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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCCTTGGCACCTCTTTACTACAGAGGAGCTGCTGCTGCAGTTGTTGTCTACGACATAACTAGTCCAGAATCATTTAGCAAAGCACAATACTGGGTGAAGgtatgctatcgccaaattatctgcttttctgatgtctggttgattgattactctttctatcttttactatgagtttgtattttttgcccgaaactgttct...

Basic information

species Oryza sativa
transcript LOC_Os03g05740.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g05740.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM5G863105_T01 (Zea mays), 5'ss of exon 1
TGCCTTGGCACCTCTTTACTACAGAGGAGCTGCTGCTGCAGTTGTTGTCTACGACATAACTAGTCCAGAATCATTTAGCAAAGCACAATACTGGGTGAAGgtatgctatcgccaaattatctgcttttctgatgtctggt--tgattgattactctttct----atcttttactatgagtttgtattttttgcccgaaactgttct
             ||||||||||||||||||||||||||| |||||||||| |  ||||  ||||| || ||||||||||||||||| || ||||| ||||||  ||||   |||    ||| || ||||||  |||  |  |   |    || |   |     ||    || |||  |  | |   | | ||   |||||     
------------ACTTTACTACAGAGGAGCTGCTGCTGCAATTGTTGTCTATGGTATAATGAGTCCGGAGTCATTTAGCAAAGCACATTATTGGGTAAAGgtaaactataagcaaccc-tctactcttctgagctcttatgcttgctccccacccccaccccaaattccctattatcggcctctgcatct-gcttaaaactc----

upper sequence: LOC_Os03g05740.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G362088_T02 (Zea mays), 5'ss of exon 6
TGCCTTGGCACCTCTTTACTACAGAGGAGCTGCTGCTGCAGTTGTTGTCTACGACATAACTAGTCCAGAATCATTTAGCAAAGCACAATACTGGGTGAAGgtatgctatcgccaaattatctgcttttctgatgtctggttgattgattactctttctatcttttactatgagtttgtattttttgcccgaaactgttct----
||||||||| || ||||||||||||||||||||||||||| |||||||||| || ||||| ||||| |||||||||||||||||||| || ||||| ||||||   |||   |||    ||| || ||||||  |||  |   ||| ||  |||  | ||    || |||     |||   | || |  ||| || |  |    
TGCCTTGGCGCCACTTTACTACAGAGGAGCTGCTGCTGCAATTGTTGTCTATGATATAACAAGTCCGGAATCATTTAGCAAAGCACAGTATTGGGTAAAGgtaaagtataagcaaccc-tctactcttctgagttcttatcc-ttggtt-ttctccccattccctattatcgacctgtgcatctt-cttgaagctctgatgtaa

upper sequence: LOC_Os03g05740.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA20G32320.1 (Glycine max), 5'ss of exon 5
TGCCTTGGCACCTCTTTACTACAGAGGAGCTGCTGCTGCAGTTGTTGTCTACGACATAACTAGTCCAGAATCATTTAGCAAAGCACAATACTGGGTGAAGgtatgctatcgccaaattatctgcttttctgatgtctggttgattgattactctttctatcttttactatgagtttgtattttttgcccgaaactgttct-----
||| || ||||| || || ||| | || || || | ||||||| |||| || || ||||| || |||||||| || ||||||||||| |||||||| ||||||   | ||    |  | | || || | |  ||||   ||  ||| ||    |   ||| |   | | ||| |   |||   |  |   ||| |   ||     
TGCGTTAGCACCACTCTATTACCGTGGTGCAGCAGTTGCAGTTATTGTTTATGATATAACAAGCCCAGAATCTTTCAGCAAAGCACAGTACTGGGTTAAGgtagattttcagtta-ctgtatggttctatattgtc--atttcttg-ttttgttagttatttgaaattttgaatg-atatgaataacaaaaaattcccctattat

upper sequence: LOC_Os03g05740.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA10G35230.3 (Glycine max), 5'ss of exon 5
TGCCTTGGCACCTCTTTACTACAGAGGAGCTGCTGCTGCAGTTGTTGTCTACGACATAACTAGTCCAGAATCATTTAGCAAAGCACAATACTGGGTGAAGgtatgctatcgccaaattatctgcttttctgatgtc--tggttgattgattactctttctatcttttac----tatgagtttgtattttttgcccgaaactgttct
||| || ||||| || || ||| | || || || | ||||||| |||| || || ||||| || |||||||| || ||||||||||| |||||||| ||||||   |  |    | || | || || | |  ||||  |  ||| ||  ||| |  ||  |  ||||      ||||| |    |    || ||| |   |     
TGCGTTAGCACCGCTATATTACCGTGGTGCAGCAGTTGCAGTTATTGTTTATGATATAACAAGCCCAGAATCTTTCAGCAAAGCACAGTACTGGGTTAAGgtagatttgcagtta-ttgtatggttctatattgtcatttcttgttttgttagttatttgaaattttgaatgatatgaataacaaacaattcccctatcat-----

upper sequence: LOC_Os03g05740.1 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv13s0019g04680.t01 (Vitis vinifera), 5'ss of exon 5
TGCCTTGGCACCTCTTTACTACAGAGGAGCTGCTGCTGCAGTTGTTGTCTACGACATAACTAGTCCAGAATCATTTAGCAAAGCACAATACTGGGTGAAGgtatgctatcgccaaattatctgcttttctgatgtctggttgattgattactcttt--ctatcttttactatgagtttgtattttttgcccgaaactgttct
|||  ||||||| ||||||||  |||| ||||| | ||||||||| || || || ||||| || ||||||||||| | ||||||||| || ||||| |||||||  | |      |  |  |||  |  | || | |   || ||  ||  |  ||   ||| | |   | |  | |||  |  |||        || ||  
TGCGCTGGCACCACTTTACTATCGAGGTGCTGCAGTTGCAGTTGTAGTGTATGATATAACAAGCCCAGAATCATTCAACAAAGCACAGTATTGGGTTAAGgtatctttttttagtaggaagtgcaatagt-atttatttctgtttctttcttgcttaattatttctatttctttgcttgcttcatttatttatttcttttt-

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|11565095|gb|AU165731.1|AU165731
EST:     ACGACATAACTAGTCCAGAATCATTTAGCAAAGCACAATACTGGGTGAAG                         GAACTTCAAAAACATGGTAGTCCTGATATTATCATGGTTTTGGTTGGTAAT
genomic: ACGACATAACTAGTCCAGAATCATTTAGCAAAGCACAATACTGGGTGAAGgtatgctatc ... tatattgcagGAACTTCAAAAACATGGTAGTCCTGATATTATCATGGTTTTGGTTGGTAAT
EST: gi|3760086|gb|C97344.1|C97344
EST:     ACGACATAACTAGTCCAGAATCATTTAGCAAAGCACAATACTGGGTGAAG                         GAACTTCAAAAACATGGTANTCCTGATATTATCATGGT
genomic: ACGACATAACTAGTCCAGAATCATTTAGCAAAGCACAATACTGGGTGAAGgtatgctatc ... tatattgcagGAACTTCAAAAACATGGTAGTCCTGATATTATCATGGT
EST: gi|6782805|gb|C99985.1|C99985
EST:     ACGACATAACTAGTCCAGAATCATTTAGCAAAGCACAATACTGGGTGAAG                         GAACTTCAAAAACATGGTAGTCCTGATATTATCATGGTTTTGGTTGGTAAT
genomic: ACGACATAACTAGTCCAGAATCATTTAGCAAAGCACAATACTGGGTGAAGgtatgctatc ... tatattgcagGAACTTCAAAAACATGGTAGTCCTGATATTATCATGGTTTTGGTTGGTAAT
EST: gi|55412383|gb|CV724759.1|CV724759
EST:     ACGACATAACTAGTCCAGAATCATTTAGCAAAGCACAATACTGGGTGAAG                         GAACTTCAAAAACATGGTAGTCCTGATATTATCATGGTTTTGGTTGGTAAT
genomic: ACGACATAACTAGTCCAGAATCATTTAGCAAAGCACAATACTGGGTGAAGgtatgctatc ... tatattgcagGAACTTCAAAAACATGGTAGTCCTGATATTATCATGGTTTTGGTTGGTAAT
EST: gi|300216317|gb|HO088102.1|HO088102
EST:     ACGACATAACTAGTCCAGAATCATTTAGCAAAGCACAATACTGGGTGAAG                         GAACTTCAAAAACATGGTAGTCCTGATATTATCATGGTTTTGGTTGGTAAT
genomic: ACGACATAACTAGTCCAGAATCATTTAGCAAAGCACAATACTGGGTGAAGgtatgctatc ... tatattgcagGAACTTCAAAAACATGGTAGTCCTGATATTATCATGGTTTTGGTTGGTAAT
EST: gi|25803490|gb|CA759389.1|CA759389
EST:     ACGACATAACTAGTCCAGAATCATTTAGCAAAGCACAATACTGGGTGAAG                         GAACTTCAAAAACATGGTAGTCCTGATATTATCATGGTTTTGGTTGGTAAT
genomic: ACGACATAACTAGTCCAGAATCATTTAGCAAAGCACAATACTGGGTGAAGgtatgctatc ... tatattgcagGAACTTCAAAAACATGGTAGTCCTGATATTATCATGGTTTTGGTTGGTAAT
EST: gi|3760087|gb|C97345.1|C97345
EST:     GACATAACTAGTCCCAG-ATCCATTTAGCNAAGCACAATACTGGGTGAAG                         GAACTTCAAAAACATGGTAGTCCTGATATTATCCATGGTTTTGGTTGGTNA
genomic: GACATAACTAGT-CCAGAAT-CATTTAGCAAAGCACAATACTGGGTGAAGgtatgctatc ... tatattgcagGAACTTCAAAAACATGGTAGTCCTGATATTAT-CATGGTTTTGGTTGGTAA
EST: gi|88264996|gb|CI368770.1|CI368770
EST:     AAAGCACAATACTGGGTGAAG                         GAACTTCAAAAACATGGTAGTCCTGATATTATCATGGTTTTGGTTGGTAAT
genomic: AAAGCACAATACTGGGTGAAGgtatgctatc ... tatattgcagGAACTTCAAAAACATGGTAGTCCTGATATTATCATGGTTTTGGTTGGTAAT
EST: gi|33666789|gb|CF297756.1|CF297756
EST:     TCCAGAATCATTTAGCAAAGCACAATACTGGGTGAAG                         GAACTTCAAAAAACATGGTAGTCCTGATATTATCATGGTTTTGGTTGGTAA
genomic: TCCAGAATCATTTAGCAAAGCACAATACTGGGTGAAGgtatgctatc ... tatattgcagGAACTTC-AAAAACATGGTAGTCCTGATATTATCATGGTTTTGGTTGGTAA

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: 64 (upstream exon), 73 (downstream exon)
Score: 30

TGCCTTGGCACCTCTTTACTACAGAGGAGCTGCTGCTGCAGTTGTTGTCTACGACATAACTAGTCCAGAATCATTTAGCAAAGCACAATACTGGGTGAAGgtatgctatc ... tatattgcagGAACTTCAAAAACATGGTAGTCCTGATATTATCATGGTTTTGGTTGGTAATAAAGCTGATCTACATGAAAATCGACATGTATCTTCTCAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCCTTGGCACCTCTTTACTACAGAGGAGCTGCTGCTGCAGTTGTTGTCTACGACATAACTAGTCCAGAATCATTTAGCAAAGCACAATACTGGGTGAAGgtatgctatcgccaaattatctgcttttctgatgtctggttgattgattactctttctatcttttactatgagtttgtattttttgcccgaaactgttct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG