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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggaggttccatcctacccttttctggactctcatgtctcattgctttacaccattgtaatcctttgtcatttactttaatttactggtacagTTCCTGTGGCGTCCGAGACCACCGTCGCTGCTGACCCCTGAAAAGGAAGACGAGATTGCGAAGAACCTGAGGAAGTACAGCAAGAAGTACGAGCAAGAGG

Basic information

species Oryza sativa
transcript LOC_Os10g41960.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g41960.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G174757_T01 (Zea mays), 3'ss of exon 10
gtatggaggttccatcctacccttttctggactctcatgtctcattgctttacaccattgtaatcctt------tgtcatttactttaatttac---tggtacagTTCCTGTGGCGTCCGAGACCACCGTCGCTGCTGACCCCTGAAAAGGAAGACGAGATTGCGAAGAACCTGAGGAAGTACAGCAAGAAGTACGAGCAAGAGG
   |  | |||| ||| | | | ||| ||||          ||| || | || || |||||  ||  |      | || ||||| |  | | |    ||||||||||  | ||||| |||||||| || || || |||||  | || |||||||| |||||  | | |||||||| |||||| |||||||||||||| ||||| |
--gtaaatgttcaatcattctccttt-tggat----gcagttcaatgatatatacaattgtcttctgtggtaagtatcttttacatggactgaacggtggtacagTTTATATGGCGCCCGAGACCGCCCTCACTACTGACGGCCGAGAAGGAAGAAGAGATCTCAAGGAACCTGAAGAAGTATAGCAAGAAGTACGAACAAGAAG

upper sequence: LOC_Os10g41960.1 (Oryza sativa), 3'ss of exon 10
lower sequence: AT5G27640.1 (Arabidopsis thaliana), 3'ss of exon 11
gtatggaggttccatcctacccttttctggactctcatgtctcattgctttacaccattgtaatcctttgtcatttactttaatttactggtacagTTCCTGTGGCGTCCGAGACCACCGTCGCTGCTGACCCCTGAAAAGGAAGACGAGATTGCGAAGAACCTGAGGAAGTACAGCAAGAAGTACGAGCAAGAGG
||||| |           || |  |  |  ||   |||    |||| |  |   | | |  |||        ||||   |    ||  |   ||||||    |||||||| ||||| || ||  |  ||||  | || |||||||| ||||| || |||| ||||| |||||||||||||||||| |||  |||||
gtatgtaa--caagaaaaactcggtcttaaacgagcatcgtccattccgatgt-ctaataaaat--------atttgtgtatggttggttacacagTTGGCTTGGCGTCCAAGACCTCCATCATTCTTGACTGCAGAGAAGGAAGAAGAGATAGCAAAGACCCTGAAGAAGTACAGCAAGAAGTATGAGGCAGAGG

upper sequence: LOC_Os10g41960.1 (Oryza sativa), 3'ss of exon 10
lower sequence: AT5G25780.1 (Arabidopsis thaliana), 3'ss of exon 10
gtatggaggttccatcctacccttttctggactctcatgtctcattgctttacaccattgtaatcctttgtcatttactttaatttactggtacagTTCCTGTGGCGTCCGAGACCACCGTCGCTGCTGACCCCTGAAAAGGAAGACGAGATTGCGAAGAACCTGAGGAAGTACAGCAAGAAGTACGAGCAAGAGG
||||| |      |    || |  |     |||  |||    ||||     |   | |  |||         ||||   |    ||  |   ||||||    |||||||| |||||  | ||  |  ||||  | || |||||||| ||||| || |||||||||||||| |||||||||| ||| |||  |||||
gtatgtaa-caataaaaaactcggtctcaaactagcatcatccattttcagatgtc-taataa------aatatttgtgtatggttggttacacagTTGGCTTGGCGTCCAAGACCGGCATCATTCTTGACTGCGGAGAAGGAAGAAGAGATAGCAAAGAACCTGAGGAATTACAGCAAGAGGTATGAGGCAGAGG

upper sequence: LOC_Os10g41960.1 (Oryza sativa), 3'ss of exon 10
lower sequence: PP1S130_248V6.3 (Physcomitrella patens), 3'ss of exon 9
gtatggaggt--tccatcctacccttttctggactctcatgt-ctcattgctttacaccattgtaatcctttgtcatttactttaatttactggta--cagTTCCTGTGGCGTCCGAGACCACCGTCGCTGCTGACCCCTGAAAAGGAAGACGAGATTGCGAAGAACCTGAGGAAGTACAGCAAGAAGTACGAGCAAGAGG
 | | || ||   | |    |   |   ||||| |   |  | || || | ||   |    || | |   |  | |   || |  ||||  |   |  |||||  |||||||||| ||||| ||  | || || || || ||  | || |  |||||||| ||||||||| | |||||||||||||||||||||   || |
-tttcgacgtgaccgaattgatggtcacctggaattagacatgcttatggattagtatgtgtgcattatgtcattaacaacatacattttttttcaaccagTTTTTGTGGCGTCCAAGACCCCCCACACTTCTTACTCCCGAGGATGAGGCTGAGATTGCCAAGAACCTGCGCAAGTACAGCAAGAAGTACGAGGCTGACG

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|86480590|gb|CI123223.1|CI123223
EST:     AAGCAACTTTACAAGGTGTCAAAGGACCACTTCTTTCAG                         TTCCTGTGGCGTCCGAGACCACCGTCGCTGCTGACCCCTGAAAAGGAAGAC
genomic: AAGCAACTTTACAAGGTGTCAAAGGACCACTTCTTTCAGgtatggaggt ... actggtacagTTCCTGTGGCGTCCGAGACCACCGTCGCTGCTGACCCCTGAAAAGGAAGAC
EST: gi|89165532|gb|CI102622.1|CI102622
EST:     ACTTCTTTCAG                         TTCCTGTGGCGTCCGAGACCACCGTCGCTGCTGACCCCTGAAAAGGAAGAC
genomic: ACTTCTTTCAGgtatggaggt ... actggtacagTTCCTGTGGCGTCCGAGACCACCGTCGCTGCTGACCCCTGAAAAGGAAGAC
EST: gi|88998539|gb|CI259872.1|CI259872
EST:     CTTTCAGTGGCAAGCAACTTTACAAGGTGTCAAAGGACCACTTCTTTCAG                         TTCCTGTGGCGTCCGAGACCACCGTCGCTGCTGACCCCTGAAAAGGAAGAC
genomic: CTTTCAGTGGCAAGCAACTTTACAAGGTGTCAAAGGACCACTTCTTTCAGgtatggaggt ... actggtacagTTCCTGTGGCGTCCGAGACCACCGTCGCTGCTGACCCCTGAAAAGGAAGAC
EST: gi|58682866|gb|CK071553.1|CK071553
EST:     CTTTCAGTGGCAAGCAACTTTACAAGGTGTCAAAGGACCACTTCTTTCAG                         TTCCTGTGGCGTCCGAGACCACCGTCGCTGCTGACCCCTGAAAAGGAAGAC
genomic: CTTTCAGTGGCAAGCAACTTTACAAGGTGTCAAAGGACCACTTCTTTCAGgtatggaggt ... actggtacagTTCCTGTGGCGTCCGAGACCACCGTCGCTGCTGACCCCTGAAAAGGAAGAC
EST: gi|87036433|gb|CI191055.1|CI191055
EST:     CTTTCAGTGGCAAGCAACTTTACAAGGTGTCAAAGGACCACTTCTTTCAG                         TTCCTGTGGCGTCCGAGACCACCGTCGCTGCTGACCCCTGAAAAGGAAGAC
genomic: CTTTCAGTGGCAAGCAACTTTACAAGGTGTCAAAGGACCACTTCTTTCAGgtatggaggt ... actggtacagTTCCTGTGGCGTCCGAGACCACCGTCGCTGCTGACCCCTGAAAAGGAAGAC
EST: gi|86480631|gb|CI123264.1|CI123264
EST:     CTTTCAGTGGCAAGCAACTTTACAAGGTGTCAAAGGACCACTTCTTTCAG                         TTCCTGTGGCGTCCGAGACCACCGTCGCTGCTGACCCCTGAAAAGGAAGAC
genomic: CTTTCAGTGGCAAGCAACTTTACAAGGTGTCAAAGGACCACTTCTTTCAGgtatggaggt ... actggtacagTTCCTGTGGCGTCCGAGACCACCGTCGCTGCTGACCCCTGAAAAGGAAGAC
EST: gi|86477297|gb|CI119930.1|CI119930
EST:     CTTTCAGTGGCAAGCAACTTTACAAGGTGTCAAAGGACCACTTCTTTCAG                         TTCCTGTGGCGTCCGAGACCACCGTCGCTGCTGACCCCTGAAAAGGAAGAC
genomic: CTTTCAGTGGCAAGCAACTTTACAAGGTGTCAAAGGACCACTTCTTTCAGgtatggaggt ... actggtacagTTCCTGTGGCGTCCGAGACCACCGTCGCTGCTGACCCCTGAAAAGGAAGAC
EST: gi|86481269|gb|CI123902.1|CI123902
EST:     CTTTCAGTGGCAAGCAACTTTACAAGGTGTCAAAGGACCACTTCTTTCAG                         TTCCTGTGGCGTCCGAGACCACCGTCGCTGCTGACCCCTGAAAAGGAAGAC
genomic: CTTTCAGTGGCAAGCAACTTTACAAGGTGTCAAAGGACCACTTCTTTCAGgtatggaggt ... actggtacagTTCCTGTGGCGTCCGAGACCACCGTCGCTGCTGACCCCTGAAAAGGAAGAC
EST: gi|87018934|gb|CI256819.1|CI256819
EST:     CTTTCAGTGGCAAGCAACTTTACAAGGTGTCAAAGGACCACTTCTTTCAG                         TTCCTGTGGCGTCCGAGACCACCGTCGCTGCTGACCCCTGAAAAGGAAGAC
genomic: CTTTCAGTGGCAAGCAACTTTACAAGGTGTCAAAGGACCACTTCTTTCAGgtatggaggt ... actggtacagTTCCTGTGGCGTCCGAGACCACCGTCGCTGCTGACCCCTGAAAAGGAAGAC
EST: gi|88837414|gb|CI078774.1|CI078774
EST:     GTGTCAAAGGACCACTTCTTTCAG                         TTCCTGTGGCGTCCGAGACCACTGTCGCTGCTGACCCCTGAAAAGGAAGAC
genomic: GTGTCAAAGGACCACTTCTTTCAGgtatggaggt ... actggtacagTTCCTGTGGCGTCCGAGACCACCGTCGCTGCTGACCCCTGAAAAGGAAGAC
EST: gi|88902689|gb|CI088227.1|CI088227
EST:     CACTTCTTTCAG                         TTCCTGTGGCGTCCGAGACCACGGTCGCTGCTGACCCCTGAAAAGGAAGAC
genomic: CACTTCTTTCAGgtatggaggt ... actggtacagTTCCTGTGGCGTCCGAGACCACCGTCGCTGCTGACCCCTGAAAAGGAAGAC
EST: gi|87021533|gb|CI274140.1|CI274140
EST:     CTTTCAGTGGCAAGCAACTTTACAAGGTGTCAAAGGACCACTTCTTTCAG                         TTCCTGTGGCGTCCGAGACCACCGTCGCTGCTGACCCCTGAAAAGGAGGAC
genomic: CTTTCAGTGGCAAGCAACTTTACAAGGTGTCAAAGGACCACTTCTTTCAGgtatggaggt ... actggtacagTTCCTGTGGCGTCCGAGACCACCGTCGCTGCTGACCCCTGAAAAGGAAGAC
EST: gi|86481284|gb|CI123917.1|CI123917
EST:     TTTCAGTGGCAAGCAACTTTACCAAGGTGTCAAAGGACCACTTCTTTCAG                         TTCCTGTGGCGTCCGAGACCACCGTCGCTGCTGACCCCTGAAAAGGAAGAC
genomic: TTTCAGTGGCAAGCAACTTTA-CAAGGTGTCAAAGGACCACTTCTTTCAGgtatggaggt ... actggtacagTTCCTGTGGCGTCCGAGACCACCGTCGCTGCTGACCCCTGAAAAGGAAGAC

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), 66 (downstream exon)
Score: 15

ATCTGCAGTTACCTCAGTCCATGAAATGGAGAATGGTTTCCAAATATGGTCTTTCAGTGGCAAGCAACTTTACAAGGTGTCAAAGGACCACTTCTTTCAGgtatggaggt ... actggtacagTTCCTGTGGCGTCCGAGACCACCGTCGCTGCTGACCCCTGAAAAGGAAGACGAGATTGCGAAGAACCTGAGGAAGTACAGCAAGAAGTACGAGCAAGAGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcattgctttacaccattgtaatcctttgtcatttactttaatttactggtacagTTCCTGTGGCGTCCGAGACCACCGTCGCTGCTGACCCCTGAAAAGGAAGACGAGATTGCGAAGAACCTGAGGAAGTACAGCAAGAAGTACGAGCAAGAGG
                                    ctttaat  putative branch site (score: 15)
                         tttgtcatttacttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggaggttccatcctacccttttctggactctcatgtctcattgctttacaccattgtaatcctttgtcatttactttaatttactggtacagTTCCTGTGGCGTCCGAGACCACCGTCGCTGCTGACCCCTGAAAAGGAAGACGAGATTGCGAAGAACCTGAGGAAGTACAGCAAGAAGTACGAGCAAGAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
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