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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtttgctaattttgttttgttgcagtcaatttctcacatgcatccctttattttatacagaatataatcattcacttcccatgtcactttttttacacagGCTTTTAGTCGGTGCCCTCTTCCTATTCCTTGCAGTACCTTCAACAGTGATGGGTCGATATTTGCTTATGCA

Basic information

species Oryza sativa
transcript LOC_Os08g07960.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g07960.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G058498_T01 (Zea mays), 3'ss of exon 9
gtttgctaattttgttttgttgcagtcaatttctcacat-gcatccctttattttatacagaatataatcattcacttcccatgt-cactttttttacacagGCTTTTAGTCGGTGCCCTCTTCCTATTCCTTGCAGTACCTTCAACAGTGATGGGTCGATATTTGCTTATGCA
 || |      |||||||  | | |  | |     ||||  | | || ||||||| || |  | |||  |||||| | |   |    ||| ||| |  ||||||||||||| | ||||| ||||| ||||||||||||||||||||||||||||| || |||||||||||||| 
attggaactgcttgtttttatcctgaaattcgtatacattaccttccattattttgtagatgacata--cattcattccattttcgtactatttctgtacagGCTTTTAGTAGATGCCCCCTTCCCATTCCTTGCAGTACCTTCAACAGTGATGGTTCCATATTTGCTTATGCG

upper sequence: LOC_Os08g07960.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA08G19260.1 (Glycine max), 3'ss of exon 8
gtt-tgctaattttgttttg---ttgcagtcaatttctcac--atgcatccctttattttatacagaatataatcattcacttccc--atgtcac--tttttttacacagGCTTTTAGTCGGTGCCCTCTTCCTATTCCTTGCAGTACCTTCAACAGTGATGGGTCGATATTTGCTTATGCA
||| | | | |||| ||      || || |||||| || ||  |  |||    |  |  |||       |||||||    |||  |  |||  |   | | ||    |||||  |     | |||   || ||||||||||||||||||||||||| |||||| || |||||||||||  ||
gttattccatttttattaaacacttccattcaattcctaaccaacacatattgtagtgatatttttggcataatcacatgcttatctaatgcaaacgtgtcttgtttcagGCCATGTTGAGATGCAGCCTACCTATTCCTTGCAGTACCTTCAACAATGATGGTTCAATATTTGCTTACTCA

upper sequence: LOC_Os08g07960.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA15G05740.1 (Glycine max), 3'ss of exon 8
gtt-tgctaattttgttttg---ttgcagtcaattt---ctcacatgcatccctttattttatacagaatataatcattcacttcccatgtca-ctttttttaca-cagGCTTTTAGTCGGTGCCCTCTTCCTATTCCTTGCAGTACCTTCAACAGTGATGGGTCGATATTTGCTTATGCA
||| | | | |||| ||      || || |||||     || |||   ||   |  | | | |   | |||    ||| |   ||  |||  | ||| | |||   |||||  |     | |||   |  ||||||||||||||||||||||||| |||||| || |||||||||||  ||
gttattccatttttattaaacacttccattcaatcctaactgacacatattgttgcaatatttttggcataattacatgcttatctaatgcaaacttgtcttatttcagGCCATGTTGAGATGCAGCCAACCTATTCCTTGCAGTACCTTCAACAATGATGGTTCAATATTTGCTTACTCA

upper sequence: LOC_Os08g07960.1 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv12s0055g00900.t01 (Vitis vinifera), 3'ss of exon 9
gtttgctaattttgttttgttgca-gtcaatttctcacatgcatccctttattttatacagaatataatcattcacttcccatgtcacttttttta---cacagGCTTTTAGTCGGTGCCCTCTTCCTATTCCTTGCAGTACCTTCAACAGTGATGGGTCGATATTTGCTTATGCA
     |   |||| |||| || ||  ||||  |  || ||    |   || |||     |||| ||     |     ||  |    | ||  | |      |||||| |     |||||  ||  ||||| ||||||||||| ||||||| |||||| ||||||||||| ||| | 
---gacctttttttttttcttccatatcaagctggcaaat-tgccgacttttttgggctagaacatccctttgtttgtctgactctatttggtctgattttcagGCTATGTCAAGGTGCAGTCAACCTATACCTTGCAGTACTTTCAACAATGATGGATCGATATTTGCATATTCG

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|29681301|gb|CB677576.1|CB677576
EST:     CAGATGGCGCATTTAATTTCTGGGATAAGGATAGCAAACAAAGACTGAAG                         GCTTTTAGTCGGTGCCCTCTTCCTATTCCTTGCAGTACCTTCAACAGTGAT
genomic: CAGATGGCGCATTTAATTTCTGGGATAAGGATAGCAAACAAAGACTGAAGgtttgatgtt ... ttttacacagGCTTTTAGTCGGTGCCCTCTTCCTATTCCTTGCAGTACCTTCAACAGTGAT
EST: gi|86496217|gb|CI138850.1|CI138850
EST:     CAGATGGCGCATTTAATTTCTGGGATAAGGATAGCAAACAAAGACTGAAG                         GCTTTTAGTCGGTGCCCTCTTCCTATTCCTTGCAGTACCTTCAACAGTGAT
genomic: CAGATGGCGCATTTAATTTCTGGGATAAGGATAGCAAACAAAGACTGAAGgtttgatgtt ... ttttacacagGCTTTTAGTCGGTGCCCTCTTCCTATTCCTTGCAGTACCTTCAACAGTGAT
EST: gi|86494783|gb|CI137416.1|CI137416
EST:     CAGATGGCGCATTTAATTTCTGGGATAAGGATAGCAAACAAAGACTGAAG                         GCTTTTAGTCGGTGCCCTCTTCCTATTCCTTGCAGTACCTTCAACAGTGAT
genomic: CAGATGGCGCATTTAATTTCTGGGATAAGGATAGCAAACAAAGACTGAAGgtttgatgtt ... ttttacacagGCTTTTAGTCGGTGCCCTCTTCCTATTCCTTGCAGTACCTTCAACAGTGAT
EST: gi|33805337|gb|CF328546.1|CF328546
EST:     CAGATGGCGCATTTAATTTCTGGGATAAGGATAGCAAACAAAGACTGAAG                         GCTTTTAGTCGGTGCCCTCTTCCTATTCCTTGCAGTACCTTCAACAGTGAT
genomic: CAGATGGCGCATTTAATTTCTGGGATAAGGATAGCAAACAAAGACTGAAGgtttgatgtt ... ttttacacagGCTTTTAGTCGGTGCCCTCTTCCTATTCCTTGCAGTACCTTCAACAGTGAT
EST: gi|86498360|gb|CI140993.1|CI140993
EST:     CAGATGGCGCATTTAATTTCTGGGATAAGGATAGCAAACAAAGACTGAAG                         GCTTTTAGTCGGTGCCCTCTTCCTATTCCTTGCAGTACCTTCAACAGTGAT
genomic: CAGATGGCGCATTTAATTTCTGGGATAAGGATAGCAAACAAAGACTGAAGgtttgatgtt ... ttttacacagGCTTTTAGTCGGTGCCCTCTTCCTATTCCTTGCAGTACCTTCAACAGTGAT
EST: gi|86597807|gb|CI276593.1|CI276593
EST:     CAGATGGCGCATTTAATTTCTGGGATAAGGATAGCAAACAAAGACTGAAG                         GCTTTTAGTCGGTGCCCTCTTCCTATTCCTTGCAGTACCTTCAACAGTGAT
genomic: CAGATGGCGCATTTAATTTCTGGGATAAGGATAGCAAACAAAGACTGAAGgtttgatgtt ... ttttacacagGCTTTTAGTCGGTGCCCTCTTCCTATTCCTTGCAGTACCTTCAACAGTGAT
EST: gi|86503924|gb|CI146557.1|CI146557
EST:     AGATGGCGCATTTAATTTCTGGGATAAGGATAGCAAACAAAGACTGAAG                         GCTTTTAGTCGGTGCCCTCTTCCTATTCCTTGCAGTACCTTCAACAGTGAT
genomic: AGATGGCGCATTTAATTTCTGGGATAAGGATAGCAAACAAAGACTGAAGgtttgatgtt ... ttttacacagGCTTTTAGTCGGTGCCCTCTTCCTATTCCTTGCAGTACCTTCAACAGTGAT
EST: gi|86498473|gb|CI141106.1|CI141106
EST:     CAGATGGCGCATTTAATTTCTGGGATAAGGATAGCAAACCAAGACTGAAG                         GCTTTTAGTCGGTGCCCTCTTCCTATTCCTTGCAGTACCTTCAACAGTGAT
genomic: CAGATGGCGCATTTAATTTCTGGGATAAGGATAGCAAACAAAGACTGAAGgtttgatgtt ... ttttacacagGCTTTTAGTCGGTGCCCTCTTCCTATTCCTTGCAGTACCTTCAACAGTGAT
EST: gi|86495339|gb|CI137972.1|CI137972
EST:     CAGATGGCGCATTTAATTTCTGGGATAAGGATAGCAAACAAAGACTGAAG                         GCTTTTAGTCGGTGCCCTCTTCCTATTCCTTGCAGTACCTTCAACAGTGAT
genomic: CAGATGGCGCATTTAATTTCTGGGATAAGGATAGCAAACAAAGACTGAAGgtttgatgtt ... ttttacacagGCTTTTAGTCGGTGCCCTCTTCCTATTCCTTGCAGTACCTTCAACAGTGAT
EST: gi|86504575|gb|CI147208.1|CI147208
EST:     GCATTTAATTTCTGGGATAAGGATAGCAAACAAAGATTGAAG                         GCTTTTAGTCGGTGCCCTCTTCCTATTCCTTGCAGTACCTTCAACAGTGAT
genomic: GCATTTAATTTCTGGGATAAGGATAGCAAACAAAGACTGAAGgtttgatgtt ... ttttacacagGCTTTTAGTCGGTGCCCTCTTCCTATTCCTTGCAGTACCTTCAACAGTGAT
EST: gi|87007439|gb|CI279110.1|CI279110
EST:     CAGATGGCGCATTTAATTTCTGGGATAAGGATAGCAAACAAAGACTGAAG                         GCTTTTAGTCGGTGCCCTCTTCCTATTCCTTGCAGTACCTTCAACAGTGAT
genomic: CAGATGGCGCATTTAATTTCTGGGATAAGGATAGCAAACAAAGACTGAAGgtttgatgtt ... ttttacacagGCTTTTAGTCGGTGCCCTCTTCCTATTCCTTGCAGTACCTTCAACAGTGAT
EST: gi|86494277|gb|CI136910.1|CI136910
EST:     CAGATGGCGCATTTAATTTCTGGGATAAGGATAGCAAACAAAGACTGAAG                         GCTTTTAGTCGGTGCCCTCTTCCTATTCCTTGCAGTACCTTCAACAATGAT
genomic: CAGATGGCGCATTTAATTTCTGGGATAAGGATAGCAAACAAAGACTGAAGgtttgatgtt ... ttttacacagGCTTTTAGTCGGTGCCCTCTTCCTATTCCTTGCAGTACCTTCAACAGTGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttattttatacagaatataatcattcacttcccatgtcactttttttacacagGCTTTTAGTCGGTGCCCTCTTCCTATTCCTTGCAGTACCTTCAACAGTGATGGGTCGATATTTGCTTATGCA
                                      tcacttttttt  CT-rich tract
     ttttatacagaatata  TA-rich tract