Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttgagtgctgaacaatttcagtgttatctgtcagattgggatcccataaacacattgtgtaatttagctttctgtgcatttgcatgatgactgaatggctgtgttgatcatttgggcacagGTGAGCGACACGGAGCTTTGCTGCATCTGCTTCGACCAGGCTTGCACCATTGAGGTGCAAGACTGTGGACATCAAATGTGTGCACCGTGCACGCTGGCAC

Basic information

species Oryza sativa
transcript LOC_Os05g02130.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g02130.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G069162_T03 (Zea mays), 3'ss of exon 7
gtatttgagtgctgaacaatttcagtgttatctgtcagattgggatcccataaacacattgtgtaatttagctttctgtgcatttgcatgatgactgaatggctgtgttgatcatttgggcacagGTGAGCGACACGGAGCTTTGCTGCATCTGCTTCGACCAGGCTTGCACCATTGAGGTGCAAGACTGTGGACATCAAATGTGTGCACCGTGCACGCTGGCAC
                        || |  | |||  ||  |    |  | |||         | ||  |  |    |  |||||    | | |||   || |||| |   |||    |||    |  |||||| ||||||| ||||||||||||||||||||||| ||||| || |||||||| ||||| || || || ||||| || ||||||||||      
------------------------gtatgctttgt--gaccg----ctgacaaatgtgggacctgatgca--tcatcgcccattt-tgcgctcact---tgactgt-tcactcac--agGCCAGCGCCAGCGACGCGGAGCTGTGCTGCATCTGCTTCGACCAGGCGTGCACGATGGAGGTGCAGGACTGCGGGCACCAGATGTGCGCGCCGTGCACGC------

upper sequence: LOC_Os05g02130.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G141922_T01 (Zea mays), 3'ss of exon 7
------gtatttgagtgctgaacaatttcagtgttatctgtca-gattgggatc-ccataaacacattgtgtaatttagctttctgtgcatttgcatgatgactgaatggctgtgttgatcatttgggc------acagGTGAGCGACACGGAGCTTTGCTGCATCTGCTTCGACCAGGCTTGCACCATTGAGGTGCAAGACTGTGGACATCAAATGTGTGCACCGTGCACGCTGGCAC
      || ||       ||     |  || |   ||    |  |||    |||  ||| | |   | |||   |   | |   || | |   |    || ||  |  | |  | |   |||| || ||      |||||  ||||||  |||||| ||||||||||||||||| ||||| |||| ||| |||||||| ||||| || || || ||||| ||  ||||||| ||||| |
gtacgcgtgttcattcagtgctttgtgacaatccaatgaaccttgatcatcatcatcatcatctggtggtgcgttgctggtaaatgaggaacggatgcatcacccaccgaccct-tccttcatctgtgctgactcacagGCCAGCGACGGGGAGCTGTGCTGCATCTGCTTCGAGCAGGCGTGCAGCATCGAGGTGCAGGACTGCGGGCACCAGATGTGCGCGGCGTGCACACTGGCGC

upper sequence: LOC_Os05g02130.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv06s0004g04550.t01 (Vitis vinifera), 3'ss of exon 7
gtatttgagtgctgaacaatttcagtgttatctgtcagattgggatcccataaacacattgtgtaat-ttagctt-tctgtgcatttgcatgatgactgaatggctg--tgttgatcatttgggcacagGTGAGCGACACGGAGCTTTGCTGCATCTGCTTCGACCAGGCTTGCACCATTGAGGTGCAAGACTGTGGACATCAAATGTGTGCACCGTGCACGCTGGCAC
                              ||| |  |    ||  || || | |   |  |||  | ||||  | |   ||||    || || | || | | | |   ||||    | |      ||||  || || || |||||||||||||| |||||||| ||||  ||||| ||||| || |||||||| || || || ||||| || |  ||||| || || |
----------------------------cgtct-ttggtcctggtcccaattatcttctcctgttctgttagtctattcttgcaagaacaagaggtctcagttgttcattgtttgataatatcttgcagGCCAGTGAAACAGAGCTTTGCTGCATATGCTTCGATCAGGTGTGCACAATTGAAGTCCAAGACTGCGGTCACCAGATGTGCGCTCAATGCACACTAGCCC

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|58659990|gb|CK048670.1|CK048670
EST:     CATCCCCTTCGCCCGGTGATGACAGTGCCGATGACGATGCATGCTCAGAG                         GTGAGCGACACGGAGCTCTGCTGCATCTGCTTCGACCAGGCTTGCACCATT
genomic: CATCCCCTTCGCCCGGTGATGACAGTGCCGATGACGATGCATGCTCAGAGgtatttgagt ... ttgggcacagGTGAGCGACACGGAGCTTTGCTGCATCTGCTTCGACCAGGCTTGCACCATT
EST: gi|29637639|gb|CB642648.1|CB642648
EST:     CATCCCCTTCGCCCGGTGATGACAGTGCCGATGACGATGCATGCTCAGAG                         GTGAGCGACACGGAGCTTTGCTGCATCTGCTTCGACCAGGCTTGCACCATT
genomic: CATCCCCTTCGCCCGGTGATGACAGTGCCGATGACGATGCATGCTCAGAGgtatttgagt ... ttgggcacagGTGAGCGACACGGAGCTTTGCTGCATCTGCTTCGACCAGGCTTGCACCATT
EST: gi|33812673|gb|CF332225.1|CF332225
EST:     CCGATGACGATGCATGCTCAGAG                         GTGAGCGACACGGAGCTTTGCTGCATCTGCTTCGACCAGGCTTGCACCATT
genomic: CCGATGACGATGCATGCTCAGAGgtatttgagt ... ttgggcacagGTGAGCGACACGGAGCTTTGCTGCATCTGCTTCGACCAGGCTTGCACCATT
EST: gi|33677416|gb|CF305655.1|CF305655
EST:     CATCCCCTTCGCCCGGTGATGACAGTGCCGATGACGATGCATGCTCAGAG                         GTGAGCGACACGGAGCTTTGCTGCATCTGCTTCGACCAGGCTTGCACCATT
genomic: CATCCCCTTCGCCCGGTGATGACAGTGCCGATGACGATGCATGCTCAGAGgtatttgagt ... ttgggcacagGTGAGCGACACGGAGCTTTGCTGCATCTGCTTCGACCAGGCTTGCACCATT
EST: gi|66918338|gb|CX105186.1|CX105186
EST:     CATCCCCTTCGCCCGGTGATGACAGTGCCGATGACGATGCATGCTCAGAG                         GTGAGCGACACGGAGCTCTGCTGCATCTGCTTCGACCAGGCTTGCACCNAT
genomic: CATCCCCTTCGCCCGGTGATGACAGTGCCGATGACGATGCATGCTCAGAGgtatttgagt ... ttgggcacagGTGAGCGACACGGAGCTTTGCTGCATCTGCTTCGACCAGGCTTGCACC-AT
EST: gi|33809660|gb|CF330722.1|CF330722
EST:     CCGATGACGATTTTTGCTCAGAG                         GTGAGCGACACGGAGCTTTGCTGCATCTGCTTCGACCAGGCTTGCACCATT
genomic: CCGATGACGATGCATGCTCAGAGgtatttgagt ... ttgggcacagGTGAGCGACACGGAGCTTTGCTGCATCTGCTTCGACCAGGCTTGCACCATT
EST: gi|38473861|gb|CF957993.1|CF957993
EST:     CATCCCCTTCGCCCGGTGATGACAGTGCCGATGACGATGCATGCTCAGAG                         GTGAGCGACACGGAGCTCTGCTGCATCTGCTTCGACCAGGCTTGCACCATT
genomic: CATCCCCTTCGCCCGGTGATGACAGTGCCGATGACGATGCATGCTCAGAGgtatttgagt ... ttgggcacagGTGAGCGACACGGAGCTTTGCTGCATCTGCTTCGACCAGGCTTGCACCATT

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: 60 (upstream exon), 51 (downstream exon)
Score: 8

CAACAGGGAGAGGGAGAAGAAAATCCTGAATGGCACAAAGTACTCCCTGCCATCCCCTTCGCCCGGTGATGACAGTGCCGATGACGATGCATGCTCAGAGgtatttgagt ... ttgggcacagGTGAGCGACACGGAGCTTTGCTGCATCTGCTTCGACCAGGCTTGCACCATTGAGGTGCAAGACTGTGGACATCAAATGTGTGCACCGTGCACGCTGGCAC




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctttctgtgcatttgcatgatgactgaatggctgtgttgatcatttgggcacagGTGAGCGACACGGAGCTTTGCTGCATCTGCTTCGACCAGGCTTGCACCATTGAGGTGCAAGACTGTGGACATCAAATGTGTGCACCGTGCACGCTGGCAC
                                   tgttgat  putative branch site (score: 8)
                                        atcattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttgagtgctgaacaatttcagtgttatctgtcagattgggatcccataaacacattgtgtaatttagctttctgtgcatttgcatgatgactgaatggctgtgttgatcatttgggcacagGTGAGCGACACGGAGCTTTGCTGCATCTGCTTCGACCAGGCTTGCACCATTGAGGTGCAAGACTGTGGACATCAAATGTGTGCACCGTGCACGCTGGCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA