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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtttttttatattgattcagctggttatcccttcttggataacctttatatattttttatcaaatttaaattaattgccttttagctcatttgttccttgattaataactaatgtaaattgccaactgtgtctatgactgcagTGCATGACAAACAATTAGTGAATGACATTCCAGTTGAGAAGCTGTTAGTTCATGATGTACCAGTTGACATTATCTGCACTCCAACTCAGGTCATATTCAC

Basic information

species Oryza sativa
transcript LOC_Os12g07020.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g07020.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G001904_T01 (Zea mays), 3'ss of exon 2
gtgagtttttttatattgattcagctggttatcccttcttggataacctttatatatttt-ttatcaaatttaaattaattgccttttagctcatttgttccttgattaataactaatgtaaattgccaactgtgtctatgactgcagTGCATGACAAACAATTAGTGAATGACATTCCAGTTGAGAAGCTGTTAGTTCATGATGTACCAGTTGACATTATCTGCACTCCAACTCAGGTCATATTCAC
                                 ||||||||  | |  |  | |  |  |    | |  || |||    |     ||||| |  |            ||   |||||  ||||| ||||||| | ||||||  | ||||||||||||| || |||||  ||||||||||||| ||||||||| ||||||||||||| |||||||||||||||||||| || ||||||||||| |||||
---------------------------------ccttcttgattgaaatgcagagctcctaccgttacgttcaaaaaggta----tttagtttgt----------gctagccactaacataaat-gccaactatttctatgcttacagTGCATGACAAGCAGTTAGTTGATGACATTCCAGTGGAGAAGCTGCTAGTTCATGATGTGCCAGTTGACATTATCTGCACCCCTACTCAGGTCATCTTCAC

upper sequence: LOC_Os12g07020.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA02G08860.1 (Glycine max), 3'ss of exon 5
gtgagtttttttatattgattcagctggttatcccttcttggataacctttatatattttttatcaaatttaaattaattgccttttagctcatttgttccttgattaataactaatgtaaattgccaactgtgtctatgactgcagTGCATGACAAACAATTAGTGAATGACATTCCAGTTGAGAAGCTGTTAGTTCATGATGTACCAGTTGACATTATCTGCACTCCAACTCAGGTCATATTCAC
                             | | |  || |   ||   | |   |||| ||   ||  | |||| |  ||||  |||  ||  |||      || |  |||||      | ||||  ||||      |    |||||||||||||   ||||| ||| | || ||||| ||||| ||||||||| | ||||| |||||||| || || || || |||||||| |||||||| |||||
--------------------------taatgtgcagtcatatttattatctgcttattctt-gccatgtgtaaaat--ttgcaatttgtcttcttt------tggtatataac------atattgagaact------acccttgcagTGCATGACTGCCAATTGGTGGACGATATTCCTGTTGAAAAGCTGTTAATCCATGACGTACCAGTGGATATCATTTGTACTCCAACACAGGTCATTTTCAC

upper sequence: LOC_Os12g07020.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA16G27960.1 (Glycine max), 3'ss of exon 4
gtgagtttttttatattgattcagctggttatcccttcttggataacctttatatattttttatcaaatttaaattaattgccttttagctcatttgttccttgattaataactaatgtaaattgccaactgtgtctatgactgcagTGCATGACAAACAATTAGTGAATGACATTCCAGTTGAGAAGCTGTTAGTTCATGATGTACCAGTTGACATTATCTGCACTCCAACTCAGGTCATATTCAC
                             | | |  || |    |   | | | |||| ||   ||  | |||| |  ||||  |||  ||  |||      || |  |||||      | | ||  ||||      |    |||||||||||||   ||||| ||| |||| ||||||||||| ||||||||| | |||||||||||||| || || || || || || || |||||||| || ||
--------------------------taatgtgcggtcatattcattatctgtttattctt-gccatgtgtaaaat--ttgcaatttctcttcttt------tggtatataac------atactgagaact------acccttgcagTGCATGACTGCCAATTGGTGGATGATATTCCAGTTGAAAAGCTGTTAATCCATGATGTACCAGTGGATATCATTTGTACCCCGACACAGGTCATTTTTAC

upper sequence: LOC_Os12g07020.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv18s0072g00300.t01 (Vitis vinifera), 3'ss of exon 4
gtgagtttttttatattgattcagctggttatcccttcttggataacctttatatattttttatcaaatt--taaattaattgccttttagctcatttgttccttgattaataactaatg-taaattgccaactgtgtctatgactgcagTGCATGACAAACAATTAGTGAATGACATTCCAGTTGAGAAGCTGTTAGTTCATGATGTACCAGTTGACATTATCTGCACTCCAACTCAGGTCATATTCAC
                                                  ||||| |         | ||  ||  ||     ||    | | | | | || |||  ||  ||| ||  | |  |||        | |||     |||||| |||||  | ||||| ||  |||| ||||| ||||||||||||||| | ||||| || |||||||| ||||| ||||| ||||| || ||||| || ||
--------------------------------------------------tatatgtggccatctgatttgttatcttcccctccccccaccccctctttttctttttttctaattatcgcttcattattttgattctctgattttgcagTACATGATGAGCAATTGGTCGATGATATTCCTGTTGAGAAGCTGTTAATCCATGACGTGCCAGTTGATATTATATGCACCCCAACCCAAGTCATTTTTAC

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|157650239|gb|EX449873.1|EX449873
EST:     GCTGCGTTATATGGGATCTATAAGCGATTCAACCATGATAGTAACAACTG                         TGCATGACAAACAATTAGTGAATGACATTCCAGTTGAGAAGCTGTTAGTTC
genomic: GCTGCGTTATATGGGATCTATAAGCGATTCAACCATGATAGTAACAACTGgtgagttttt ... atgactgcagTGCATGACAAACAATTAGTGAATGACATTCCAGTTGAGAAGCTGTTAGTTC
EST: gi|29666613|gb|CB662888.1|CB662888
EST:     GCTGCGTTATATGGGATCTATAAGCGATTCAACCATGATAGTAACAACTG                         TGCATGACAAACAATTAGTGAATGACATTCCAGTTGAGAAGCTGTTAGTTC
genomic: GCTGCGTTATATGGGATCTATAAGCGATTCAACCATGATAGTAACAACTGgtgagttttt ... atgactgcagTGCATGACAAACAATTAGTGAATGACATTCCAGTTGAGAAGCTGTTAGTTC
EST: gi|86848842|gb|CI295675.1|CI295675
EST:     GCTGCGTTATATGGGATCTATAAGCGATTCAACCATGATAGTAACAACTG                         TGCATGACAAACAATTAGTGAATGACATTCCAGTTGAGAAGCTGTTAGTTC
genomic: GCTGCGTTATATGGGATCTATAAGCGATTCAACCATGATAGTAACAACTGgtgagttttt ... atgactgcagTGCATGACAAACAATTAGTGAATGACATTCCAGTTGAGAAGCTGTTAGTTC
EST: gi|86503583|gb|CI146216.1|CI146216
EST:     GCTGCGTTATATGGGATCTATAAGCGATTCAACCATGATAGTAACAACTG                         TGCATGACAAACAATTAGTGAATGACATTCCAGTTGAGAAGCTGTTAGTTC
genomic: GCTGCGTTATATGGGATCTATAAGCGATTCAACCATGATAGTAACAACTGgtgagttttt ... atgactgcagTGCATGACAAACAATTAGTGAATGACATTCCAGTTGAGAAGCTGTTAGTTC
EST: gi|29658507|gb|CB654782.1|CB654782
EST:     GCTGCGTTATATGGGATCTATAAGCGATTCAACCATGATAGTAACAACTG                         TGCATGACAAACAATTAGTGAATGACATTCCAGTTGAGAAGCTGTTAGTTC
genomic: GCTGCGTTATATGGGATCTATAAGCGATTCAACCATGATAGTAACAACTGgtgagttttt ... atgactgcagTGCATGACAAACAATTAGTGAATGACATTCCAGTTGAGAAGCTGTTAGTTC
EST: gi|86493868|gb|CI136501.1|CI136501
EST:     GCTGCGTTATATGGGATCTATAAGCGATTCAACCATGATAGTAACAACTG                         TGCATGACAAACAATTAGTGAATGACATTCCAGTTGAGAAGCTGTTAGTTC
genomic: GCTGCGTTATATGGGATCTATAAGCGATTCAACCATGATAGTAACAACTGgtgagttttt ... atgactgcagTGCATGACAAACAATTAGTGAATGACATTCCAGTTGAGAAGCTGTTAGTTC

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), 70 (downstream exon)
Score: 28

GGATTTGCAGAGCTGGAATATGGGATGCTGCGTTATATGGGATCTATAAGCGATTCAACCATGATAGTAACAACTGgtgagttttt ... atgactgcagTGCATGACAAACAATTAGTGAATGACATTCCAGTTGAGAAGCTGTTAGTTCATGATGTACCAGTTGACATTATCTGCACTCCAACTCAGGTCATATTCAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttgttccttgattaataactaatgtaaattgccaactgtgtctatgactgcagTGCATGACAAACAATTAGTGAATGACATTCCAGTTGAGAAGCTGTTAGTTCATGATGTACCAGTTGACATTATCTGCACTCCAACTCAGGTCATATTCAC
         ttgattaataactaat  TA-rich tract