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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttatagtgctcatgcgctcatgcttagttttgcaagccaaaactggaatgtagtttaactatatctgctgatcttgatttctaatactatttatttccagTTGATCCTGAGGATATTCCATTGGAGAAGGTTCAAGCTAAATCTTCTGGAAGTGTTCTGCCATATGTGGGCGTTGCTTGTTTGGGGGCTATTTTATTTGG

Basic information

species Oryza sativa
transcript LOC_Os01g04190.4
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g04190.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G153704_T03 (Zea mays), 3'ss of exon 2
--ttatagtgctcatgcgctcatgcttagttttgcaagccaaaactggaatgtagtttaactatatctgc-tgatcttgatttctaatactatttatttccagTTGATCCTGAGGATATTCCATTGGAGAAGGTTCAAGCTAAATCTTCTGGAAGTGTTCTGCCATATGTGGGCGTTGCTTGTTTGGGGGCTATTTTATTTGG
    ||  |  ||||  || ||   ||  |  ||||||   ||| ||  |  |  | |  |  | ||||| |  |||  | |  |   |||||   ||| ||||||| ||||| ||||||||||||||||||||||||| |||||| || |||  ||||||||||||||| |||||||||||||||||||||||| | |||||
gcagatgtttttcatctgcacacttttc-tactgcaagtttaaa-tgacagatgatgtt-cagtctctgcattctctcaactcatttgactatccttttacagTTGACCCTGAAGATATTCCATTGGAGAAGGTTCAAGTTAAATCCTCAGGACATGTTCTGCCATATGTTGGCGTTGCTTGTTTGGGGGCTATTCTGTTTGG

upper sequence: LOC_Os01g04190.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G098011_T02 (Zea mays), 3'ss of exon 2
----ttatagtgctcatgcgctcatg-cttagttttgcaagccaaaactgga-atgtagtttaactatatctgctgatcttgatttctaatactatttatttccagTTGATCCTGAGGATATTCCATTGGAGAAGGTTCAAGCTAAATCTTCTGGAAGTGTTCTGCCATATGTGGGCGTTGCTTGTTTGGGGGCTATTTTATTTGG
      ||| || ||||| || | |  |||  |  | |||    |||  | | |||  |||||    |  ||||||||||   |  ||   ||||  | | | ||||||| ||||| ||||||||| ||||||||||||||| |||||| || |||  |||| |||||||||| || ||||||||||||||||||||| | |||||
ttgcagataatgttcatgtgcacttaactttctactacaaatttaaatggcagatggtgtttag---tccctgctgatctc--tcgctttgactacct-tatacagTTGACCCTGAAGATATTCCACTGGAGAAGGTTCAAGTTAAATCCTCAGGACATGTTATGCCATATGTTGGTGTTGCTTGTTTGGGGGCTATTCTGTTTGG

upper sequence: LOC_Os01g04190.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA13G07780.1 (Glycine max), 3'ss of exon 2
ttatagtgctcatgcgctcatgcttagttttgcaagccaa--aactggaatgta-gtttaactatatctgctgatcttgatttctaatactatttatttccagTTG---ATCCTGAGGATATTCCATTGGAGAAGGTTCAAGCTAAATCTTCTGGAAGTGTTCTGCCATATGTGGGCGTTGCTTGTTTGGGGGCTATTTTATTTGG
   | |    | |    |     |    | ||  | |     | |||  |  ||   ||   | |   | | |||  | ||    | ||  ||| | || ||| ||   |   ||| ||| ||      |  |    ||| |  ||||||||||||| |||||| |||||||| || ||||||||  | || || ||||||||   
---ttggaaacttagatttgaattgcaatatgataactttctagctgttacatatacttgtatgttcttacagatactcatagaaagtaaaattgagttgcagATGGAAACATTGAAGATGTTGTTCCAGCTACTCCTCAGGGCAAATCTTCTGGAAATGTTCTACCATATGTTGGTGTTGCTTGCCTCGGAGCCATTTTATT---

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|88738909|gb|CI762417.1|CI762417
EST:     CGGCCCGCGCTCGAGCCCGCGCTACTCCCGCGTGCGCGCCACCGCCACAG                         TTGATCCTGAGGATATTCCATTGGAGAAGGTTCAAGCTAAATCTTCTGGAA
genomic: CGGCCCGCGCTCGAGCCCGCGCTACTCCCGCGTGCGCGCCACCGCCACAGgtgcgtcctc ... ttatttccagTTGATCCTGAGGATATTCCATTGGAGAAGGTTCAAGCTAAATCTTCTGGAA
EST: gi|88385512|gb|CI564172.1|CI564172
EST:     CGGCCCGCGCTCGAGCCCGCGCTACTCCCGCGTGCGCGCCACCGCCACAG                         TTGATCCTGAGGATATTCCATTGGAGAAGGTTCAAGCTAAATCTTCTGGAA
genomic: CGGCCCGCGCTCGAGCCCGCGCTACTCCCGCGTGCGCGCCACCGCCACAGgtgcgtcctc ... ttatttccagTTGATCCTGAGGATATTCCATTGGAGAAGGTTCAAGCTAAATCTTCTGGAA
EST: gi|86849748|gb|CI301637.1|CI301637
EST:     CGGCCCGCGCTCGAGCCCGCGCTACTCCCGCGTGCGCGCCACCGCCACAG                         TTGATCCTGAGGATATTCCATTGGAGAAGGTTCAAGCTAAATCTTCTGGAA
genomic: CGGCCCGCGCTCGAGCCCGCGCTACTCCCGCGTGCGCGCCACCGCCACAGgtgcgtcctc ... ttatttccagTTGATCCTGAGGATATTCCATTGGAGAAGGTTCAAGCTAAATCTTCTGGAA
EST: gi|88368202|gb|CI575084.1|CI575084
EST:     CGGCCCGCGCTCGAGCCCGCGCTACTCCCGCGTGCGCGCCACCGCCACAG                         TTGATCCTGAGGATATTCCATTGGAGAAGGTTCAAGCTAAATCTTCTGGAA
genomic: CGGCCCGCGCTCGAGCCCGCGCTACTCCCGCGTGCGCGCCACCGCCACAGgtgcgtcctc ... ttatttccagTTGATCCTGAGGATATTCCATTGGAGAAGGTTCAAGCTAAATCTTCTGGAA
EST: gi|88745134|gb|CI768494.1|CI768494
EST:     GGCCCGCGCTCGAGCCCGCGCTACTCCCGCGGTGCGCGCCACCGCCACAG                         TTGATCCTGAGGATATTCCATTGGAGAAGGTTCAAGCTAAATCTTCTGGAA
genomic: GGCCCGCGCTCGAGCCCGCGCTACTCCCGCG-TGCGCGCCACCGCCACAGgtgcgtcctc ... ttatttccagTTGATCCTGAGGATATTCCATTGGAGAAGGTTCAAGCTAAATCTTCTGGAA
EST: gi|86832143|gb|CI305369.1|CI305369
EST:     CGGCCCGCGCTCGAGCCCGCGCTACTCCCGCGTGCGCGCCACCGCCACAG                         TTGATCCTGAGGATATTCCATTGGAGAAGGTTCAAGCTAAATCTTCTGGAA
genomic: CGGCCCGCGCTCGAGCCCGCGCTACTCCCGCGTGCGCGCCACCGCCACAGgtgcgtcctc ... ttatttccagTTGATCCTGAGGATATTCCATTGGAGAAGGTTCAAGCTAAATCTTCTGGAA
EST: gi|88732120|gb|CI757297.1|CI757297
EST:     CGGCCCGCGCTCGAGCCCGCGCTACTCCCGCGTGCGCCCCACCGCCACAG                         TTGATCCTGAGGATATTCCATTGGAGAAGGTTCAAGCTAAATCTTCTGGAA
genomic: CGGCCCGCGCTCGAGCCCGCGCTACTCCCGCGTGCGCGCCACCGCCACAGgtgcgtcctc ... ttatttccagTTGATCCTGAGGATATTCCATTGGAGAAGGTTCAAGCTAAATCTTCTGGAA
EST: gi|300215629|gb|HO088255.1|HO088255
EST:     CGCGCTACT-CCGCGTGCGCGCCACCGCCACAG                         TTGATCCTGAGGATATTCCCTTGTTAGAAGGTTCAAGCTAAATCTTCTGGA
genomic: CGCGCTACTCCCGCGTGCGCGCCACCGCCACAGgtgcgtcctc ... ttatttccagTTGATCCTGAGGATATTCCATTG-GAGAAGGTTCAAGCTAAATCTTCTGGA
EST: gi|88740564|gb|CI764072.1|CI764072
EST:     CGGCCCGCGCTCGAGCCCGCGCTACTCCCGCGTGCGCGCCACCGCCACAG                         TTGATCCTGAGGATATTCCATTGGAGAAGGTTCAAGCTAAATCTTCTGGAA
genomic: CGGCCCGCGCTCGAGCCCGCGCTACTCCCGCGTGCGCGCCACCGCCACAGgtgcgtcctc ... ttatttccagTTGATCCTGAGGATATTCCATTGGAGAAGGTTCAAGCTAAATCTTCTGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaatgtagtttaactatatctgctgatcttgatttctaatactatttatttccagTTGATCCTGAGGATATTCCATTGGAGAAGGTTCAAGCTAAATCTTCTGGAAGTGTTCTGCCATATGTGGGCGTTGCTTGTTTGGGGGCTATTTTATTTGG
                                 ttctaat  putative branch site (score: 2)
                                            tttatttcc  putative PPT
                            ttgatttctaatacta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttatagtgctcatgcgctcatgcttagttttgcaagccaaaactggaatgtagtttaactatatctgctgatcttgatttctaatactatttatttccagTTGATCCTGAGGATATTCCATTGGAGAAGGTTCAAGCTAAATCTTCTGGAAGTGTTCTGCCATATGTGGGCGTTGCTTGTTTGGGGGCTATTTTATTTGG

- -tagtgct
- - - - - catgcgc
- - - - - - - - - catgctt
- - - - - - - - - - - - - - - tgcaagc
- - - - - - - - - - - - - - - - - - - - - -tggaatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctgat