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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCATCACACGTTTGCAACTGCTGGATCAGATGGCGCATTTAATTTCTGGGATAAGGATAGCAAACAAAGACTGAAGgtttgatgttggctcttttgaagttccatttgtactggttattgcacttgtatttttgttcccttgagtattcagtgatttttaatagtcataattgctt...

Basic information

species Oryza sativa
transcript LOC_Os08g07960.2
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g07960.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G058498_T01 (Zea mays), 5'ss of exon 9
GTTCATCACACGTTTGCAACTGCTGGATCAGATGGCGCATTTAATTTCTGGGATAAGGATAGCAAACAAAGACTGAAGgt---ttgatgt---tggctcttt-tgaagttccatttgtactggttattgcacttgtatttttgttcccttgagtattcagtgatttttaatagtcataattgctt
|| |||||||| ||||||||||||||||| || || || || || |||||||||||||||||||| || || || |||||      || |   ||||| ||| |  | || || ||||  ||||   ||   ||| |||| |||| | | || ||| |  |||||||   | ||  | | || ||
GTCCATCACACATTTGCAACTGCTGGATCTGACGGTGCTTTCAACTTCTGGGATAAGGATAGCAAGCAGAGGCTAAAGgtagaccaatttccatggctttttgttgattttcacttgtgttggtagctg---ttg-atttctgttgcatcgattatcct-tgattttgtgttgt--ttactggtt

upper sequence: LOC_Os08g07960.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA15G05740.1 (Glycine max), 5'ss of exon 8
GTTCATCACACGTTTGCAACTGCTGGATCAGATGGCGCATTTAATTTCTGGGATAAGGATAGCAAACAAAGACTGAAGgtttgatgttggctcttttgaagttccatttg-tactggttattgcac----ttgtatttttgttcccttgagtattcagtgatttttaatagtcataattgctt----
|| || ||||| ||||||||| |||| || ||||| || || ||||| |||||||||||||| ||||| || || ||||||      |   | ||    | |||||||   | ||   |    ||     ||| | | || ||  | | | ||     | || |     |  | |   |  ||    
GTACACCACACATTTGCAACTTCTGGTTCTGATGGTGCTTTCAATTTTTGGGATAAGGATAGTAAACAGAGGCTCAAGgttattccatttttattaaacacttccattcaatcctaactgacacatattgttgcaatatttttggcataattacatgcttatctaatgcaaacttgtcttatttcag

upper sequence: LOC_Os08g07960.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA02G13780.1 (Glycine max), 5'ss of exon 8
GTTCATCACACGTTTGCAACTGCTGGATCAGATGGCGCATTTAATTTCTGGGATAAGGATAGCAAACAAAGACTGAAGgtttgatgttggctcttttgaagttccatttgtactggttattgcacttgtatttttgttcccttgagtattcagtg---atttttaatagtcataattgctt-
|| |||||||| ||||||||||||||||| ||||| || |||||||||||||||||||| || ||||| ||||| |||||||  || |  |||| ||  |   |  ||   ||  ||  || | ||| |     || ||  | || | | ||      | ||||  |  |    || |  | 
GTACATCACACTTTTGCAACTGCTGGATCTGATGGTGCTTTTAATTTCTGGGATAAGGACAGTAAACAGAGACTCAAGgtttcttgctttctctattaca---ctcttctcacctgtcctttc-cttctgaaactgatctttggaatttccaaaacatacttttttttttttgtatagtata

upper sequence: LOC_Os08g07960.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA08G19260.1 (Glycine max), 5'ss of exon 8
GTTCATCACACGTTTGCAACTGCTGGATCAGATGGCGCATTTAATTTCTGGGATAAGGATAGCAAACAAAGACTGAAGgtttgatgttggctcttttgaagttccatttg--tactggttattgcac-ttgtatttttgttcccttgagtattcagtgatttttaatagtcataattgctt-------
|| || ||||| ||||||||| |||| || ||||| || || ||||| |||||||||||||| |||||  | || ||||||      |   | ||    | |||||||    | ||    |   ||  ||||| |  | ||      |  ||    || || |  |  |  |   |  |||       
GTACACCACACATTTGCAACTTCTGGTTCTGATGGTGCTTTCAATTTTTGGGATAAGGATAGTAAACAGCGGCTCAAGgttattccatttttattaaacacttccattcaattcctaaccaacacatattgtagtgatatttttggcataatcacatgcttatctaatgcaaacgtgtcttgtttcag

upper sequence: LOC_Os08g07960.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA01G09290.1 (Glycine max), 5'ss of exon 8
GTTCATCACACGTTTGCAACTGCTGGATCAGATGGCGCATTTAATTTCTGGGATAAGGATAGCAAACAAAGACTGAAGgtttgatgttggctctt-ttgaagttccatttgtactggttattgcacttgtatttttgttcccttgagtattcagtgatttttaatagtcataattgctt-
|| |||||||| ||||||||||||||||| ||||| || ||||||||||||||||| || || ||||| ||||| ||||||   || |  ||||  || |    |  ||   ||  ||  || | ||| |     || ||  | || | | ||     |  |  |  |  |  ||  || 
GTACATCACACTTTTGCAACTGCTGGATCTGATGGTGCTTTTAATTTCTGGGATAAAGACAGTAAACAGAGACTCAAGgttcc-tgctttctctaattaatacactcttctcacctgtcctttc-cttctgaaactgatctttggaatttccaaaacatacttgtgttttttttttattt

upper sequence: LOC_Os08g07960.1 (Oryza sativa), 5'ss of exon 9
lower sequence: AT1G80670.1 (Arabidopsis thaliana), 5'ss of exon 9
GTTCATCACACGTTTGCAACTGCTGGATCAGATGGCGCATTTAATTTCTGGGATAAGGATAGCAAACAAAGACTGAAGgtttgatgttggctcttttgaagttccatttgtactggttattgcacttgtatttttgttcccttgagtattcagtgatttttaatagtcataattgctt
|| |||  ||| |||||||||||||| |||||||| || || ||||||||||| || ||||| ||||||||||| ||||| |  |  |  ||   ||||  ||  |||| |  |    |  | | || | |    |||       |||||| |||  |    | ||            
GTACATGGCACTTTTGCAACTGCTGGGTCAGATGGTGCTTTCAATTTCTGGGACAAAGATAGTAAACAAAGACTCAAGgtattttcctc-ctgcattgattttttattt-tgttaaccaa-gtaattatctaacagtttt-----gtattctgtg--tccccacag------------

upper sequence: LOC_Os08g07960.1 (Oryza sativa), 5'ss of exon 9
lower sequence: Vv09s0002g09150.t01 (Vitis vinifera), 5'ss of exon 8
GTTCATCACACGTTTGCAACTGCTGGATCAGATGGCGCATTTAATTTCTGGGATAAGGATAGCAAACAAAGACTGAAGgtttgatgttggctcttttgaagttc---catttgtactggt-tattgcacttgtatttttgtt--cccttgagtattcagtgatttttaatagtcataattgctt
|| ||||| || ||||||||||| || || ||||| || |||||||| ||||| |||||||| ||||| ||||| |||||            ||||     ||     |||| | | | | | ||     ||| |||| |||  | ||| |    | |   ||  ||  | ||   |       
GTGCATCATACATTTGCAACTGCAGGGTCTGATGGTGCTTTTAATTTTTGGGACAAGGATAGTAAACAGAGACTTAAGgtgcctcccaaatactttcagtttttgaatatttttcccgttctgttatttctgtgttttagttgtcacttcatacatgaactatcgttcctggtttcat------

upper sequence: LOC_Os08g07960.1 (Oryza sativa), 5'ss of exon 9
lower sequence: Vv12s0055g00900.t01 (Vitis vinifera), 5'ss of exon 9
GTTCATCACACGTTTGCAACTGCTGGATCAGATGGCGCATTTAATTTCTGGGATAAGGATAGCAAACAAAGACTGAAGgt---ttgatgttggctcttttgaagttccatttgtactggttattg--cacttgtatttttgttcccttgagtattcagtgatttttaatagtcataattgctt
|| |||||||| ||||| ||||| || || || || || |||||||||||||| |||||||| ||||| ||||| |||||    | | |    |  |||||||  |    || |  | ||| | |  ||||  || | || |    ||    ||||  |  ||||||     | |||| |   
GTGCATCACACATTTGCCACTGCAGGCTCTGACGGTGCTTTTAATTTCTGGGACAAGGATAGTAAACAGAGACTCAAGgtaatctcaaggattcctttttgaatatgttcttctcgttgttttcggacactgttactcttctattattctagattctattgttttta----ccctaatcgga-

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

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTCATCACACGTTTGCAACTGCTGGATCAGATGGCGCATTTAATTTCTGGGATAAGGATAGCAAACAAAGACTGAAGgtttgatgttggctcttttgaagttccatttgtactggttattgcacttgtatttttgttcccttgagtattcagtgatttttaatagtcataattgctt

- - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG