||||||||| |||||||| || ||||||||||||||||||||||||||||||||||    ||
gtgaagtctagagcttg-----tggttattgctttatgagtcaaaacatatgttagatagtgaatcatatgtcatcttacttttcagATTGGCTGGATCTATGGATCAGTTACAGAAGATATTCTAACTGGTTTCAAGATGCATTGTCATGGTTGGCGGTCAATTTACTGCATACCTAAACGGGTTG

upper sequence: LOC_Os07g24190.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G028353_T02 (Zea mays), 3'ss of exon 12
gtaaggactggagcctgattgctgttaactggttaattgattgaaacatttcttaactagttaattatat------ctttgttgcagATTGGCTGGATCTACGGATCAGTTACAGAAGATATTCTAACTGGTTTTAAGATGCACTGCCATGGTTGGCGGTCAATTTACTGCATACCTAAACTACCTG
|||| | || |||||||     || | | ||||| ||   |  |||||| | |||  |||| ||| ||||       |   || ||||||||||||||||| |||||||||||||| ||||||||||||||||| |||||||| || ||||||||||||||||||||||||||||||||||  ||||
gtaaagtcttgagcctg-----tggttattggttgatgagtcaaaacatatgttacatagtgaatcatatgatattttccttttcagATTGGCTGGATCTATGGATCAGTTACAGAGGATATTCTAACTGGTTTCAAGATGCATTGTCATGGTTGGCGGTCAATTTACTGCATACCTAAACGGCCTG

upper sequence: LOC_Os07g24190.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G025231_T01 (Zea mays), 3'ss of exon 12
gtaaggactggagcctgattgctgttaactggttaattgattgaaacatttcttaactagttaattatatctt------tgttgcagATTGGCTGGATCTACGGATCAGTTACAGAAGATATTCTAACTGGTTTTAAGATGCACTGCCATGGTTGGCGGTCAATTTACTGCATACCTAAACTACCTG----------------------
|| | | || |||| ||     || | | || || ||   |  |||||| | |||  |||| ||| |||| |         || ||||||||||||||||| |||||||||||||||||||||||||||||||| |||||||| || ||||||||||||||||||||||||||||||||||    ||                      
gtgaagtctagagcttg-----tggttattgctttatgagtcaaaacatatgttagatagtgaatcatatgtcatcttacttttcagattggctggatctatggatcagTTACAGAAGATATTCTAACTGGTTTCAAGATGCATTGTCATGGTTGGCGGTCAATTTACTGCATACCTAAACGGGTTGCATTCAAAGGTTCTGCACCTCT

upper sequence: LOC_Os07g24190.2 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv03s0038g04250.t01 (Vitis vinifera), 3'ss of exon 12
----------gtaaggactggagcctg-attgctgttaactggttaattgattg---------aaacatttcttaactagttaattatatctttgttgcagATTGGCTGGATCTACGGATCAGTTACAGAAGATATTCTAACTGGTTTTAAGATGCACTGCCATGGTTGGCGGTCAATTTACTGCATACCTAAACTACCTG
           |  | | ||   |||| |  | |  |  ||   || |||||           | | |||||  |||||  |   | |  ||||  | ||| | || |||||||| ||||| ||||||||||||||  | || |||||||| ||||| |||||||| ||||| || || |||||||| ||| |    || |
tttttctaggttttgcattgctccctgtaaggttactggctatctatttgatcctgtttttctagaaatttcaaaactaacttcat-tgccttttattcagGTGGGTTGGATCTATGGATCTGTTACAGAAGATATCTTGACAGGTTTTAAAATGCATTGCCATGGATGGCGATCCATATACTGCATCCCTGACAGGCCAG

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|29632757|gb|CB637766.1|CB637766
EST:     TTCATGTCATAAGCTGTGGGTACGAAGATAAGACATACTGGGGGAAAGAG                         ATTGGCTGGATCTACTGATCAGCTACAGAAGATATTCTAACTGGT
genomic: TTCATGTCATAAGCTGTGGGTACGAAGATAAGACAGACTGGGGGAAAGAGgtaaggactg ... tttgttgcagATTGGCTGGATCTACGGATCAGTTACAGAAGATATTCTAACTGGT
EST: gi|15008337|gb|AU222725.1|AU222725
EST:     TTCATGTCATAAGCTGTGGGTACGAAGATAAGACAGACTGGGGGAAAGAG                         ATTGGCTGGATCTACGGATCAGTTACAGAAGATATTCTAACTGGTTTTAAG
genomic: TTCATGTCATAAGCTGTGGGTACGAAGATAAGACAGACTGGGGGAAAGAGgtaaggactg ... tttgttgcagATTGGCTGGATCTACGGATCAGTTACAGAAGATATTCTAACTGGTTTTAAG
EST: gi|58607492|gb|CK035525.1|CK035525
EST:     TTCATGTCATAAGCTGTGGGTACGAAGATAAGACAGACTGGGGGAAAGAG                         ATTGGCTGGATCTACGGATCAGTTACAGAAGATATTCTAACTGGTTTAAAG
genomic: TTCATGTCATAAGCTGTGGGTACGAAGATAAGACAGACTGGGGGAAAGAGgtaaggactg ... tttgttgcagATTGGCTGGATCTACGGATCAGTTACAGAAGATATTCTAACTGGTTTTAAG
EST: gi|86882518|gb|CI327259.1|CI327259
EST:     TTCATGTCATAAGCTGTGGGTACGAAGATAAGACAGACTGGGGG-AAGAG                         ATTGGCTGGATCTACGGATCAGTTACAGAAGATATTCTAACTGGTTTTAAT
genomic: TTCATGTCATAAGCTGTGGGTACGAAGATAAGACAGACTGGGGGAAAGAGgtaaggactg ... tttgttgcagATTGGCTGGATCTACGGATCAGTTACAGAAGATATTCTAACTGGTTTTAAG
EST: gi|163928491|gb|EG711376.1|EG711376
EST:     CAGACTGGGGGAAAGAG                         ATTGGCTGGATCTACGGATCAGTTACAGAAGATATTCTAACTGGTTTTAAG
genomic: CAGACTGGGGGAAAGAGgtaaggactg ... tttgttgcagATTGGCTGGATCTACGGATCAGTTACAGAAGATATTCTAACTGGTTTTAAG
EST: gi|29675228|gb|CB671503.1|CB671503
EST:     TTCATGTCATAAGCTGTGGGTACGAAGATAAGACAGACTGGGGGAAAGAG                         ATTGGCTGGATCTACGGATCAGTTACAGAAGATATTCTAACTGGTTTTAAG
genomic: TTCATGTCATAAGCTGTGGGTACGAAGATAAGACAGACTGGGGGAAAGAGgtaaggactg ... tttgttgcagATTGGCTGGATCTACGGATCAGTTACAGAAGATATTCTAACTGGTTTTAAG
EST: gi|29628005|gb|CB633016.1|CB633016
EST:     TTCATGTCATAAGCTGTGGGTACGAAGATAAGACAGACTGGGGGAAAGAG                         ATTGGCTGGATCTACGGATCAGTTACAGAAGATATTCTAACTGGTTTTAAG
genomic: TTCATGTCATAAGCTGTGGGTACGAAGATAAGACAGACTGGGGGAAAGAGgtaaggactg ... tttgttgcagATTGGCTGGATCTACGGATCAGTTACAGAAGATATTCTAACTGGTTTTAAG
EST: gi|86876412|gb|CI318407.1|CI318407
EST:     TTCATGTCATAAGCTGTGGGTACGAAGATAAGACAGACTGGGGGAAAGAG                         ATTGGCTGGATCTACGGATCAGTTACAGAAGATATTCTAACTGGTTTTAAG
genomic: TTCATGTCATAAGCTGTGGGTACGAAGATAAGACAGACTGGGGGAAAGAGgtaaggactg ... tttgttgcagATTGGCTGGATCTACGGATCAGTTACAGAAGATATTCTAACTGGTTTTAAG

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), 73 (downstream exon)
Score: 56

TGGTGGAACCTTGAAAAGTGCGAGTCCAGCATCTCTTCTAAAGGAAGCAATTCATGTCATAAGCTGTGGGTACGAAGATAAGACAGACTGGGGGAAAGAGgtaaggactg ... tttgttgcagATTGGCTGGATCTACGGATCAGTTACAGAAGATATTCTAACTGGTTTTAAGATGCACTGCCATGGTTGGCGGTCAATTTACTGCATACCTAAACTACCTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aactggttaattgattgaaacatttcttaactagttaattatatctttgttgcagATTGGCTGGATCTACGGATCAGTTACAGAAGATATTCTAACTGGTTTTAAGATGCACTGCCATGGTTGGCGGTCAATTTACTGCATACCTAAACTACCTG
                                           tctttgtt  CT-rich tract
                 aaacatttcttaacta  TA-rich tract