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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgctcttcccgtctgtgtttgtgcttgtagtctttatttctttttagttttgctgaatatttctggtcaaaagaacttttgttgctgatcactgaagtatgctgtctgaaacttttgtgcaccatggattctattaatgtaacaagcaatttatttctagGAAGGGATTGCTTTTGTTTGATGCCAACTGGAGGTGGAAAATCAATGTGCTATCAGATTCCTGCTCTAGTGAAGTCAGGCATTGTTCTTGTTATCTCACC

Basic information

species Oryza sativa
transcript LOC_Os02g54020.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g54020.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G039683_T01 (Zea mays), 3'ss of exon 2
gtgctcttcccgtctgtgtttgtgcttgtagtctttatttctttttagttttgctgaatatttctggtcaaaagaacttttgttgctgatcactgaagtatgctgtctgaaacttttgtgcaccatggattctatt-aatgtaacaagcaatttatttctagGAAGGGATTGCTTTTGTTTGATGCCAACTGGAGGTGGAAAATCAATGTGCTATCAGATTCCTGCTCTAGTGAAGTCAGGCATTGTTCTTGTTATCTCACC
||| | |||||| | || || | | || | ||| | ||| | || || |||| | ||| |||| || | || ||| | | |||||||| | ||| || |||||||||||||||||||||||||| |||||||| || ||||||||||||||||| ||||| ||||| |||||||||||||||| || |||||
--------------------------------------gtctgctcg--cttgctgcgctcgtgtgttcttat-atctgtaattggttggcacc----tgtgttg-ctgagatgttttcaacgtatgggttttgtttaatatgttatacaatttatgtgcagGGAGAGATTGCTTTTGTTTGATGCCAACTGGTGGTGGAAAGTCCATGTGCTATCAGATTCCAGCTCTGGTGAAAACAGGCATTGTTCTTGTCATTTCACC

upper sequence: LOC_Os02g54020.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT4G35740.1 (Arabidopsis thaliana), 3'ss of exon 1
gtgctcttcccgtctgtgtttgtgcttgtagtctttatttctttttagttttgctgaatatttctggtcaaaagaacttttgttgctgatcactgaagtatgctgtctgaaacttttgtgcaccatggattctattaatgtaacaagcaatttatttctagGAAGGGATTGCTTTTGTTTGATGCCAACTGGAGGTGGAAAATCAATGTGCTATCAGATTCCTGCTCTAGTGAAGTCAGGCATTGTTCTTGTTATCTCACC
|| | | | |||| | | | | | || | | | ||| | | | || | | | || | | ||| |||||||||||||||||| ||||||||||| ||||| |||||||| || || |||||||| ||||| ||| || | || || || |||||| | || ||
------------------------------------------------------------------gtaagtcgtaatttttctcttttactccggagaaaattagaatgattgttttagaattctctgttttgtgattg----atgagatt-------agGAAGGGATTGCTTTTGCTTGATGCCAACGGGAGGAGGAAAATCGATTTGTTATCAGATACCTGCATTAGCTAAACCTGGAATCGTCCTTGTTGTGTCTCC

upper sequence: LOC_Os02g54020.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv11s0016g00850.t01 (Vitis vinifera), 3'ss of exon 1
gtgctcttcccgtctgtgtttgtgcttgtagtctttatttctttttagttttgctgaatatttctggtcaaaagaacttttgttgctgatcactgaagtatgctgtctgaaacttttgtgcaccatg-----gattctattaatgtaacaagcaatttatt-tctagGAAGGGATTGCTTTTGTTTGATGCCAACTGGAGGTGGAAAATCAATGTGCTATCAGATTCCTGCTCTAGTGAAGTCAGGCATTGTTCTTGTTATCTCACC
|||| || | | | | | || | | ||| || || |||| | || || | |||| || || || | ||| || | |||||| ||||| |||||| | |||||||| ||||| ||||| |||||||| |||||||||||||| || | || |||| ||||| || || | | ||
----------------------------------------------------------------cagtcagaaagagtgtag--agttatgttggcgatcctttgtatggaatttttttaaacagtgatttgggttctgttgat-tagtgctaattttcttgtgcagGAAGAGATTGTTTTTGTCTCATGCCAACAGGAGGAGGAAAGTCAATGTGTTATCAGATTCCTGCACTGGCAAAACCAGGGATTGTGCTCGTGGTTTGTCC

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|88314892|gb|CI608351.1|CI608351
EST:     TTCAGGCTTTCGAGGAAAGCAACTACAGGCTATAGAAGCTGTTCTTTCAG                         GAAGGGATTGCTTTTGTTTGATGCCAACCTGGAGGTGGAAAATCAATGTGC
genomic: TTCAGGCTTTCGAGGAAAGCAACTAGAGGCTATAGAAGCTGTTCTTTCAGgtgctcttcc ... ttatttctagGAAGGGATTGCTTTTGTTTGATGCCAAC-TGGAGGTGGAAAATCAATGTGC
EST: gi|88730102|gb|CI753717.1|CI753717
EST:     TTCAGGCTTCCGAGGAAAGCAACTAGAGGCTATAGAACCTGTCCTTCCAG                         GAAGGGATTGCTTTTGTTTGATGCCAACTGGAGGTGGAAAATCAATGTGCT
genomic: TTCAGGCTTTCGAGGAAAGCAACTAGAGGCTATAGAAGCTGTTCTTTCAGgtgctcttcc ... ttatttctagGAAGGGATTGCTTTTGTTTGATGCCAACTGGAGGTGGAAAATCAATGTGCT
EST: gi|88729634|gb|CI751437.1|CI751437
EST:     TTCAGGCTTTCGAGGAAAGCAACTAGAGGCTATAGAAGCTGTTCTTTCAG                         GAAGGGATTGCTTTTGTTTGATGCCAACTGGAGGTGGAAAATCAATGTGCT
genomic: TTCAGGCTTTCGAGGAAAGCAACTAGAGGCTATAGAAGCTGTTCTTTCAGgtgctcttcc ... ttatttctagGAAGGGATTGCTTTTGTTTGATGCCAACTGGAGGTGGAAAATCAATGTGCT
EST: gi|88369281|gb|CI577744.1|CI577744
EST:     TTCAGGCTTTCGAGGAAAGCAACTAGAGGCTATAGAAGCTGTTCTTTCAG                         GAAGGGATTGCTTTTGTTTGATGCCAACTGGAGGTGGAAAATCAATGTGCT
genomic: TTCAGGCTTTCGAGGAAAGCAACTAGAGGCTATAGAAGCTGTTCTTTCAGgtgctcttcc ... ttatttctagGAAGGGATTGCTTTTGTTTGATGCCAACTGGAGGTGGAAAATCAATGTGCT

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: 57 (upstream exon), 74 (downstream exon)
Score: 7

AAGAAAGCTCCTCAGGAGCTGGAGAACGTCTTGAAGCAACATTTCGGATATTCAGGCTTTCGAGGAAAGCAACTAGAGGCTATAGAAGCTGTTCTTTCAGgtgctcttcc ... ttatttctagGAAGGGATTGCTTTTGTTTGATGCCAACTGGAGGTGGAAAATCAATGTGCTATCAGATTCCTGCTCTAGTGAAGTCAGGCATTGTTCTTGTTATCTCACC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgaaacttttgtgcaccatggattctattaatgtaacaagcaatttatttctagGAAGGGATTGCTTTTGTTTGATGCCAACTGGAGGTGGAAAATCAATGTGCTATCAGATTCCTGCTCTAGTGAAGTCAGGCATTGTTCTTGTTATCTCACC
                                            tttatttct  CT-rich tract
 attctattaatgtaa  TA-rich tract