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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacccaagactttatttaaccatgttatagatcgaatactatctgctagggtaagtcctgacagtaacataaacctgttccttagGTGATTATGGGAAAATAATATCTTGGAATACGACCTCGTGGACGAGAATTGGGTCAAATAAAATAACACGTGAGGCAATTTCAGCATTTGCTGTCTCGCC

Basic information

species Oryza sativa
transcript LOC_Os11g39650.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g39650.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G011364_T01 (Zea mays), 3'ss of exon 6
gtaac-ccaagactttatttaaccatgttatagatcgaatactatctgctagggtaagtcctgacagtaac---ataaacctgttccttagGTGATTATGGGAAAATAATATCTTGGAATACGACCTCGTGGACGAGAATTGGGTCAAATAAAATAACACGTGAGGCAATTTCAGCATTTGCTGTCTCGCC
|| ||   |||  || | || |||  |||| | || ||||     |  | ||  ||||  |||||| |  |   | ||   || |  ||||| |||||||| |||||| | ||||||||||| ||||| ||||||||||  || ||||| |||||||| ||||||||||||||||| |||||||| || ||
gtgacattaaggtttaagttgacctagttacaaattgaat-taggcaacaagcttaaggtctgacaatgcctgaacaatattgatttttagGCGATTATGGAAAAATAGTGTCTTGGAATACTACCTCATGGACGAGAACCGGATCAAAGAAAATAACTCGTGAGGCAATTTCAGCTTTTGCTGTGTCACC

upper sequence: LOC_Os11g39650.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G041642_T03 (Zea mays), 3'ss of exon 5
gtaacccaagactttat-ttaaccatgttatagatcgaatactatctgctagggtaagtcctgacagtaacata--aacctgttccttagGTGATTATGGGAAAATAATATCTTGGAATACGACCTCGTGGACGAGAATTGGGTCAAATAAAATAACACGTGAGGCAATTTCAGCATTTGCTGTCTCGCC
|| ||   |   ||||  || | |  |||| | |  ||||     |  | ||  ||||   || || || |  |  ||  | ||  |||||||||||||| |||||| ||||||||||||| ||||| ||||| ||||  || ||||| |||||||| ||||||||||||||||| ||||| || |||||
gtgacattaaggtttacgttgatctagttacaaactgaat-taggcaacaagcttaaggtttggcaatacctgagtaatattttttttagGTGATTATGGAAAAATAGTATCTTGGAATACTACCTCATGGACAAGAACAGGATCAAAGAAAATAACTCGTGAGGCAATTTCAGCGTTTGCGGTGTCGCC
















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|29675265|gb|CB671540.1|CB671540
EST:     TCTAATCAGACTGACAACAGTCAGATCCTCTTTGTTTACAGCGATGCAAG                         GTGATTATGGGAAAATAATATCTTGGAATACGACCTCGTGGACGAGAATTG
genomic: TCTAATCAGACTGACAACAGTCAGATCCTCTTTG-TTACAGCGATGCAAGgtaacccaag ... tgttccttagGTGATTATGGGAAAATAATATCTTGGAATACGACCTCGTGGACGAGAATTG
EST: gi|33795266|gb|CF323505.1|CF323505
EST:     CTCTAATCTGACTGACAACAGTCAGATCCTCTTTGTTACAGCGATGCAAG                         GTGATTATGGGAAAATAATATCTTGGAATACGACCTCGTGGACGAGAATTG
genomic: CTCTAATCAGACTGACAACAGTCAGATCCTCTTTGTTACAGCGATGCAAGgtaacccaag ... tgttccttagGTGATTATGGGAAAATAATATCTTGGAATACGACCTCGTGGACGAGAATTG
EST: gi|29665512|gb|CB661787.1|CB661787
EST:     TCAGACTGACAACAGTCAGATCCTCTTTGTTACAGCGATGCAAG                         GTGATTATGGGAAAATAATATCTTGGAATACGACCTCGTGGACGAGAATTG
genomic: TCAGACTGACAACAGTCAGATCCTCTTTGTTACAGCGATGCAAGgtaacccaag ... tgttccttagGTGATTATGGGAAAATAATATCTTGGAATACGACCTCGTGGACGAGAATTG
EST: gi|29671178|gb|CB667453.1|CB667453
EST:     TCAGACTGACAACAGTCAGATCCTCTTTGTTACAGCGATGCAAG                         GTGATTATGGGAAAATAATATCTTGGAATACGACCTCGTGGACGAGAATTG
genomic: TCAGACTGACAACAGTCAGATCCTCTTTGTTACAGCGATGCAAGgtaacccaag ... tgttccttagGTGATTATGGGAAAATAATATCTTGGAATACGACCTCGTGGACGAGAATTG
EST: gi|218487277|gb|FG955018.1|FG955018
EST:     GATCCTCTTTGTTACAGCGATGCAAG                         GTGATTATGGGAAAATAATATCTTGGAATACGACCTCGNTGGACGAGAATT
genomic: GATCCTCTTTGTTACAGCGATGCAAGgtaacccaag ... tgttccttagGTGATTATGGGAAAATAATATCTTGGAATACGACCTCG-TGGACGAGAATT
EST: gi|218488104|gb|FG955050.1|FG955050
EST:     CTCTAATCAGACTGACAACAGTCAGATCCTCTTTGTTACAGCGATGCAAG                         GTGATTATGGGAAAATAATATCTTGGAATACGACCTCGTGGACGAGAATTG
genomic: CTCTAATCAGACTGACAACAGTCAGATCCTCTTTGTTACAGCGATGCAAGgtaacccaag ... tgttccttagGTGATTATGGGAAAATAATATCTTGGAATACGACCTCGTGGACGAGAATTG
EST: gi|58686189|gb|CK074876.1|CK074876
EST:     CTCTAATCAGACTGACAACAGTCAGATCCTCTTTGTTACAGCGATGCAAG                         GTGATTATGGGAAAATAATATCTTGGAATACGACCTCGTGGACGAGAATTG
genomic: CTCTAATCAGACTGACAACAGTCAGATCCTCTTTGTTACAGCGATGCAAGgtaacccaag ... tgttccttagGTGATTATGGGAAAATAATATCTTGGAATACGACCTCGTGGACGAGAATTG

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: 69 (upstream exon), 64 (downstream exon)
Score: 35

GGAGAAATATTTGGTTTCTGCAGATTCTCTAATCAGACTGACAACAGTCAGATCCTCTTTGTTACAGCGATGCAAGgtaacccaag ... tgttccttagGTGATTATGGGAAAATAATATCTTGGAATACGACCTCGTGGACGAGAATTGGGTCAAATAAAATAACACGTGAGGCAATTTCAGCATTTGCTGTCTCGCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcgaatactatctgctagggtaagtcctgacagtaacataaacctgttccttagGTGATTATGGGAAAATAATATCTTGGAATACGACCTCGTGGACGAGAATTGGGTCAAATAAAATAACACGTGAGGCAATTTCAGCATTTGCTGTCTCGCC
                               cagtaac  putative branch site (score: 35)
                                           cctgttcctt  putative PPT
                                  taacataaa  TA-rich tract