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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgatgtccattttagctgaatccctggatctaattgccgatatctactatgtttggtattaccattttcttacagttgttaatgtgacttcagGCTATTGCCAACTTATCGGTGAATGCCAAGGTTGCAAAGGCAGTTGCAGACGAGGGAGGTATCACAATACTAACCAATTTGGCCAGGTCAATGAATCGGC

Basic information

species Oryza sativa
transcript LOC_Os10g41360.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g41360.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G028796_T01 (Zea mays), 3'ss of exon 1
gtaatgatgtccattttagctgaatccctggatctaattgccgatatctactatgtttggtattaccattttcttacagttgttaatgtgacttc--agGCTATTGCCAACTTATCGGTGAATGCCAAGGTTGCAAAGGCAGTTGCAGACGAGGGAGGTATCACAATACTAACCAATTTGGCCAGGTCAATGAATCGGC
               |||| ||  || ||    ||  |      ||       || |||   ||||||| |||| ||| | |||||||  ||     |||||||||||||||| || |||||| |||||||||| |||||||||||||| || || || || |||||||| ||  |||| |||| ||| |||||| |||
-----------gtaattagttgtttctctctgcctgttattttttagtgttcttgcttgcatttaccatcttctcacattagttaatgccaccatgaagGCTATTGCCAACTTGTCAGTGAATACCAAGGTTGCCAAGGCAGTTGCAGATGAAGGCGGCATTACAATACTCACTGATTTAGCCAAGTCGATGAATAGGC

upper sequence: LOC_Os10g41360.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G079031_T03 (Zea mays), 3'ss of exon 1
gtaatgatgtccattttagctgaatccctggatctaattgccgatatctactatgtttggtattaccattttcttacagttgttaatgtgac--ttcagGCTATTGCCAACTTATCGGTGAATGCCAAGGTTGCAAAGGCAGTTGCAGACGAGGGAGGTATCACAATACTAACCAATTTGGCCAGGTCAATGAATCGGC
             |  ||  |   |||     ||   | |    ||       || |||   ||||||| |||| ||| | |||||||| ||  | ||||||||||||||||| || |||||| |||||||||| |||||||||||||| || || || || |||||||| |  ||||| |||| ||| |||||| |||
------------gtaataaattgttcctctcttcccttcgtatttagtgttcttgcttgcatttaccatcttctcacattagttaatgtcaccatgcagGCTATTGCCAACTTGTCAGTGAATACCAAGGTTGCCAAGGCAGTTGCAGATGAAGGCGGCATTACAATACTCATTAATTTAGCCAAGTCGATGAATAGGC

upper sequence: LOC_Os10g41360.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv15s0021g01810.t01 (Vitis vinifera), 3'ss of exon 2
---gtaatgatgtccattttagctgaatccctggatctaattgccgatatct-actatgtttggtattaccattttcttacagttg---ttaatgtgacttcagGCTATTGCCAACTTATCGGTGAATGCCAAGGTTGCAAAGGCAGTTGCAGACGAGGGAGGTATCACAATACTAACCAATTTGGCCAGGTCAATGAATCGGC
     | |  ||||  | |||  |||| |     || |  ||   ||| |   | |    |||     |||| |||  |    |      |  ||    |  |||||||||||||||| |||||||||||||| |||||||| || |||||||| || ||||| ||||  |||||  ||| |||||| ||||| |||||  || 
acaagattagtgtcattatta--tgaaacttgacattt--ttattgattttggattgaagttgtggaaaccaatttaatttgttaaaatctgttgcatatgtagGCTATTGCCAACTTGTCGGTGAATGCCAATGTTGCAAAAGCTGTTGCAGATGAAGGAGGAATCAATATACTTTCCAGTTTGGCTAGGTCCATGAACAGGT

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|29642133|gb|CB647140.1|CB647140
EST:     TGGACCTTGCAAGGTGTTCAAGGGAGAGTGCACAGTCAGAAGCAGCAAAG                         GCTATTGCCAACTTATCGGTGAATGCCAAGGTTGCAAAGGCAGTTGCAGAC
genomic: TGGACCTTGCAAGGTGTTCAAGGGAGAGTGCACAGTCAGAAGCAGCAAAGgtaatgatgt ... gtgacttcagGCTATTGCCAACTTATCGGTGAATGCCAAGGTTGCAAAGGCAGTTGCAGAC
EST: gi|87017043|gb|CI286179.1|CI286179
EST:     TGGACCTTGCAAGGTGTTCAAGGGAGAGTGCACAGTCAGAAGCAGCAAAG                         GCTATTGCCAACTTATCGGTGAATGCCAAGGTTGCAAAGGCAGTTGCA
genomic: TGGACCTTGCAAGGTGTTCAAGGGAGAGTGCACAGTCAGAAGCAGCAAAGgtaatgatgt ... gtgacttcagGCTATTGCCAACTTATCGGTGAATGCCAAGGTTGCAAAGGCAGTTGCA
EST: gi|29627762|gb|CB632773.1|CB632773
EST:     TGGACCTTGCAAGGTGTTCAAGGGAGAGTGCACAGTCAGAAGCAGCAAAG                         GCTATTGCCAACTTATCGGTGAATGCCAAGGTTGCAAAGGCAGTTGCAGAC
genomic: TGGACCTTGCAAGGTGTTCAAGGGAGAGTGCACAGTCAGAAGCAGCAAAGgtaatgatgt ... gtgacttcagGCTATTGCCAACTTATCGGTGAATGCCAAGGTTGCAAAGGCAGTTGCAGAC
EST: gi|88414832|gb|CI604190.1|CI604190
EST:     TGGACCTTGCAAGGTGTTCAAGGGAGAGTGCACAGTCAGAAGCAGCAAAG                         GCTATTGCCAACTTATCGGTGAATG
genomic: TGGACCTTGCAAGGTGTTCAAGGGAGAGTGCACAGTCAGAAGCAGCAAAGgtaatgatgt ... gtgacttcagGCTATTGCCAACTTATCGGTGAATG
EST: gi|29635379|gb|CB640388.1|CB640388
EST:     TGGACCTTGCAAGGTGTTCAAGGGAGAGTGCACAGTCAGAAGCAGCAAAG                         GCTATTGCCAACTTATCGGTGAATGCCAAGGTTGCAAAGGCAGTTGCAGAC
genomic: TGGACCTTGCAAGGTGTTCAAGGGAGAGTGCACAGTCAGAAGCAGCAAAGgtaatgatgt ... gtgacttcagGCTATTGCCAACTTATCGGTGAATGCCAAGGTTGCAAAGGCAGTTGCAGAC

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: 75 (upstream exon), 68 (downstream exon)
Score: 11

TGCTGCAAGATCAGAGGCAGTGATGCGTGTTGGGGGCATTCCAATGCTACTGGACCTTGCAAGGTGTTCAAGGGAGAGTGCACAGTCAGAAGCAGCAAAGgtaatgatgt ... gtgacttcagGCTATTGCCAACTTATCGGTGAATGCCAAGGTTGCAAAGGCAGTTGCAGACGAGGGAGGTATCACAATACTAACCAATTTGGCCAGGTCAATGAATCGGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatatctactatgtttggtattaccattttcttacagttgttaatgtgacttcagGCTATTGCCAACTTATCGGTGAATGCCAAGGTTGCAAAGGCAGTTGCAGACGAGGGAGGTATCACAATACTAACCAATTTGGCCAGGTCAATGAATCGGC
                         attttctta  TA-rich tract