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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgcattcctcgctttaaatttctggttacatggttttaatatatcaaccttctactagcagtgatcaaataagtctagaatttcattttactcaatatcaacgatatgtttaatgtacctttgtaaagtttgaactccatgatttaacgttcgattgtttggaattgctttcagGTTGTCTATGAGCATCATCCTCGACCAAAGCAGCTCATAGTTGAGAATGATCTTCCTCAAAAGCTACAAAACCTGATCGAAGAACGAAGGGATGGGCAAC

Basic information

species Oryza sativa
transcript LOC_Os04g56530.1
intron # 23
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g56530.1 (Oryza sativa), 3'ss of exon 23
lower sequence: GRMZM2G017654_T01 (Zea mays), 3'ss of exon 23
gtttgcattcctcgctttaaatttctggttacatggttttaatatatcaaccttctactagcagtgatcaaataagtctagaatttcattttac--tcaatatcaacgatatgtttaatgtacctttgtaaagtttgaactccatgatttaacgttcgattgtttggaattgctttcagGTTGTCTATGAGCATCATCCTCGACCAAAGCAGCTCATAGTTGAGAATGATCTTCCTCAAAAGCTACAAAACCTGATCGAAGAACGAAGGGATGGGCAAC
                                                                |       |     |||   ||      ||  ||| | | |  || ||  ||   |||  |||||| ||| | ||||   || ||||              | | ||  || ||||||||||||||||| |||||||||||||| ||||||||||| |||||||| || ||||| |||||||| ||||| || ||||| || |||||||| ||||
--------------------------------------------------------------gtttgatgcctggccttagctgttagccggacgctcactgtgagtgaaataattctggtag-tttgtagagtctaaactttgtggttta-------------cgtatttttttccagGTTGTCTATGAGCACCATCCTCGACCAAAACAGCTCATAGTAGAGAATGACCTCCCTCAGAAGCTACAGAACCTCATTGAAGAGCGCAGGGATGGACAAC

upper sequence: LOC_Os04g56530.1 (Oryza sativa), 3'ss of exon 23
lower sequence: GRMZM2G084586_T01 (Zea mays), 3'ss of exon 9
gtttgcattcctcgctttaaatttctggttacatggttttaatatatcaaccttctactagcagtgatcaaataagtctagaatttcattttactcaatatcaacgatatgtttaatgtacctttgtaaagtttgaactccatgatttaacgttcgattgtttggaattgctttcagGTTGTCTATGAGCATCATCCTCGACCAAAGCAGCTCATAGTTGAGAATGATCTTCCTCAAAAGCTACAAAACCTGATCGAAGAACGAAGGGATGGGCAAC
                                                    | || |      | | |   ||   ||  | ||| |     |||| | | |  || ||| ||   |||  |||||| ||| | ||       ||||         ||||||  |  | ||| |||||||||||||||||||||||||||||||| ||| ||||||| |||||||| || ||||| ||||||||||||||||| |||||||| |||| ||| ||||
-------------------------------------------------gtttgctgcctagccttagctgttagtcctgaagttttaggacgctcactgtgattgaaatgattctagtag-tttgtagagtctcaa-------attt--------gttgtttacatattcttccagGTTGTCTATGAGCATCATCCTCGACCAAAACAGGTCATAGTAGAGAATGACCTCCCTCAGAAGCTACAAAACCTGATTGAAGAACGCAGGGGTGGACAAC

upper sequence: LOC_Os04g56530.1 (Oryza sativa), 3'ss of exon 23
lower sequence: Vv01s0011g02270.t01 (Vitis vinifera), 3'ss of exon 23
gtttgcattcctcgctttaaatttctggttacatggttttaatatatcaaccttctactagcagtgatcaaataagtctagaatttcattttactcaatatcaacgatatgtttaatgtacctttgtaaagtttgaactccatgatttaacgttcgattgtttggaattgctttcagGTTGTCTATGAGCATCATCCTCGACCAAAGCAGCTCATAGTTGAGAATGATCTTCCTCAAAAGCTACAAAACCTGATCGAAGAACGAAGGGATGGGCAAC
                                                                         |  || | |     ||| | || || ||      | | | | | | |   || |  |||||     ||| |||||    |   |    |||    |     |||  ||| |||||||| ||||| || |||||||| || || || ||||||||||| ||||| ||||| || || ||||| || || || || ||||||||||
------------------------------------------------------------------------aagttccacagaaatattcttctgaacattc----tgtttctta-gcattattattgagttttgtagccaggatttgtattaaaagctattgtttgtatcggcagTCTGTTTATGAGCACCATCCACGGCCAAAGCAACTGATCGTGGAGAATGATCTGCCTCAGAAGCTTCAGAATCTGATTGAGGAGCGCAGAGATGGGCAAC

upper sequence: LOC_Os04g56530.1 (Oryza sativa), 3'ss of exon 23
lower sequence: PP1S99_12V6.1 (Physcomitrella patens), 3'ss of exon 26
gtttgcattcctcgctttaaatttctggttacatggttttaatatatcaaccttctactagcagtgatcaaataagtctagaatttcattttactcaatatcaacgatatgtttaatgtacctttgtaaagtttgaactccatgatttaacgttcgattgtttggaattgctttcagGTTGTCTATGAGCATCATCCTCGACCAAAGCAGCTCATAGTTGAGAATGATCTTCCTCAAAAGCTACAAAACCTGATCGAAGAACGAAGGGATGGGCAAC
                                                        |||  || |||  || ||   | || | |  | |||      ||  |  || || |  ||   ||  | | |  ||     || | |||      |   ||  || |       ||| |||||||| ||||||||||| || || ||||||||||||||||  ||| | ||  | ||    | ||||||||| || ||||||||| || | |||||| | |
--------------------------------------------------------act--caatga--aagtattacgaggaatggagtttt-----taggactgaaatttggaaaccacactggcactgtagtcgctacctga------ggctgaacgtgtt------cttgcagGTTGTTTATGAGCATCACCCGCGTCCAAAGCAGCTCATAGCGGAGCACGACTTGCCATCCAGGCTACAAAAGCTCATCGAAGAAAGACGTGATGGGGAGC

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|66928095|gb|CX114943.1|CX114943
EST:     TTGACCACCGAGAAGCTATTGCCCGTTTGACACTGCTAAAATTAATAAAG                         GTTGTCTATGAGCATCATCCTCGACCAAAGCAGCTCATAGTTGAGAATGAT
genomic: TTGACCACCGAGAAGCTATTGCCCGTTTGACACTGCTAAAATTAATAAAGgtttgcattc ... ttgctttcagGTTGTCTATGAGCATCATCCTCGACCAAAGCAGCTCATAGTTGAGAATGAT
EST: gi|58686297|gb|CK074984.1|CK074984
EST:     TTGACCACCGAGAAGCTATTGCCCGTTTGACACTGCTAAAATTAATAAAG                         GTTGTCTATGAGCATCATCCTCGACCAAAGCAGCTCATAGTTGAGAATGAT
genomic: TTGACCACCGAGAAGCTATTGCCCGTTTGACACTGCTAAAATTAATAAAGgtttgcattc ... ttgctttcagGTTGTCTATGAGCATCATCCTCGACCAAAGCAGCTCATAGTTGAGAATGAT
EST: gi|29622113|gb|CB627124.1|CB627124
EST:     TTGACCACCGAGAAGCTATTGCCCGTTTGACACTGCTAAAATTAATAAAG                         GTTGTCTATGAGCATCATCCTCGACCAAAGCAGCTCATAGTTGAGAATGAT
genomic: TTGACCACCGAGAAGCTATTGCCCGTTTGACACTGCTAAAATTAATAAAGgtttgcattc ... ttgctttcagGTTGTCTATGAGCATCATCCTCGACCAAAGCAGCTCATAGTTGAGAATGAT
EST: gi|88976274|gb|CI024491.1|CI024491
EST:     TGCCCGTTTGACACTGCTAAAATTAATAAAG                         GTTGTCTATGAGCATCATCCTCGACCAAAGCAGCTCATAGTTGAGAATGAT
genomic: TGCCCGTTTGACACTGCTAAAATTAATAAAGgtttgcattc ... ttgctttcagGTTGTCTATGAGCATCATCCTCGACCAAAGCAGCTCATAGTTGAGAATGAT
EST: gi|117220975|gb|CT845486.1|CT845486
EST:     TTGACCACCGAGAAGCTATTGCCCGTTTGACACTGCTAAAATTAATAAAG                         GTTGTCTATGAGCATCATCCTCGACCAAAGCAGCTCATAGTTGAGAATGAT
genomic: TTGACCACCGAGAAGCTATTGCCCGTTTGACACTGCTAAAATTAATAAAGgtttgcattc ... ttgctttcagGTTGTCTATGAGCATCATCCTCGACCAAAGCAGCTCATAGTTGAGAATGAT
EST: gi|4714791|gb|AU055908.1|AU055908
EST:     TGACCACCGAGAAGCTATTGCCCGTTTGACACTGCTAAAATTAATAAAG                         GTTGTCTATGAGCATCATCCTCGACCAAAGCAGCTCATAGTTGAGAATGAT
genomic: TGACCACCGAGAAGCTATTGCCCGTTTGACACTGCTAAAATTAATAAAGgtttgcattc ... ttgctttcagGTTGTCTATGAGCATCATCCTCGACCAAAGCAGCTCATAGTTGAGAATGAT
EST: gi|86881828|gb|CI324110.1|CI324110
EST:     AAGCTA-TGCCCGGTTGACACGGCTAAAATTAATAAAG                         GTTGTCTATGAGCATCATCCTCGACCAAACCAGCTGATAGTTGAGAAT-AT
genomic: AAGCTATTGCCCGTTTGACACTGCTAAAATTAATAAAGgtttgcattc ... ttgctttcagGTTGTCTATGAGCATCATCCTCGACCAAAGCAGCTCATAGTTGAGAATGAT

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), 71 (downstream exon)
Score: 43

AAATACAGCAATGGCTACCAATGGTTTAACGACACTGCTTATTGCAAGGCTTGACCACCGAGAAGCTATTGCCCGTTTGACACTGCTAAAATTAATAAAGgtttgcattc ... ttgctttcagGTTGTCTATGAGCATCATCCTCGACCAAAGCAGCTCATAGTTGAGAATGATCTTCCTCAAAAGCTACAAAACCTGATCGAAGAACGAAGGGATGGGCAAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtaaagtttgaactccatgatttaacgttcgattgtttggaattgctttcagGTTGTCTATGAGCATCATCCTCGACCAAAGCAGCTCATAGTTGAGAATGATCTTCCTCAAAAGCTACAAAACCTGATCGAAGAACGAAGGGATGGGCAAC
                      atttaac  putative branch site (score: 43)
                                             ttgctttc  putative PPT
                   atgatttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgcattcctcgctttaaatttctggttacatggttttaatatatcaaccttctactagcagtgatcaaataagtctagaatttcattttactcaatatcaacgatatgtttaatgtacctttgtaaagtttgaactccatgatttaacgttcgattgtttggaattgctttcagGTTGTCTATGAGCATCATCCTCGACCAAAGCAGCTCATAGTTGAGAATGATCTTCCTCAAAAGCTACAAAACCTGATCGAAGAACGAAGGGATGGGCAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC