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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtttggataatggaatttttggagtagttctttctgtttgggagttcacttggtgattaacttgatcataattccatgcagTGACATGAGCCAAAATAATCTTGGGGGTGGCCAAAATATTCAATACAATCTTCCAAATAAGAAGCTTGAGAGGCT

Basic information

species Oryza sativa
transcript LOC_Os10g25090.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g25090.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G004572_T01 (Zea mays), 3'ss of exon 3
gtgagtttggataatggaatttt--tggagtagttctttctgtttgggagttcacttggt----gattaacttgatcataattccatgcagTGACATGAGCCAAAATAATCTTGGGGGTGGCCAAAATATTCAATACAATCTTCCAAATAAGAAGCTTGAGAGGCT
||||| ||   | |||    | |  || |||  |  |   ||| ||| ||||    | ||    || ||  ||||||| |||    ||||| ||||||||||| || ||||| || ||||||||| | |||| ||||||||||||||||||||||||||| || ||
gtgagcttcatttatgtctctctcttgcagtgctgttccgtgtctggcagttttactagtttctgactaggttgatcacaatctattgcagAGACATGAGCCACAACAATCTCGGTGGTGGCCAACAGATTCCATACAATCTTCCAAATAAGAAGCTTGAAAGACT
















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|88369294|gb|CI577757.1|CI577757
EST:     TCGGGGAATCTGGCCTACAATATGAACACCATGGAGTCCCTAGTTGAGCT                         TGACATGAGCCAAAATAATCTTGGGGGTGGCCAAAATATTCAATACAATCT
genomic: TCGGGGAATCTGGCCTACAATATGAACACCATGGAGTCCCTAGTTGAGCTgtgagtttgg ... ttccatgcagTGACATGAGCCAAAATAATCTTGGGGGTGGCCAAAATATTCAATACAATCT
EST: gi|88311529|gb|CI572585.1|CI572585
EST:     TCGGGGAATCTGGCCTACAATATGAACACCATGGAGTCCCTAGTTGAGCT                         TGACATGAGCCAAAATAATCTTGGGGGTGGGCAAAATATTCAATACAATCT
genomic: TCGGGGAATCTGGCCTACAATATGAACACCATGGAGTCCCTAGTTGAGCTgtgagtttgg ... ttccatgcagTGACATGAGCCAAAATAATCTTGGGGGTGGCCAAAATATTCAATACAATCT
EST: gi|86888413|gb|CI303695.1|CI303695
EST:     TCGGGGAATCTGGCCTACAATATGAACACCATGGAGTCCCTAGTTGAGCT                         TGACATGAGCCAAA
genomic: TCGGGGAATCTGGCCTACAATATGAACACCATGGAGTCCCTAGTTGAGCTgtgagtttgg ... ttccatgcagTGACATGAGCCAAA
EST: gi|88449338|gb|CI582210.1|CI582210
EST:     TCGGGGAATCTGGCCTACAATATGAACACCATGGAGTCCCTAGTTGAGCT                         TGACATGAGCCAAAATAATCTTGGGGGTGGCCAAAATATTCAATACAATCT
genomic: TCGGGGAATCTGGCCTACAATATGAACACCATGGAGTCCCTAGTTGAGCTgtgagtttgg ... ttccatgcagTGACATGAGCCAAAATAATCTTGGGGGTGGCCAAAATATTCAATACAATCT
EST: gi|88730221|gb|CI753836.1|CI753836
EST:     TCGGGGAATCTGGCCTACAATATGAACACCATGGAGTCCCTAGTTGAGCT                         TGACATGAGCCAAAATAATCTTGGGGGTGGCCAAAATATTCAATACAATCT
genomic: TCGGGGAATCTGGCCTACAATATGAACACCATGGAGTCCCTAGTTGAGCTgtgagtttgg ... ttccatgcagTGACATGAGCCAAAATAATCTTGGGGGTGGCCAAAATATTCAATACAATCT
EST: gi|88385785|gb|CI566647.1|CI566647
EST:     TCGGGGAATCTGGCCTACAATATGAACACCATGGAGTCCCTAGTTGAGTT                         TGACATGAGCCAAAATAATCTTGGGGGTGGCCAAAATATT-AATACAATCT
genomic: TCGGGGAATCTGGCCTACAATATGAACACCATGGAGTCCCTAGTTGAGCTgtgagtttgg ... ttccatgcagTGACATGAGCCAAAATAATCTTGGGGGTGGCCAAAATATTCAATACAATCT
EST: gi|88406193|gb|CI593973.1|CI593973
EST:     TCGGGGAATCTGGCCTACAATATGAACACCATGGAGTCCCTAGTTGAGCT                         TGACATGAGCCAAAATAATCTTGGGGGTGGCCAAAATATTCAATACAATCT
genomic: TCGGGGAATCTGGCCTACAATATGAACACCATGGAGTCCCTAGTTGAGCTgtgagtttgg ... ttccatgcagTGACATGAGCCAAAATAATCTTGGGGGTGGCCAAAATATTCAATACAATCT
EST: gi|6507597|gb|AU064258.2|AU064258
EST:     TCGGGGAATCTGGCCTACAATATGAACACCATGGAGTCCCTAGTTGAGCT                         TGACATGAGCCAAAATAATCTTGGGGGTGGCCAAAATATTCAATACAATCT
genomic: TCGGGGAATCTGGCCTACAATATGAACACCATGGAGTCCCTAGTTGAGCTgtgagtttgg ... ttccatgcagTGACATGAGCCAAAATAATCTTGGGGGTGGCCAAAATATTCAATACAATCT
EST: gi|88298922|gb|CI567925.1|CI567925
EST:     TCGGGGAATCTGGCCTACAATATGAACACCATGGAGTCCCTAGTTGAGCT                         TGACATGAGCCAAAATAATCTTGGGGGTGGCCAAAATATTCAATACAATCT
genomic: TCGGGGAATCTGGCCTACAATATGAACACCATGGAGTCCCTAGTTGAGCTgtgagtttgg ... ttccatgcagTGACATGAGCCAAAATAATCTTGGGGGTGGCCAAAATATTCAATACAATCT
EST: gi|88720186|gb|CI743485.1|CI743485
EST:     CCGGGGAATCTGGCCTACAATATGAA-ACCATGGAGTCCCTAGTTGAGCT                         TGACATGAGCCAAAATAATCTTGGGG-TGGCCACAATATTCAATACAATCT
genomic: TCGGGGAATCTGGCCTACAATATGAACACCATGGAGTCCCTAGTTGAGCTgtgagtttgg ... ttccatgcagTGACATGAGCCAAAATAATCTTGGGGGTGGCCAAAATATTCAATACAATCT
EST: gi|88298740|gb|CI565937.1|CI565937
EST:     TCGGGGAATCTGGCCTAAAATATGAACACCATGGAGTCCCTAGTTGAGCT                         TGACATGAGCCAAAATAATCTTGGGGGTGGCCAAAATATTCAATACAATCT
genomic: TCGGGGAATCTGGCCTACAATATGAACACCATGGAGTCCCTAGTTGAGCTgtgagtttgg ... ttccatgcagTGACATGAGCCAAAATAATCTTGGGGGTGGCCAAAATATTCAATACAATCT
EST: gi|88371283|gb|CI600131.1|CI600131
EST:     TCGGGGAATCTGGCCTACAATATGAACACCATGGAGTCCCTAGTTGAGCT                         TGACATGAGCCAAAATAATCTTGGGGGTGGCCAAAATATTCAATACAATCT
genomic: TCGGGGAATCTGGCCTACAATATGAACACCATGGAGTCCCTAGTTGAGCTgtgagtttgg ... ttccatgcagTGACATGAGCCAAAATAATCTTGGGGGTGGCCAAAATATTCAATACAATCT
EST: gi|88314468|gb|CI604952.1|CI604952
EST:     TCGGGGAATCTGGCCTACAATATGAACACCATGGAGTCCCTAGTTGAGCT                         TGACATGAGCCAAAATAATCTTGGGGGTGGCCAAAATATTCAATACAATCT
genomic: TCGGGGAATCTGGCCTACAATATGAACACCATGGAGTCCCTAGTTGAGCTgtgagtttgg ... ttccatgcagTGACATGAGCCAAAATAATCTTGGGGGTGGCCAAAATATTCAATACAATCT
EST: gi|88422824|gb|CI573986.1|CI573986
EST:     TCGGGGAATCTGGCCTACAATATGAACACCATGGAGTCCCTAGTTGAGCT                         TGACATGAGCCAAAATAATCTTGGGGGTGGCCAAAATATTCAATACAATCT
genomic: TCGGGGAATCTGGCCTACAATATGAACACCATGGAGTCCCTAGTTGAGCTgtgagtttgg ... ttccatgcagTGACATGAGCCAAAATAATCTTGGGGGTGGCCAAAATATTCAATACAATCT
EST: gi|88428401|gb|CI564869.1|CI564869
EST:     TCGGGGAATCTGGCCTACAATATGAACACCATGGAGTCCCTAGTTGAGCT                         TGACATGAGCCAAAATAATCTTGGGGGTGGCCAAAATATTCAATACAATCT
genomic: TCGGGGAATCTGGCCTACAATATGAACACCATGGAGTCCCTAGTTGAGCTgtgagtttgg ... ttccatgcagTGACATGAGCCAAAATAATCTTGGGGGTGGCCAAAATATTCAATACAATCT
EST: gi|88392563|gb|CI625385.1|CI625385
EST:     TCGGGGAATCTGGCCTACAATATGAACACCATGGAGTCCCTAGTTGAGCT                         TGACATGAGCCAAAATAATCTTGGGGGTGGCCAAAATATTCAATACAATCT
genomic: TCGGGGAATCTGGCCTACAATATGAACACCATGGAGTCCCTAGTTGAGCTgtgagtttgg ... ttccatgcagTGACATGAGCCAAAATAATCTTGGGGGTGGCCAAAATATTCAATACAATCT
EST: gi|88721915|gb|CI743427.1|CI743427
EST:     TCGGGGAATCTGGCCTACAATATGAACACCATGGAGTCCCTAGTTGAGCT                         TGACATGAGCCAAAATAATCTTGGGGGTGGCCAAAATATTCAATACAATCT
genomic: TCGGGGAATCTGGCCTACAATATGAACACCATGGAGTCCCTAGTTGAGCTgtgagtttgg ... ttccatgcagTGACATGAGCCAAAATAATCTTGGGGGTGGCCAAAATATTCAATACAATCT
EST: gi|88425544|gb|CI569268.1|CI569268
EST:     TCGGGGAATCTGGCCTACAATATGAACACCATGGAGTCCCTAGTTGAGCT                         TGACATGAGCCAAAATAATCTTGGGGGTGGCCAAAATATTCAATACAATCT
genomic: TCGGGGAATCTGGCCTACAATATGAACACCATGGAGTCCCTAGTTGAGCTgtgagtttgg ... ttccatgcagTGACATGAGCCAAAATAATCTTGGGGGTGGCCAAAATATTCAATACAATCT
EST: gi|88395348|gb|CI611265.1|CI611265
EST:     TCGGGGAATCTGGCCTACAATATGAACACCATGGAGTCCCTACTTGAGCT                         TGACATGAGCCAAAATAATCTTGGGGGTGGCCAAAATATTCAATACAATCT
genomic: TCGGGGAATCTGGCCTACAATATGAACACCATGGAGTCCCTAGTTGAGCTgtgagtttgg ... ttccatgcagTGACATGAGCCAAAATAATCTTGGGGGTGGCCAAAATATTCAATACAATCT
EST: gi|88385459|gb|CI564119.1|CI564119
EST:     TCGGGGAATCTGGCCTACAATATGAACACCATGGAGTCCCTAGTTGAGCT                         TGACATGAGCCAAAATAATCTTGGGGGTGGCCAAAATATTCAATACAATCT
genomic: TCGGGGAATCTGGCCTACAATATGAACACCATGGAGTCCCTAGTTGAGCTgtgagtttgg ... ttccatgcagTGACATGAGCCAAAATAATCTTGGGGGTGGCCAAAATATTCAATACAATCT
EST: gi|88402885|gb|CI613333.1|CI613333
EST:     TCGGGGAATCTGGCCTACAATATGAACACCATGGAGTCCCTAGTTGAGCT                         TGACATGAGCCAAAATAATCTTGGGGGTGGC-AAAATATTCAATACAATCT
genomic: TCGGGGAATCTGGCCTACAATATGAACACCATGGAGTCCCTAGTTGAGCTgtgagtttgg ... ttccatgcagTGACATGAGCCAAAATAATCTTGGGGGTGGCCAAAATATTCAATACAATCT
EST: gi|88368294|gb|CI577565.1|CI577565
EST:     TCGGGGAATCTGGCCTACAATATGAACACCATGGAGTCCCTAGTTGAGCT                         TGACATGAGCCAAAATAATCTTGGGGGTGGCCAAAATATTCAATACAATCT
genomic: TCGGGGAATCTGGCCTACAATATGAACACCATGGAGTCCCTAGTTGAGCTgtgagtttgg ... ttccatgcagTGACATGAGCCAAAATAATCTTGGGGGTGGCCAAAATATTCAATACAATCT
EST: gi|88300565|gb|CI587369.1|CI587369
EST:     TCGGGGAATCTGGCCTACAATATGAACACCATGGAGTCCCTAGTTGAGCT                         TGACATGAGCCAAAATAATCTTGGGGGTGGCCAAAATATTCAATACAATCT
genomic: TCGGGGAATCTGGCCTACAATATGAACACCATGGAGTCCCTAGTTGAGCTgtgagtttgg ... ttccatgcagTGACATGAGCCAAAATAATCTTGGGGGTGGCCAAAATATTCAATACAATCT
EST: gi|88401962|gb|CI593674.1|CI593674
EST:     TCGGGGAATTTGGCCTACAATATTAACACCATGGAGTGCCTAGTTGAGCT                         TGACATGAGCCAAAATAATCTTGGGGGTGGCCAAAATATTCAATACAATCT
genomic: TCGGGGAATCTGGCCTACAATATGAACACCATGGAGTCCCTAGTTGAGCTgtgagtttgg ... ttccatgcagTGACATGAGCCAAAATAATCTTGGGGGTGGCCAAAATATTCAATACAATCT
EST: gi|88405784|gb|CI609683.1|CI609683
EST:     TCGGGGAATCTGGCCTACAATATGAACACCATGGAGTCCCTAGTTGAGCT                         TGACATGAGCCAAAATAATCTTGGGGGTGGCCAAAATATTCAATACAATCT
genomic: TCGGGGAATCTGGCCTACAATATGAACACCATGGAGTCCCTAGTTGAGCTgtgagtttgg ... ttccatgcagTGACATGAGCCAAAATAATCTTGGGGGTGGCCAAAATATTCAATACAATCT
EST: gi|29631005|gb|CB636014.1|CB636014
EST:     TCGGGGAATCTGGCCTACAATATGAACACCATGGAGTCCCTAGTTGAGCT                         TGACATGAGCCAAAATAATCTTGGGGGTGGCCAAAATATTCAATACAATCT
genomic: TCGGGGAATCTGGCCTACAATATGAACACCATGGAGTCCCTAGTTGAGCTgtgagtttgg ... ttccatgcagTGACATGAGCCAAAATAATCTTGGGGGTGGCCAAAATATTCAATACAATCT
EST: gi|88430712|gb|CI596826.1|CI596826
EST:     TCGGGGAATCTGGCCTACAATATGAACACCATGGAGTCCCTAGTTGAGCT                         TGACATGAGCCAAAATAATCTTGGGGGTGGCCAAAATATTCAATACAATCT
genomic: TCGGGGAATCTGGCCTACAATATGAACACCATGGAGTCCCTAGTTGAGCTgtgagtttgg ... ttccatgcagTGACATGAGCCAAAATAATCTTGGGGGTGGCCAAAATATTCAATACAATCT
EST: gi|88412193|gb|CI573469.1|CI573469
EST:     TCGGGGAATCTGGCCTACAATATGAACACCATGGAGTCCCTAGTTGAGCT                         TGACATGAGCCAAAATAATCTTGGGGGTGGCCAAAATATTCAATACAATCT
genomic: TCGGGGAATCTGGCCTACAATATGAACACCATGGAGTCCCTAGTTGAGCTgtgagtttgg ... ttccatgcagTGACATGAGCCAAAATAATCTTGGGGGTGGCCAAAATATTCAATACAATCT
EST: gi|88415116|gb|CI583939.1|CI583939
EST:     TCGGGGAATCTGGCCTACAATATGAACACCATGGAGTCCCTAGTTGAGCT                         TGACATGAGCCAAAATAATCTTGGGGGTGGCCAAAATATTCAATACAATCT
genomic: TCGGGGAATCTGGCCTACAATATGAACACCATGGAGTCCCTAGTTGAGCTgtgagtttgg ... ttccatgcagTGACATGAGCCAAAATAATCTTGGGGGTGGCCAAAATATTCAATACAATCT
EST: gi|88396144|gb|CI595692.1|CI595692
EST:     TCGGGGAATCTGGCCTACAATATGAACACCATGGAGTCCCTAGTTGAGCT                         TGACATGAGCCAAAATAATCTTGGGGGTGGCCAAAATATTCAATACAATCT
genomic: TCGGGGAATCTGGCCTACAATATGAACACCATGGAGTCCCTAGTTGAGCTgtgagtttgg ... ttccatgcagTGACATGAGCCAAAATAATCTTGGGGGTGGCCAAAATATTCAATACAATCT
EST: gi|88426869|gb|CI584232.1|CI584232
EST:     TCGGGGAATCTGGCCTGCAATATGAACACCATGGAGTCCCTAGTTGAGCT                         TGACATGAGCCAAAATAATCTTGGGGGTGGCCAAAATATCCAATACAACCT
genomic: TCGGGGAATCTGGCCTACAATATGAACACCATGGAGTCCCTAGTTGAGCTgtgagtttgg ... ttccatgcagTGACATGAGCCAAAATAATCTTGGGGGTGGCCAAAATATTCAATACAATCT
EST: gi|88314779|gb|CI608238.1|CI608238
EST:     TCGGGGAATCTGGCCTACAATATGAACACCATGGAGTCCCTAGTTGAGCT                         TGACATGAGCCAAAATAATCTTGGGGGTGGC-AAAATATTCAATACAATCT
genomic: TCGGGGAATCTGGCCTACAATATGAACACCATGGAGTCCCTAGTTGAGCTgtgagtttgg ... ttccatgcagTGACATGAGCCAAAATAATCTTGGGGGTGGCCAAAATATTCAATACAATCT

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), 68 (downstream exon)
Score: 20

TAAATTGCCGAGCTTGGGGCTTTCGGGGAATCTGGCCTACAATATGAACACCATGGAGTCCCTAGTTGAGCTgtgagtttgg ... ttccatgcagTGACATGAGCCAAAATAATCTTGGGGGTGGCCAAAATATTCAATACAATCTTCCAAATAAGAAGCTTGAGAGGCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttctttctgtttgggagttcacttggtgattaacttgatcataattccatgcagTGACATGAGCCAAAATAATCTTGGGGGTGGCCAAAATATTCAATACAATCTTCCAAATAAGAAGCTTGAGAGGCT
                                      atcataatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtttggataatggaatttttggagtagttctttctgtttgggagttcacttggtgattaacttgatcataattccatgcagTGACATGAGCCAAAATAATCTTGGGGGTGGCCAAAATATTCAATACAATCTTCCAAATAAGAAGCTTGAGAGGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG