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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caagacctatggtaaccatgcctaaacaaattagaagatccccttcctttctcttcatctcctagtgcgacgataatatttggttgtttgatcctcgcagATGATGAAGAAGAGGCACAAGATTGAGAGGGACCTGAGCATTGGTGAGGAGGTTGGGTGGTCGAAGAATGTTCAGGTGGCAAAAAACAACCCTACCCTTG

Basic information

species Oryza sativa
transcript LOC_Os12g37060.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g37060.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G106906_T01 (Zea mays), 3'ss of exon 2
caagacctatggtaaccatgcctaaacaaattagaagatccccttcctttctcttcatctcctagtgcgacgataat--atttggttgtttgatcctcgcagATGATGAAGAAGAGGCACAAGATTGAGAGGGACCTGAGCATTGGTGAGGAGGTTGGGTGGTCGAAGAATGTTCAGGTGGCAAAAAACAACCCTACCCTTG
   ||  | ||  ||| |     | || || ||||| || ||||    | ||     | |  |   || |    | |  |  |||||| | | | |||||||||||||||||||||||||||||| ||| |||||||||| || || ||||| || || ||||| |||||    |||||||| |||  |||||| ||||| |
-gggaagtctga-aactaatttgagactaactagaacatgccctcttctcctacatcttttttcacgcaatttcacttgacgtggttgatcgctgctcgcagATGATGAAGAAGAGGCACAAGATCGAGCGGGACCTGAGTATCGGCGAGGAAGTCGGATGGTCAAAGAACCAGCAGGTGGCTAAATCCAACCCCACCCTCG
















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|89194863|gb|CI003327.1|CI003327
EST:     TTGGCTTCGACCTCTCCAACCTGCTCGTGTTCACCCCCATGACCATCGAG                         ATGATGAAGAAGAGGCACAAGATTGAGAGGGACCTGAGCATTGGTGAGGAG
genomic: TTGGCTTCGACCTCTCCAACCTGCTCGTGTTCACCCCCATGACCATCGAGgtcagctatt ... atcctcgcagATGATGAAGAAGAGGCACAAGATTGAGAGGGACCTGAGCATTGGTGAGGAG
EST: gi|86417461|gb|CI031670.1|CI031670
EST:     TTGGCTTCGACCTCTCCAACCTGCTCGTGTTCACCCCCATGACCATCGAG                         ATGATGAAGAAGAGGCACAAGATTGAGAGGGACCTGAGCATTGGTGAGGAG
genomic: TTGGCTTCGACCTCTCCAACCTGCTCGTGTTCACCCCCATGACCATCGAGgtcagctatt ... atcctcgcagATGATGAAGAAGAGGCACAAGATTGAGAGGGACCTGAGCATTGGTGAGGAG
EST: gi|89197557|gb|CI012338.1|CI012338
EST:     CTCGTGTTCACCCCCATGACCATCGAG                         ATGATGAAGAAGAGGCACAAGATTGAGAGGGACCTGAGCATTGGTGAGGAG
genomic: CTCGTGTTCACCCCCATGACCATCGAGgtcagctatt ... atcctcgcagATGATGAAGAAGAGGCACAAGATTGAGAGGGACCTGAGCATTGGTGAGGAG
EST: gi|88839587|gb|CI005375.1|CI005375
EST:     TTGGCTTCGACCTCTCCAACCTGCTCGTGTTCACCCCCATGACNATCGAG                         ATGATGAAGAAGAGGCACAAGATTGAGAGGGACCTGAGCATTGGTGAGGAG
genomic: TTGGCTTCGACCTCTCCAACCTGCTCGTGTTCACCCCCATGACCATCGAGgtcagctatt ... atcctcgcagATGATGAAGAAGAGGCACAAGATTGAGAGGGACCTGAGCATTGGTGAGGAG
EST: gi|88841501|gb|CI005581.1|CI005581
EST:     TTGGCTTCGACCTCTCCAACCTGCTCGTGTTCACCCCCATGACCATCGAG                         ATGATGAAGAAGAGGCACAAGATTGAGAGGGACCTGAGCATTGGTGAGGAG
genomic: TTGGCTTCGACCTCTCCAACCTGCTCGTGTTCACCCCCATGACCATCGAGgtcagctatt ... atcctcgcagATGATGAAGAAGAGGCACAAGATTGAGAGGGACCTGAGCATTGGTGAGGAG
EST: gi|89190388|gb|CI015353.1|CI015353
EST:     CTGCTCGTGTTCACCCCCATGACCATCGAG                         ATGATGAAGAAGAGGCACAAGATTGAGAGGGACCTGAGCATTGGTGAGGAG
genomic: CTGCTCGTGTTCACCCCCATGACCATCGAGgtcagctatt ... atcctcgcagATGATGAAGAAGAGGCACAAGATTGAGAGGGACCTGAGCATTGGTGAGGAG
EST: gi|86855406|gb|CI266935.1|CI266935
EST:     TTGGCTTCGACCTCTCCAACCTGCTCGTGTTCACCCCCATGACCATCGAG                         ATGATGAAGAAGAGGCACAAGATTGAGAGGGACCTGAGCATTGGTGAGGAG
genomic: TTGGCTTCGACCTCTCCAACCTGCTCGTGTTCACCCCCATGACCATCGAGgtcagctatt ... atcctcgcagATGATGAAGAAGAGGCACAAGATTGAGAGGGACCTGAGCATTGGTGAGGAG
EST: gi|38479221|gb|CF963354.1|CF963354
EST:     TTGGCTTCGACCTCTCCAACCTGCTCGTGTTCACCCCCATGACNATCGAG                         ATGATGAAGAAGAGGCACAAGATTGAGAGGGACCTGAGCATTGGTGAGGAG
genomic: TTGGCTTCGACCTCTCCAACCTGCTCGTGTTCACCCCCATGACCATCGAGgtcagctatt ... atcctcgcagATGATGAAGAAGAGGCACAAGATTGAGAGGGACCTGAGCATTGGTGAGGAG
EST: gi|86545260|gb|CI185466.1|CI185466
EST:     CTCTCCTACCTGCTCGTGTTCACCCCCATGACCATCGAG                         ATGATGAAGAAGAGGCACAAGATTGAGAGGGACCTGAGCATTTGGTGAGGA
genomic: CTCTCCAACCTGCTCGTGTTCACCCCCATGACCATCGAGgtcagctatt ... atcctcgcagATGATGAAGAAGAGGCACAAGATTGAGAGGGACCTGAGCA-TTGGTGAGGA
EST: gi|86545703|gb|CI185909.1|CI185909
EST:     GTGTTCACCCCCATGACCATCGAG                         ATGATGAAGAAGAGGCACAAGATTGAGAGGGACCTGAGCATTGGTGAGGAG
genomic: GTGTTCACCCCCATGACCATCGAGgtcagctatt ... atcctcgcagATGATGAAGAAGAGGCACAAGATTGAGAGGGACCTGAGCATTGGTGAGGAG
EST: gi|87013767|gb|CI269266.1|CI269266
EST:     CTCGTGTTCACCCCCATGACCATCGAG                         ATGATGAAGAAGAGGCACAAGATTGAGAGGGACCTGAGCATTGGTGAGGAG
genomic: CTCGTGTTCACCCCCATGACCATCGAGgtcagctatt ... atcctcgcagATGATGAAGAAGAGGCACAAGATTGAGAGGGACCTGAGCATTGGTGAGGAG
EST: gi|86545683|gb|CI185889.1|CI185889
EST:     TGTTCACCCCCATGACCATCGAG                         ATGATGAAGAAGAGGCACAAGATTGAGAGGGACCTGAGCATTGGTGAGGAG
genomic: TGTTCACCCCCATGACCATCGAGgtcagctatt ... atcctcgcagATGATGAAGAAGAGGCACAAGATTGAGAGGGACCTGAGCATTGGTGAGGAG
EST: gi|14192263|gb|AU184474.1|AU184474
EST:     TTGGCTTCGACCTCTCCAACCTGCTCGTGTTCACCCCCATGACCATCGAG                         ATGATGAAGAAGAGGCACAAGATTGAGAGGGACCTGAGCATTGGTGAGGAG
genomic: TTGGCTTCGACCTCTCCAACCTGCTCGTGTTCACCCCCATGACCATCGAGgtcagctatt ... atcctcgcagATGATGAAGAAGAGGCACAAGATTGAGAGGGACCTGAGCATTGGTGAGGAG
EST: gi|88201362|gb|CI201717.1|CI201717
EST:     GTTCACCCCCATGACCATCGAG                         ATGATGAAGAAGAGGCACAAGATTGAGAGGGACCTGAGCATTGGTGAGGAG
genomic: GTTCACCCCCATGACCATCGAGgtcagctatt ... atcctcgcagATGATGAAGAAGAGGCACAAGATTGAGAGGGACCTGAGCATTGGTGAGGAG
EST: gi|7274063|gb|AU032861.2|AU032861
EST:     TTGGCTTCGACCTCTCCAACCTGCTCGTGTTCACCCCCATGACCATCGAG                         ATGATGAAGAAGAGGCACAAGATTGAGTAGGGGACCTGGAGCATTGGTGAG
genomic: TTGGCTTCGACCTCTCCAACCTGCTCGTGTTCACCCCCATGACCATCGAGgtcagctatt ... atcctcgcagATGATGAAGAAGAGGCACAAGATTGAG-AGGG-ACCTG-AGCATTGGTGAG
EST: gi|88843712|gb|CI010970.1|CI010970
EST:     TTGGCTTCGACCTCTCCAACCTGCTCGTGTTCACCCCCATGACCATCGAG                         ATGATGAAGAAGAGGCACAAGATTGAGAGGGACCTGAGCATTGGTGAGGAG
genomic: TTGGCTTCGACCTCTCCAACCTGCTCGTGTTCACCCCCATGACCATCGAGgtcagctatt ... atcctcgcagATGATGAAGAAGAGGCACAAGATTGAGAGGGACCTGAGCATTGGTGAGGAG
EST: gi|88251840|gb|CI349077.1|CI349077
EST:     ACCCCCATGACCATCGAG                         ATGATGAAGAAGAGGCACAAGATTGAGAGGGACCTGAGCATTGGTGAGGAG
genomic: ACCCCCATGACCATCGAGgtcagctatt ... atcctcgcagATGATGAAGAAGAGGCACAAGATTGAGAGGGACCTGAGCATTGGTGAGGAG
EST: gi|88987097|gb|CI034138.1|CI034138
EST:     CCCATGACCATCGAG                         ATGATGAAGAAGAGGCACAAGATTGAGAGGGACCTGAGCATTGGTGAGGAG
genomic: CCCATGACCATCGAGgtcagctatt ... atcctcgcagATGATGAAGAAGAGGCACAAGATTGAGAGGGACCTGAGCATTGGTGAGGAG
EST: gi|87019259|gb|CI279769.1|CI279769
EST:     TTGGCTTCGACCTCTCCAACCTGCTCGTGTTCACCCCCATGACCATCGAG                         ATGATGAAGAAGAGGCACAAGATTGAGAGGGACCTGAGCATTGGTGAGGAG
genomic: TTGGCTTCGACCTCTCCAACCTGCTCGTGTTCACCCCCATGACCATCGAGgtcagctatt ... atcctcgcagATGATGAAGAAGAGGCACAAGATTGAGAGGGACCTGAGCATTGGTGAGGAG
EST: gi|88217738|gb|CI217587.1|CI217587
EST:     TTGGCTTCGACCTCTCCAACCTGCTCGTGTTCACCCCCATGACCATCGAG                         ATGATGAAGAAGAGGCACAAGATTGAGAGGGACCTGAGCATTGGTGAGGGG
genomic: TTGGCTTCGACCTCTCCAACCTGCTCGTGTTCACCCCCATGACCATCGAGgtcagctatt ... atcctcgcagATGATGAAGAAGAGGCACAAGATTGAGAGGGACCTGAGCATTGGTGAGGAG
EST: gi|86502901|gb|CI145534.1|CI145534
EST:     TTGGCTTCGACCTCTCCAACCTGCTCGTGTTCACCCCCATGACCATCGAG                         ATGATGAAGAAGAGGCACAAGATTGAGAGGGACCTGAGCATTGGTGAGGAG
genomic: TTGGCTTCGACCTCTCCAACCTGCTCGTGTTCACCCCCATGACCATCGAGgtcagctatt ... atcctcgcagATGATGAAGAAGAGGCACAAGATTGAGAGGGACCTGAGCATTGGTGAGGAG
EST: gi|86413559|gb|CI019144.1|CI019144
EST:     CATGACCATCGAG                         ATGATGAAGAAGAGGCACAAGATTGAGAGGGACCTGAGCATTGGTGAGGAG
genomic: CATGACCATCGAGgtcagctatt ... atcctcgcagATGATGAAGAAGAGGCACAAGATTGAGAGGGACCTGAGCATTGGTGAGGAG
EST: gi|88966135|gb|CI013011.1|CI013011
EST:     TTGGCTTCGACCTCTCCAACCTGCTCGTGTTCACCCCCATGACCATCGAG                         ATGATGAAGAAGAGGCACAAGATTGAGAGGGACCTGAGCATTGGTGAGGAG
genomic: TTGGCTTCGACCTCTCCAACCTGCTCGTGTTCACCCCCATGACCATCGAGgtcagctatt ... atcctcgcagATGATGAAGAAGAGGCACAAGATTGAGAGGGACCTGAGCATTGGTGAGGAG
EST: gi|14192264|gb|AU184475.1|AU184475
EST:     CCCCCATGACCATCGAG                         ATGATGAAGAAGAGGCNCAAGATTGAGAGGGACCTGAGCATTGGTGAGGAG
genomic: CCCCCATGACCATCGAGgtcagctatt ... atcctcgcagATGATGAAGAAGAGGCACAAGATTGAGAGGGACCTGAGCATTGGTGAGGAG
EST: gi|109711765|gb|CI028935.1|CI028935
EST:     TTGGCTTCGACCTCTCCAACCTGCTCGTGTTCACCCCCATGACCATCGAG                         ATGATGAAGAAGAGGCACAAGATTGAGAGGGACCTGAGCATTGGTGAGGAG
genomic: TTGGCTTCGACCTCTCCAACCTGCTCGTGTTCACCCCCATGACCATCGAGgtcagctatt ... atcctcgcagATGATGAAGAAGAGGCACAAGATTGAGAGGGACCTGAGCATTGGTGAGGAG
EST: gi|15008972|gb|AU223360.1|AU223360
EST:     TTGGCTTCGACCTCTCCAACCTGCTCGTGTTCACCCCCATGACCATCGAG                         ATGATGAAGAAGAGGCACAAGATTGAGAGGGACCTGAGCATTGGTGAGGAG
genomic: TTGGCTTCGACCTCTCCAACCTGCTCGTGTTCACCCCCATGACCATCGAGgtcagctatt ... atcctcgcagATGATGAAGAAGAGGCACAAGATTGAGAGGGACCTGAGCATTGGTGAGGAG

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), 44 (downstream exon)
Score: 8

GACGGCGTCCACCGTCGAGCGCTACCAGCTCGGCTTCCTCCTCGCCGCCCTTGGCTTCGACCTCTCCAACCTGCTCGTGTTCACCCCCATGACCATCGAGgtcagctatt ... atcctcgcagATGATGAAGAAGAGGCACAAGATTGAGAGGGACCTGAGCATTGGTGAGGAGGTTGGGTGGTCGAAGAATGTTCAGGTGGCAAAAAACAACCCTACCCTTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctttctcttcatctcctagtgcgacgataatatttggttgtttgatcctcgcagATGATGAAGAAGAGGCACAAGATTGAGAGGGACCTGAGCATTGGTGAGGAGGTTGGGTGGTCGAAGAATGTTCAGGTGGCAAAAAACAACCCTACCCTTG
                                        gtttgat  putative branch site (score: 8)
                                              tcctcgc  CT-rich tract
                           ataatattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caagacctatggtaaccatgcctaaacaaattagaagatccccttcctttctcttcatctcctagtgcgacgataatatttggttgtttgatcctcgcagATGATGAAGAAGAGGCACAAGATTGAGAGGGACCTGAGCATTGGTGAGGAGGTTGGGTGGTCGAAGAATGTTCAGGTGGCAAAAAACAACCCTACCCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - catgcct
- - - - - - - - - - - -aaacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgtttg