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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcaccattctaccttcaaatctttgatcaaaaccatgatgccatcaatggcattgtgttcaatttgttcaggagatatgatgagttgggttctaatggagtgcaatgcaaatgtttgtgtttttgtttgtctttcagGTTGATCTTGTTGGAGGTTATTATGATGCAGGGGACAATGTCAAGTTTGGGTTGCCAATGGCGTTCACGGTGACCATGATGTCGTGGAGCATATTAGAGT

Basic information

species Oryza sativa
transcript LOC_Os05g12150.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g12150.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G143747_T01 (Zea mays), 3'ss of exon 1
gtatgcaccattctaccttcaaatctttgatcaaaaccatgatgccatcaatggcattgtgttcaatttgttcaggagatatgatgagttgggttctaatggagtgcaatgcaaatgtttgtgtttttgtttgtctttcagGTTGATCTTGTTGGAGGTTATTATGATGCAGGGGACAATGTCAAGTTTGGGTTGCCAATGGCGTTCACGGTGACCATGATGTCGTGGAGCATATTAGAGT
|||||||| | | | || | || || | | || | || || | || || | | | | | | || ||| | || | | | | | ||| |||||| | | | ||||| || || || ||||| || || || ||||| ||||| || ||||| || |||| |||||||||||||||||||||||||||||| |||| | ||||
gtatgcacaacgcgtctctcgttgcattaattagcaa------gcaagcattgtgaccatgg-cagctgggttcgtcgctgtgctgaacacgatttttgt----tttggttc----ttttatgttttgtctcgccggacagGTGGACCTCGTCGGAGGGTACTACGACGCAGGCGACAACGTGAAGTTCGGCCTGCCCATGGCGTTCACGGTGACCATGATGTCGTGGGGCATCCTGGAGT

upper sequence: LOC_Os05g12150.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA05G36930.1 (Glycine max), 3'ss of exon 1
gtatgcaccattctaccttcaaatctttgatcaaaaccatgatgccatcaatggcattgtgttcaatttgttcaggagatatgatgagttgggttctaatggagtgcaatgcaaatgtttgtgtttttgtttgtctttcagGTTGATCTTGTTGGAGGTTATTATGATGCAGGGGACAATGTCAAGTTTGGGTTGCCAATGGCGTTCACGGTGACCATGATGTCGTGGAGCATATTAGAGT
| | |||| | | | || | ||| | | | | | | ||| || | ||||| ||| | || || | ||||| ||||| |||||||| || |||||||||||||||||||| ||||| ||||| || |||||||| || || || ||||||||||||||||| | || |
--------------------------------------gtaagcttttcaa---ctctttttttagtttagtttagtt-tctcactttcctcacccaaattcag---gttacaaattattg-atgttaaattata---cagGTGGATCTAGTTGGAGGGTACTATGATGCAGGGGACAATGTGAAGTTCGGGTTACCCATGGCGTTTACCGTTACGATGATGTCGTGGAGCATCATTGAAT

upper sequence: LOC_Os05g12150.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA08G02610.1 (Glycine max), 3'ss of exon 1
gtatgcaccattctaccttcaaatctttgatcaaaaccatgatgccatcaatggcattgtgttcaatttgttcaggagatatgatgagttgggttctaatggagtgcaatgcaaatgtttgtgtttttgtttgtcttt-cagGTTGATCTTGTTGGAGGTTATTATGATGCAGGGGACAATGTCAAGTTTGGGTTGCCAATGGCGTTCACGGTGACCATGATGTCGTGGAGCATATTAGAGT
| ||| || | | | | | | | | ||| | | | | | | || |||| |||| | | ||||| ||||| |||||||| || |||||||||||||||||||| ||||| ||||| || |||||||| || || || ||||||||||||||||| | || |
--------------------------------------------------------gtaagtttaagaactcttttactttagtttactca--cccaaattctttctagtcctagttttcatgttgatgttaaattatgcagGTGGATCTAGTTGGAGGGTACTATGATGCAGGGGACAATGTGAAGTTCGGGTTACCCATGGCGTTTACCGTTACGATGATGTCGTGGAGCATCATTGAAT

upper sequence: LOC_Os05g12150.1 (Oryza sativa), 3'ss of exon 1
lower sequence: AT1G64390.1 (Arabidopsis thaliana), 3'ss of exon 1
---------------------------------------------------gtatgcaccattctaccttcaaatct---ttgatcaaaaccatgatgccatcaat-ggcattgtgttcaattt--gttcaggagatatgatgagttgggttctaatggagtgcaatgca--aatgtttgtgtttttgtttgtctttcagGTTGATCTTGTTGGAGGTTATTATGATGCAGGGGACAATGTCAAGTTTGGGTTGCCAATGGCGTTCACGGTGACCATGATGTCGTGGAGCATATTAGAGT
|| ||| | || | | | | | | || || | || | | | | ||| || | | ||| |||||| | | | | || | | | || || || | | | | || | ||| |||||| |||| || |||||||| || || || || |||||||| || ||||| || || ||||| ||||||||||| |||||| ||||||| | | ||||
gtatgtctctccctctctgtctctctctttctagattttgtttccgacattgt-tgctctgttttccacttgattttgagtttattcagacaacatttcagtaaattagctatagatctgttttccgttcagacaacgtcgtcaccaacattgt--tcgtgtttcatacagtactaactagaatcttttgtgttgatcagGTGAATCTGGTCGGAGGTTACTACGACGCCGGAGACAATGTGAAATTTGGATTACCGATGGCTTTCACGGTGACGATGATGGCGTGGAGTGTGATTGAGT

upper sequence: LOC_Os05g12150.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv02s0025g01380.t01 (Vitis vinifera), 3'ss of exon 3
------gtatgcaccattctaccttcaaatctttgatcaaaaccatgatgccatcaatggcattgtgttcaatttgttcaggagatatgatgagttgggttctaatggagtgcaatgcaaatgtttgtgtttttgtttgtctttcagGTTGATCTTGTTGGAGGTTATTATGATGCAGGGGACAATGTCAAGTTTGGGTTGCCAATGGCGTTCACGGTGACCATGATGTCGTGGAGCATATTAGAGT
|| ||| || | || |||| | ||| || |||| || | ||| ||| | | | || ||| ||| | | || ||| | | ||| || ||| |||| ||| | |||| ||||| || ||||| |||||||||||||| |||||||| |||||||| | || ||||| ||||| || || |||||||| ||||||||| | ||||
gtaagttcattttccactccaactcaaaatttctgaa-aagcccattgtgg-aacaagacaattataattgaattattcc----atacaaccaaatgtgttgaagttttttgctat---aatctttgagtt----------atgtagGTGGATCTGGTGGGAGGATATTATGATGCAGGTGACAATGTGAAGTTTGGCCTACCCATGGCATTCACCGTTACAATGATGTCATGGAGCATAGTGGAGT

upper sequence: LOC_Os05g12150.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S176_127V6.1 (Physcomitrella patens), 3'ss of exon 2
-----------------------gtatgcaccattctaccttcaaatctttgatcaaaaccatgatgccatcaatggcattgtgttcaatttgttcaggagatatgatgagt-tgggttctaatgg--agtgcaatgcaaatgtttgtgtttttgtttgtctttcagGTTGATCTTGTTGGAGGTTATTATGATGCAGGGGACAATGTCAAGTTTGGGTTGCCAATGGCGTTCACGGTGACCATGATGTCGTGGAGCATATTAGAGT
||| | | | || | | ||| ||| | | ||| | | | || | | ||||||| | | || | || | || || | | | ||| | |||| | |||| ||||| ||||| |||||||| ||||| || ||||||||||||||||| ||||| |||| ||||| || |||||| |||||||||| | | ||||
gtaagaccttcgtttcgcgttctagatgggtgactgttttatcttaagcatagaaaaagttgtgaagaggatgtagacat-gctcgccagctgacaattaaatatgatatatgtaggatatagtcattggttcatttgctttacgattatttgtacttgtaatgtagGTGGATCTGGTTGGTGGTTATTACGATGCTGGTGACAATGTCAAGTTTGGCTTGCCTCTGGCATTCACTGTTACCATGCTGTCGTGGAGTGTTCTTGAGT

upper sequence: LOC_Os05g12150.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S37_355V6.1 (Physcomitrella patens), 3'ss of exon 1
gtatgcaccattctaccttcaaatctttgatcaaaaccatgatgccatcaatggcattgtgtt-caatttgttcaggagatatgatgagttgggttctaatggagtgcaatgcaaatgtttgtgtttttgtttgtctttcagGTTGATCTTGTTGGAGGTTATTATGATGCAGGGGACAATGTCAAGTTTGGGTTGCCAATGGCGTTCACGGTGACCATGATGTCGTGGAGCATATTAGAGT
| || | || || | || | | ||| ||| || | | | | || | || || | || | || || || | |||| ||||| | | ||||||| ||| |||||||| || |||||||| ||||||||||||| ||| |||| |||||||| || | || ||| | || ||||| || | || |
--------------gtaagtggcacattccttgaactcacaacagtttc--tcgtgttgcgttgcagtaccgcaatgtcgcagaataa--tgtgtcgtgatagctcacactgt--atctgtgtggcgttgtt--ccgtgtagGTTGACCTTTCGGGAGGTTACTACGATGCAGGAGACAATGTCAAGTATGGTCTGCCGATGGCGTTTACCATTACTATGCTCTCTTGGAGTGTAATTGAAT

upper sequence: LOC_Os05g12150.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ12750 (Selaginella moellendorffii), 3'ss of exon 1
gtatgcaccattctaccttcaaatctttgatcaaaaccatgatgccatcaatggcattgtgttcaatttgttcaggagatatgatgagttgggttctaatggagtgcaatgcaaatgtttgtgtttttgtttgtctttcagGTTGATCTTGTTGGAGGTTATTATGATGCAGGGGACAATGTCAAGTTTGGGTTGCCAATGGCGTTCACGGTGACCATGATGTCGTGGAGCATATTAGAGT
| | | | ||| || | | || | | || | | | | || ||| || || || || || | || | ||| || || ||||| ||| | |||||||| ||||| || || || ||||||||||||||||| |||| ||||| ||||| | |||||||||||||||||| | ||||
--------------------------------atagata-gctgcattcgaggatatctttccc---tttcggatgtgcctttgcgaattgagtactt-tgcgttgtggtg--attgatggtggcgctg--gaactaccagGTGGATTTGGTTGGAGGGTATTACGACGCGGGCGACAATGTCAAGTTTGGCCTGCCCATGGCCTTCACCATCACCATGATGTCGTGGAGCGCCATCGAGT

upper sequence: LOC_Os05g12150.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ13916 (Selaginella moellendorffii), 3'ss of exon 1
gtatgcaccattctaccttcaaatctttgatcaaaaccatgatgccatcaatggcattgtgttcaatttgttcaggagatatgatgagttgggttctaatggagtgcaatgcaaatgtttgtgtttttgtttgtctttcagGTTGATCTTGTTGGAGGTTATTATGATGCAGGGGACAATGTCAAGTTTGGGTTGCCAATGGCGTTCACGGTGACCATGATGTCGTGGAGCATATTAGAGT
| | | ||| || | | || | | || | | | | || ||| || || || || || | || | ||| || || ||||| ||| | |||||||| ||||| || || || ||||||||||||||||| |||| ||||| ||||| | |||||||||||||||||| | ||||
--------------------------------gtagata-gctgcattctaggatatctttccc---tttcggatgtgcctttgcgaattgagtactt-tgcgttgtggtg--attgatggtggcgctg--gaactaccagGTGGATTTGGTTGGAGGGTATTACGACGCGGGCGACAATGTCAAGTTTGGTCTGCCCATGGCCTTCACCATCACCATGATGTCGTGGAGCGCCATCGAGT

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|86900869|gb|CI304074.1|CI304074
EST:     GGGTCTCCTGGAGAGCCAGCTCTGGCCTCTTTGATGGAAAGGCCAATGGA                         GTTGATCTTGTTGGAGGTTATTATGATGC
genomic: GGGTCTCCTGGAGAGCCAGCTCTGGCCTCTTTGATGGAAAGGCCAATGGAgtatgcacca ... tgtctttcagGTTGATCTTGTTGGAGGTTATTATGATGC
EST: gi|88364046|gb|CI610390.1|CI610390
EST:     GGGTCTCCTGGAGAGCCAGCTCTGGCCTCTTTGATGGAAAGGCCAATGGA                         GTTGATCTTGTTGGAGGTTATTATGATGCAGGGGACAATGTCAAGTTTGGG
genomic: GGGTCTCCTGGAGAGCCAGCTCTGGCCTCTTTGATGGAAAGGCCAATGGAgtatgcacca ... tgtctttcagGTTGATCTTGTTGGAGGTTATTATGATGCAGGGGACAATGTCAAGTTTGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttgggttctaatggagtgcaatgcaaatgtttgtgtttttgtttgtctttcagGTTGATCTTGTTGGAGGTTATTATGATGCAGGGGACAATGTCAAGTTTGGGTTGCCAATGGCGTTCACGGTGACCATGATGTCGTGGAGCATATTAGAGT
       ttctaat  putative branch site (score: 2)
 tttttgtttgtctttc  putative PPT
 tttttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcaccattctaccttcaaatctttgatcaaaaccatgatgccatcaatggcattgtgttcaatttgttcaggagatatgatgagttgggttctaatggagtgcaatgcaaatgtttgtgtttttgtttgtctttcagGTTGATCTTGTTGGAGGTTATTATGATGCAGGGGACAATGTCAAGTTTGGGTTGCCAATGGCGTTCACGGTGACCATGATGTCGTGGAGCATATTAGAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA