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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgcaatattcttttgcttttctgttcattgtgcttttattaatcacttgcgtacttgatgtaatccggcggtgcttaaccattaagttactgttaatagATCTGCGGGATGATAAGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTATTTCCACTGCTCAG

Basic information

species Oryza sativa
transcript LOC_Os02g58730.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g58730.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G375002_T02 (Zea mays), 3'ss of exon 3
atgcaatattcttttgcttttctgttcattgtgcttttattaatcacttg--cgtacttgatgtaatc--cggcggtgcttaaccattaagttactgttaatagATCTGCGGGATGATAAGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTATTTCCACTGCTCAG
 ||  |      | ||  |         |  ||| |    |||||| | |  | |  ||  | ||  |  | ||| |||||||| ||| |||||||  ||| ||||||||| ||||||||||| ||||| || ||||||||||||||||| || ||||||||||| |||
-tgtga-gcaaatatgtctgaaaacatgtgatgcctca--taatcagtggatctttgttcttttagccgacagcgttgcttaacaatttagttacttgtaacagATCTGCGTGATGATAAGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAATTTCCACTGCCCAG
















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|3763167|gb|AU029919.1|AU029919
EST:     AAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTTGGAACAAAGCTTG                         ATCTGCGGGATGATAAGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTA
genomic: AAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTTGGAACAAAGCTTGgtatgccctt ... ctgttaatagATCTGCGGGATGATAAGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTA
EST: gi|33802327|gb|CF327037.1|CF327037
EST:     AAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTTGGAACAAAGCTTG                         ATCTGCGGGATGATAAGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTA
genomic: AAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTTGGAACAAAGCTTGgtatgccctt ... ctgttaatagATCTGCGGGATGATAAGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTA
EST: gi|163918056|gb|EG713984.1|EG713984
EST:     TCTCGTTGGAACAAAGCTTG                         ATCTGCGGGATGATAAGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTA
genomic: TCTCGTTGGAACAAAGCTTGgtatgccctt ... ctgttaatagATCTGCGGGATGATAAGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTA
EST: gi|88832933|gb|CI369823.1|CI369823
EST:     AAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTTGGAACAAAGCTTG                         ATCTGCGGGATGATAAGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTA
genomic: AAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTTGGAACAAAGCTTGgtatgccctt ... ctgttaatagATCTGCGGGATGATAAGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTA
EST: gi|86861523|gb|CI328204.1|CI328204
EST:     CGTTGGAACAAAGCTTG                         ATCTGCGGGATGATAAGCAATTTTTCGTAGATCACCCCTGGTGCTGTACCT
genomic: CGTTGGAACAAAGCTTGgtatgccctt ... ctgttaatagATCTGCGGGATGATAAGCAATTTTTCGTAGATCA-CCCTGGTGCTGTACCT
EST: gi|11233552|gb|AU164964.1|AU164964
EST:     AAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTTGGAACAAAGCTTG                         ATCTGCGGGATGATAAGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTA
genomic: AAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTTGGAACAAAGCTTGgtatgccctt ... ctgttaatagATCTGCGGGATGATAAGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTA
EST: gi|58593555|gb|CF991863.1|CF991863
EST:     AAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTTGGAACAAAGCTTG                         ATCTGCGGGATGATAAGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTA
genomic: AAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTTGGAACAAAGCTTGgtatgccctt ... ctgttaatagATCTGCGGGATGATAAGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTA
EST: gi|58594206|gb|CF992514.1|CF992514
EST:     AAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTTGGAACAAAGCTTG                         ATCTGCGGGATGATAAGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTA
genomic: AAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTTGGAACAAAGCTTGgtatgccctt ... ctgttaatagATCTGCGGGATGATAAGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTA
EST: gi|25807453|gb|CA763414.1|CA763414
EST:     AAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTTGGAACAAAGCTTG                         ATCTGCGGGATGATAAGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTA
genomic: AAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTTGGAACAAAGCTTGgtatgccctt ... ctgttaatagATCTGCGGGATGATAAGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTA
EST: gi|218494722|gb|FG969779.1|FG969779
EST:     AAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTTGGAACAAAGCTTG                         ATCTGCGGGATGATAAGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTA
genomic: AAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTTGGAACAAAGCTTGgtatgccctt ... ctgttaatagATCTGCGGGATGATAAGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTA
EST: gi|163920990|gb|EG710403.1|EG710403
EST:     AAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTTGGAACAAAGCTTG                         ATCTGCGGGAT
genomic: AAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTTGGAACAAAGCTTGgtatgccctt ... ctgttaatagATCTGCGGGAT
EST: gi|14980894|gb|BI305572.1|BI305572
EST:     AAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTTGGAACAAAGCTTG                         ATCTGCGGGATGATAAGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTA
genomic: AAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTTGGAACAAAGCTTGgtatgccctt ... ctgttaatagATCTGCGGGATGATAAGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTA
EST: gi|117226289|gb|CT846197.1|CT846197
EST:     AAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTTGGAACAAAGCTTG                         ATCTGCGGGATGATAAGCAATTTTTTGTAGATCACCCTGGTGCTGTACCTA
genomic: AAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTTGGAACAAAGCTTGgtatgccctt ... ctgttaatagATCTGCGGGATGATAAGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTA
EST: gi|86415824|gb|CI029835.1|CI029835
EST:     AAGGCATTATGCTCCTGGTGTGCCCATAATTCTCGTTGGAACAAAGCTTG                         ATCTGCGGGATGATAAGCNATTTTTCGTAGATCACCCTGGTGCTGTACCTA
genomic: AAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTTGGAACAAAGCTTGgtatgccctt ... ctgttaatagATCTGCGGGATGATAAGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTA
EST: gi|163929342|gb|EG713767.1|EG713767
EST:     GTGCCAATAATTCTCGTTGGAACAAAGCTTG                         ATCTGCGGGATGATAAGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTA
genomic: GTGCCAATAATTCTCGTTGGAACAAAGCTTGgtatgccctt ... ctgttaatagATCTGCGGGATGATAAGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTA
EST: gi|7134822|gb|AU082691.1|AU082691
EST:     AAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTTGGAACAAAGCTTG                         ATCTGCGGGATGATAAGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTA
genomic: AAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTTGGAACAAAGCTTGgtatgccctt ... ctgttaatagATCTGCGGGATGATAAGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTA
EST: gi|86599058|gb|CI355675.1|CI355675
EST:     GGTGTGCCAATAATTCTCGTTGGAACAAAGCTTG                         ATCTGCGGGATGATAAGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTA
genomic: GGTGTGCCAATAATTCTCGTTGGAACAAAGCTTGgtatgccctt ... ctgttaatagATCTGCGGGATGATAAGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTA
EST: gi|2431385|gb|C73805.1|C73805
EST:     AAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTTGGAACAAAGCTTG                         ATCTGCGGGATGATAAGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTA
genomic: AAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTTGGAACAAAGCTTGgtatgccctt ... ctgttaatagATCTGCGGGATGATAAGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTA
EST: gi|218499440|gb|FG950955.1|FG950955
EST:     AAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTTGGAACAAAGCTTG                         ATCTGCGGGATGATAAGCAATTTTTCGTAAATCACCCTGGTGCTGTACCTA
genomic: AAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTTGGAACAAAGCTTGgtatgccctt ... ctgttaatagATCTGCGGGATGATAAGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTA
EST: gi|88251317|gb|CI349745.1|CI349745
EST:     TGGAACAAAGCTTG                         ATCTGCGGGATGATAAGCAATTTTTCGTAGATCACACTGGTGCTGTACCTA
genomic: TGGAACAAAGCTTGgtatgccctt ... ctgttaatagATCTGCGGGATGATAAGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTA
EST: gi|218483315|gb|FG958115.1|FG958115
EST:     AAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTTGGAACAAAGCTTG                         ATCTGCGGGATGATAAGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTA
genomic: AAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTTGGAACAAAGCTTGgtatgccctt ... ctgttaatagATCTGCGGGATGATAAGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTA
EST: gi|33802329|gb|CF327038.1|CF327038
EST:     AAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTTGGAACAAAGCTTG                         ATCTGCGGGATGATAAGCAATTTTTCGTAGATCACCCCTGGTGCTGTACCT
genomic: AAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTTGGAACAAAGCTTGgtatgccctt ... ctgttaatagATCTGCGGGATGATAAGCAATTTTTCGTAGATCA-CCCTGGTGCTGTACCT
EST: gi|86598350|gb|CI354967.1|CI354967
EST:     ATAATTCTAGTT-GAACAAAGCTTA                         ATCTGCGGGATGATAAGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTA
genomic: ATAATTCTCGTTGGAACAAAGCTTGgtatgccctt ... ctgttaatagATCTGCGGGATGATAAGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTA
EST: gi|30228239|gb|CB966130.1|CB966130
EST:     AAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTTGGAACAAAGCTTG                         ATCTGCGGGATGATAAGCNATTTTTCGTAGATCACCCTGGTGCTGTACCTA
genomic: AAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTTGGAACAAAGCTTGgtatgccctt ... ctgttaatagATCTGCGGGATGATAAGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTA

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), 65 (downstream exon)
Score: 62

TGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTTGGAACAAAGCTTGgtatgccctt ... ctgttaatagATCTGCGGGATGATAAGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTATTTCCACTGCTCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttgcgtacttgatgtaatccggcggtgcttaaccattaagttactgttaatagATCTGCGGGATGATAAGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTATTTCCACTGCTCAG
                            gcttaac  putative branch site (score: 62)
                                    attaagtta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgcaatattcttttgcttttctgttcattgtgcttttattaatcacttgcgtacttgatgtaatccggcggtgcttaaccattaagttactgttaatagATCTGCGGGATGATAAGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTATTTCCACTGCTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - cttttgc
- - - - - - - - - -ttctgtt
- - - - - - - - - - - - - -attgtgc
- - - - - - - - - - - - - - - - - - - - - - cacttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - cttgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcttaa