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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgaatgcatattcgttgttcttctttccttttttgttttgacaggaagttcttccttcctaattggtattagtttcttattgtataatcgtctaatctgattcctgaatttgattaatccctcctttcttaactagATTGATGCGCATGTCGGTGGTGTAAATGACATTGCATTTGCCCATCCAAATAAGCAGCTATGTATAATAACCTGCGGAGATGACAAGACAATTAAG

Basic information

species Oryza sativa
transcript LOC_Os03g14980.2
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g14980.1 (Oryza sativa), 3'ss of exon 12
lower sequence: AC203920.3_FGT004 (Zea mays), 3'ss of exon 5
gtatgaatgcatattcgttgttcttctttccttttttgttttgacaggaagttcttccttcctaattggtattagtttcttattgtataatcgtctaatctgattcctgaatttgattaatccctcctttcttaactagATTGATGCGCATGTCGGTGGTGTAAATGACATTGCATTTG---CCCATCCAAA-TAAGCAGCTATGTATAATAACCTGCGGAGATGACAAGACAATTAAG
                        | |  |    | | | || |       | | || |   |  ||||| |  |||   | ||||||| | | |||   || ||| |   ||||| |||| |  | |   ||    |||||||||| ||| | |||||||||||||||||||||||||    | | |     |  ||| |     ||  | ||     | | |      ||   |   
-----------------------gtttgactgcatgtttcttaattctttctacctcatagatgtttggtgt--gttctcttttgtatagttgactatgttggttcatatttttgactaatgcg-cttgctttcttcagATTGATGCACATATTGGTGGTGTAAATGACATTGCATTTGGATTCTACCTTGCCTGGGCAACGCAACATTTTCACTCTTTGTGCTTCTTGAACTTCTTCC

upper sequence: LOC_Os03g14980.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G030422_T01 (Zea mays), 3'ss of exon 12
gtatgaatgcatattcgttgttcttctttccttttttgttttgacaggaagttcttccttcctaattggtattagtttcttattgtataatcgtctaatctgattcctgaatttgattaatccctcctttcttaactagATTGATGCGCATGTCGGTGGTGTAAATGACATTGCATTTGCCCATCCAAATAAGCAGCTATGTATAATAACCTGCGGAGATGACAAGACAATTAAG
                              ||||        | | |  |||| ||  |   |  ||||| ||  |||  | ||||| ||||  |||   || ||| |  |||||| ||   | | |||||||    |||||||||| ||||| ||||||||||||||||| |||||||| |||||||||||||||||||||||||| || || |||||||| ||||||||||||
------------------------------ctttccctccccggctg--agttttt--tagttgtttggtgtt--ttttcttttgtacaatcaactacattggttcttatatttgactatcgcttgctttctt---cagATTGATGCACATGTTGGTGGTGTAAATGACATAGCATTTGCTCATCCAAATAAGCAGCTATGTATAATTACATGTGGAGATGATAAGACAATTAAG

upper sequence: LOC_Os03g14980.1 (Oryza sativa), 3'ss of exon 12
lower sequence: AC192595.3_FGT001 (Zea mays), 3'ss of exon 6
gtatgaatgcatattcgttgttcttctttccttttttgttttgacaggaagttcttccttcctaattggtattagtttcttattgtataatcgtctaatctgattcctgaatttgattaatccctcctttcttaactagATTGATGCGCATGTCGGTGGTGTAAATGACATTGCATTTG---CCCATCCAAAT-AAGCAGCTATGTATAATAACCTGCGGAGATGACAAGACAATTAAG
|| ||| ||||| ||  ||  |  | | | | |  | | | |                       ||||| |  |||   | ||||||| | | |||   || ||| |   ||||| |||| |  | |   ||    |||||||||| ||| | |||||||||||||||||||||||||    | | |    |   ||| |     ||  | ||     | | |      ||   |   
gtttgagtgcatgtttcttaattctttctacctcatagatgt-----------------------ttggtgt--gttctcttttgtatagttgactatgttggttcatatttttgactaatgcg-cttgctttcttcagATTGATGCACATATTGGTGGTGTAAATGACATTGCATTTGGATTCTACCTTGCTTGGGCAACACAACATTTTCACTCTTCGTGCTTCTTGAACTTCTTCC

upper sequence: LOC_Os03g14980.1 (Oryza sativa), 3'ss of exon 12
lower sequence: EFJ37833 (Selaginella moellendorffii), 3'ss of exon 11
gtatgaatgcatattcgttgttcttctttccttttttgttttgacaggaagttcttccttcctaattggtattagtttcttattgtataatcgtctaatctgattcctgaatttgattaatccctcctttcttaactagATTGATGCGCATGTCGGTGGTGTAAATGACATTGCATTTGCCCATCCAAATAAGCAGCTATGTATAATAACCTGCGGAGATGACAAGACAATTAAG
                                                                        ||  | |  ||||| ||  | |    | |||   | |||     || |    | || |   ||| |||||||||||||||| ||  |||| || ||  ||||||||||||||||||| ||||| || || |||||  | || || |||||||| || || |||
-----------------------------------------------------------------------gtatgtacgcattgtttatacct----tgtgacgac-gaaaacacttgaatgtttctcttccaac-agATTGATGCGCATGTGGGGAGTGTGAACGATCTTGCATTTGCCCATCCAAACAAGCAACTGTGCATAATTTCTTGTGGCGATGACAAAACGATCAAG

upper sequence: LOC_Os03g14980.1 (Oryza sativa), 3'ss of exon 12
lower sequence: EFJ32018 (Selaginella moellendorffii), 3'ss of exon 11
gtatgaatgcatattcgttgttcttctttccttttttgttttgacaggaagttcttccttcctaattggtattagtttcttattgtataatcgtctaatctgattcctgaatttgattaatccctcctttcttaactagATTGATGCGCATGTCGGTGGTGTAAATGACATTGCATTTGCCCATCCAAATAAGCAGCTATGTATAATAACCTGCGGAGATGACAAGACAATTAAG
                                                                        ||  | |  ||||| ||  | |    | |||   | |||     || |    | || |   ||| |||||||||||||||| ||  |||| || ||  ||||||||||||||||||| ||||| || || || ||  | || || |||||||| || || |||
-----------------------------------------------------------------------gtatgtacgcattgtttatacct----tgtgaagac-gaaaacacttgaatgtttctcttccaac-agATTGATGCGCATGTGGGGAGTGTGAACGATCTTGCATTTGCCCATCCAAACAAGCAACTGTGCATCATTTCTTGTGGCGATGACAAAACGATCAAG

upper sequence: LOC_Os03g14980.1 (Oryza sativa), 3'ss of exon 12
lower sequence: EFJ35798 (Selaginella moellendorffii), 3'ss of exon 11
gtatgaatgcatattcgttgttcttctttccttttttgttttgacaggaagttcttccttcctaattggtattagtttcttattgtataatcgtctaatctgattcctgaatttgattaatccctcctttcttaactagATTGATGCGCATGTCGGTGGTGTAAATGACATTGCATTTGCCCATCCAAATAAGCAGCTATGTATAATAACCTGCGGAGATGACAAGACAATTAAG
                                                                        ||  | |  ||||| ||  | |    | |||   |  ||     | |||   ||  |||  |   |||||||||||||||| ||  |||| || ||  ||||||||||||||||||| ||||| || || || ||  | || || |||||||| || || |||
-----------------------------------------------------------------------gtatgtacgcattgtttatacct----tgtgaagacgaaaacacctgaatgtttctcttccaa--cagATTGATGCGCATGTGGGGAGTGTGAACGATCTTGCATTTGCCCATCCAAACAAGCAACTGTGCATTATTTCTTGTGGCGATGACAAAACGATCAAG

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|58661057|gb|CK049737.1|CK049737
EST:     TACAGATCTATTCATACCATGGCGGTGATGATATCAGGCAGCACTTGGAG                         ATTGATGCGCATGTCGGTGGTGTAAATGACATTGCATTTGCCCATCCAAAT
genomic: TACAGATCTATTCATACCATGGCGGTGATGATATCAGGCAGCACTTGGAGgtatgaatgc ... tcttaactagATTGATGCGCATGTCGGTGGTGTAAATGACATTGCATTTGCCCATCCAAAT
EST: gi|58693082|gb|CK081769.1|CK081769
EST:     TACAGATCTATTCATACCATGGCGGTGATGATATCAGGCAGCACTTGGAG                         ATTGATGCGCATGTCGGTGGTGTAAATGACATT
genomic: TACAGATCTATTCATACCATGGCGGTGATGATATCAGGCAGCACTTGGAGgtatgaatgc ... tcttaactagATTGATGCGCATGTCGGTGGTGTAAATGACATT
EST: gi|58666485|gb|CK055171.1|CK055171
EST:     TACAGATCTATTCATACCATGGCGGTGATGATATCAGGCAGCACTTGGAG                         ATTGATGCGCATGTCGGTGGTGTAAATGACATTGCATTTGCCCATCCAAAT
genomic: TACAGATCTATTCATACCATGGCGGTGATGATATCAGGCAGCACTTGGAGgtatgaatgc ... tcttaactagATTGATGCGCATGTCGGTGGTGTAAATGACATTGCATTTGCCCATCCAAAT
EST: gi|88356140|gb|CI627588.1|CI627588
EST:     TACAGATCTATTCATACCATGGCGGTGATGATATCAGGCAGCACTTGGAG                         ATTGATGCGCATGTCGGTGGTGTAAATGACATTGCATTTGCCCATCCAAAT
genomic: TACAGATCTATTCATACCATGGCGGTGATGATATCAGGCAGCACTTGGAGgtatgaatgc ... tcttaactagATTGATGCGCATGTCGGTGGTGTAAATGACATTGCATTTGCCCATCCAAAT
EST: gi|58673842|gb|CK062528.1|CK062528
EST:     TACAGATCTATTCATACCATGGCGGTGATGATATCAGGCAGCACTTGGAG                         ATTGATGCGCATGTCGGTGGTGTAAATGACATTGCATTTGCCCATCCAAAT
genomic: TACAGATCTATTCATACCATGGCGGTGATGATATCAGGCAGCACTTGGAGgtatgaatgc ... tcttaactagATTGATGCGCATGTCGGTGGTGTAAATGACATTGCATTTGCCCATCCAAAT
EST: gi|29628402|gb|CB633413.1|CB633413
EST:     TACAGATCTATTCATACCATGGCGGTGATGATATCAGGCAGCACTTGGAG                         ATTGATGCGCATGTCGGTGGTGTAAATGACATTGCATTTGCCCATCCAAAT
genomic: TACAGATCTATTCATACCATGGCGGTGATGATATCAGGCAGCACTTGGAGgtatgaatgc ... tcttaactagATTGATGCGCATGTCGGTGGTGTAAATGACATTGCATTTGCCCATCCAAAT
EST: gi|29625346|gb|CB630357.1|CB630357
EST:     TACAGATCTATTCATACCATGGCGGTGATGATATCAGGCAGCACTTGGAG                         ATTGATGCGCATGTCGGTGGTGTAAATGACATTGCATTTGCCCATCCAAAT
genomic: TACAGATCTATTCATACCATGGCGGTGATGATATCAGGCAGCACTTGGAGgtatgaatgc ... tcttaactagATTGATGCGCATGTCGGTGGTGTAAATGACATTGCATTTGCCCATCCAAAT
EST: gi|58667991|gb|CK056677.1|CK056677
EST:     TACAGATCTATTCATACCATGGCGGTGATGATATCAGGCAGCACTTGGAG                         ATTGATGCGCATGTCGGTGGTGTAAATGACATTGCATTTGCCCATCCAAAT
genomic: TACAGATCTATTCATACCATGGCGGTGATGATATCAGGCAGCACTTGGAGgtatgaatgc ... tcttaactagATTGATGCGCATGTCGGTGGTGTAAATGACATTGCATTTGCCCATCCAAAT
EST: gi|29622174|gb|CB627185.1|CB627185
EST:     TACAGATCTATTCATACCATGGCGGTGATGATATCAGGCAGCACTTGGAG                         ATTGATGCGCATGTCGGTGGTGTAAATGACATTGCATTTGCCCATCCAAAT
genomic: TACAGATCTATTCATACCATGGCGGTGATGATATCAGGCAGCACTTGGAGgtatgaatgc ... tcttaactagATTGATGCGCATGTCGGTGGTGTAAATGACATTGCATTTGCCCATCCAAAT
EST: gi|29631515|gb|CB636524.1|CB636524
EST:     TACAGATCTATTCATACCATGGCGGTGATGATATCAGGCAGCACTTGGAG                         ATTGATGCGCATGTCGGTGGTGTAAATGACATTGCATTTGCCCATCCAAAT
genomic: TACAGATCTATTCATACCATGGCGGTGATGATATCAGGCAGCACTTGGAGgtatgaatgc ... tcttaactagATTGATGCGCATGTCGGTGGTGTAAATGACATTGCATTTGCCCATCCAAAT
EST: gi|163927939|gb|EG712951.1|EG712951
EST:     TACAGATCTATTCATACCATGGCGGTGATGATATCAGGCAGCACTTGGAG                         ATTGATGCGCATGTCGGTGGTGTAAATGACATTGCATTTGCCCATCCAAAT
genomic: TACAGATCTATTCATACCATGGCGGTGATGATATCAGGCAGCACTTGGAGgtatgaatgc ... tcttaactagATTGATGCGCATGTCGGTGGTGTAAATGACATTGCATTTGCCCATCCAAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtataatcgtctaatctgattcctgaatttgattaatccctcctttcttaactagATTGATGCGCATGTCGGTGGTGTAAATGACATTGCATTTGCCCATCCAAATAAGCAGCTATGTATAATAACCTGCGGAGATGACAAGACAATTAAG
                              gattaat  putative branch site (score: 3)
                                ttaatccctcctttct  CT-rich tract
                       tgaatttgattaat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgaatgcatattcgttgttcttctttccttttttgttttgacaggaagttcttccttcctaattggtattagtttcttattgtataatcgtctaatctgattcctgaatttgattaatccctcctttcttaactagATTGATGCGCATGTCGGTGGTGTAAATGACATTGCATTTGCCCATCCAAATAAGCAGCTATGTATAATAACCTGCGGAGATGACAAGACAATTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG