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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatatgcagagtccactagactttacactaagctgccaaacgatgaaccatgctgattttcctccttctctccagTACTTCTCAAATACTATATCTCGGCTCCTGCTGCCTGTGGATGGTGCCCACCCCTCAGCTTGTGAAGATATGGGATCAGCAGTATCTGTTGTTGAGGCTG

Basic information

species Oryza sativa
transcript LOC_Os12g13590.2
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g13590.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM5G823484_T01 (Zea mays), 3'ss of exon 3
gtaatatgcagag-tccactagactttacactaagctgccaaacga------tgaaccatgct--gattttcctccttc-tctccagTACTTCTCAAATACTATATCTCGGCTCCTGCTGCCTGTGGATGGTGCCCACCCCTCAGCTTGTGAAGATATGGGATCAGCAGTATCTGTTGTTGAGGCTG
||||| | |   | ||||  |   |  |  ||  |||  || | ||      | || ||||||   ||||  ||  ||| |||  |||||||||||||||| |||||||||||| |||| ||||| |||||||| || || || ||||||||||||||||| ||||||||||| || ||||||||||
gtaatcttcgctgatccatcaagttgcaaccttggcttgcatatgaagtcaataaagcatgcttgaatttctctgtttcctctgtagTACTTCTCAAATACCATATCTCGGCTCTTGCTACCTGTTGATGGTGCTCATCCGTCTGCTTGTGAAGATATGGGGTCAGCAGTATCAGTAGTTGAGGCTG

upper sequence: LOC_Os12g13590.1 (Oryza sativa), 3'ss of exon 17
lower sequence: Vv15s0046g02200.t01 (Vitis vinifera), 3'ss of exon 17
-------------------gtaatatgcagagtccactagactttac--actaagctgccaaacgatgaaccatgc--tgatttt--cctccttctctccagTACTTCTCAAATACTATATCTCGGCTCCTGCTGCCTGTGGATGGTGCCCACCCCTCAGCTTGTGAAGATATGGGATCAGCAGTATCTGTTGTTGAGGCTG
                   |   | | |  | |    |  | | | |  |  |   ||   |   ||  |   ||   | | ||   |  | || ||| ||||||||  ||||  |||||||||||||  | ||||||||||||||||||||  | ||  | |||||||| ||||   ||||  | ||   ||  ||  |||
gttcgttagatggccgaatgccttttactcaattattttaattatgctcatgagaatgattagaaatttattttgaaataaattggactgctttttctgcagTACTTTGCAAACTCTATATCTCGGCTTTTACTGCCTGTGGATGGTGCCCATGCTTCTTCCTGTGAAGAAATGGCTACAGCTATGTCCAGTGCAGAAACTG
















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|33822211|gb|CF336920.1|CF336920
EST:     ATGANTTGCTGTGCNAGCGTTGTGCTAGCAGTGTGGCTATTCTTCAGCAG                         TACTTCTCAAATACTATATCTCGGCTCCTGCTNGCCTGTGGATGGTGCCCA
genomic: ATGA-TTGCTGTGC-AGCGTTGTGCTAGCAGTGTGGCTATTCTTCAGCAGgtaatatgca ... ttctctccagTACTTCTCAAATACTATATCTCGGCTCCTGCT-GCCTGTGGATGGTGCCCA
EST: gi|29669745|gb|CB666020.1|CB666020
EST:     TCATGATTGCTGTGCAGCGTTGTGCTAGCAGTGTGGCTATTCTTCAGCAG                         TACTTCTCAAATAATATATCTCGGCTCCTGCTGCCTGTGGATGGTGCCCAC
genomic: TCATGATTGCTGTGCAGCGTTGTGCTAGCAGTGTGGCTATTCTTCAGCAGgtaatatgca ... ttctctccagTACTTCTCAAATACTATATCTCGGCTCCTGCTGCCTGTGGATGGTGCCCAC
EST: gi|33822202|gb|CF336916.1|CF336916
EST:     TCATGATTGCTGTGCAGCGTTGTGCTAGCAGTGTGGCTATTCTTCAGCAG                         TACTTCTCAAATACTATATCTCGGCTCCTGCTGCCTGTGGATGGTGCCCAC
genomic: TCATGATTGCTGTGCAGCGTTGTGCTAGCAGTGTGGCTATTCTTCAGCAGgtaatatgca ... ttctctccagTACTTCTCAAATACTATATCTCGGCTCCTGCTGCCTGTGGATGGTGCCCAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttacactaagctgccaaacgatgaaccatgctgattttcctccttctctccagTACTTCTCAAATACTATATCTCGGCTCCTGCTGCCTGTGGATGGTGCCCACCCCTCAGCTTGTGAAGATATGGGATCAGCAGTATCTGTTGTTGAGGCTG
                              tgctgat  putative branch site (score: 3)
                              tgctgattttcctcct  CT-rich tract
                                 tgatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatatgcagagtccactagactttacactaagctgccaaacgatgaaccatgctgattttcctccttctctccagTACTTCTCAAATACTATATCTCGGCTCCTGCTGCCTGTGGATGGTGCCCACCCCTCAGCTTGTGAAGATATGGGATCAGCAGTATCTGTTGTTGAGGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA