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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcctgatgatcgtattcttgtttgttgcaaaatcatatacatagtacatctacttatctgaactttgtatgattctttcttcagAGGTATGTTTAATAAAGAAAGAATTGCAAAGATGAAGAAAGGTGTAATCATTGTGAATAATGCTCGAGGAGCAATCATGGATACCCAGGCGGTTGCAGAC

Basic information

species Oryza sativa
transcript LOC_Os06g29180.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g29180.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G362021_T01 (Zea mays), 3'ss of exon 4
gttcctgatgatcgtattcttgtttgttgcaaaatcatatacatagtacatctacttatctgaactttgtatgat-tctttcttcagAGGTATGTTTAATAAAGAAAGAATTGCAAAGATGAAGAAAGGTGTAATCATTGTGAATAATGCTCGAGGAGCAATCATGGATACCCAGGCGGTTGCAGAC
|||  |  | ||| | | | ||    || ||||||  | |  | ||||       || |||||  ||||| || | | ||| |||||||| |||||||| ||||| || ||||||||||||||||||||||||||  |||||||||||||||||||||||||||||||| | |  || || ||||| 
gtttgtattcatcatgtacctgacatttccaaaatagtttg-acagta-------ttttctgagttttgtttgctgttttttttcagAGGCATGTTTAACAAAGAGAGGATTGCAAAGATGAAGAAAGGTGTAATTGTTGTGAATAATGCTCGAGGAGCAATCATGGATGCTCGAGCAGTCGCAGAT

upper sequence: LOC_Os06g29180.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G147714_T01 (Zea mays), 3'ss of exon 4
gttcctgatgatcgtattcttgtttgttgcaaaatcatatacatagtacatctacttatctgaactttgtatg--attctttcttcagAGGTATGTTTAATAAAGAAAGAATTGCAAAGATGAAGAAAGGTGTAATCATTGTGAATAATGCTCGAGGAGCAATCATGGATACCCAGGCGGTTGCAGAC
|||  |  | ||| | | | ||    || ||||||  | |  | ||||       || |||||  ||||| ||   || ||| |||||||| |||||||| ||||| || ||||||||||||||||||||||||||  |||||||||||||||||||||||||||||||| | |  || || ||||| 
gtttgtattcatcatgtacctgacatttccaaaatagtttg-acagta-------ttttctgagttttgtttgctgtttttttttcagAGGCATGTTTAACAAAGAGAGGATTGCAAAGATGAAGAAAGGTGTAATTGTTGTGAATAATGCTCGAGGAGCAATCATGGATGCTCGAGCAGTCGCAGAT

upper sequence: LOC_Os06g29180.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G418005_T01 (Zea mays), 3'ss of exon 2
gttcctgatgatcgtattcttgtttgttgcaaaatcatatacatagtacatctacttatctgaactttgtatgat-tctttcttcagAGGTATGTTTAATAAAGAAAGAATTGCAAAGATGAAGAAAGGTGTAATCATTGTGAATAATGCTCGAGGAGCAATCATGGATACCCAGGCGGTTGCAGAC
|||  |  | ||| | | | ||    || ||||||  | |  | ||||       || |||||  ||||| || | | ||| |||||||| |||||||| ||||| || ||||||||||||||||||||||||||  |||||||||||||||||||||||||||||||| | |  || || | ||| 
gtttgtattcatcatgtacctgacatttccaaaatagtttg-acagta-------ttttctgagttttgtttgctgttttttttcagAGGCATGTTTAACAAAGAGAGGATTGCAAAGATGAAGAAAGGTGTAATTGTTGTGAATAATGCTCGAGGAGCAATCATGGATGCTCGAGCAGTCGTAGAT

upper sequence: LOC_Os06g29180.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G049811_T01 (Zea mays), 3'ss of exon 3
gttcctgatgatcgtattcttgtttgttgcaaaatcatatacatagtacatctacttatctgaactttgtatg--attctttcttcagAGGTATGTTTAATAAAGAAAGAATTGCAAAGATGAAGAAAGGTGTAATCATTGTGAATAATGCTCGAGGAGCAATCATGGATACCCAGGCGGTTGCAGAC
|||  |  | ||| | | | ||    || ||||||  | |  | | ||       || |||||  ||||| ||   || ||| |||||||| |||||||| ||||| || ||||||||||||||||||||||||||  |||| ||||||||||||||||||||||||||| | || || || ||||| 
gtttgtattcatcatgtacctgacatttccaaaatagtttg-acaata-------ttttctgagttttgtttgctgtttttttttcagAGGCATGTTTAACAAAGAGAGGATTGCAAAGATGAAGAAAGGTGTAATTGTTGTAAATAATGCTCGAGGAGCAATCATGGATGCTCAAGCAGTCGCAGAT

upper sequence: LOC_Os06g29180.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G423972_T02 (Zea mays), 3'ss of exon 2
gttcctgatgatcgtattcttgtttgttgcaaaatcatatacatagtacatctacttatctgaactttgtatgat-tctttcttcagAGGTATGTTTAATAAAGAAAGAATTGCAAAGATGAAGAAAGGTGTAATCATTGTGAATAATGCTCGAGGAGCAATCATGGATACCCAGGCGGTTGCAGAC
|||  |  | | | | | | ||    || ||||||  | |  | ||||       || |||||  ||||| || | | ||| |||||||| |||||||| ||||| || ||||||||||||||| || |||||||  |||||||||||||||||||||||||||||||| | |  || || ||||| 
gtttgtattcaccatgtacctgacatttccaaaatagtctg-acagta-------ttttctgagttttgtttgctgttttttttcagAGGCATGTTTAACAAAGAGAGGATTGCAAAGATGAAGGAACGTGTAATTGTTGTGAATAATGCTCGAGGAGCAATCATGGATGCTCGAGCAGTCGCAGAT

upper sequence: LOC_Os06g29180.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv14s0066g01320.t01 (Vitis vinifera), 3'ss of exon 3
-------------------gttcctgatgatcgtattcttgtttgttgcaaaatcatatacatagtacatctacttatctgaactttgtatgattctttcttcagAGGTATGTTTAATAAAGAAAGAATTGCAAAGATGAAGAAAGGTGTAATCATTGTGAATAATGCTCGAGGAGCAATCATGGATACCCAGGCGGTTGCAGAC
                    | | |||   | | ||     ||   | ||||||        | | ||    | ||||| ||| ||||      |  |  |||||||| ||||| || ||||| || ||||||||| |||| || || ||  | ||||| || |||||||||||||||||||||||||| || || ||||| || 
gccccctttcatataccatttgcttgaatctagcatggcaattc--tacaaaatttgtgttgttgaaccctaaattatcagaattttg---atcttgtaattcagAGGAATGTTCAACAAAGAGAGGATTGCAAAGTTGAAAAAGGGAGTTCTAATTGTTAACAATGCTCGAGGAGCAATCATGGATACACAAGCTGTTGCCGAT

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|14575034|gb|AU197513.1|AU197513
EST:     CCAAAGTGTGATGTCATTGTGATCAATACACCTCTTACAGAGAAAACAAG                         AGGTATGTTTAATAAAGAAA
genomic: CCAAAGTGTGATGTCATTGTGATCAATACACCTCTTACAGAGAAAACAAGgttcctgatg ... ctttcttcagAGGTATGTTTAATAAAGAAA
EST: gi|29669367|gb|CB665642.1|CB665642
EST:     CCAAAGTGTGATGTCATTGTGATCAATACACCTCTTACAGAGAAAACAAG                         AGGTATGTTTAATAAAGAAAGAATTGCAAAGATGAAGAAAGGTGTAATCAT
genomic: CCAAAGTGTGATGTCATTGTGATCAATACACCTCTTACAGAGAAAACAAGgttcctgatg ... ctttcttcagAGGTATGTTTAATAAAGAAAGAATTGCAAAGATGAAGAAAGGTGTAATCAT
EST: gi|58661899|gb|CK050579.1|CK050579
EST:     CCAAAGTGTGATGTCATTGTGATCAATACACCTCTTACAGAGAAAACAAG                         AGGTATGTTTAATAAAGAAAGAATTGCAAAGATGAAGAAAGGTGTAATCAT
genomic: CCAAAGTGTGATGTCATTGTGATCAATACACCTCTTACAGAGAAAACAAGgttcctgatg ... ctttcttcagAGGTATGTTTAATAAAGAAAGAATTGCAAAGATGAAGAAAGGTGTAATCAT
EST: gi|86601912|gb|CI258588.1|CI258588
EST:     TCTTACAGAGAAAACAAG                         AGGTATGTTTAATAAAGAAAGAATTGCAAAGATGAAGAAAGGTGTAATCAT
genomic: TCTTACAGAGAAAACAAGgttcctgatg ... ctttcttcagAGGTATGTTTAATAAAGAAAGAATTGCAAAGATGAAGAAAGGTGTAATCAT
EST: gi|88432183|gb|CI563014.1|CI563014
EST:     CCAAAGTGTGATGTCATTGTGATCAATACACCTCTTACAGAGAAAACAAG                         AGGTATGTTTAATAAAGAAAGAATTGC
genomic: CCAAAGTGTGATGTCATTGTGATCAATACACCTCTTACAGAGAAAACAAGgttcctgatg ... ctttcttcagAGGTATGTTTAATAAAGAAAGAATTGC
EST: gi|29659276|gb|CB655551.1|CB655551
EST:     CCAAAGTGTGATGTCATTGTGATCAATACACCTCTTACAGAGAAAACAAG                         AGGTATGTTTAATAAAGAAAGAATTGCAAAGATGAAGAAAGGTGTAATCAT
genomic: CCAAAGTGTGATGTCATTGTGATCAATACACCTCTTACAGAGAAAACAAGgttcctgatg ... ctttcttcagAGGTATGTTTAATAAAGAAAGAATTGCAAAGATGAAGAAAGGTGTAATCAT
EST: gi|29646500|gb|CB651507.1|CB651507
EST:     CCAAAGTGTGATGTCATTGTGATCAATACACCTCTTACAGAGAAAACAAG                         AGGTATGTTTAATAAAGAAAGAATTGCAAAGATGAAGAAAGGTGTAATCAT
genomic: CCAAAGTGTGATGTCATTGTGATCAATACACCTCTTACAGAGAAAACAAGgttcctgatg ... ctttcttcagAGGTATGTTTAATAAAGAAAGAATTGCAAAGATGAAGAAAGGTGTAATCAT
EST: gi|427637|gb|D23770.1|D23770
EST:     CCAAAGTGTGATGTCATTGTGATCAATACACCTCTTACAGAGAAAACAAG                         AGGTATGTTTAATAAAGAAAGAATTGCAAAGATGAAGAAAGGTGTAATCAT
genomic: CCAAAGTGTGATGTCATTGTGATCAATACACCTCTTACAGAGAAAACAAGgttcctgatg ... ctttcttcagAGGTATGTTTAATAAAGAAAGAATTGCAAAGATGAAGAAAGGTGTAATCAT
EST: gi|29666820|gb|CB663095.1|CB663095
EST:     ATGTCATTGTGATCAATACACTTCTTACAGAGAAAACAAG                         AGGTATGTTTAATAAAGAAAGAATTGCAAAGATGAAGAAAGGTGTAATCAT
genomic: ATGTCATTGTGATCAATACACCTCTTACAGAGAAAACAAGgttcctgatg ... ctttcttcagAGGTATGTTTAATAAAGAAAGAATTGCAAAGATGAAGAAAGGTGTAATCAT
EST: gi|29662259|gb|CB658534.1|CB658534
EST:     CCAAAGTGTGATGTCATTGTGATCAATACACCTCTTACAGAGAAAACAAG                         AGGTATGTTTAATAAAGAAAGAATTGCAAAGATGAAGAAAGGTGTAATCAT
genomic: CCAAAGTGTGATGTCATTGTGATCAATACACCTCTTACAGAGAAAACAAGgttcctgatg ... ctttcttcagAGGTATGTTTAATAAAGAAAGAATTGCAAAGATGAAGAAAGGTGTAATCAT
EST: gi|11173099|gb|AU164612.1|AU164612
EST:     CAAAGTGTGATGTCATTGTGATCAATACACCTCTTACAGAGAAAANCAAG                         AGGTATGTTTAATAAAGAAAGAATTTGCAAAGATGAAGAAAGGTGTAATC
genomic: CAAAGTGTGATGTCATTGTGATCAATACACCTCTTACAGAGAAAA-CAAGgttcctgatg ... ctttcttcagAGGTATGTTTAATAAAGAAAGAA-TTGCAAAGATGAAGAAAGGTGTAATC
EST: gi|58696127|gb|CK084814.1|CK084814
EST:     TGTGATCAATACACCTCTTACAGAGAAAACAAG                         AGGTATGTTTAATAAAGAAAGAATTGCAAAGATGAAGAAAGGTGTAATCAT
genomic: TGTGATCAATACACCTCTTACAGAGAAAACAAGgttcctgatg ... ctttcttcagAGGTATGTTTAATAAAGAAAGAATTGCAAAGATGAAGAAAGGTGTAATCAT
EST: gi|2311656|gb|C27811.1|C27811
EST:     CCAAAGTGTGATGTCATTGTGATCAATACACCTCTTACAGAGAAAACAAG                         AGGTATGTTTAATAAAGAAAGAATTGCAAAGATGAAGAAAGGTGTAATCAT
genomic: CCAAAGTGTGATGTCATTGTGATCAATACACCTCTTACAGAGAAAACAAGgttcctgatg ... ctttcttcagAGGTATGTTTAATAAAGAAAGAATTGCAAAGATGAAGAAAGGTGTAATCAT
EST: gi|313079527|gb|HO213085.1|HO213085
EST:     CCAAAGTGTGATGTCATTGTGATCAATACACCTCTTACAGAGAAAACAAG                         AGGTATGTTTAATAAAGAAAGAATTGCAAAGATGAAGAAAGGTGTAATCAT
genomic: CCAAAGTGTGATGTCATTGTGATCAATACACCTCTTACAGAGAAAACAAGgttcctgatg ... ctttcttcagAGGTATGTTTAATAAAGAAAGAATTGCAAAGATGAAGAAAGGTGTAATCAT
EST: gi|86823497|gb|CI256438.1|CI256438
EST:     CCAAAGTGTGATGTCATTGTGATCAATACACCTCTTACAGAGAAAACAAG                         AGGTATGTTTAATAAAGAAAGAATTGCAAAGATGAAGAAAGGTGTAATCAT
genomic: CCAAAGTGTGATGTCATTGTGATCAATACACCTCTTACAGAGAAAACAAGgttcctgatg ... ctttcttcagAGGTATGTTTAATAAAGAAAGAATTGCAAAGATGAAGAAAGGTGTAATCAT
EST: gi|29658973|gb|CB655248.1|CB655248
EST:     CCAAAGTGTGATGTCATTGTGATCAATACACCTCTTACAGAGAAAACAAG                         AGGTATGTTTAATAAAGAAAGAATTGCAAAGATGAAGAAAGGTGTAATCAT
genomic: CCAAAGTGTGATGTCATTGTGATCAATACACCTCTTACAGAGAAAACAAGgttcctgatg ... ctttcttcagAGGTATGTTTAATAAAGAAAGAATTGCAAAGATGAAGAAAGGTGTAATCAT
EST: gi|29663026|gb|CB659301.1|CB659301
EST:     ATGTCATTGTGATCAATACACCTCTTACAGAGAAAACAAG                         AGGTATGTTTAATAAAGAAAGAATTGCAAAGATGAAGAAAGGTGTAATCAT
genomic: ATGTCATTGTGATCAATACACCTCTTACAGAGAAAACAAGgttcctgatg ... ctttcttcagAGGTATGTTTAATAAAGAAAGAATTGCAAAGATGAAGAAAGGTGTAATCAT
EST: gi|163918002|gb|EG714772.1|EG714772
EST:     CCAAAGTGTGATGTCATTGTGATCAATACACCTCTTACAGAGAAAACAAG                         AGGTATGTTTAATAAACAAAGAATTGCAAAGATGAAGAAAGGTGTAATCAT
genomic: CCAAAGTGTGATGTCATTGTGATCAATACACCTCTTACAGAGAAAACAAGgttcctgatg ... ctttcttcagAGGTATGTTTAATAAAGAAAGAATTGCAAAGATGAAGAAAGGTGTAATCAT

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: 72 (upstream exon), 73 (downstream exon)
Score: 180

TTGAGAAAGAAATTGGGGCCAAATATGAAGAGGATCTCGATGCTATGCTTCCAAAGTGTGATGTCATTGTGATCAATACACCTCTTACAGAGAAAACAAGgttcctgatg ... ctttcttcagAGGTATGTTTAATAAAGAAAGAATTGCAAAGATGAAGAAAGGTGTAATCATTGTGAATAATGCTCGAGGAGCAATCATGGATACCCAGGCGGTTGCAGAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatcatatacatagtacatctacttatctgaactttgtatgattctttcttcagAGGTATGTTTAATAAAGAAAGAATTGCAAAGATGAAGAAAGGTGTAATCATTGTGAATAATGCTCGAGGAGCAATCATGGATACCCAGGCGGTTGCAGAC
                                           ttctttcttc  CT-rich tract
     atatacata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcctgatgatcgtattcttgtttgttgcaaaatcatatacatagtacatctacttatctgaactttgtatgattctttcttcagAGGTATGTTTAATAAAGAAAGAATTGCAAAGATGAAGAAAGGTGTAATCATTGTGAATAATGCTCGAGGAGCAATCATGGATACCCAGGCGGTTGCAGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA