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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgaatgattcctagaaggctggtagataagctttggctatctttggaaagaaatttgtttgaagtgtatcttttgtccgctaacatttaagatgataccagtctgttctgatggttgagtgatattccatgtccattacagGTAACTGTATCTAAGGACGACACTGTTATTCTTGATGGAGCTGGAGACAAGAAATCCATTGAAGAGAGGGCTGAGCAG

Basic information

species Oryza sativa
transcript LOC_Os10g32550.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g32550.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G416120_T01 (Zea mays), 3'ss of exon 10
----------------------------gtatgaat---gattcctagaaggctggtagataagctttggctatctttggaaaga--aatttgtttgaagtgt----atcttttgtccgctaacatttaagatgataccagtctgttctgatggttgagtgatattccatgtccattacagGTAACTGTATCTAAGGACGACACTGTTATTCTTGATGGAGCTGGAGACAAGAAATCCATTGAAGAGAGGGCTGAGCAG
                             |||  ||   |||| |   ||   |      ||||     |   |||      ||   | | |  |  ||||      |||| ||||      |||| |    ||||   |  || || |    | ||| |||   | | | | || ||||||| ||||| |||||||| |||||||||||||||||||| ||||||||||| || || |||||||||||||| || |||
gtatagtagatgatttaaaaggatttttctattgatttggattgcagcaaccttcagccttaagtcacagtattctaacatgagctcagtgttgtgcaagtaccaaaatctgttgtgtttgtacatgtgctttgatgtaatactattttatgtgctgaatga--cttccttttcaatacagGTGACTGTCTCTAAGGATGACACTGTTATTCTTGATGGCGCTGGAGACAAAAAGTCTATTGAAGAGAGGGCAGACCAG

upper sequence: LOC_Os10g32550.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G458208_T01 (Zea mays), 3'ss of exon 10
-------------------------------------------------gtatgaatgattcctagaaggctggta-gataagctttggctatctttggaaagaaatttgtttgaagtgtatcttttgtccgctaacatttaagatgataccagtctgttctgatggttgagtgatattccatgtccattacagGTAACTGTATCTAAGGACGACACTGTTATTCTTGATGGAGCTGGAGACAAGAAATCCATTGA-AGAGAGGGCTGAGCAG----
                                                 || || ||          || |||  | | ||  ||      |||||   | ||   | || | | |    ||  | | || |||  || ||  | |   |     || || |    | ||| ||| ||||| | | || | ||||| ||||| |||||||  | | ||||||||||||||||||| ||||||||||| |||||  | ||||| |  |    ||    
gtataatccaggatttaataggatattctattttctgacatgtttattggtttggattgcaatcttcagactgtcacggtattctcacatgatctt---acagtgttgtgctagtaccaaatgctat-tctgcttgcacttttgctttgatagtgctattttatgtgctgaatga-attcc-ttttcaatgcagGTGACTGTCTCTAAGGTTGCCCCTGTTATTCTTGATGGAGCCGGAGACAAGAAGTCCATGAAGAGAGACGAATCTCTAGAAAC

upper sequence: LOC_Os10g32550.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA10G33680.1 (Glycine max), 3'ss of exon 11
gtatgaatgattcctagaaggctggtagataagctttggctatctttggaaagaaatttgtttgaagtgtatcttttgtccgctaacatttaagatgataccagtctgttctgatggttgagtgatattccatgtccattacagGTAACTGTATCTAAGGACGACACTGTTATTCTTGATGGAGCTGGAGACAAGAAATCCATTGAAGAGAGGGCTGAGCAG
                                           ||||  ||||||| |    | || | | ||| || |  ||  | | |       |    |     ||  ||    ||| | |  |||  | |   ||  || ||||  | |||||||| |||||||| || |||||||||||||| || |||||| | |||||||| ||   |||||||
------------------------------------------gctttttaaagaaagtgtcattaaatttctctattctatgcccatactattttcaaggttaaatgatttagaaaactgaataaggttctgtat--gttttagATAACAATTTCTAAGGATGACACTGTCATCCTTGATGGAGCTGGTGATAAGAAAGCAATTGAAGAAAGAAGTGAGCAG

upper sequence: LOC_Os10g32550.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA20G19980.1 (Glycine max), 3'ss of exon 11
gtatgaatgattcctagaaggctggtagataagctttggctatctttggaaagaaatttgtttgaagtgtatcttttgtccgctaacatttaagatgataccagtctgttctgatggttgagtgatattccatgtccattacagGTAACTGTATCTAAGGACGACACTGTTATTCTTGATGGAGCTGGAGACAAGAAATCCATTGAAGAGAGGGCTGAGCAG
                                    ||  |    ||||||     |||  |||| ||  ||| || ||   || | | |    ||      |   ||    ||    ||| | |  ||| ||     || ||| |||| || |||||||| |||||||| |||||||||||||| || ||||||||| |  |||| || ||    ||||||
------------------------------------tgtgtgatattggaatatgttttcattga-gttcatcattcgtatcctgatact--gcatagggttaacgtg----gacaactgacttaggttc-ataatgtttgcagATAACAGTTTCTAAGGATGACACTGTCATTCTTGATGGAGCGGGTGACAAGAAAGCACTTGAGGAAAGATGCGAGCAG

upper sequence: LOC_Os10g32550.1 (Oryza sativa), 3'ss of exon 11
lower sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 9
gtatgaatgattcctagaaggctggtagata-agctttggctatctttggaaagaaatttgtttgaagtgtatcttttgtccgctaacatttaagatgataccagtctgttctgatggttgagtgatattccatgtccattacagGTAACTGTATCTAAGGACGACACTGTTATTCTTGATGGAGCTGGAGACAAGAAATCCATTGAAGAGAGGGCTGAGCAG
       |      |  ||   |    |||| ||   |||      || | | ||| |   ||||     ||  || |       | ||| |       |    |  |||     | ||||||   | |           || |||| || || || |||||||||||||||||||||||||| ||||| |||||||||   ||||| || ||   ||| |||
------gtagcctttgaaaccttaactgatatagacatggtggctcttagtatgaactagatttggctattacattct------cagcatat----ccttgttggattgtaagtgtagttgagacttgtctggctatttgtatagGTTACAGTCTCCAAGGACGACACTGTTATTCTTGATGGGGCTGGCGACAAGAAAGGAATTGAGGAAAGATGTGAACAG

upper sequence: LOC_Os10g32550.1 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv05s0051g00340.t01 (Vitis vinifera), 3'ss of exon 11
gtatgaatgattcctagaaggctggtagataagctttggctatctttggaaagaaatttgtttgaagtgtatcttttg---tccgcta-acatttaagatgataccagtctgttctgatggttgagtgatattccatgtccattacagGTAACTGTATCTAAGGACGACACTGTTATTCTTGATGGAGCTGGAGACAAGAAATCCATTGAAGAGAGGGCTGAGCAG
                                            |  | |   | || ||||| || | ||  || |    |   ||  ||  ||   || ||||  ||||  | ||  |  | | | |   |   |     ||  |||| ||  ||||||||||||| |||||||| |||||||| ||||| ||||||||  ||||||| ||  ||  |||||||
--------------------------------------------tccgaatgaatatatgttttaactctaggttatagaatgaactgcaccctttgtattatacaggtct--tttgcagcataactaa--ctaggttcatgttttagGTTACAATATCTAAGGACGATACTGTTATCCTTGATGGGGCTGGTGACAAGAAGGCCATTGAGGAACGGTGTGAGCAG

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|218485224|gb|FG951291.1|FG951291
EST:     GAATGAATCTTGAGAAGTTCGAGCCTCAGATGTTGGGTACATGCAAGAAG                         GTAACTGTATCTAAGGACGACACTGTTATTCTTGATGGAGCTGGAGACAAG
genomic: GAATGAATCTTGAGAAGTTCGAGCCTCAGATGTTGGGTACATGCAAGAAGgtatgaatga ... tccattacagGTAACTGTATCTAAGGACGACACTGTTATTCTTGATGGAGCTGGAGACAAG
EST: gi|33795638|gb|CF323689.1|CF323689
EST:     GAAGTTCGAGCCTCAGATGTTGGGTACATGCAAGAAG                         GTAACTGTATCTAAGGACGACACTGTTATTCTTGATGGAGCTGGAGACAAG
genomic: GAAGTTCGAGCCTCAGATGTTGGGTACATGCAAGAAGgtatgaatga ... tccattacagGTAACTGTATCTAAGGACGACACTGTTATTCTTGATGGAGCTGGAGACAAG
EST: gi|58675082|gb|CK063769.1|CK063769
EST:     GAATGAATCTTGAGAAGTTCGAGCCTCAGATGTTGGGTACATGCAAGAAG                         GTAACTGTATCTAAGGACGACACTGTTATTCTTGATGGAGCTGGAGACAAG
genomic: GAATGAATCTTGAGAAGTTCGAGCCTCAGATGTTGGGTACATGCAAGAAGgtatgaatga ... tccattacagGTAACTGTATCTAAGGACGACACTGTTATTCTTGATGGAGCTGGAGACAAG
EST: gi|428132|gb|D24280.1|D24280
EST:     AATGAATCTTGAGAAGTTCGAGCCTCAAGATGTTGGGTACATGCAAGNAG                         GTAACTGTATCTAANGGNCGGCACTGTTAT
genomic: AATGAATCTTGAGAAGTTCGAGCCTCA-GATGTTGGGTACATGCAAGAAGgtatgaatga ... tccattacagGTAACTGTATCTAA-GGACGACACTGTTAT
EST: gi|55411061|gb|CV723437.1|CV723437
EST:     GAATGAATCTTGAGAAGTTCGAGCCTCAGATGTTGGGTACATGCAAGAAG                         GTAACTGTATCTAAGGACGACACTGTTATTCTTGATGGAGCTGGAGACAAG
genomic: GAATGAATCTTGAGAAGTTCGAGCCTCAGATGTTGGGTACATGCAAGAAGgtatgaatga ... tccattacagGTAACTGTATCTAAGGACGACACTGTTATTCTTGATGGAGCTGGAGACAAG
EST: gi|218483700|gb|FG965930.1|FG965930
EST:     ATCTTGAGAAGTTCGAGCCTCAGATGTTGGGTACATGCAAGAAG                         GTAACTGTATCTAAGGACGACACTGTTATTCTTGATGGAGCTGGAGACAAG
genomic: ATCTTGAGAAGTTCGAGCCTCAGATGTTGGGTACATGCAAGAAGgtatgaatga ... tccattacagGTAACTGTATCTAAGGACGACACTGTTATTCTTGATGGAGCTGGAGACAAG
EST: gi|27576373|gb|CA999067.1|CA999067
EST:     GAATGAATCTTGAGAAGTTCGAGCCTCAGATGTTGGGTACATGCAAGAAG                         GTAACTGTATCTAAGGACGACACTGTTATTCTTGATGGAGCTGGAGACAAG
genomic: GAATGAATCTTGAGAAGTTCGAGCCTCAGATGTTGGGTACATGCAAGAAGgtatgaatga ... tccattacagGTAACTGTATCTAAGGACGACACTGTTATTCTTGATGGAGCTGGAGACAAG
EST: gi|58692466|gb|CK081153.1|CK081153
EST:     GAATGAATCTTGAGAAGTTCGAGCCTCAGATGTTGGGTACATGCAAGAAG                         GTAACTGTATCTAAGGACGACACTGTTATTCTTGATGGAGCTGGAGACAAG
genomic: GAATGAATCTTGAGAAGTTCGAGCCTCAGATGTTGGGTACATGCAAGAAGgtatgaatga ... tccattacagGTAACTGTATCTAAGGACGACACTGTTATTCTTGATGGAGCTGGAGACAAG
EST: gi|27546502|gb|CA764746.2|CA764746
EST:     GAATGAATCTTGAGAAGTTCGAGCCTCAGATGTTGGGTACATGCAAGAGG                         GTAACTGTATCTAAGGACGACACTGTTATTCTTGATGGAGCTGGAGACAAG
genomic: GAATGAATCTTGAGAAGTTCGAGCCTCAGATGTTGGGTACATGCAAGAAGgtatgaatga ... tccattacagGTAACTGTATCTAAGGACGACACTGTTATTCTTGATGGAGCTGGAGACAAG
EST: gi|55411724|gb|CV724100.1|CV724100
EST:     GAATGAATCTTGAGAAGTTCGAGCCTCAGATGTTGGGTACATGCAAGAAG                         GTAACTGTATCTAAGGACGACACTGTTATTCTTGATGGAGCTGGAGACAAG
genomic: GAATGAATCTTGAGAAGTTCGAGCCTCAGATGTTGGGTACATGCAAGAAGgtatgaatga ... tccattacagGTAACTGTATCTAAGGACGACACTGTTATTCTTGATGGAGCTGGAGACAAG
EST: gi|58663314|gb|CK052000.1|CK052000
EST:     GAATGAATCTTGAGAAGTTCGAGCCTCAGATGTTGGGTACATGCAAGAAG                         GTAACTGTATCTAAGGACGACACTGTTATTCTTGATGGAGCTGGAGACAAG
genomic: GAATGAATCTTGAGAAGTTCGAGCCTCAGATGTTGGGTACATGCAAGAAGgtatgaatga ... tccattacagGTAACTGTATCTAAGGACGACACTGTTATTCTTGATGGAGCTGGAGACAAG
EST: gi|25803762|gb|CA759723.1|CA759723
EST:     GAGAAGTTCGAGCCTCAGATGTTGGGTACATGCAAGAAG                         GTAACTGTATCTAAGGACGACACTGTTATTCTTGATGGAGCTGGAGACAAG
genomic: GAGAAGTTCGAGCCTCAGATGTTGGGTACATGCAAGAAGgtatgaatga ... tccattacagGTAACTGTATCTAAGGACGACACTGTTATTCTTGATGGAGCTGGAGACAAG
EST: gi|33796275|gb|CF324004.1|CF324004
EST:     GAATGAATCTTGAGAAGTTCGAGCCTCAGATGTTGGGTACATGCAAGAAG                         GTAACTGTATCTAAGGACGACACTGTTATTCTTGATGGAGCTGGAGACAAG
genomic: GAATGAATCTTGAGAAGTTCGAGCCTCAGATGTTGGGTACATGCAAGAAGgtatgaatga ... tccattacagGTAACTGTATCTAAGGACGACACTGTTATTCTTGATGGAGCTGGAGACAAG

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: 61 (upstream exon), 71 (downstream exon)
Score: 105

GTCATAACTGAAGAGCTAGGAATGAATCTTGAGAAGTTCGAGCCTCAGATGTTGGGTACATGCAAGAAGgtatgaatga ... tccattacagGTAACTGTATCTAAGGACGACACTGTTATTCTTGATGGAGCTGGAGACAAGAAATCCATTGAAGAGAGGGCTGAGCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaagatgataccagtctgttctgatggttgagtgatattccatgtccattacagGTAACTGTATCTAAGGACGACACTGTTATTCTTGATGGAGCTGGAGACAAGAAATCCATTGAAGAGAGGGCTGAGCAG
                   ttctgat  putative branch site (score: 105)
                                 tgatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgaatgattcctagaaggctggtagataagctttggctatctttggaaagaaatttgtttgaagtgtatcttttgtccgctaacatttaagatgataccagtctgttctgatggttgagtgatattccatgtccattacagGTAACTGTATCTAAGGACGACACTGTTATTCTTGATGGAGCTGGAGACAAGAAATCCATTGAAGAGAGGGCTGAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG