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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGTCTGTCCTTTATGTATGATGGTGTACCTCTTCTAGCTATGTTGGATGAATATGTCATGCTAAGGCAGGAAAGGGAAGAAGATAAGAAAAGAATGAGGgtgagtgccacttcctctttaaatgttgaatccattttcttgaacacgtatcacccttgagcgttgatcgaattcttttaaatctcgtgttgagtcatgt...

Basic information

species Oryza sativa
transcript LOC_Os06g20370.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g20370.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G101874_T01 (Zea mays), 5'ss of exon 10
TGGTCTGTCCTTTATGTATGATGGTGTACCTCTTCTAGCTATGTTGGATGAATATGTCATGCTAAGGCAGGAAAGGGAAGAAGATAAGAAAAGAATGAGGgtgagtgccacttcctctttaaatgttgaatccattttcttgaacacgtatcacccttgagcgttgatcgaattcttttaaatctcgtgttgagtcatgt-
||||||||||||||||||||||||||||||||||||||||||||||||||| ||||  ||||| || || |||||||||||||| |||||||||||| |||| ||||  |  | |||||||||| | ||| ||| | ||      | |      |  | |  ||  ||    |||| ||    |   || | ||||  || 
TGGTCTGTCCTTTATGTATGATGGTGTACCTCTTCTAGCTATGTTGGATGAGTATGCTATGCTCAGACAAGAAAGGGAAGAAGAAAAGAAAAGAATGCGGgttagtgtgatatgctctttaaatctagaagccactatcacctggatgacaattcaattattgtccattacgttctgtttggacctatgct-agtctggtc

upper sequence: LOC_Os06g20370.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G465169_T02 (Zea mays), 5'ss of exon 9
TGGTCTGTCCTTTATGTATGATGGTGTACCTCTTCTAGCTATGTTGGATGAATATGTCATGCTAAGGCAGGAAAGGGAAGAAGATAAGAAAAGAATGAGGgtgagtgccacttcctctttaaatgttgaatccattttcttgaacacgtatcacccttgagcgttgatcgaattcttttaaatctcgtgttgagtcatgt
||||||||| ||||||||||||||||||||||||||||||||||||||||| ||||| ||||| |||||||||||||||||||| |||||||||| | |||| ||||  |  | |||||||||| | ||||||||| ||      | |      | || |  ||  || || |||| ||    |   || ||     || 
TGGTCTGTCTTTTATGTATGATGGTGTACCTCTTCTAGCTATGTTGGATGAGTATGTTATGCTCAGGCAGGAAAGGGAAGAAGAGAAGAAAAGAACGCGGgtaagtgtgatatgctctttaaatctagaatccattatcacctggatgccaattcatttattgtccattgagttctgtttggacctatgctggagtctgg

upper sequence: LOC_Os06g20370.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA02G46450.3 (Glycine max), 5'ss of exon 9
TGGTCTGTCCTTTATGTATGATGGTGTACCTCTTCTAGCTATGTTGGATGAATATGTCATGCTAAGGCAGGAAAGGGAAGAAGATAAGAAAAGAATGAGGgtgagtgccacttcctctttaaatgttgaatccattttcttgaacacgtatcacccttgagcgttgatcgaattcttttaaatctcgtgttgagtcatgt-
|||  |||| ||||  ||||||||||| |||||||| || ||||| |||||||||| |||||| || || ||| ||||||| || ||    || |||||||| |||  ||||       | | |      |    ||   | |             ||||||  |    || |  |  |||  |      |  |  | |  
TGGCATGTCATTTACATATGATGGTGTTCCTCTTCTTGCCATGTTAGATGAATATGCCATGCTCAGACATGAACGGGAAGAGGAAAAACGGAGGATGAGGgtaagtaacactaataagatgattaggatttaggattgactcattttcagcttgatttgagcacttgctga-taataataagaccaccactctgcgaggaa

upper sequence: LOC_Os06g20370.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA08G43450.1 (Glycine max), 5'ss of exon 16
------------------------------TGGTCTGTCCTTTATGTATGATGGTGTACCTCTTCTAGCTATGTTGGATGAATATGTCATGCTAAGGCAGGAAAGGGAAGAAGATAAGAAAAGAATGAGGgtgagtgccacttcctctttaaatgttgaatccattttcttgaacacgtatcacccttgagcgttgat---cgaattcttttaaatctcgtgttgagtcatgt------------
                              ||   |||| || |  ||||||||||| |||||||| ||||||||||||||||||| |||||| ||||| | | ||||||| ||  |   ||| |||  ||| |||  || |       | | |     |     ||     || |  | |  | ||||    |  |      |      | || | ||        |||| |            
TGCTAAAACTCGTGTTTGGGAAGAAGCACCTGACATGTCATTCACATATGATGGTGTTCCTCTTCTTGCTATGTTGGATGAATATGCCATGCTCAGGCATgtatgggaagaggaagaatgaaggatgcaggtaagtttcattgatgggatgattagaataattgattatcaaaataattttagcacttgctaataaaaaagtaagcaaagtgaactatcaaaagagttcatatcacattctttag

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|58653743|gb|CK042423.1|CK042423
EST:     AATATGTCATGCTAAGGCAGGAAAGGGAAGAAGATAAGAAAAGAATGAGG                         GAACAAAAGCGCTACATCGAGCAACAACTGAACACCGACCATGAAGGGCCA
genomic: AATATGTCATGCTAAGGCAGGAAAGGGAAGAAGATAAGAAAAGAATGAGGgtgagtgcca ... cacatcccagGAACAAAAGCGCTACATCGAGCAACAACTGAACACCGACCATGAAGGGCCA
EST: gi|86478689|gb|CI121322.1|CI121322
EST:     AATATGTCATGCTAAGGCAGGAAAGGGAAGAAGATAAGAAAAGAATGAGG                         GAACAAAAGCGCTACATCGAGCAACAACTGAACACCGACCATGAAGGGCCA
genomic: AATATGTCATGCTAAGGCAGGAAAGGGAAGAAGATAAGAAAAGAATGAGGgtgagtgcca ... cacatcccagGAACAAAAGCGCTACATCGAGCAACAACTGAACACCGACCATGAAGGGCCA
EST: gi|4878729|gb|AU063028.1|AU063028
EST:     AATATGTCATGCTAAGGCAGGAAAGGGAAGAAGATAAGAAAAGAATGAGG                         GAACAAAAGCGCTACATCGAGCAACAACTGAACACCGACCATGAAGGGCCA
genomic: AATATGTCATGCTAAGGCAGGAAAGGGAAGAAGATAAGAAAAGAATGAGGgtgagtgcca ... cacatcccagGAACAAAAGCGCTACATCGAGCAACAACTGAACACCGACCATGAAGGGCCA
EST: gi|87014008|gb|CI273198.1|CI273198
EST:     AATATGTCATGCTAAGGCAGGAAAGGGAAGAAGATAAGAAAAGAATGAGG                         GAACAAAAGCGCTACATCGAGCAACAACTGAACACCGACCATGAAGGGCCA
genomic: AATATGTCATGCTAAGGCAGGAAAGGGAAGAAGATAAGAAAAGAATGAGGgtgagtgcca ... cacatcccagGAACAAAAGCGCTACATCGAGCAACAACTGAACACCGACCATGAAGGGCCA
EST: gi|88583042|gb|CI699517.1|CI699517
EST:     AATATGTCATGCTAAGGCAGGAAAGGGAAGAAGATAAGAAAAGAATGAGG                         GAACAAAAGCGCTACATCGAGCAACAACTGAACACCGACCATGAAGGGCCA
genomic: AATATGTCATGCTAAGGCAGGAAAGGGAAGAAGATAAGAAAAGAATGAGGgtgagtgcca ... cacatcccagGAACAAAAGCGCTACATCGAGCAACAACTGAACACCGACCATGAAGGGCCA
EST: gi|58686116|gb|CK074803.1|CK074803
EST:     ATAAGAAAAGAATGAGG                         GAACAAAAGCGCTACATCGAGCAACAACTGAACACCGACCATGAAGGGCCA
genomic: ATAAGAAAAGAATGAGGgtgagtgcca ... cacatcccagGAACAAAAGCGCTACATCGAGCAACAACTGAACACCGACCATGAAGGGCCA
EST: gi|58665982|gb|CK054668.1|CK054668
EST:     GCAGGAAAGGGAAGAAGATAAGAAAAGAATGAGG                         GAACAAAAGCGCTACATCGAGCAACAACTGAACACCGACCATGAAGGGCCA
genomic: GCAGGAAAGGGAAGAAGATAAGAAAAGAATGAGGgtgagtgcca ... cacatcccagGAACAAAAGCGCTACATCGAGCAACAACTGAACACCGACCATGAAGGGCCA
EST: gi|58680503|gb|CK069190.1|CK069190
EST:     AGGAAAGGGAAGAAGATAAGAAAAGAATGAGG                         GAACAAAAGCGCTACATCGAGCAACAACTGAACACCGACCATGAAGGGCCA
genomic: AGGAAAGGGAAGAAGATAAGAAAAGAATGAGGgtgagtgcca ... cacatcccagGAACAAAAGCGCTACATCGAGCAACAACTGAACACCGACCATGAAGGGCCA
EST: gi|87031673|gb|CI259857.1|CI259857
EST:     AATATGTCATGCTAAGGCAGGAAAGGGAAGAAGATAAGAAAAGAATGAGG                         GAACAAAAGCGCTACATCGAGCAACAACTGAACACCGACCATGAAGGGCCA
genomic: AATATGTCATGCTAAGGCAGGAAAGGGAAGAAGATAAGAAAAGAATGAGGgtgagtgcca ... cacatcccagGAACAAAAGCGCTACATCGAGCAACAACTGAACACCGACCATGAAGGGCCA
EST: gi|218496732|gb|FG958311.1|FG958311
EST:     AATATGTCATGCTAAGGCAGGAAAGGGAAGAAGATAAGAAAAGAATGAGG                         GAACAAAAGCGCTACATCGAGCAACAACTGAACACCGACCATGAAGGGCCA
genomic: AATATGTCATGCTAAGGCAGGAAAGGGAAGAAGATAAGAAAAGAATGAGGgtgagtgcca ... cacatcccagGAACAAAAGCGCTACATCGAGCAACAACTGAACACCGACCATGAAGGGCCA
EST: gi|58678983|gb|CK067670.1|CK067670
EST:     AATATGTCATGCTAAGGCAGGAAAGGGAAGAAGATAAGAAAAGAATGAGG                         GAACAAAAGCGCTACATCGAGCAACAACTGTACACCGACCATGAAGGGCCA
genomic: AATATGTCATGCTAAGGCAGGAAAGGGAAGAAGATAAGAAAAGAATGAGGgtgagtgcca ... cacatcccagGAACAAAAGCGCTACATCGAGCAACAACTGAACACCGACCATGAAGGGCCA
EST: gi|88586562|gb|CI704268.1|CI704268
EST:     AATATGTCATGCTAAGGCAGGAAAGGGAAGAAGATAAGAAAAGAATGAGG                         GAACAAAAGCGCTACATCGAGCAACAACTGAACACCGACCATGAAGGGCCA
genomic: AATATGTCATGCTAAGGCAGGAAAGGGAAGAAGATAAGAAAAGAATGAGGgtgagtgcca ... cacatcccagGAACAAAAGCGCTACATCGAGCAACAACTGAACACCGACCATGAAGGGCCA

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: 48 (upstream exon), 59 (downstream exon)
Score: 24

TGGTCTGTCCTTTATGTATGATGGTGTACCTCTTCTAGCTATGTTGGATGAATATGTCATGCTAAGGCAGGAAAGGGAAGAAGATAAGAAAAGAATGAGGgtgagtgcca ... cacatcccagGAACAAAAGCGCTACATCGAGCAACAACTGAACACCGACCATGAAGGGCCATTTGGTTCACGTGTGAGCCCTAACAGACCAGTCAGTGCAAAGAAGGTAC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGTCTGTCCTTTATGTATGATGGTGTACCTCTTCTAGCTATGTTGGATGAATATGTCATGCTAAGGCAGGAAAGGGAAGAAGATAAGAAAAGAATGAGGgtgagtgccacttcctctttaaatgttgaatccattttcttgaacacgtatcacccttgagcgttgatcgaattcttttaaatctcgtgttgagtcatgt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttcctc