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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTCCCTTGACCCGAAGAAATTCGTGGGTGTAGCTTCTGCGCCTGATGCGGTAGAATATCTTCATTCTGGCAAGAGTGTTGGCAAGgtaccatcgcttatatgatgaaatatgattctgttcttatcttctcaaatgtgacttaatagatttttcttctggaacctttccag

Basic information

species Oryza sativa
transcript LOC_Os09g28570.1
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g28570.1 (Oryza sativa), 5'ss of exon 17
lower sequence: GRMZM2G479068_T01 (Zea mays), 5'ss of exon 5
GTTTCCCTTGACCCGAAGAAATTCGTGGGTGTAGCTTCTGCGCCTGATGCGGTAGAATATCTTCATTCTGGCAAGAGTGTTGGCAAGgtaccatcgcttatatgatga-aat-atgattctgttcttatcttctcaaatgtgacttaatagatttttcttctggaacctttccag-----------------
|| | | ||||||| ||||||||||||||||| ||||| | | | ||||| ||||||||||| |||||||||| |||||||||||||||||  | | || ||  |  | ||| ||||  ||||| || |  |   ||| |  ||||   |    ||||  |||  | ||||||||                 
GTCTTCGTTGACCCCAAGAAATTCGTGGGTGTTGCTTCCGTGGCAGATGCAGTAGAATATCTCCATTCTGGCAGGAGTGTTGGCAAGgtacggtggtttctacaagcacaatgatgaacctgtttttgttgtagtaaa-gcaacttgcaa----tttccactgttatctttccaggtcgttgtttgcatgga

upper sequence: LOC_Os09g28570.1 (Oryza sativa), 5'ss of exon 17
lower sequence: GRMZM2G147191_T02 (Zea mays), 5'ss of exon 17
GTTTCCCTTGACCCGAAGAAATTCGTGGGTGTAGCTTCTGCGCCTGATGCGGTAGAATATCTTCATTCTGGCAAGAGTGTTGGCAAGgtacca-tcgcttat------atgatgaaatatgattctgttcttatcttctcaaatgtgacttaatagatttttcttctggaacctttccag
|||||||| ||||| ||| ||||| ||||||| ||||| |     |||||||| ||||||||||||||||||||||||||||||||||||  | | |  | |       |||    ||  || ||||| |  |||||| |||        | | || ||||  | ||| ||| ||| |||
GTTTCCCTAGACCCCAAGCAATTCTTGGGTGTTGCTTCAGTCGTAGATGCGGTCGAATATCTTCATTCTGGCAAGAGTGTTGGCAAGgtataagttgtctgtctatctgtgacagcatgagaatctgtcccaatcttcgcaa-------cttacaggttttcatcctg-aactttttcag
















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|88451227|gb|CI534220.1|CI534220
EST:     CGGTAGAATATCTTCATTCTGGCAAGAGTGTTGGCAAG                         GTTGTTGTGTGCATTGATCCGTCATACAGTCAGACCCTTGCTAAGCTATAG
genomic: CGGTAGAATATCTTCATTCTGGCAAGAGTGTTGGCAAGgtaccatcgc ... acctttccagGTTGTTGTGTGCATTGATCCGTCATACAGTCAGACCCTTGCTAAGCTATAG
EST: gi|88416128|gb|CI538284.1|CI538284
EST:     CTGCGCCTGATGCGGTAGAATATCTTCATTCTGGCAAGAGTGTTGGCAAG                         GTTGTTGTGTGCATTGATCCGTCATACAGTCAGACCCTTGCTAAGCTATAG
genomic: CTGCGCCTGATGCGGTAGAATATCTTCATTCTGGCAAGAGTGTTGGCAAGgtaccatcgc ... acctttccagGTTGTTGTGTGCATTGATCCGTCATACAGTCAGACCCTTGCTAAGCTATAG
EST: gi|86881108|gb|CI339289.1|CI339289
EST:     CTGCGCCTGATGCGGTAGAATATCTTCATTCTGGCAAGAGTGTTGGCAAG                         GTTGTTGTGTGCATTGATCCGTCATACAGTCAGACCCTTGCTAAGCTATAG
genomic: CTGCGCCTGATGCGGTAGAATATCTTCATTCTGGCAAGAGTGTTGGCAAGgtaccatcgc ... acctttccagGTTGTTGTGTGCATTGATCCGTCATACAGTCAGACCCTTGCTAAGCTATAG
EST: gi|86876432|gb|CI318417.1|CI318417
EST:     TGCGCCTGATGCGGTAGAATATCTTCATTCTGGCAAGAGTGGTTGGCAAG                         GTTGTTGTGTGCATTGATCCGTCATACAGTCAGACCCTTGCTAAGCTATA
genomic: TGCGCCTGATGCGGTAGAATATCTTCATTCTGGCAAGAGT-GTTGGCAAGgtaccatcgc ... acctttccagGTTGTTGTGTGCATTGATCCGTCATACAGTCAGACCCTTGCTAAGCTATA
EST: gi|88322986|gb|CI548080.1|CI548080
EST:     CTGCGCCTGATGCGGTAGAATATCTTCATTCTGGCAAGAGTGTTGGCAAG                         GTTGTTGTGTGCATTGATCCGTCATACAGTCAGACCCTTGCTAAGCTATAG
genomic: CTGCGCCTGATGCGGTAGAATATCTTCATTCTGGCAAGAGTGTTGGCAAGgtaccatcgc ... acctttccagGTTGTTGTGTGCATTGATCCGTCATACAGTCAGACCCTTGCTAAGCTATAG
EST: gi|88366773|gb|CI558947.1|CI558947
EST:     CTGCGCCTGATGCGGTAGAATATCTTCATTCTGGCAAGAGTGTTGGCAAG                         GTTGTTGTGTGCATTGATCCGTCATACAGTCAGACCCTTGCTAAGCTATAG
genomic: CTGCGCCTGATGCGGTAGAATATCTTCATTCTGGCAAGAGTGTTGGCAAGgtaccatcgc ... acctttccagGTTGTTGTGTGCATTGATCCGTCATACAGTCAGACCCTTGCTAAGCTATAG
EST: gi|88267019|gb|CI378954.1|CI378954
EST:     CTGCGCCTGATGCGGTAGAATATCTTCATTCTGGCAAGAGTGTTGGCAAG                         GTTGTTGTGTGCATTGATCCGTCATACAGTCAGACCCTTGCTAAGCTATAG
genomic: CTGCGCCTGATGCGGTAGAATATCTTCATTCTGGCAAGAGTGTTGGCAAGgtaccatcgc ... acctttccagGTTGTTGTGTGCATTGATCCGTCATACAGTCAGACCCTTGCTAAGCTATAG
EST: gi|88274323|gb|CI394729.1|CI394729
EST:     CTGCGCCTGATGCGGTAGAAAATCTTCATTCTGGCAAGAGTGTTGGCAAG                         GTTGTTGTGTGCATTGATCCGTCAAACAGTCAGACCCTTGCTAAGCAATAG
genomic: CTGCGCCTGATGCGGTAGAATATCTTCATTCTGGCAAGAGTGTTGGCAAGgtaccatcgc ... acctttccagGTTGTTGTGTGCATTGATCCGTCATACAGTCAGACCCTTGCTAAGCTATAG
EST: gi|86870214|gb|CI319320.1|CI319320
EST:     CTGCGCCTGATGCGGTAGAATATCTTCATTCTGGCAAGAGTGTTGGCAAG                         GTTGTTGTGTGCATTGATCCGTCATACAGTCAGACCCTTGCTAAGCTATAG
genomic: CTGCGCCTGATGCGGTAGAATATCTTCATTCTGGCAAGAGTGTTGGCAAGgtaccatcgc ... acctttccagGTTGTTGTGTGCATTGATCCGTCATACAGTCAGACCCTTGCTAAGCTATAG
EST: gi|86488890|gb|CI131523.1|CI131523
EST:     CTGCGCCTGATGCGGTAGAATATCTTCATTCTGGCAAGAGTGTTGGCAAG                         GTTGTTGTGTGCATTGATCCGTCATACAGTCAGACCCTTGCTAAGCTATAG
genomic: CTGCGCCTGATGCGGTAGAATATCTTCATTCTGGCAAGAGTGTTGGCAAGgtaccatcgc ... acctttccagGTTGTTGTGTGCATTGATCCGTCATACAGTCAGACCCTTGCTAAGCTATAG
EST: gi|86870421|gb|CI320517.1|CI320517
EST:     CTGCCCCTGATGCGGTAGAATATCTTCATTCTGCCAAGAGTGTTGGCAAG                         GTTGTTGTGTGCATTGATCCGTCATACAGTCAGACCCTTGCTAAGCTATAG
genomic: CTGCGCCTGATGCGGTAGAATATCTTCATTCTGGCAAGAGTGTTGGCAAGgtaccatcgc ... acctttccagGTTGTTGTGTGCATTGATCCGTCATACAGTCAGACCCTTGCTAAGCTATAG
EST: gi|88269934|gb|CI381232.1|CI381232
EST:     TGCGCCTGATGCGGTAGAATATCTTCATTCTGGCAAGAGGTGTTGGCAAG                         GTTGTTGTGTGCATTGATCCGTCATACAGTCAGACCCTTGCTAAGGTATAG
genomic: TGCGCCTGATGCGGTAGAATATCTTCATTCTGGCAAGA-GTGTTGGCAAGgtaccatcgc ... acctttccagGTTGTTGTGTGCATTGATCCGTCATACAGTCAGACCCTTGCTAAGCTATAG
EST: gi|88446675|gb|CI526508.1|CI526508
EST:     CTGCGCCTGATGCGGTAGAATATCTTCATTCTGGCAAGAGTGTTGGCAAG                         GTTGTTGTGTGCATTGATCCGTCATACAGTCAGACCCTTGCTAAGCTATAG
genomic: CTGCGCCTGATGCGGTAGAATATCTTCATTCTGGCAAGAGTGTTGGCAAGgtaccatcgc ... acctttccagGTTGTTGTGTGCATTGATCCGTCATACAGTCAGACCCTTGCTAAGCTATAG
EST: gi|29670808|gb|CB667083.1|CB667083
EST:     CTGCGCCTGATGCGGTAGAATATCTTCATTCTGGCAAGAGTGTTGGCAAG                         GTTGTTGTGTGCATTGATCCGTCATACAGTCAGACCCTTGCTAAGCTATAG
genomic: CTGCGCCTGATGCGGTAGAATATCTTCATTCTGGCAAGAGTGTTGGCAAGgtaccatcgc ... acctttccagGTTGTTGTGTGCATTGATCCGTCATACAGTCAGACCCTTGCTAAGCTATAG
EST: gi|86865386|gb|CI330890.1|CI330890
EST:     TGCGCCTGATGCGGTAGAATATCTTCATTCTGGCAAGAGTGTTGGGCAAG                         GTTGTTGTGTGCATTGATCCGTCATACAGTCAGACCCTTGCTAAGCTATA
genomic: TGCGCCTGATGCGGTAGAATATCTTCATTCTGGCAAGAGTGTT-GGCAAGgtaccatcgc ... acctttccagGTTGTTGTGTGCATTGATCCGTCATACAGTCAGACCCTTGCTAAGCTATA
EST: gi|88295049|gb|CI523003.1|CI523003
EST:     GGCAAGAGTGTTGGCAAG                         GTTGTTGTGTGCATTGATCCGTCATACAGTCAGACCCTTGCTAAGCTATAG
genomic: GGCAAGAGTGTTGGCAAGgtaccatcgc ... acctttccagGTTGTTGTGTGCATTGATCCGTCATACAGTCAGACCCTTGCTAAGCTATAG
EST: gi|88834245|gb|CI000609.1|CI000609
EST:     CTGCGCCTGATGCGGTAGAATATCTTCATTCTGGCAAGAGTGTTGGCAAG                         GTTGTTGTGTGCATTGATCCGTCATACAGTCAGACCCTTGCTAAGCTATAG
genomic: CTGCGCCTGATGCGGTAGAATATCTTCATTCTGGCAAGAGTGTTGGCAAGgtaccatcgc ... acctttccagGTTGTTGTGTGCATTGATCCGTCATACAGTCAGACCCTTGCTAAGCTATAG
EST: gi|86885914|gb|CI319762.1|CI319762
EST:     CTGCGCCTGATGCGGTAGAATATCTTCATTCTGGCAAGAGTGTTGGCAAG                         GTTGTTGTGTGCATTGATCCCTCATACAGTCAGACCCTTGCTAAGCTATAG
genomic: CTGCGCCTGATGCGGTAGAATATCTTCATTCTGGCAAGAGTGTTGGCAAGgtaccatcgc ... acctttccagGTTGTTGTGTGCATTGATCCGTCATACAGTCAGACCCTTGCTAAGCTATAG
EST: gi|88254018|gb|CI352644.1|CI352644
EST:     CTGCGCCTGATGCGGTAGAATATCTTCATTCTGGCAAGAGTGTTGGCAAG                         GTTGTTGTGTGCATTGATCCGTCATACAGTCAGACCCTTGCTAAGCTATAG
genomic: CTGCGCCTGATGCGGTAGAATATCTTCATTCTGGCAAGAGTGTTGGCAAGgtaccatcgc ... acctttccagGTTGTTGTGTGCATTGATCCGTCATACAGTCAGACCCTTGCTAAGCTATAG
EST: gi|86416489|gb|CI030500.1|CI030500
EST:     CTGCGCCTGATGCGGTAGAATATCTTCATTCTGGCAAGAGTGTTGGCAAG                         GTTGTTGTGTGCATTGATCCGTCATACAGTCAGACCCTTGCTAAGCTATAG
genomic: CTGCGCCTGATGCGGTAGAATATCTTCATTCTGGCAAGAGTGTTGGCAAGgtaccatcgc ... acctttccagGTTGTTGTGTGCATTGATCCGTCATACAGTCAGACCCTTGCTAAGCTATAG
EST: gi|13165263|gb|AU174060.1|AU174060
EST:     CTGCGCCTGATGCGGTAGAATATCTTCATTCTGGCAAGAGTGTTGGCAAG                         GTTGTTGTGTGCATTGATCCGTCATACAGTCAGACCCTTGCTAAGCTATAG
genomic: CTGCGCCTGATGCGGTAGAATATCTTCATTCTGGCAAGAGTGTTGGCAAGgtaccatcgc ... acctttccagGTTGTTGTGTGCATTGATCCGTCATACAGTCAGACCCTTGCTAAGCTATAG
EST: gi|88254109|gb|CI352735.1|CI352735
EST:     CTGCGCCTGATGCGGTAGAATATCTTCATTCTGGCAAGAGTGTTGGCAAG                         GTTGTTGTGTGCATTGATCCGTCATACAGTCAGACCCTTGCTAAGCTATAG
genomic: CTGCGCCTGATGCGGTAGAATATCTTCATTCTGGCAAGAGTGTTGGCAAGgtaccatcgc ... acctttccagGTTGTTGTGTGCATTGATCCGTCATACAGTCAGACCCTTGCTAAGCTATAG
EST: gi|86837438|gb|CI345680.1|CI345680
EST:     CTGCGCCTGATGCGGTAGAATATCTTCATTCTGGCAAGAGTGTTGGCAAG                         GTTGTTGTGTGCATTGATCCGTCATACAGTCAGACCCTTGCTAAGCTATAG
genomic: CTGCGCCTGATGCGGTAGAATATCTTCATTCTGGCAAGAGTGTTGGCAAGgtaccatcgc ... acctttccagGTTGTTGTGTGCATTGATCCGTCATACAGTCAGACCCTTGCTAAGCTATAG
EST: gi|66913912|gb|CX100760.1|CX100760
EST:     CTGCGCCTGATGCGGTAGAATATCTTCATTCTGGCAAGAGTGTTGGCAAG                         GTTGTTGTGTGCATTGATCCGTCATACAGTCAGACCCTTGCTAAGCTATAG
genomic: CTGCGCCTGATGCGGTAGAATATCTTCATTCTGGCAAGAGTGTTGGCAAGgtaccatcgc ... acctttccagGTTGTTGTGTGCATTGATCCGTCATACAGTCAGACCCTTGCTAAGCTATAG
EST: gi|88383425|gb|CI540838.1|CI540838
EST:     CTGCGCCTGATGCGGTAGAATATCTTCATTCTGGCAAGAGTGTTGGCAAG                         GTTGTTGTGTGCATTGATCCGTCATACAGTCAGACCCTTGCTAAGCTATAG
genomic: CTGCGCCTGATGCGGTAGAATATCTTCATTCTGGCAAGAGTGTTGGCAAGgtaccatcgc ... acctttccagGTTGTTGTGTGCATTGATCCGTCATACAGTCAGACCCTTGCTAAGCTATAG
EST: gi|33800750|gb|CF326245.1|CF326245
EST:     CTGCGCCTGATGCGGTAGAATATCTTCATTCTGGCAAGAGTGTTGGCAAG                         GTTGTTGTGTGCATTGATCCGTCATACAGTCAGACCCTTGCTAAGCTATAG
genomic: CTGCGCCTGATGCGGTAGAATATCTTCATTCTGGCAAGAGTGTTGGCAAGgtaccatcgc ... acctttccagGTTGTTGTGTGCATTGATCCGTCATACAGTCAGACCCTTGCTAAGCTATAG
EST: gi|29675620|gb|CB671895.1|CB671895
EST:     CTGCGCCTGATGCGGTAGAATATCTTCATTCTGGCAAGAGTGTTGGCAAG                         GTTGTTGTGTGCATTGATCCGTCATACAGTCAGACCCTTGCTAAGCTATAG
genomic: CTGCGCCTGATGCGGTAGAATATCTTCATTCTGGCAAGAGTGTTGGCAAGgtaccatcgc ... acctttccagGTTGTTGTGTGCATTGATCCGTCATACAGTCAGACCCTTGCTAAGCTATAG
EST: gi|88289413|gb|CI555775.1|CI555775
EST:     CTGCGCCTGATGCGGTAGAATATCTTCATTCTGGCAAGAGTGTTGGCAAG                         GTTGTTGTGTGCATTGATCCGTCATACAGTCAGACCCTTGCTAAGCTATAG
genomic: CTGCGCCTGATGCGGTAGAATATCTTCATTCTGGCAAGAGTGTTGGCAAGgtaccatcgc ... acctttccagGTTGTTGTGTGCATTGATCCGTCATACAGTCAGACCCTTGCTAAGCTATAG
EST: gi|87009274|gb|CI313747.1|CI313747
EST:     TGCGCCTGATGCGGTAGAATATCTTCATTCTGCCAAGAGTGTTGGCCAAG                         GTTGTTGTGTGCATTGATCCGTCATACAGTCAGACCCTTGCTAAGCTATA
genomic: TGCGCCTGATGCGGTAGAATATCTTCATTCTGGCAAGAGTGTTGG-CAAGgtaccatcgc ... acctttccagGTTGTTGTGTGCATTGATCCGTCATACAGTCAGACCCTTGCTAAGCTATA
EST: gi|88411630|gb|CI521353.1|CI521353
EST:     CTGCGCCTGATGCGGTAGAATATCTTCATTCTGGCAAGAGTGTTGGCAAG                         GTTGTTGTGTGCATTGATCCGTCATACAGTCAGACCCTTGCTAAGCTATAG
genomic: CTGCGCCTGATGCGGTAGAATATCTTCATTCTGGCAAGAGTGTTGGCAAGgtaccatcgc ... acctttccagGTTGTTGTGTGCATTGATCCGTCATACAGTCAGACCCTTGCTAAGCTATAG
EST: gi|88265497|gb|CI376399.1|CI376399
EST:     CTGCGCCTGATGCGGTAGAATATCTTCATTCTGGCAAGAGTGTTGGCAAG                         GTTGTTGTGTGCATTGATCCGTCATACAGTCAGACCCTTGCTAAGCTATAG
genomic: CTGCGCCTGATGCGGTAGAATATCTTCATTCTGGCAAGAGTGTTGGCAAGgtaccatcgc ... acctttccagGTTGTTGTGTGCATTGATCCGTCATACAGTCAGACCCTTGCTAAGCTATAG

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: 75 (upstream exon), 61 (downstream exon)
Score: 23

GTTTCCCTTGACCCGAAGAAATTCGTGGGTGTAGCTTCTGCGCCTGATGCGGTAGAATATCTTCATTCTGGCAAGAGTGTTGGCAAGgtaccatcgc ... acctttccagGTTGTTGTGTGCATTGATCCGTCATACAGTCAGACCCTTGCTAAGCTATAGTCTGTGGACATGAGATACATCATATTTCATCGTCTAGTCACGAGGAAGA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTTCCCTTGACCCGAAGAAATTCGTGGGTGTAGCTTCTGCGCCTGATGCGGTAGAATATCTTCATTCTGGCAAGAGTGTTGGCAAGgtaccatcgcttatatgatgaaatatgattctgttcttatcttctcaaatgtgacttaatagatttttcttctggaacctttccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA