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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGTGAGAGTATGGAGAATGCATTGCGGGCATGCTGCAAAGGTATAAAAATTGGGAAGATTCTTATTCACAGGGAAGGAGACAATGGCAAACAGgtttggtttaatctacttttggcattatttgttggagttagtcaaattactaagctcttgattccttgcag

Basic information

species Oryza sativa
transcript LOC_Os02g17320.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g17320.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G034143_T01 (Zea mays), 5'ss of exon 12
TGGTGAGAGTATGGAGAATGCATTGCGGGCATGCTGCAAAGGTATAAAAATTGGGAAGATTCTTATTCACAGGGAAGGAGACAATGGCAAACAGgtttggtttaatctacttttggcattatttgttggagttagtcaaattactaagctct--tgattccttgcag
||| || || ||||||||||| || || |||||||| ||||||||||| ||||||||||||||||||||  ||||||||||||||||  ||||||| || |||| || ||||||| |||    |||| | || ||||||||||||||| |||  |  ||  ||||||
TGGCGAAAGCATGGAGAATGCGTTACGAGCATGCTGTAAAGGTATAAAGATTGGGAAGATTCTTATTCATCGGGAAGGAGACAATGGACAACAGgtctgattta-tcaacttttgccatg---tgttagggtgagtcaaattactaagatctattttttttttgcag

upper sequence: LOC_Os02g17320.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G169462_T01 (Zea mays), 5'ss of exon 11
TGGTGAGAGTATGGAGAATGCATTGCGGGCATGCTGCAAAGGTATAAAAATTGGGAAGATTCTTATTCACAGGGAAGGAGACAATGGCAAACAGgtttggtttaatctacttttggcattatttgttggagttagtcaaattactaagctcttgattcctt-gcag
||| || ||||||||||||||| | || |||||||| ||||||||||| ||||||||||||||||||||  ||||||| ||||||||  ||||||| ||| ||| || ||||||| |||    |||| | || ||||||||||||||| |||  ||| ||| ||||
TGGCGAAAGTATGGAGAATGCACTACGTGCATGCTGTAAAGGTATAAAGATTGGGAAGATTCTTATTCATCGGGAAGGTGACAATGGACAACAGgtctggctta-tcaacttttgccatg---tgttagggtgagtcaaattactaagatctaaatttctttgcag

upper sequence: LOC_Os02g17320.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GLYMA02G47270.1 (Glycine max), 5'ss of exon 12
TGGTGAGAGTATGGAGAATGCATTGCGGGCATGCTGCAAAGGTATAAAAATTGGGAAGATTCTTATTCACAGGGAAGGAGACAATGGCAAACAGgtttg--gttta-atctacttttggcattatttgt--tggagttagtcaa--attactaagctcttgattccttgcag--------------------------------
||| ||||||||||| |||||  | || ||||||||||||||||| || |||||||| ||||||||||| || ||||| ||||||||  ||||||||||   | |   | |    ||||   ||  |||   ||| | | |  |  || ||||   ||||  ||  |||  |                                
TGGGGAGAGTATGGAAAATGCTCTACGAGCATGCTGCAAAGGTATCAAGATTGGGAAAATTCTTATTCATAGAGAAGGTGACAATGGTCAACAGgtttgtcatctgtgtgtgtgcttgggtatacctgtgtcggattcatttcatgatcactagtgtcttttttttttggtgattcactaacttgtcctttgattattgagcag

upper sequence: LOC_Os02g17320.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GLYMA18G08180.1 (Glycine max), 5'ss of exon 12
TGGTGAGAGTATGGAGAATGCATTGCGGGCATGCTGCAAAGGTATAAAAATTGGGAAGATTCTTATTCACAGGGAAGGAGACAATGGCAAACAGgtttggt----ttaatctact-tttggcatta---tttgttggagttagtcaaatta----ctaagctcttgattccttg-cag-
||| ||||||||||||||||| ||| | |||||||| |||||||| || |||||||| ||| | |||||||| ||||| ||||||||  | |||||| | |    |  |||||   ||||| |  |   | ||||  | || || | | |     || |    ||||||  |   ||| 
TGGGGAGAGTATGGAGAATGCTTTGAGAGCATGCTGTAAAGGTATCAAGATTGGGAAAATTTTAATTCACAGAGAAGGTGACAATGGTCAGCAGGttagttcatctgcatctatggtttggtacaaatctctgtttcatttggtgatactgacatcttatgctttgattaatgatcagc

upper sequence: LOC_Os02g17320.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GLYMA14G01480.1 (Glycine max), 5'ss of exon 9
------TGGTGAGAGTATGGAGAATGCATTGCGGGCATGCTGCAAAGGTATAAAAATTGGGAAGATTCTTATTCACAGGGAAGGAGACAATGGCAAACAGgtttggt-ttaatctacttttggcattatttgttggagttagtcaa--attactaagctcttg-attccttgcag----------------------------------
      ||| ||||||||||| ||||| || || ||||||||||||||||| || |||||||| ||||||||||| || ||||| ||||||||  ||||||||||   ||    |    ||||   || |  || || | | |  |  || |||||  | |    ||  ||   |                                  
TTTCAGTGGGGAGAGTATGGAAAATGCTTTACGAGCATGCTGCAAAGGTATCAAGATTGGGAAAATTCTTATTCATAGAGAAGGTGACAATGGTCAACAGgtttgtcatttgcgtgtgcttgggtatactgttttgattcatttcatgatcactaacttgtcctgttttttttggtgattcactaacttgtcctttgattattgagcag

upper sequence: LOC_Os02g17320.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GLYMA08G45270.1 (Glycine max), 5'ss of exon 12
TGGTGAGAGTATGGAGAATGCATTGCGGGCATGCTGCAAAGGTATAAAAATTGGGAAGATTCTTATTCACAGGGAAGGAGACAATGGCAAACAGgtttggt----ttaatctact-tttggcatta---tttgttggagttagtcaaattactaagctcttgattccttgcag-----
||| ||||||||||||||||| ||| | |||||||| ||||||||||| |||||||| ||| | |||||||| ||||| ||||||||  | |||||| | |    |  |||||   ||||| |  |   | ||||  | || || | | |  ||   | |   ||  |    |     
TGGGGAGAGTATGGAGAATGCTTTGAGAGCATGCTGTAAAGGTATAAAGATTGGGAAAATTTTAATTCACAGAGAAGGTGACAATGGTCAGCAGgttagttcatctgcatctatggtttggtacaaatctctgtttcacttggtgatactgatatcttatgctttgatcaatgatcag

upper sequence: LOC_Os02g17320.1 (Oryza sativa), 5'ss of exon 12
lower sequence: AT1G55810.1 (Arabidopsis thaliana), 5'ss of exon 12
TGGTGAGAGTATGGAGAATGCATTGCGGGCATGCTGCAAAGGTATAAAAATTGGGAAGATTCTTATTCACAGGGAAGGAGACAATGGCAAACAGgtttggtttaatctacttttggcattatttgttggagttagtcaaattactaagctcttgattccttgcag
 ||||||||||||||||| ||  |  | |||||||||||||| || ||||||||||||||||| ||||| || ||||| ||||||||  ||||||||||  ||    | || |   ||| | || |   |  || | |   ||  || |   ||   |    |||
CGGTGAGAGTATGGAGAACGCTCTTAGAGCATGCTGCAAAGGCATCAAAATTGGGAAGATTCTGATTCATAGAGAAGGCGACAATGGTCAACAGgtttgtgtt--ctttctctgctcatcacttctcctaactattta--ctaacaa-caaatggcactcaccag

upper sequence: LOC_Os02g17320.1 (Oryza sativa), 5'ss of exon 12
lower sequence: AT1G55810.2 (Arabidopsis thaliana), 5'ss of exon 11
TGGTGAGAGTATGGAGAATGCATTGCGGGCATGCTGCAAAGGTATAAAAATTGGGAAGATTCTTATTCACAGGGAAGGAGACAATGGCAAACAGgtttggtttaatctacttttggcattatttgttggagttagtca--aattactaa--gctcttgattccttgcag--------
 ||||||||||||||||| ||  |  | |||||||||||||| || ||||||||||||||||| ||||| || ||||| ||||||||  ||||||||||  ||    | || |   ||| | || |   |  || | |  ||  || ||  || ||      |||            
CGGTGAGAGTATGGAGAACGCTCTTAGAGCATGCTGCAAAGGCATCAAAATTGGGAAGATTCTGATTCATAGAGAAGGCGACAATGGTCAACAGgtttgtgtt--ctttctctgctcatcacttctcctaactatttactaacaacaaatggcactcaccagcttatctacgagaag

upper sequence: LOC_Os02g17320.1 (Oryza sativa), 5'ss of exon 12
lower sequence: AT4G26510.2 (Arabidopsis thaliana), 5'ss of exon 12
TGGTGAGAGTATGGAGAATGCATTGCGGGCATGCTGCAAAGGTATAAAAATTGGGAAGATTCTTATTCACAGGGAAGGAGACAATGGCAAACAGgtttg-gtttaatctacttttggcattatttgttggagttagtcaaattactaagctcttgattcct-tgcag
||||||||| ||||||||||| || || ||||| ||||||||||| || || |||||||| || |||||||| ||||| ||||||||  |||||||    |  | |      |||      |  ||||    ||  |||   |  | |  |||  ||  || |||||
TGGTGAGAGCATGGAGAATGCGTTACGAGCATGTTGCAAAGGTATCAAGATCGGGAAGATCCTAATTCACAGAGAAGGTGACAATGGTCAACAGgtaaacgagtcactcctatttcattccaggtgttctgtttcatca--ctgttgatgtctgtatcactgtgcag

upper sequence: LOC_Os02g17320.1 (Oryza sativa), 5'ss of exon 12
lower sequence: Vv19s0015g01730.t01 (Vitis vinifera), 5'ss of exon 12
TGGTGAGAGTATGGAGAATGCATTGCGGGCATGCTGCAAAGGTATAAAAATTGGGAAGATTCTTATTCACAGGGAAGGAGACAATGGCAAACAGgtttggtttaatctacttttggcattat--ttgttggagttagtcaaat-tactaagctcttgattccttgcag---------------------------------------------------
||||||||||||||||||||| ||||| ||||| ||||||||||| |||||||||||||||||||| || |||||||| || || ||  | |||||| ||    ||||   | |  |  |||  ||||      |   || |   ||||  | | ||  | |    |                                                    
TGGTGAGAGTATGGAGAATGCTTTGCGAGCATGTTGCAAAGGTATCAAAATTGGGAAGATTCTTATCCATAGGGAAGGGGATAACGGTCAGCAGgtt-ggacagatctctctctctctgtatccttgtctcccatgcacagacacactacacacatgcatgcacagatatctatctactaacattttgactgtttttttatgtttcaatgactggacag

upper sequence: LOC_Os02g17320.1 (Oryza sativa), 5'ss of exon 12
lower sequence: PP1S83_234V6.1 (Physcomitrella patens), 5'ss of exon 12
TGGTGAGAGTATGGAGAATGCATTGCGGGCATGCTGCAAAGGTATAAAAATTGGGAAGATTCTTATTCACAGGGAAGGAGACAATGGCAAACAGgtttggtttaatctactt---ttgg--------cattatttgttggagttagtcaaattactaagctcttgattccttgcag-----------------------------------------------------------------------------------
 || ||||| |||||||||||| ||||||| ||||||||||| || || ||||| |||||| | || ||  | |||||||| |||||  ||||||| |   | ||| || |    ||||        || ||||| |    | | ||   | || | | ||||| |||   | |||                                                                                   
CGGGGAGAGCATGGAGAATGCACTGCGGGCGTGCTGCAAAGGCATCAAGATTGGAAAGATTTTGATACATCGCGAAGGAGATAATGGGCAACAGgtatcagtcaatttaatcgtgttggatggtgttcactatttttccctgattgtacgaatattca-ctcttcatttggttcagtaatgatcagtcttagacttccagcgaggtcaacaatgcaactcatcctttgtttaggctgacttaatttttgcactttgcag

upper sequence: LOC_Os02g17320.1 (Oryza sativa), 5'ss of exon 12
lower sequence: PP1S19_94V6.1 (Physcomitrella patens), 5'ss of exon 11
TGGTGAGAGTATGGAGAATGCATTGCGGGCATGCTGCAAAGGTATAAAAATTGGGAAGATTCTTATTCACAGGGAAGGAGACAATGGCAAACAGgt-ttggtttaatctactt---ttggcattatttgttggagttagtcaaattactaagctcttgattccttgcag--------------------------------------------------------------------------------------------------
||| ||||||||||||||||| |||||||| || ||||| || || || ||||| |||||||| || ||| |||| |||||  | || || |||||  | |||  || |  ||    | | || |    |||   ||  |||  ||   |   | |  || |  || |                                                                                                   
TGGAGAGAGTATGGAGAATGCTTTGCGGGCGTGTTGCAAGGGCATCAAGATTGGAAAGATTCTAATACACCGGGAGGGAGATGACGGGAAGCAGgtacttgttggatgtgattggtcttgtatcacgc-ttgcttttcttcatcttttcatattttcaatacgctgaatccgaatatgttaagttcattcaaggctgcacagaatcgcaaatgttgaaagtttggagctacttcatctgttaaaagtggctgatggtgatgatgcag

upper sequence: LOC_Os02g17320.1 (Oryza sativa), 5'ss of exon 12
lower sequence: EFJ17251 (Selaginella moellendorffii), 5'ss of exon 10
TGGTGAGAGTATGGAGAATGCATTGCGGGCATGCTGCAAAGGTATAAAAATTGGGAAGATTCTTATTCACAGGGAAGGAGACAATGGCAAACAGgt----------------------ttggtttaatctacttttggcattatttgttggagttagtcaaattactaagctcttgattccttgcag-------
 || ||  |||||||||| ||  |||| || || ||||| || |||||||| || ||||||||||| ||| |||| || |||||||| ||||| ||                      |||                                                                         
CGGGGAACGTATGGAGAACGCTCTGCGTGCCTGTTGCAAGGGAATAAAAATCGGCAAGATTCTTATACACCGGGAGGGCGACAATGGAAAACAAgtaaaagcttcatcagagcagccattgacannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn

upper sequence: LOC_Os02g17320.1 (Oryza sativa), 5'ss of exon 12
lower sequence: EFJ31180 (Selaginella moellendorffii), 5'ss of exon 11
TGGTGAGAGTATGGAGAATGCATTGCGGGCATGCTGCAAAGGTATAAAAATTGGGAAGATTCTTATTCACAGGGAAGGAGACAATGGCAAACAGgtttggtttaatctacttttggcattatttgttggagttagtcaaattactaagctcttgattccttgcag
 || || ||||||||||| ||  |||| || || ||||| || |||||||| || ||||||||||| ||| ||||||| |||||||| ||||| ||       || || | |  |  |  |    |||   | | |    |||||      ||  |     ||||
CGGAGAAAGTATGGAGAACGCTCTGCGTGCCTGTTGCAAGGGAATAAAAATCGGCAAGATTCTTATACACCGGGAAGGCGACAATGGAAAACAAgta-----aaaccttcatcag--agcagccattgacatgatttc--ttacttcttcttttctctgacgcag

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|29633369|gb|CB638378.1|CB638378
EST:     TAAAAATTGGGAAGATTCTTATTCACAGGGAAGGAGACAATGGCAAACAG                         CTAATCTATCACAATTTACCGAAAGATATTGCAAACAGGCATGTGCTGTTG
genomic: TAAAAATTGGGAAGATTCTTATTCACAGGGAAGGAGACAATGGCAAACAGgtttggttta ... ttccttgcagCTAATCTATCACAATTTACCGAAAGATATTGCAAACAGGCATGTGCTGTTG
EST: gi|87037876|gb|CI192498.1|CI192498
EST:     TAAAAATTGGGAAGATTCTTATTCACAGGGAAGGAGACAATGGCAAACAG                         CTAATCTATCACAATTTACCGAAAGATATTGCAAACAGGCATGTGCTGTTG
genomic: TAAAAATTGGGAAGATTCTTATTCACAGGGAAGGAGACAATGGCAAACAGgtttggttta ... ttccttgcagCTAATCTATCACAATTTACCGAAAGATATTGCAAACAGGCATGTGCTGTTG
EST: gi|3760815|gb|C98069.1|C98069
EST:     TAAAAATTGGGAAGATTCTTATTCACAGGGAAGGAGACAATGGCAAACAG                         CTAATCTATCACAATTTACCGAAAGATATTGCAAACAGGCATGTGCTGTTG
genomic: TAAAAATTGGGAAGATTCTTATTCACAGGGAAGGAGACAATGGCAAACAGgtttggttta ... ttccttgcagCTAATCTATCACAATTTACCGAAAGATATTGCAAACAGGCATGTGCTGTTG
EST: gi|87029276|gb|CI276544.1|CI276544
EST:     TAAAAATTGGGAAGATTCTTATTCACAGGGAAGGAGACAATGGCAAACAG                         CTAATCTATCACAATTTACCGAAAGATATTGCAAACAGGCATGTGCTGTTG
genomic: TAAAAATTGGGAAGATTCTTATTCACAGGGAAGGAGACAATGGCAAACAGgtttggttta ... ttccttgcagCTAATCTATCACAATTTACCGAAAGATATTGCAAACAGGCATGTGCTGTTG
EST: gi|86498530|gb|CI141163.1|CI141163
EST:     TAAAAATTGGGAAGATTCTTATTCACAGGGAAGGAGACAATGGCAAACAG                         CTAATCTATCACAATTTACCGAAAGATATTGCAAACAGGCATGTGCTGTTG
genomic: TAAAAATTGGGAAGATTCTTATTCACAGGGAAGGAGACAATGGCAAACAGgtttggttta ... ttccttgcagCTAATCTATCACAATTTACCGAAAGATATTGCAAACAGGCATGTGCTGTTG
EST: gi|29675373|gb|CB671648.1|CB671648
EST:     TAAAAATTGGGAAGATTCTTATTCACAGGGAAGGAGACAATGGCAAACAG                         CTAATCTATCACAATTTACCGAAAGATATTGCAAACAGGCATGTGCTGTTG
genomic: TAAAAATTGGGAAGATTCTTATTCACAGGGAAGGAGACAATGGCAAACAGgtttggttta ... ttccttgcagCTAATCTATCACAATTTACCGAAAGATATTGCAAACAGGCATGTGCTGTTG
EST: gi|29627016|gb|CB632027.1|CB632027
EST:     TAAAAATTGGGAAGATTCTTATTCACAGGGAAGGAGACAATGGCAAACAG                         CTAATCTATCACAATTTACCGAAAGATATTGCAAACAGGCATGTGCTGTTG
genomic: TAAAAATTGGGAAGATTCTTATTCACAGGGAAGGAGACAATGGCAAACAGgtttggttta ... ttccttgcagCTAATCTATCACAATTTACCGAAAGATATTGCAAACAGGCATGTGCTGTTG
EST: gi|86537180|gb|CI177386.1|CI177386
EST:     GACAATGGCAAACAG                         CTAATCTATCACAATTTACCGAAAGATATTGCAAACAGGCATGTGCTGTTG
genomic: GACAATGGCAAACAGgtttggttta ... ttccttgcagCTAATCTATCACAATTTACCGAAAGATATTGCAAACAGGCATGTGCTGTTG
EST: gi|29643326|gb|CB648333.1|CB648333
EST:     AGATTCTTATTCTCAGGGAAGGAGACAATGGCGAGCCAG                         CTAATCTATCACAATTTGCCGAAAGATATTGCAAACAGGCATGTGCTGTT
genomic: AGATTCTTATTCACAGGGAAGGAGACAATGGC-AAACAGgtttggttta ... ttccttgcagCTAATCTATCACAATTTACCGAAAGATATTGCAAACAGGCATGTGCTGTT
EST: gi|86536638|gb|CI176844.1|CI176844
EST:     AGACAATGTCAAACAG                         CTAATCTATCACAATTTACCGAAAGATATTGCAAACAGGCATGTGCTGTTG
genomic: AGACAATGGCAAACAGgtttggttta ... ttccttgcagCTAATCTATCACAATTTACCGAAAGATATTGCAAACAGGCATGTGCTGTTG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 63 (upstream exon), 70 (downstream exon)
Score: 42

TGGTGAGAGTATGGAGAATGCATTGCGGGCATGCTGCAAAGGTATAAAAATTGGGAAGATTCTTATTCACAGGGAAGGAGACAATGGCAAACAGgtttggttta ... ttccttgcagCTAATCTATCACAATTTACCGAAAGATATTGCAAACAGGCATGTGCTGTTGTTGGATCCCATACTGGGAACAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGTGAGAGTATGGAGAATGCATTGCGGGCATGCTGCAAAGGTATAAAAATTGGGAAGATTCTTATTCACAGGGAAGGAGACAATGGCAAACAGgtttggtttaatctacttttggcattatttgttggagttagtcaaattactaagctcttgattccttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA