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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgatgcctaaccacatgttgaaatgctatacgttttctgccagttttagctaatttctttttctgcgttaatgcagGTTCATTTTTTCCGTCCGGTTCCCAAGGAATATCTTCATTCTGCAGAACTGAGAGATATCATGCAATTTGGGAGCAGCAATACCGCTGTTTTCTTTAAAA

Basic information

species Oryza sativa
transcript LOC_Os04g57140.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g57140.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G423861_T01 (Zea mays), 3'ss of exon 10
gtctgatgcctaaccacatgttg-aaatgctatacgttttctgccagttttagctaatttctt-tttctgcgttaatgcagGTTCATTTTTTCCGTCCGGTTCCCAAGGAATATCTTCATTCTGCAGAACTGAGAGATATCATGCAATTTGGGAGCAGCAATACCGCTGTTTTCTTTAAAA
|||||||  || ||||   | || |||    |||   ||||||  |  |  | || || |    ||| ||| | |||||||||||| ||||||||||| |||||||||||||||||||||||||||||| | ||||| |||||||||||||| ||||||||||| ||||||||||||||||
gtctgat--ctcaccatgcgatggaaacttcatattctttctgttaagtaaaactgatcttgaatttatgcatgaatgcagGTTCACTTTTTCCGTCCAGTTCCCAAGGAATATCTTCATTCTGCAGAATTAAGAGACATCATGCAATTTGGTAGCAGCAATACTGCTGTTTTCTTTAAAA

upper sequence: LOC_Os04g57140.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G070273_T01 (Zea mays), 3'ss of exon 9
gtctgatgcctaaccacatgttgaaatgct-atacgttttctgccagttttagctaatttctt-tttctgcgttaatgcagGTTCATTTTTTCCGTCCGGTTCCCAAGGAATATCTTCATTCTGCAGAACTGAGAGATATCATGCAATTTGGGAGCAGCAATACCGCTGTTTTCTTTAAAA
||||||| |   ||||  |  || ||   | |||   ||||||| |  |  | || |  |    ||||||| | |||||||||||| |||||||| ||||||||||||||||||||||||||||||||||| ||||| |||||||||||||| ||||||||||| ||||| ||||||||||
gtctgat-ctcgaccatgtaatggaagcttcatattctttctgctaagtaaaactgaccttgaatttctgcatgaatgcagGTTCACTTTTTCCGCCCGGTTCCCAAGGAATATCTTCATTCTGCAGAACTAAGAGACATCATGCAATTTGGTAGCAGCAATACTGCTGTCTTCTTTAAAA

upper sequence: LOC_Os04g57140.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA11G09480.1 (Glycine max), 3'ss of exon 11
---------gtctgatgcctaaccacatgttgaaatgctatacgttttctgccag-------------ttttagctaatttctttttc--tgcgttaatgc-agGTTCATTTTTTCCGTCCGGTTCCCAAGGAATATCTTCATTCTGCAGAACTGAGAGATATCATGCAATTTGGGAGCAGCAATACCGCTGTTTTCTTTAAAA
            ||||    |     |  ||  || | |  |  |||  |   |              |||||  | | |  |||||   |   ||| | | |||| |||||||||||||| ||||| ||||||||| | || ||||| ||| ||||||| || ||||||||||| ||||||||||| || || || |||||||
gtaagactaacatgatttaaattttaagattataaggtttaaaatttctttttaaaaacgaattgtgcttttaattgaatgtttttttaataaattattcccagGTCCATTTTTTCCGTCCCGTTCCAAAGGAATATATGCACTCTGCTGAATTGAGAGACATAATGCAATTTGGAAGCAGCAATACTGCAGTATTTTTTAAAA

upper sequence: LOC_Os04g57140.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA16G21340.1 (Glycine max), 3'ss of exon 14
---------------------------------gtctgatgcctaaccacatgttgaaat-gctatacgttttctgccagttttagctaatttctttttctgc--gttaa-tgcagGTTCATTTTTTCCGTCCGGTTCCCAAGGAATATCTTCATTCTGCAGAACTGAGAGATATCATGCAATTTGGGAGCAGCAATACCGCTGTTTTCTTTAAAA
                                       |   ||      | ||  |||   || |   |         |||||  |   || ||| |       ||   |  || |||||||||||||||| ||||| ||||||||| | || || || ||  ||||||| || ||||||||||| ||||||||||| || || || |||||||
gtatgactaaacaaaaaaataactagttaaactaaacattatatagtttactattacaattattaaaaaatgaactgtgcttttaattgtgttttttcttgatcaattggctatagATTCATTTTTTCCGTCCAGTTCCTAAGGAATATTTGCACTCAGCTGAGTTGAGAGACATAATGCAATTTGGAAGCAGCAATACTGCAGTCTTTTTTAAAA

upper sequence: LOC_Os04g57140.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA09G32740.1 (Glycine max), 3'ss of exon 11
------------------------------------gtctgatgcctaaccacatgttgaaatgctatacgttttctgccagttttagctaatttctttttctgcgttaatgcagGTTCATTTTTTCCGTCCGGTTCCCAAGGAATATCTTCATTCTGCAGAACTGAGAGATATCATGCAATTTGGGAGCAGCAATACCGCTGTTTTCTTTAAAA
                                     | |  |   | |  |||  |   || |    |  | | ||   | || |      ||||||  ||    |   |  || |||||||||||||||| ||||| ||||||||| | || || || ||  ||||||| || ||||||||||| ||||| ||||| || || ||||||||||
gtatgactaaatgaaaaactagttaaactaaacattatatagtttatcattacaattattaaagaatgaattgtgcttttaattgtgtgccttttcttgatccat-tggctatagATTCATTTTTTCCGTCCAGTTCCTAAGGAATATTTGCACTCAGCTGAGTTGAGAGACATAATGCAATTTGGAAGCAGTAATACTGCAGTCTTCTTTAAAA

upper sequence: LOC_Os04g57140.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA01G35950.1 (Glycine max), 3'ss of exon 11
-------------gtctgatgcctaac--cacatgttgaaatgctatacgttttctgccagttttagctaatttctttttctgcgttaatgc-agGTTCATTTTTTCCGTCCGGTTCCCAAGGAATATCTTCATTCTGCAGAACTGAGAGATATCATGCAATTTGGGAGCAGCAATACCGCTGTTTTCTTTAAAA
             |  | |    ||||   | | | |  ||  ||     ||     | | || |    | ||| |||   |   ||| | | |||| ||||||||||||||  |||| ||||||||| | || ||||| ||  |||| || || ||||||||||| ||||||||||| || || || |||||||
gtaatactaacatgattaaattttaacactataaggtttaaaacttctttttaaaaactaattgtttgaattttttttcaataaattattcccagGTCCATTTTTTCCGTCCCATTCCAAAGGAATATATGCACTCTGCTGAGTTGAGGGACATAATGCAATTTGGAAGCAGCAATACTGCAGTATTTTTTAAAA

upper sequence: LOC_Os04g57140.1 (Oryza sativa), 3'ss of exon 9
lower sequence: AT5G65930.1 (Arabidopsis thaliana), 3'ss of exon 8
--------------------------gtctgatgcctaaccacatgttgaaatgctatacgttttctgccagtttt-----agctaatttctttttctgcgttaatgcagGTTCATTTTTTCCGTCCGGTTCCCAAGGAATATCTTCATTCTGCAGAACTGAGAGATATCATGCAATTTGGGAGCAGCAATACCGCTGTTTTCTTTAAAA
                           | |||     ||  |  ||||    |  | |    ||     |  | ||     |  | | ||  || | ||| ||  || ||||||| ||||| || |||||||| || |||||||| || ||||| |||||  | || |||||||||||||| ||||| || || ||||| || || ||||
gttagtctcaatataaatgttatacattatgactttaaaaaaactgttattgttgtttggaattcaaatctatgttgttggatttgaatttgttgtttgctttcttgtagGTTCACTTTTTTCGACCGGTTCCTAAAGAATATCTGCACTCTGCTGAACTACGTGACATCATGCAATTTGGCAGCAGTAACACTGCTGTCTTTTTCAAAA

upper sequence: LOC_Os04g57140.1 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 10
----------------------------gtctg---atgcctaaccacatgttgaaatgctatacgttttctgccagttttagctaatttctttttctgcgttaatgcagGTTCATTTTTTCCGTCCGGTTCCCAAGGAATATCTTCATTCTGCAGAACTGAGAGATATCATGCAATTTGGGAGCAGCAATACCGCTGTTTTCTTTAAAA
                             ||||   ||  | ||    |||||  |||  ||||  | |  ||| |         |||||  || |   | ||    |||||||||||||||||||| ||||| || || ||| | |||||||| ||||| |||||||| ||||||||||| ||||||||||| ||||| || ||||| |
gtgagtcagagttatattattataatgtatctgtacattgcaaatttgatgtttgaat--tatagatctattgcaacagaacatgaatttgattgtt--cattctcacagGTTCATTTTTTCCGTCCAGTTCCAAAAGAGTATTTGCATTCTGCTGAACTAAGAGATATAATGCAATTTGGTAGCAGCAATACTGCTGTATTTTTTAAGA

upper sequence: LOC_Os04g57140.1 (Oryza sativa), 3'ss of exon 9
lower sequence: PP1S83_25V6.1 (Physcomitrella patens), 3'ss of exon 11
--------------------------------------------------------------------------------------------------------------------gtctg-atgcctaaccacatgttgaaatgctatacgttttctgccagttttagctaatttcttttt--ctgcgttaatg-cagGTTCATTTTTTCCGTCCGGTTCCCAAGGAATATCTTCATTCTGCAGAACTGAGAGATATCATGCAATTTGGGAGCAGCAATACCGCTGTTTTCTTTAAAA
                                                                                                                    | ||  | | ||  |   |  ||| | |   ||   || | | ||| | | |  |  ||| ||| |   | |  |  || ||||| || |||||  | |||||||| ||||| ||||| || ||||||||  || ||||||||||||| ||||| || || || || ||||| || |||||||
gtaagtttcatggacctgtagctaagtgggttagctttgctgagtttcgcaattccttattatcaagtcagtttgcatggtcttcgtgtttttagagctttgtgtcatgttaagcagactacacgtctt-ctgtaacttgtagtctgattttttctattccattctcactttgtttttttctattttcactcttggcagGTGCACTTTTTTAGACCGGTTCCAAAGGAGTATCTACACTCTGCAGAGTTGCGAGATATCATGCAGTTTGGCAGTAGTAACACTGCTGTATTTTTTAAAA

upper sequence: LOC_Os04g57140.1 (Oryza sativa), 3'ss of exon 9
lower sequence: EFJ30174 (Selaginella moellendorffii), 3'ss of exon 10
gtctgatgcctaaccacatgttgaaatgctatacgttttctgccagttttagctaatttctttttctgcgttaatgcagGTTCATTTTTTCCGTCCGGTTCCCAAGGAATATCTTCATTCTGCAGAACTGAGAGATATCATGCAATTTGGGAGCAGCAATACCGCTGTTTTCTTTAAAA
                 | ||  || |  ||| | | |||   | |||||  |  || | ||| |      |||  ||||||||||||||||| || || || || |||||| | ||||| || || |||||||| |||||||||||||| || ||||||||||| || || |||||||
---------------gtacgtgcaagta-tattcatgttcg--ctgttttgac--atgtgtttct------taa--cagGTTCATTTTTTCCGGCCAGTACCTAAAGAATATTTACATTCGGCTGAGCTGAGAGACATCATGCAATTTGGAAGTAGCAATACCGCAGTGTTTTTTAAAA

upper sequence: LOC_Os04g57140.1 (Oryza sativa), 3'ss of exon 9
lower sequence: EFJ06058 (Selaginella moellendorffii), 3'ss of exon 10
gtctgatgcctaaccacatgttgaaatgctatacgttttctgccagttttagctaatttctttttctgcgttaatgcagGTTCATTTTTTCCGTCCGGTTCCCAAGGAATATCTTCATTCTGCAGAACTGAGAGATATCATGCAATTTGGGAGCAGCAATACCGCTGTTTTCTTTAAAA
                 | ||  || |  ||| | | |||   | |||||  |  || | ||| |      |||  ||||||||||||||||| || || || || |||||| | ||||| || || || ||||| |||||||||||||| || ||||||||||| || || |||||||
---------------gtacgtgcaagta-tattcatgttcg--cggttttgac--atgtgtttct------taa--cagGTTCATTTTTTCCGGCCAGTACCTAAAGAATATTTACATTCGGCTGAGCTTAGAGACATCATGCAATTTGGAAGTAGCAATACCGCAGTGTTTTTTAAAA

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|58671897|gb|CK060583.1|CK060583
EST:     CAATAGGACTTTTACCTGGAAGAATCATTCTGGGAATAAACAAACGAGGG                         GTTCATTTTTTCCGTCCGGTTCCCAAGGAATATCTTCATTCTGCAGAACTG
genomic: CAATAGGACTTTTACCTGGAAGAATCATTCTGGGAATAAACAAACGAGGGgtctgatgcc ... gttaatgcagGTTCATTTTTTCCGTCCGGTTCCCAAGGAATATCTTCATTCTGCAGAACTG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgctatacgttttctgccagttttagctaatttctttttctgcgttaatgcagGTTCATTTTTTCCGTCCGGTTCCCAAGGAATATCTTCATTCTGCAGAACTGAGAGATATCATGCAATTTGGGAGCAGCAATACCGCTGTTTTCTTTAAAA
                                tttctttttctgcgtt  CT-rich tract
                             taatttctttttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgatgcctaaccacatgttgaaatgctatacgttttctgccagttttagctaatttctttttctgcgttaatgcagGTTCATTTTTTCCGTCCGGTTCCCAAGGAATATCTTCATTCTGCAGAACTGAGAGATATCATGCAATTTGGGAGCAGCAATACCGCTGTTTTCTTTAAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT