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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acttacaaagctcctggatttggttttgtttcacgtccactgtgatgattcctcttttaatgtcatattaatgtttcccttttattgttatgataaacagAAGTGATGCGGATGTCTACAGTCAGGCTGCATCAAATCTTGTTTCAGGTAGCAACCTAGAACAGACAATCCAACAAATTCTTGACATGGGTGGTGGCACC

Basic information

species Oryza sativa
transcript LOC_Os06g15360.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g15360.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G035417_T01 (Zea mays), 3'ss of exon 5
-----acttacaaagctcctggatttggttttgtttcacgtccactgtgatgattcctcttttaatgtcatattaatgtttcccttttattgttatgataaacagAAGTGATGCGGATGTCTACAGTCAGGCTGCATCAAATCTTGTTTCAGGTAGCAACCTAGAACAGACAATCCAACAAATTCTTGACATGGGTGGTGGCACC
      | |  |||||           ||||| |||        ||||  ||  || |  | ||    || | ||||  | | |||| ||     || |  ||||   |||||| ||||| ||||||||||| || ||||| ||||| || || | ||| ||||||||||| ||||||||||||||||||||||||||||| || 
attggtccttgaaagcctacatcaaaagttttctttatttcttgctgttctg--tcgtagtctag---cacagtaatcctgctctttcatgtggctgttctacagTGATGATGCTGATGTGTACAGTCAGGCAGCTTCAAACCTTGTATCTGGCAACAATCTAGAACAGACTATCCAACAAATTCTTGACATGGGTGGTGGTACA
















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|29629490|gb|CB634499.1|CB634499
EST:     TCTGCCACTCCAGCTGCTGCTGCCACTCCAGCTGCTGCTGTGACCGCATC                         AAGTGATGCGGATGTCTACAGTCAGGCTGCATCAAATCTTGTTTCAGGTAG
genomic: TCTGCCACTCCAGCTGCTGCTGCCACTCCAGCTGCTGCTGTGACCGCATCgtaagctccc ... tgataaacagAAGTGATGCGGATGTCTACAGTCAGGCTGCATCAAATCTTGTTTCAGGTAG
EST: gi|58682592|gb|CK071279.1|CK071279
EST:     TCTGCCACTCCAGCTGCTGCTGCCACTCCAGCTGCTGCTGTGACCGCATC                         ---TGATGCGGATGTCTACAGTCAGGCTGCATCAAATCTTGTTTCAGGTAG
genomic: TCTGCCACTCCAGCTGCTGCTGCCACTCCAGCTGCTGCTGTGACCGCATCgtaagctccc ... tgataaacagAAGTGATGCGGATGTCTACAGTCAGGCTGCATCAAATCTTGTTTCAGGTAG
EST: gi|58665658|gb|CK054344.1|CK054344
EST:     TCTGCCACTCCAGCTGCTGCTGCCACTCCAGCTGCTGCTGTGACCGCATC                         AAGTGATGCGGATGTCTACAGTCAGGCTGCATCAAATCTTGTTTCAGGTAG
genomic: TCTGCCACTCCAGCTGCTGCTGCCACTCCAGCTGCTGCTGTGACCGCATCgtaagctccc ... tgataaacagAAGTGATGCGGATGTCTACAGTCAGGCTGCATCAAATCTTGTTTCAGGTAG
EST: gi|29643232|gb|CB648239.1|CB648239
EST:     TCTGCCACTCCAGCTGCTGCTGCCACTCCAGCTGCTGCTGTGACCGCATC                         AAGTGATGCGGATGTCTACAGTCAGGCTGCATCAAATCTTGTTTCAGGTAG
genomic: TCTGCCACTCCAGCTGCTGCTGCCACTCCAGCTGCTGCTGTGACCGCATCgtaagctccc ... tgataaacagAAGTGATGCGGATGTCTACAGTCAGGCTGCATCAAATCTTGTTTCAGGTAG
EST: gi|33654535|gb|CF277149.1|CF277149
EST:     TCTGCCACTCCAGCTGCTGCTGCCACTCCAGCTGCTGCTGTGACCGCATC                         AAGNTGATGCGGATGTCTACAGTCAGGCTGCATCAAATCTTGTTTCAGGTA
genomic: TCTGCCACTCCAGCTGCTGCTGCCACTCCAGCTGCTGCTGTGACCGCATCgtaagctccc ... tgataaacagAAG-TGATGCGGATGTCTACAGTCAGGCTGCATCAAATCTTGTTTCAGGTA
EST: gi|29655833|gb|CB652108.1|CB652108
EST:     TCTGCCACTCCAGCTGCTGCTGCCACTCCAGCTGCTGCTGTGACCGCATC                         AAGTGATGCGGATGTCTACAGTCAGGCTGCATCAAATCTTGTTTCAGGTAG
genomic: TCTGCCACTCCAGCTGCTGCTGCCACTCCAGCTGCTGCTGTGACCGCATCgtaagctccc ... tgataaacagAAGTGATGCGGATGTCTACAGTCAGGCTGCATCAAATCTTGTTTCAGGTAG
EST: gi|33656015|gb|CF278629.1|CF278629
EST:     TCTGCCACTCCAGCTGCTGCTGCCACTCCAGCTGCTGCTGTGACCGCATC                         AAGTGATGCGGATGTCTACAGT
genomic: TCTGCCACTCCAGCTGCTGCTGCCACTCCAGCTGCTGCTGTGACCGCATCgtaagctccc ... tgataaacagAAGTGATGCGGATGTCTACAGT
EST: gi|58670606|gb|CK059292.1|CK059292
EST:     TCTGCCACTCCAGCTGCTGCTGCCACTCCAGCTGCTGCTGTGACCGCATC                         AAGTGATGCGGATGTCTACAGTCAGGCTGCATCAAATCTTGTTTCAGGTAG
genomic: TCTGCCACTCCAGCTGCTGCTGCCACTCCAGCTGCTGCTGTGACCGCATCgtaagctccc ... tgataaacagAAGTGATGCGGATGTCTACAGTCAGGCTGCATCAAATCTTGTTTCAGGTAG
EST: gi|58670896|gb|CK059582.1|CK059582
EST:     TCTGCCACTCCAGCTGCTGCTGCCACTCCAGCTGCTGCTGTGACCGCATC                         AAGTGATGCGGATGTCTACAGTCAGGCTGCATCAAATCTTGTTTCAGGTAG
genomic: TCTGCCACTCCAGCTGCTGCTGCCACTCCAGCTGCTGCTGTGACCGCATCgtaagctccc ... tgataaacagAAGTGATGCGGATGTCTACAGTCAGGCTGCATCAAATCTTGTTTCAGGTAG
EST: gi|29631166|gb|CB636175.1|CB636175
EST:     TCTGCCACTCCAGCTGCTGCTGCCACTCCAGCTGCTGCTGTGACCGCATC                         AAGTGATGCGGATGTCTACAGTCAGGCTGCATCAAATCTTGTTTCAGGTAG
genomic: TCTGCCACTCCAGCTGCTGCTGCCACTCCAGCTGCTGCTGTGACCGCATCgtaagctccc ... tgataaacagAAGTGATGCGGATGTCTACAGTCAGGCTGCATCAAATCTTGTTTCAGGTAG
EST: gi|29669284|gb|CB665559.1|CB665559
EST:     TCTGCCACTCCAGCTGCTGCTGCCACTCCAGCTGCTGCTGTGACCGCATC                         AAGTGATGCGGATGTCTACAGTCTGGCTGCATCAAATCTTGTTTCAGGTAG
genomic: TCTGCCACTCCAGCTGCTGCTGCCACTCCAGCTGCTGCTGTGACCGCATCgtaagctccc ... tgataaacagAAGTGATGCGGATGTCTACAGTCAGGCTGCATCAAATCTTGTTTCAGGTAG
EST: gi|29636049|gb|CB641058.1|CB641058
EST:     TCTGCCACTCCAGCTGCTGCTGCCACTCCAGCTGCTGCTGTGACCGCATC                         AAGTGATGCGGATGTCTACAGTCAGGCTGCATCACATCTTGTTTTAAGTAG
genomic: TCTGCCACTCCAGCTGCTGCTGCCACTCCAGCTGCTGCTGTGACCGCATCgtaagctccc ... tgataaacagAAGTGATGCGGATGTCTACAGTCAGGCTGCATCAAATCTTGTTTCAGGTAG
EST: gi|29673854|gb|CB670129.1|CB670129
EST:     TCTGCCACTCCAGCTGCTGCTGCCACTCCAGCTGCTGCTGTGACCGCATC                         AAGTGATGCGGATGTCTACAGTCAGGCTGCATCAAATCTTGTTTCAGGTAG
genomic: TCTGCCACTCCAGCTGCTGCTGCCACTCCAGCTGCTGCTGTGACCGCATCgtaagctccc ... tgataaacagAAGTGATGCGGATGTCTACAGTCAGGCTGCATCAAATCTTGTTTCAGGTAG
EST: gi|218502296|gb|FG962509.1|FG962509
EST:     TCTGCCACTCCAGCTGCTGCTGCCACTCCAGCTGCTGCTGTGACCGCATC                         AAGTGATGCGGATGTCTACAGTCAGGCTGCATCAAATCTTGTTTCAGGTAG
genomic: TCTGCCACTCCAGCTGCTGCTGCCACTCCAGCTGCTGCTGTGACCGCATCgtaagctccc ... tgataaacagAAGTGATGCGGATGTCTACAGTCAGGCTGCATCAAATCTTGTTTCAGGTAG
EST: gi|58586179|gb|CF984487.1|CF984487
EST:     TCTGCCACTCCAGCTGCTGCTGCCACTCCAGCTGCTGCTGTGACCGCATC                         AAGTGATGCGGATGTCTACAGTCAGGCTGCATCAAATCTTGTTTCAGGT
genomic: TCTGCCACTCCAGCTGCTGCTGCCACTCCAGCTGCTGCTGTGACCGCATCgtaagctccc ... tgataaacagAAGTGATGCGGATGTCTACAGTCAGGCTGCATCAAATCTTGTTTCAGGT
EST: gi|700253|gb|D46544.1|D46544
EST:     TCTGCCACTCCAGCTGCTGCTGCCACTCCAGCTGCTGCTGTGACCGCATC                         AAGTGATGCGGATGTCTACAGTCAGGNTGCATCAAATCTTGTTTCAGGTAG
genomic: TCTGCCACTCCAGCTGCTGCTGCCACTCCAGCTGCTGCTGTGACCGCATCgtaagctccc ... tgataaacagAAGTGATGCGGATGTCTACAGTCAGGCTGCATCAAATCTTGTTTCAGGTAG
EST: gi|29657664|gb|CB653939.1|CB653939
EST:     TCTGCCACTCCAGCTGCTGCTGCCACTCCAGCTGCTGCTGTGACCGCATC                         AAGTGATGCGGATGTCTACAGTCAGGCTGCATCAAATCTTGTTTCAGGTAG
genomic: TCTGCCACTCCAGCTGCTGCTGCCACTCCAGCTGCTGCTGTGACCGCATCgtaagctccc ... tgataaacagAAGTGATGCGGATGTCTACAGTCAGGCTGCATCAAATCTTGTTTCAGGTAG
EST: gi|117226238|gb|CT846174.1|CT846174
EST:     TCTGCCACTCCAGCTGCTGCTGCCACTCCAGCTGCTGCTGTGACCGCATC                         AAGTGATGCGGATGTCTACAGTCAGGCTGCATCAAATCTTGTTTCAGGTAG
genomic: TCTGCCACTCCAGCTGCTGCTGCCACTCCAGCTGCTGCTGTGACCGCATCgtaagctccc ... tgataaacagAAGTGATGCGGATGTCTACAGTCAGGCTGCATCAAATCTTGTTTCAGGTAG
EST: gi|58611993|gb|CK039705.1|CK039705
EST:     TCTGCCACTCCAGCTGCTGCTGCCACTCCAGCTGCTGCTGTGACCGCATC                         AAGTGATGCGGATGTCTACAGTCAGGCTGCATCAAATCTTGTTTCAGGTAG
genomic: TCTGCCACTCCAGCTGCTGCTGCCACTCCAGCTGCTGCTGTGACCGCATCgtaagctccc ... tgataaacagAAGTGATGCGGATGTCTACAGTCAGGCTGCATCAAATCTTGTTTCAGGTAG
EST: gi|29670071|gb|CB666346.1|CB666346
EST:     TCTGCCACTCCAGCTGCTGCTGCCACTCCAGCTGCTGCTGTGACCGCATC                         AAGTGATGCGGATGTCTACAGTCAGGCTGCATCAAATCTTGTTTCAGGTAG
genomic: TCTGCCACTCCAGCTGCTGCTGCCACTCCAGCTGCTGCTGTGACCGCATCgtaagctccc ... tgataaacagAAGTGATGCGGATGTCTACAGTCAGGCTGCATCAAATCTTGTTTCAGGTAG
EST: gi|29668712|gb|CB664987.1|CB664987
EST:     TCTGCCACTCCAGCTGCTGCTGCCACTCCAGCTGCTGCTGTGACCGCATC                         AAGTGATGCGGATGTCTACAGTCAGGCTGCATCAAATCTTGTTTCAAGTAG
genomic: TCTGCCACTCCAGCTGCTGCTGCCACTCCAGCTGCTGCTGTGACCGCATCgtaagctccc ... tgataaacagAAGTGATGCGGATGTCTACAGTCAGGCTGCATCAAATCTTGTTTCAGGTAG
EST: gi|29658464|gb|CB654739.1|CB654739
EST:     TCTGCCTCTCCGGCTGCTGCTGCCACTCCAGCTGCTGCTGTGACCGCATC                         AGGCTGATGCGGATGTTTACGGTCAGGCTGCATCAAATCTTGTTTCATGTA
genomic: TCTGCCACTCCAGCTGCTGCTGCCACTCCAGCTGCTGCTGTGACCGCATCgtaagctccc ... tgataaacagAAG-TGATGCGGATGTCTACAGTCAGGCTGCATCAAATCTTGTTTCAGGTA
EST: gi|29632660|gb|CB637669.1|CB637669
EST:     TCTGCCACTCCAGCTGCTGCTGCCACTCCAGCTGCTGCTGTGACCGCATC                         AAGTGATGCNGATGTCTACAGTCACGCTGCATCAAATCTTG
genomic: TCTGCCACTCCAGCTGCTGCTGCCACTCCAGCTGCTGCTGTGACCGCATCgtaagctccc ... tgataaacagAAGTGATGCGGATGTCTACAGTCAGGCTGCATCAAATCTTG
EST: gi|29643186|gb|CB648193.1|CB648193
EST:     TCTGCCACTCCAGCTGCTGCTGCCACTCCAGCTGCTGCTGTGACCGCATC                         AAGTGATGCGGATGTCTACAGTCAGGCTGCATCAAATCTTGTTTCAGGTAG
genomic: TCTGCCACTCCAGCTGCTGCTGCCACTCCAGCTGCTGCTGTGACCGCATCgtaagctccc ... tgataaacagAAGTGATGCGGATGTCTACAGTCAGGCTGCATCAAATCTTGTTTCAGGTAG
EST: gi|29660320|gb|CB656595.1|CB656595
EST:     TCTGCCACTCCAGCTGCTGCTGCCACTCCAGCTGCTGCTGTGACCGCATC                         AAGTGATGCGGATGTCTACAGTCAGGCTGCATCAAATCTTGTTTCAGGTAG
genomic: TCTGCCACTCCAGCTGCTGCTGCCACTCCAGCTGCTGCTGTGACCGCATCgtaagctccc ... tgataaacagAAGTGATGCGGATGTCTACAGTCAGGCTGCATCAAATCTTGTTTCAGGTAG
EST: gi|58596519|gb|CK007047.1|CK007047
EST:     TCTGCCACTCCAGCTGCTGCTGCCACTCCAGCTGCTGCTGTGACCGCATC                         AAGTGATGCGGATGTCTACAGTCAGGCTGCATCAAATCTTGTTTCAGGTAG
genomic: TCTGCCACTCCAGCTGCTGCTGCCACTCCAGCTGCTGCTGTGACCGCATCgtaagctccc ... tgataaacagAAGTGATGCGGATGTCTACAGTCAGGCTGCATCAAATCTTGTTTCAGGTAG
EST: gi|29631164|gb|CB636173.1|CB636173
EST:     TCTGCCACTCCAGCTGCTGCTGCCACTCCAGCTGCTGCTGTGACCGCATC                         AAGTGATGNCGGATGTCTACAGTCAGGCTGCATCAAATCTTG
genomic: TCTGCCACTCCAGCTGCTGCTGCCACTCCAGCTGCTGCTGTGACCGCATCgtaagctccc ... tgataaacagAAGTGATG-CGGATGTCTACAGTCAGGCTGCATCAAATCTTG
EST: gi|58667186|gb|CK055872.1|CK055872
EST:     TCTGCCACTCCAGCTGCTGCTGCCACTCCAGCTGCTGCTGTGACCGCATC                         AAGTGATGCGGATGTCTACAGTCAGGCTGCATCAAATCTTGTTTCAGGTAG
genomic: TCTGCCACTCCAGCTGCTGCTGCCACTCCAGCTGCTGCTGTGACCGCATCgtaagctccc ... tgataaacagAAGTGATGCGGATGTCTACAGTCAGGCTGCATCAAATCTTGTTTCAGGTAG

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: 63 (upstream exon), 74 (downstream exon)
Score: 23

GGCACCTCCAAGTGCACAGCCTCCAGTTGCTTCTGCCACTCCAGCTGCTGCTGCCACTCCAGCTGCTGCTGTGACCGCATCgtaagctccc ... tgataaacagAAGTGATGCGGATGTCTACAGTCAGGCTGCATCAAATCTTGTTTCAGGTAGCAACCTAGAACAGACAATCCAACAAATTCTTGACATGGGTGGTGGCACC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgattcctcttttaatgtcatattaatgtttcccttttattgttatgataaacagAAGTGATGCGGATGTCTACAGTCAGGCTGCATCAAATCTTGTTTCAGGTAGCAACCTAGAACAGACAATCCAACAAATTCTTGACATGGGTGGTGGCACC
                    tattaat  putative branch site (score: 23)
         ttttaatgtcatatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acttacaaagctcctggatttggttttgtttcacgtccactgtgatgattcctcttttaatgtcatattaatgtttcccttttattgttatgataaacagAAGTGATGCGGATGTCTACAGTCAGGCTGCATCAAATCTTGTTTCAGGTAGCAACCTAGAACAGACAATCCAACAAATTCTTGACATGGGTGGTGGCACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - -gctcctg
- - - - - - - - - - - - - tgtttca
- - - - - - - - - - - - - - - - - - - - tgtgatg