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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatttgcacaaattcaatatgtggattgcattgtactttaggatttgcttagttgcataatttgtttgttctaactgtgttattctgatccaaaattcagGTACCACTTGTGCTACTGTATTGACTAAAGCAATATTTACTGAGGGGTGCAAGTCTGTTGCTGCTGGCATGAATGCAATGGATTTAAGGCGTGGTATTTC

Basic information

species Oryza sativa
transcript LOC_Os10g32550.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g32550.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G458208_T01 (Zea mays), 3'ss of exon 3
tatttgcacaaattcaatatgtggattgcattgtactttaggatttgcttagttgcataatttgtttgttctaactgtgt-tattctga--tccaaaa--ttcagGTACCACTTGTGCTACTGTATTGACTAAAGCAATATTTACTGAGGGGTGCAAGTCTGTTGCTGCTGGCATGAATGCAATGGATTTAAGGCGTGGTATTTC
   ||| |  | |  |||| ||  | |    | || |||    | |   ||| |   | || |  || ||| ||||||   |  |||||  |||||||  |||||||||||| ||||| ||||| ||||| |||||||||||||||||||||||||| |||||||| ||||| ||||||||||||||||||||||| || || ||
--attgaatca-tgtaataagttaaattttctata-tttgaattgtatgtagcttgctgatgt-cttcttccaactgtacctgatctgacatccaaaaatttcagGTACCACATGTGCCACTGTTTTGACAAAAGCAATATTTACTGAGGGGTGCAAATCTGTTGCGGCTGGAATGAATGCAATGGATTTAAGGCGCGGAATCTC

upper sequence: LOC_Os10g32550.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G416120_T01 (Zea mays), 3'ss of exon 3
tatttgcacaaattcaatatgtggattgcattgtactttaggatttgcttagttgcataatttgtttgttctaactgtgttattctgatccaaaa-ttcagGTACCACTTGTGCTACTGTATTGACTAAAGCAATATTTACTGAGGGGTGCAAGTCTGTTGCTGCTGGCATGAATGCAATGGATTTAAGGCGTGGTATTTC
|    |  | ||   ||  | ||  |   |||||    | | || |   | |||| ||  ||| || |  ||    ||| | |  |   | |||| |||||||||||| ||||||||||| ||||| |||||||||||||||||||||||||| |||||||| ||||| |||||||||||||||||||||||||| || ||
tgaccggtctaacataaactatgcctcatattgttgaattgtatgtagcttgttg-atgctttcttcgaactgtacgtgatctgatatccaaaaaattcagGTACCACATGTGCTACTGTTTTGACAAAAGCAATATTTACTGAGGGGTGCAAATCTGTTGCGGCTGGAATGAATGCAATGGATTTAAGGCGTGGAATCTC

upper sequence: LOC_Os10g32550.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA20G33910.1 (Glycine max), 3'ss of exon 4
tatttgcacaaatt-caatatgtggattgcattgtactttaggatttgcttag--ttgcataatttgtttgttctaactgtgttattctgatccaaaatt-cagGTACCACTTGTGCTACTGTATTGACTAAAGCAATATTTACTGAGGGGTGCAAGTCTGTTGCTGCTGGCATGAATGCAATGGATTTAAGGCGTGGTATTTC
         ||  |   ||||    | || ||| |||||||  |  |  | ||  |||  || |||||   |  |||   ||    |   ||| ||  |  |||| ||||||||||||||  |  | ||||||||||||||||| || || || || || ||||| ||||| |||||||| |||||  | || || |||||   
-------gtaagctattatatccatactggattatactttattaaatcttcagcattggctactttgt---tattaataatgagggtacaatctaatttggcagGAACCACTTGTGCTACAATTCTTACTAAAGCAATATTTACGGAAGGATGTAAATCAGTTGCAGCTGGAATGAATGCGATGGACCTGAGACGAGGTATAAA

upper sequence: LOC_Os10g32550.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA10G33680.1 (Glycine max), 3'ss of exon 4
tatttgc-acaaattcaatatgtggattgcattgtactttaggatttgcttagttgcataatttgtt--tgttctaactgtgttattctga------tccaaaattcagGTACCACTTGTGCTACTGTATTGACTAAAGCAATATTTACTGAGGGGTGCAAGTCTGTTGCTGCTGGCATGAATGCAATGGATTTAAGGCGTGGTATTTC
  |  || |  |  ||  ||  ||| ||  | | || | |   || | |    |||  || ||||||  |   | ||  ||  || |  |       || ||    |||| ||||||||||||||  |  | ||||||||||||||||| || ||||| || || ||||| ||||| |||||||| |||||  | || || |||||   
-gtaagccattatatccgtac-tgggttatactttattgttaaatcttcagcattgactactttgttattaaacaaatggtaataatgagggaacattctaattggcagGAACCACTTGTGCTACAATTCTCACTAAAGCAATATTTACGGAAGGGTGTAAATCAGTTGCAGCTGGAATGAATGCGATGGACCTGAGACGAGGTATAAA

upper sequence: LOC_Os10g32550.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA10G25630.1 (Glycine max), 3'ss of exon 4
tatttgcacaaattcaatatgtggattgc--attgtactttaggatttgcttagttgcataatttgtttgttctaactgtgttattctgatccaaaattcagGTACCACTTGTGCTACTGTATTGACTAAAGCAATATTTACTGAGGGGTGCAAGTCTGTTGCTGCTGGCATGAATGCAATGGATTTAAGGCGTGGTATTTC
|     |   ||  |||      | ||||   |  ||  | |  ||||   |  |   |  ||       |  | |  |    |||   ||      | |||| ||||| || ||||| ||  | ||   ||||||||||||||| || ||||| || ||||| ||||| ||||||||||||||  | |||||||||||   
tgaagactgtaaaccaactatcagcttgctggtattatctaataatttaggtgctgttaccatgaaagaatattgag-ggaacatttcaatt-gttttgcagGAACCACGTGCGCTACAGTCCTTACACGAGCAATATTTACTGAAGGCTGCAAATCAGTTGCGGCTGGAATGAATGCAATGGACCTGAGGCGTGGTATAAG

upper sequence: LOC_Os10g32550.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv05s0051g00340.t01 (Vitis vinifera), 3'ss of exon 4
----tatttgcacaa-attcaatatgtggattgcattgtactttaggatttgcttagttgcataatttgtttgttctaactgtgttattctgatccaaaattcagGTACCACTTGTGCTACTGTATTGACTAAAGCAATATTTACTGAGGGGTGCAAGTCTGTTGCTGCTGGCATGAATGCAATGGATTTAAGGCGTGGTATTTC
    |  ||  |  | | |  |||  | |  | | |||| || |  | |||  || ||| |         | | ||| |     |  || ||||    | |||||||||||| ||||| || ||  | ||   ||||||||||||||| ||||||||||| ||||||||||| ||||||||||||||  ||||  | ||||| ||
agaatggttttatgacaatgcatac-ttgtctacgttgt-ctctgtggtttattttgtttctgttacacatagatctgatcccttatttttgat---gatttcagGTACCACCTGTGCCACAGTCCTTACCCGAGCAATATTTACTGAAGGGTGCAAGTCGGTTGCTGCTGGAATGAATGCAATGGACCTAAGAAGGGGTATCTC

upper sequence: LOC_Os10g32550.1 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S149_289V6.1 (Physcomitrella patens), 3'ss of exon 4
-----------------------------------------------------------------------------------tatttgcacaaattcaatatgtggattgcattgtactttaggatttgcttagttgcataatttgtttgttctaactgtgttattctgatccaaaa----------ttcagGTACCACTTGTGCTACTGTATTGACTAAAGCAATATTTACTGAGGGGTGCAAGTCTGTTGCTGCTGGCATGAATGCAATGGATTTAAGGCGTGGTATTTC
                                                                                      |||    ||||   | ||   |||    |   |||| |  || |   | |||    |      |  | | |     ||   ||||  | |||          | |||| || |||||||| || ||  | ||   ||| || |||  |||||| || ||||| ||||| |||||||||||||||||||| ||| |  | |||||   
gtaaagtcccggttctatctaaatttggagatatcgctcttacacgcatagttcctggacccattctttttattttgtacgaaggcttg-gggaattatttttgaaaatttatgtcaccttttgatttcggcgaattgatccacacaccttctgtgaaaacatttggctgactcgaaagaatatgttttgcagGGACAACTTGTGCAACGGTGCTCACCCGAGCTATTTTTGTTGAGGGATGTAAGTCAGTTGCAGCTGGCATGAATGCAATGGACTTACGTAGGGGTATCAA

upper sequence: LOC_Os10g32550.1 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S44_339V6.1 (Physcomitrella patens), 3'ss of exon 3
tatttgcacaaattcaatatgtggattgcattgtactttaggattt--gcttagttgcataatttgtttgttc--taactgtgttattctgatccaaaattcagGTACCACTTGTGCTACTGTATTGACTAAAGCAATATTTACTGAGGGGTGCAAGTCTGTTGCTGCTGGCATGAATGCAATGGATTTAAGGCGTGGTATTTC
    ||    |  | |       | ||| |       | ||| |||    ||||  ||  |       ||  |  |||        |   || |     | ||||||| |||   || || ||  |  ||  ||| || |||||||| || |||||||| ||||| |||||||||||||| ||||| ||  | ||||| ||| |
---ctgggtgacatgagccaacag-ttggaagaagtatcagggtttcaatttagaggcgaaccgcaaatgaacgttaaactgacagtaacgaacttttttgcagGTACAACTGCCGCAACAGTGCTTGCTCGAGCCATTTTTACTGAAGGTTGCAAGTCCGTTGCAGCTGGCATGAATGCCATGGACTTGCGCCGTGGCATTAC

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|8528178|gb|AU092993.1|AU092993
EST:     AAGCCTTGTAAAGCAGGTTGCTAATGCGACCAATGATACTGCTGGAGATG                         GTACCACTTGTGCTACTGTATTGACTAAAGCAATATTTACTGAGGGGTGCA
genomic: AAGCCTTGTAAAGCAGGTTGCTAATGCGACCAATGATACTGCTGGAGATGgtatggctgt ... caaaattcagGTACCACTTGTGCTACTGTATTGACTAAAGCAATATTTACTGAGGGGTGCA
EST: gi|58673475|gb|CK062161.1|CK062161
EST:     AAGCCTTGTAAAGCAGGTTGCTAATGCGACCAATGATACTGCTGGAGATG                         GTACCACTTGTGCTACTGTATTGACTAAAGCAAATATTTACTGAGGGGTGC
genomic: AAGCCTTGTAAAGCAGGTTGCTAATGCGACCAATGATACTGCTGGAGATGgtatggctgt ... caaaattcagGTACCACTTGTGCTACTGTATTGACTAAAGCAA-TATTTACTGAGGGGTGC
EST: gi|58685403|gb|CK074090.1|CK074090
EST:     AAGCCTTGTAAAGCAGGTTGCTAATGCGACCAATGATACTGCTGGAGATG                         GTACCACTTGTGCTACTGTATTGACTAAAGCAATATTTACTGAGGGGTGCA
genomic: AAGCCTTGTAAAGCAGGTTGCTAATGCGACCAATGATACTGCTGGAGATGgtatggctgt ... caaaattcagGTACCACTTGTGCTACTGTATTGACTAAAGCAATATTTACTGAGGGGTGCA
EST: gi|29632103|gb|CB637112.1|CB637112
EST:     AAGCCTTGTAAAGCAGGTTGCTAATGCGACCAATGATACTGCTGGAGATG                         GTACCACTTGTGCTACTGTATTGACTAAAGCAATATTTACTGAGGGGTGCA
genomic: AAGCCTTGTAAAGCAGGTTGCTAATGCGACCAATGATACTGCTGGAGATGgtatggctgt ... caaaattcagGTACCACTTGTGCTACTGTATTGACTAAAGCAATATTTACTGAGGGGTGCA
EST: gi|58652508|gb|CK041188.1|CK041188
EST:     AAGCCTTGTAAAGCAGGTTGCTAATGCGACCAATGATACTGCTGGAGATG                         GTACCACTTGTGCTACTGTATTGACTAAAGCAATATTTACTGAGGGGTGCA
genomic: AAGCCTTGTAAAGCAGGTTGCTAATGCGACCAATGATACTGCTGGAGATGgtatggctgt ... caaaattcagGTACCACTTGTGCTACTGTATTGACTAAAGCAATATTTACTGAGGGGTGCA
EST: gi|29627179|gb|CB632190.1|CB632190
EST:     AAGCCTTGTAAAGCAGGTTGCTAATGCGACCAATGATACTGCTGGAGATG                         GTACCACTTGTGCTACTGTATTGACTAAAGCAATATTTACTGAGGGGTGCA
genomic: AAGCCTTGTAAAGCAGGTTGCTAATGCGACCAATGATACTGCTGGAGATGgtatggctgt ... caaaattcagGTACCACTTGTGCTACTGTATTGACTAAAGCAATATTTACTGAGGGGTGCA
EST: gi|58691748|gb|CK080435.1|CK080435
EST:     AAGCCTTGTAAAGCAGGTTGCTAATGCGACCAATGATACTGCTGGAGATG                         GTACCACTTGTGCTACTGTATTGACTAAAGCAATATTTACTGAGGGGTGCA
genomic: AAGCCTTGTAAAGCAGGTTGCTAATGCGACCAATGATACTGCTGGAGATGgtatggctgt ... caaaattcagGTACCACTTGTGCTACTGTATTGACTAAAGCAATATTTACTGAGGGGTGCA

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: 73 (upstream exon), 69 (downstream exon)
Score: 71

ACTGTTGCCAAGAGCATTGAGTTCAAGGATAGAGTCAAGAATGTTGGTGCAAGCCTTGTAAAGCAGGTTGCTAATGCGACCAATGATACTGCTGGAGATGgtatggctgt ... caaaattcagGTACCACTTGTGCTACTGTATTGACTAAAGCAATATTTACTGAGGGGTGCAAGTCTGTTGCTGCTGGCATGAATGCAATGGATTTAAGGCGTGGTATTTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcttagttgcataatttgtttgttctaactgtgttattctgatccaaaattcagGTACCACTTGTGCTACTGTATTGACTAAAGCAATATTTACTGAGGGGTGCAAGTCTGTTGCTGCTGGCATGAATGCAATGGATTTAAGGCGTGGTATTTC
           ataatttgtttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatttgcacaaattcaatatgtggattgcattgtactttaggatttgcttagttgcataatttgtttgttctaactgtgttattctgatccaaaattcagGTACCACTTGTGCTACTGTATTGACTAAAGCAATATTTACTGAGGGGTGCAAGTCTGTTGCTGCTGGCATGAATGCAATGGATTTAAGGCGTGGTATTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - -gcacaaa
- - - - - - - - - - - - - tgcattg
- - - - - - - - - - - - - - - - - - - - - - ttgctta
- - - - - - - - - - - - - - - - - - - - - - - - - - ttgcata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtgtta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttctgat