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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaaactatctagtgttctctaaattcttagcaatcctgctgtaaaactagttattgtgcctcgaatgggtaccaaattactaatgttgcatcatcagacatgtttccttataaatgagttgtttccctaattttttagGAGGCGCTCAGGACAAGAGGGCTAAAAGATGATACGACCTGCATCGTTGTTGACATGATCCCACCTGATCAAACAATACGTCATCCATCTCCACCAAAAA

Basic information

species Oryza sativa
transcript LOC_Os01g32964.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g32964.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G173734_T01 (Zea mays), 3'ss of exon 6
gtaagaaactatctagtgttctctaaattcttagcaatcctgctgtaaaactagttattgtgcctcgaatgggtaccaaattactaatgttgcatcatcagacatgtttccttataaatgagttgttt-----ccctaattttttagGAGGCGCTCAGGACAAGAGGGCTAAAAGATGATACGACCTGCATCGTTGTTGACATGATCCCACCTGATCAAACAATACGTCATCCATCTCCACCAAAAA
||||  |  |  | | |    | |||||||||    |||||             | ||  ||| ||  |||| |  ||| ||||||   || |||||  || |||  ||  || |||   |  |  ||     |  |||| || |||||||| |||||||||||||||||||| |||||||| || ||||| ||||||||||| |||||||||| |||||||||||| | ||  ||||| || ||||
gtaaatagtttaccacttggttataaattcttgcttatcct-------------tgatgctgcttcttatggttgtcaa-ttactatcattacatcactaggcatccttttttctaacccaagtacttgtatgcaataatcttatagGAGGCACTCAGGACAAGAGGGCTAAAGGATGATACAACTTGCATTGTTGTTGACATAATCCCACCTGGTCAAACAATACGGCCTCTGTCTCCTCCTAAAA

upper sequence: LOC_Os01g32964.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA20G25360.1 (Glycine max), 3'ss of exon 8
gtaagaaactatctagtgttctctaaattcttagcaatcctgctgtaaaactagttattgtgcctcgaatgggtaccaaattactaatgttgcatcatcagacatgtttccttataaatgagt-tgtttccctaattttttagGAGGCGCTCAGGACAAGAGGGCTAAAAGATGATACGACCTGCATCGTTGTTGACATGATCCCACCTGATCAAACAATACGTCATCCATCTCCACCAAAAA
|||  |     |  |||| | |||  | | ||  |||| |||   |   | | |  |||         ||  | | ||         |||||||  | | | ||| | |||| | |  |   | | ||||     || || |||| || || || || |||||| |||| |||||||| || ||||| || |||||||| |||||||||||| |   | | |  |   || |||| ||    |
gtagtatgaactacagtgctatctgcaatttttccaattctggcttgtgatttgacattac----tacattagcatca---------tgttgcaa-agctggcatttctcctcacatgtatatatatttcaactgttattcagGAAGCACTAAGAACGAGAGGGTTAAAGGATGATACAACTTGCATAGTAGTTGACATAATCCCACCTGATAACGAATTGCCACCAACACCTCCCCCCCCCA
















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|58666920|gb|CK055606.1|CK055606
EST:     AGTGTTGCAGAGGTTTGCCTGCTGAGCTTGCTGCTAAGCAAGTTGTTAAG                         GAGGCGCTCAGGACAAGAGGGCTAAAAGATGATACGACCTGCATCGTTGTT
genomic: AGTGTTGCAGAGGTTTGCCTGCTGAGCTTGCTGCTAAGCAAGTTGTTAAGgtaagaaact ... aattttttagGAGGCGCTCAGGACAAGAGGGCTAAAAGATGATACGACCTGCATCGTTGTT
EST: gi|29630450|gb|CB635459.1|CB635459
EST:     AGTGTTGCAGAGGTTTGCCTGCTGAGCTTGCTGCTAAGCAAGTTGTTAAG                         GAGGCGCTCAGGACAAGAGGGCTAAAAGATGATACGACCTGCATCGTTGTT
genomic: AGTGTTGCAGAGGTTTGCCTGCTGAGCTTGCTGCTAAGCAAGTTGTTAAGgtaagaaact ... aattttttagGAGGCGCTCAGGACAAGAGGGCTAAAAGATGATACGACCTGCATCGTTGTT
EST: gi|44671989|gb|CR285423.1|CR285423
EST:     AGTGTTGCAGAGGTTTGCCTGCTGAGCTTGCTGCTAAGCAAGTTGTTAAG                         GAGGCGCTCAGGACAAGAGGGCTAAAAGATGATACGACCTGCATCGTTGTT
genomic: AGTGTTGCAGAGGTTTGCCTGCTGAGCTTGCTGCTAAGCAAGTTGTTAAGgtaagaaact ... aattttttagGAGGCGCTCAGGACAAGAGGGCTAAAAGATGATACGACCTGCATCGTTGTT
EST: gi|58683741|gb|CK072428.1|CK072428
EST:     CTGCTGAGCTTGCTGCTAAGCAAGTTGTTAA-                         GAGGCGCTCAGGACAAGAGGGCTAAAAGATGATACGACCTGCATCGTTGTT
genomic: CTGCTGAGCTTGCTGCTAAGCAAGTTGTTAAGgtaagaaact ... aattttttagGAGGCGCTCAGGACAAGAGGGCTAAAAGATGATACGACCTGCATCGTTGTT

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: 54 (upstream exon), 65 (downstream exon)
Score: 13

TATTGCATCAGATGGCATTTGGGATGCCTTGTCATCAGAGGCAGCTGCAAAGTGTTGCAGAGGTTTGCCTGCTGAGCTTGCTGCTAAGCAAGTTGTTAAGgtaagaaact ... aattttttagGAGGCGCTCAGGACAAGAGGGCTAAAAGATGATACGACCTGCATCGTTGTTGACATGATCCCACCTGATCAAACAATACGTCATCCATCTCCACCAAAAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttgcatcatcagacatgtttccttataaatgagttgtttccctaattttttagGAGGCGCTCAGGACAAGAGGGCTAAAAGATGATACGACCTGCATCGTTGTTGACATGATCCCACCTGATCAAACAATACGTCATCCATCTCCACCAAAAA
                                         ccctaat  putative branch site (score: 13)
                                      tttccctaatttttt  CT-rich tract
                                            taatttttta  TA-rich tract