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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttatactttaatgagagtatgagacttaggcgattaaccaccatggcttttagaacattgtttggtttgtaacaccacatctatttccttatggatgcagATATTATGTGCGGGTAAGGATCTGGCAACAGAACAAACTTTTAGTAAGATGGTTAATTTGCTAAGACAGCTTCAGACTACATTGCCTCCTTCAGTACTGG

Basic information

species Oryza sativa
transcript LOC_Os03g49420.4
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g49420.4 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G033619_T01 (Zea mays), 3'ss of exon 18
--------------------------------------------------------------------------------------------------ttatact-ttaatgagagtatgagacttaggcgattaa-ccaccatggcttttagaacattgtttggtttgtaacaccacatctatttccttatggatgcagATATTATGTGCGGGTAAGGATCTGGCAACAGAACAAACTTTTAGTAAGATGGTTAATTTGCTAAGACAGCTTCAGACTACATTGCCTCCTTCAGTACTGG
                                                                                                  ||  ||  || |  |||  || |     |||  | | | | | |   |      || |||| |||  ||   |||   |  |   |||  |   | |||||||||||||||||||| || ||||| ||||||||||| |||   || | |||||||||| | ||||| || |||||| | |||||||||||||||||| | |
gtacctttagccttttcttattttcctcaatcttgttttctttatattatcccccttctgtttcccaaggtctatggaatatggataaactgcaactcttgaaccgtttaaaagaccatcatttggaggaaactgagctatccaagtgacaggagcattatttactt---aacttgatctgccttttgtatggaatgcagATATTATGTGCGGGCAAAGATCTAGCAACAGAACAGACTGCCAGCAGGATGGTTAATCTACTAAGGCAACTTCAGGCAACATTGCCTCCTTCAGTATTAG

upper sequence: LOC_Os03g49420.4 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA19G29010.1 (Glycine max), 3'ss of exon 19
ttatacttt-aatgagagtatgagacttaggcgattaaccaccatggcttttagaacattgtttggtt-tgtaacaccacatctatttccttatggatgcagATATTATGTGCGGGTAAGGATCTGGCAACAGAACAAACTTTTAGTAAGATGGTTAATTTGCTAAGACAGCTTCAGACTACATTGCCTCCTTCAGTACTGG
   |||||| ||||  |||      |||||    |   |   || |  | |     || | ||   || |  ||       | |   ||      |||| |||| ||||||||||| || |||||||| || ||||| ||| |||||| |||| |||||||  | || ||||||||    || || || |||||    || |
--gtactttcaatgctagttct---cttagttact--gctgtca-gattctggatccacttttcccttataaaatgtttgttttgcatcgactatgatgtagATTTTATGTGCGGGAAATGATCTGGCTACCGAACAGACTGTTAGTAGGATGATTAATTTATTGAGGCAGCTTCAACAGACTTTACCACCTTCTACCCTTG

upper sequence: LOC_Os03g49420.4 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv06s0004g00500.t01 (Vitis vinifera), 3'ss of exon 19
----ttatactt-taatgagagtatgagacttaggcgattaaccaccatggcttttagaacattgtttggtttgtaacaccacatctatttccttatggatgcagATATTATGTGCGGGTAAGGATCTGGCAACAGAACAAACTTTTAGTAAGATGGTTAATTTGCTAAGACAGCTTCAGACTACATTGCCTCCTTCAGTACTGG
    |   | |   | ||  | |||      | |    ||       |   ||  | ||| | | |||  ||| |      | ||     || | ||  ||| || |  ||||||||||||||||||| |||||||| |||||  | ||   |||| | || ||||| ||||| ||||||   ||  | || |||||     |||
aatttagcagtcacattgccattatacagtatggtactttttatgttacaactgatggaaaaatctttcctttattgatgaaaat-----tcatcattaatgtagGTTCTATGTGCGGGTAAGGATCTTGCAACAGAGCAAACCATAAGCCGGATGATAAACTTGCTGAGACAACTTCAGCAGACGCTACCACCTTCCACCTTGG

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|88849788|gb|CI001494.1|CI001494
EST:     TGGGTCATAACAACCAGTATCTTCCCAAGATTGTCTCTATTTTTGCGGAG                         ATATTATGTGCGGGTAAGGATCTGGCCACAGAACAAACTTTTAGTAAGATG
genomic: TGGGTCATAACAACCAGTATCTTCCAAAGATTGTCTCTATTTTTGCGGAGgtacctattt ... atggatgcagATATTATGTGCGGGTAAGGATCTGGCAACAGAACAAACTTTTAGTAAGATG
EST: gi|86597066|gb|CI272661.1|CI272661
EST:     TGGGTCATAACCACCAGTATCTTCCAAAGATTGTCCCTATTTTTGCGGAG                         ATATTATGTGCGGGTAAGGATCTGGCAACAGAACCAACTTTTAGTAAGATG
genomic: TGGGTCATAACAACCAGTATCTTCCAAAGATTGTCTCTATTTTTGCGGAGgtacctattt ... atggatgcagATATTATGTGCGGGTAAGGATCTGGCAACAGAACAAACTTTTAGTAAGATG
EST: gi|29629841|gb|CB634850.1|CB634850
EST:     TGGGTCATAACAACCAGTATCTTCCAAAGATTGTCTCTATTTTTGCGGAG                         ATATTATGTGCGGGTAAGGATCTGGCAACAGAACAAACTTTTAGTAAGATG
genomic: TGGGTCATAACAACCAGTATCTTCCAAAGATTGTCTCTATTTTTGCGGAGgtacctattt ... atggatgcagATATTATGTGCGGGTAAGGATCTGGCAACAGAACAAACTTTTAGTAAGATG
EST: gi|27576974|gb|CA999668.1|CA999668
EST:     TGGGTCATAACAACCAGTATCTTCCAAAGATTGTCTCTATTTTTGCGGAG                         ATATTATGTGCGGGTAAGGATCTGGCAACAGAACAAACTTTTAGTAAGATG
genomic: TGGGTCATAACAACCAGTATCTTCCAAAGATTGTCTCTATTTTTGCGGAGgtacctattt ... atggatgcagATATTATGTGCGGGTAAGGATCTGGCAACAGAACAAACTTTTAGTAAGATG
EST: gi|29629241|gb|CB634252.1|CB634252
EST:     TGGGTCATAACAACCAGTATCTTCCAAAGATTGTCTCTATTTTTGCGGAG                         ATATTATGTGCGGGTAAGGATCTGGCAACAGAACAAACTTTTAGTAAGATG
genomic: TGGGTCATAACAACCAGTATCTTCCAAAGATTGTCTCTATTTTTGCGGAGgtacctattt ... atggatgcagATATTATGTGCGGGTAAGGATCTGGCAACAGAACAAACTTTTAGTAAGATG
EST: gi|29679232|gb|CB675507.1|CB675507
EST:     TGGGTCATAACAACCAGTATCTTCCAAAGATTGTCTCTATTTTTGCGGAG                         ATATTATGTGCGGGTAAGGATCTGGCAACAGAACAAACTTTTAGTAAGATG
genomic: TGGGTCATAACAACCAGTATCTTCCAAAGATTGTCTCTATTTTTGCGGAGgtacctattt ... atggatgcagATATTATGTGCGGGTAAGGATCTGGCAACAGAACAAACTTTTAGTAAGATG
EST: gi|29681491|gb|CB677766.1|CB677766
EST:     TGGGTCATAACAACCAGTATCTTCCAAAGATTGTCTTTATTTTTGCGGAG                         ATATTATGTGCGGGTAAGGATCTGGCAACAGAACAAACTTTTAGTAAGATG
genomic: TGGGTCATAACAACCAGTATCTTCCAAAGATTGTCTCTATTTTTGCGGAGgtacctattt ... atggatgcagATATTATGTGCGGGTAAGGATCTGGCAACAGAACAAACTTTTAGTAAGATG

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: 67 (upstream exon), 75 (downstream exon)
Score: 18

GTCAGATAGGGAGCTTTTGGGTCATAACAACCAGTATCTTCCAAAGATTGTCTCTATTTTTGCGGAGgtacctattt ... atggatgcagATATTATGTGCGGGTAAGGATCTGGCAACAGAACAAACTTTTAGTAAGATGGTTAATTTGCTAAGACAGCTTCAGACTACATTGCCTCCTTCAGTACTGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcttttagaacattgtttggtttgtaacaccacatctatttccttatggatgcagATATTATGTGCGGGTAAGGATCTGGCAACAGAACAAACTTTTAGTAAGATGGTTAATTTGCTAAGACAGCTTCAGACTACATTGCCTCCTTCAGTACTGG
                     ttgtaac  putative branch site (score: 18)
                                      tttccttat  putative PPT
                                 atctattt  TA-rich tract