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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaacagttatagtcctcccttcgctgacatgactttttgctgaagagttggtcatactaagtccctaactggtgttggaaatttttgtttttagGTTGCAAAAATTGAAACAGAGAAAATGCTTATTGCCATGGTTGAGACTGAATTGGAGAAGAGAAAAGCTGAGGGGAAGTACCCCGCACATTTCAGAGGCC

Basic information

species Oryza sativa
transcript LOC_Os06g13810.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g13810.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G143862_T01 (Zea mays), 3'ss of exon 3
gtaaacagttatagtcctcccttcgctgacatgactttttgctgaagagttggtcatactaag------tccctaactgg----tgttggaaatttttgtt--tttagGTTGCAAAAATTGAAACAGAGAAAATGCTTATTGCCATGGTTGAGACTGAATTGGAGAAGAGAAAAGCTGAGGGGAAGTACCCCGCACATTTCAGAGGCC
||||| | |   | |  |   ||  ||  | ||   | ||     ||  ||  |  | || |        |  |||||      || |    | | |||||  |||||||||||||||||||||| |||||||||||||||  |||||| || |||||| ||||||||||||||||||||||||  ||| | |||||||||||||| |
gtaaagactgggaatattgt-ttaactttcttggtctcttctaacaggattctttctgctgaaaggataccagtaacttagacatgctcactagtcttgttgttttagGTTGCAAAAATTGAAACTGAGAAAATGCTTATTAGCATGGTGGAAACTGAACTGGAGAAGAGAAAAGCTGAGGGGAGATACTCTGCACATTTCAGAGGAC

upper sequence: LOC_Os06g13810.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G059151_T01 (Zea mays), 3'ss of exon 10
-------------------gtaaacagttatagtcctcccttcgctgacatgactttttgctgaagagttggtcatactaagtccctaactggtgttggaaatttttgtttttagGTTGCAAAAATTGAAACAGAGAAAATGCTTATTGCCATGGTTGAGACTGAATTGGAGAAGAGAAAAGCTGAGGGGAAGTACCCCGCACATTTCAGAGGCC
                    | |||  |  ||       ||   ||| || |||| ||| |||  ||   | |   | ||||   |||     || |    |  | |  ||| |||| |||||||||||||| ||||||||||| |||  |||||| || |||||| ||||||||||||| || |||||||  ||| | |||||||||||||| |
gtaaagattgggaatattgtttaaccatcttaacttagtctcttctggcaggactcttt-ctgctgaaaggatatcagtaag---ctagaca-tgctaactaggtgttatttcagGTCGCAAAAATTGAAACCGAGAAAATGCTCATTAGCATGGTGGAAACTGAACTGGAGAAGAGAAAGGCAGAGGGGAGATACTCTGCACATTTCAGAGGGC

upper sequence: LOC_Os06g13810.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA15G11890.1 (Glycine max), 3'ss of exon 10
----gtaa-acagttatagtcctcccttcgctgacatgactttttgctgaagagttggtcatactaagtccctaactggtgttggaaatttttgtttttagGTTGCAAAAATTGAAACAGAGAAAATGCTTATTGCCATGGTTGAGACTGAATTGGAGAAGAGAAAAGCTGAGGGGAAGTACCCCGCACATTTCAGAGGCC
     |||    |||||||| ||  ||| ||||   | | ||    |           |   |      ||     |  | |||    | ||    |||||||||| || || |||||||||||||||||||||   |||||||| ||||| ||||||||||||||    || || || |||   |   | || | ||| |
gtgcctaatgttgttatagtgctatctt-gctgtgtttatttggctcctctatccaatttgaagcggcaccaatgttaatcttgcttgtattgccatttagGTTGCCAAGATAGAAACAGAGAAAATGCTTATTCAAATGGTTGAAACTGAGTTGGAGAAGAGAAAGCAAGAAGGCAAATACAATGGCGAATTTAAAGGGC

upper sequence: LOC_Os06g13810.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA17G01360.1 (Glycine max), 3'ss of exon 8
gtaaacagttatagtcctcccttcgctgacatgactttttgctgaagagttggtcatactaagtccctaactggtgttggaaatttttgtttttagGTTGCAAAAATTGAAACAGAGAAAATGCTTATTGCCATGGTTGAGACTGAATTGGAGAAGAGAAAAGCTGAGGGGAAGTACCCCG-CACATTTCAGAGGCC
        |||  ||  |    |     || | |  ||   ||| |  |    |   |||||| | |  | || || |  | ||||   |||  ||||||| || || |||||||||||||||||||||   |||||||| ||||| ||||||||||||||     ||||    ||    | |  ||||  | ||| 
----gtgcttaatgtattatagtgctatactttatcttgccctgtaatgc-aatttgactaagcctc--aatgttggtatatatttccattt--agGTTGCCAAGATAGAAACAGAGAAAATGCTTATTCAAATGGTTGAAACTGAGTTGGAGAAGAGAAAGCAACAGGGCTCATATAAAGGCGGATTTAGGGGGC-

upper sequence: LOC_Os06g13810.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA07G39380.2 (Glycine max), 3'ss of exon 10
----gtaaacagttatagtcctcccttcgctgacatgactttttgctgaagagttggtcatactaagtccctaactggtgttggaaatttttgtttttagGTTGCAAAAATTGAAACAGAGAAAATGCTTATTGCCATGGTTGAGACTGAATTGGAGAAGAGAAAAGCTGAGGGGAAGTACCCCGCACATTTCAGAGGCC
     |||    ||||||| ||    | ||||   | |  | ||||     |     |   |||||| | |  | || || |  | ||||   |||  ||||||| || || |||||||||||||||||||||   |||||||| ||||| ||||||||||||||     |||| |  ||    | |   || || || |
gtgcttaatgtattatagttctatacttgctgtgttta--tcttgcctgtaatgcaatttgactaagcctc--aatgttggtatatatttccattt--agGTTGCCAAGATAGAAACAGAGAAAATGCTTATTCAAATGGTTGAAACTGAGTTGGAGAAGAGAAAGCAACAGGGCACATATAAAGGAGGATTTAGGGGGC

upper sequence: LOC_Os06g13810.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA09G01050.1 (Glycine max), 3'ss of exon 10
----gtaa-acagttatagtcctcccttcgctgacatgactttttgctgaagagttggtcatactaagtccctaactggtgttggaaatttttgtttttagGTTGCAAAAATTGAAACAGAGAAAATGCTTATTGCCATGGTTGAGACTGAATTGGAGAAGAGAAAAGCTGAGGGGAAGTACCCCGCACATTTCAGAGGCC
     |||    ||||| || ||  ||| ||||   ||| ||    |           | | |      ||     |  | |||    | ||    |||||||||| || || |||||||||||||||||||||   |||||||| ||||| ||||||||||||||    || || || |||   |   | || | ||| |
gtgcctaatgttgttattgtgctatctt-gctgggttgatttggctcctctatccaatttaaatcggcacctatgttaatcttgcctgtattcccatttagGTTGCCAAGATAGAAACAGAGAAAATGCTTATTCAAATGGTTGAAACTGAGTTGGAGAAGAGAAAGCAAGAAGGCAAATACAAAGGCGAATTTAAAGGGC

upper sequence: LOC_Os06g13810.1 (Oryza sativa), 3'ss of exon 10
lower sequence: AT1G12000.1 (Arabidopsis thaliana), 3'ss of exon 10
gtaaacagttatagtcctcccttcgctgacatgactttttgctgaagagttggtcatactaagtccct--aactggtgttggaaatttt-tgtttt--------tagGTTGCAAAAATTGAAACAGAGAAAATGCTTATTGCCATGGTTGAGACTGAATTGGAGAAGAGAAAAGCTGAGGGGAAGTACCCCGCACATTTCAGAGGCC
||||    | || |||||  || | |  || | | |||   |   |  |  | |      |  || |   ||    | ||   |||    |||  |        |||||||| || ||||| || ||||| |||||||||   |||||||| |||||||||||||| |||||    |  ||    |||   | ||| ||||  || |
gtaattgatcatggtcctgtctcctcgtac-taaatttccaccacaatgcagttagcttcatctctcacaaatcattattaataataccatgtcctcatctcaatagGTTGCTAAGATTGAGACTGAGAAGATGCTTATTCAAATGGTTGAAACTGAATTGGAGAAAAGAAAGCAAGCTGGTGCATACAAGGGACAATTCATGGGAC

upper sequence: LOC_Os06g13810.1 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv10s0116g00360.t01 (Vitis vinifera), 3'ss of exon 10
---gtaaacagttatagtcctcccttcgctgacatgactttttgctgaagagttggtcatactaagtccctaactggtgttggaa-atttttgt-ttttagGTTGCAAAAATTGAAACAGAGAAAATGCTTATTGCCATGGTTGAGACTGAATTGGAGAAGAGAAAAGCTGAGGGGAAGTACCCCGCACATTTCAGAGGCC------
    | | |   |||  |  |   |  |   |  |||  |||   ||      |  |  |  ||  ||  |   |  || |      ||||| |   ||||||||||||||| ||||||||||||||||||||    |||||||| || || || |||||||| ||   |||||| |  |||       | | || ||| |      
gtgtttatcttatatgctagtatatgtgtgtatttgaactttacttgtttg--taattctgatagatctttggttattgataatctgtttttataccttagGTTGCAAAAATAGAAACAGAGAAAATGCTTATACAAATGGTTGAAACCGAGTTAGAGAAGAGGAAGAGTGAGGGCACATAC------AAATACAAAGGTCACTTTA

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|29689204|gb|CB685479.1|CB685479
EST:     CCATCCAGGAGCAACTTTTGCTTGAAAGAGATCCTCATGGAAATGTTCAG                         GTTGCAAAAATTGAAACAGAGAAAATGCTTATTGCCATGGTTGAGACTGAA
genomic: CCATCCAGGAGCAACTTTTGCTTGAAAGAGATCCTCATGGAAATGTTCAGgtaaacagtt ... ttgtttttagGTTGCAAAAATTGAAACAGAGAAAATGCTTATTGCCATGGTTGAGACTGAA
EST: gi|157650204|gb|EX449838.1|EX449838
EST:     CCATCCAGGAGCAACTTTTGCTTGAAAGAGATCCTCATGGAAATGTTCAG                         GTTGCAAAAATTGAAACAGAGAAAATGCTTA
genomic: CCATCCAGGAGCAACTTTTGCTTGAAAGAGATCCTCATGGAAATGTTCAGgtaaacagtt ... ttgtttttagGTTGCAAAAATTGAAACAGAGAAAATGCTTA
EST: gi|88365473|gb|CI680112.1|CI680112
EST:     CCATCCAGGAGCAACTTTTGCTTGAAAGAGATCCTCATGGAAATGTTCAG                         GTTGCAAAAATTGAAACAGAGAAAATGCTTATTGCCATGGTTGAGACTGAA
genomic: CCATCCAGGAGCAACTTTTGCTTGAAAGAGATCCTCATGGAAATGTTCAGgtaaacagtt ... ttgtttttagGTTGCAAAAATTGAAACAGAGAAAATGCTTATTGCCATGGTTGAGACTGAA
EST: gi|29678699|gb|CB674974.1|CB674974
EST:     AGGAGCAACTTTTGCTTGAAAGAGATCCTCATGGAAATGTTCAG                         GTTGCAAAAATTGAAACAGAGAAAATGCTTATTGCCATGGTTGAGACTGAA
genomic: AGGAGCAACTTTTGCTTGAAAGAGATCCTCATGGAAATGTTCAGgtaaacagtt ... ttgtttttagGTTGCAAAAATTGAAACAGAGAAAATGCTTATTGCCATGGTTGAGACTGAA
EST: gi|88369740|gb|CI680411.1|CI680411
EST:     CCATCCAGGAGCAACTTTTGCTTGAAAGAGATCCTCATGGAAATGTTCAG                         GTTGCAAAAATTGAAACAGAGAAAATGCTTATTGCCATGGTTGAGACTGAA
genomic: CCATCCAGGAGCAACTTTTGCTTGAAAGAGATCCTCATGGAAATGTTCAGgtaaacagtt ... ttgtttttagGTTGCAAAAATTGAAACAGAGAAAATGCTTATTGCCATGGTTGAGACTGAA
EST: gi|88581492|gb|CI698483.1|CI698483
EST:     CCATCCAGGAGCAACTTTTGCTTGAAAGAGATCCTCATGGAAATGTTCAG                         GTTGCAAAAATTGAAACAGAGAAAATGCTTATTGCCATGGTTGAGACTGAA
genomic: CCATCCAGGAGCAACTTTTGCTTGAAAGAGATCCTCATGGAAATGTTCAGgtaaacagtt ... ttgtttttagGTTGCAAAAATTGAAACAGAGAAAATGCTTATTGCCATGGTTGAGACTGAA
EST: gi|58687019|gb|CK075706.1|CK075706
EST:     CCATCCAGGAGCAACTTTTGCTTGAAAGAGATCCTCATGGAAATGTTCAG                         GTTGCAAAAATTGAAACAGAGAAAATGCTTATTGCCATGGTTGAGACTGAA
genomic: CCATCCAGGAGCAACTTTTGCTTGAAAGAGATCCTCATGGAAATGTTCAGgtaaacagtt ... ttgtttttagGTTGCAAAAATTGAAACAGAGAAAATGCTTATTGCCATGGTTGAGACTGAA
EST: gi|2800921|gb|AA754215.1|AA754215
EST:     CCATCCAGGAGCAACTTTTGCTTGAAAGAGAYCCTCATGGAAATGTTCAG                         GTTGCAAAMGTTGAAACAGAGAAAATGCTTATTGCC
genomic: CCATCCAGGAGCAACTTTTGCTTGAAAGAGATCCTCATGGAAATGTTCAGgtaaacagtt ... ttgtttttagGTTGCAAAAATTGAAACAGAGAAAATGCTTATTGCC
EST: gi|58672321|gb|CK061007.1|CK061007
EST:     GCTTGAAAGAGATCCTCATGGAAATGTTCAG                         GTTGCAAAAATTGAAACAGAGAAAATGCTTATTGCCATGGTTGAGACTGAA
genomic: GCTTGAAAGAGATCCTCATGGAAATGTTCAGgtaaacagtt ... ttgtttttagGTTGCAAAAATTGAAACAGAGAAAATGCTTATTGCCATGGTTGAGACTGAA
EST: gi|33796706|gb|CF324221.1|CF324221
EST:     CCATCCAGGAGCAACTTTTGCTTGAAAGAGATCCTCATGGAAATGTTCAG                         GTTGCAAAAATTGAAACAGAGAAAATGCTTATT
genomic: CCATCCAGGAGCAACTTTTGCTTGAAAGAGATCCTCATGGAAATGTTCAGgtaaacagtt ... ttgtttttagGTTGCAAAAATTGAAACAGAGAAAATGCTTATT
EST: gi|88584252|gb|CI701792.1|CI701792
EST:     CCATCCAGGAGCAACTTTTGCTTGAAAGAGATCCTCATGGAAATGTTCAG                         GTTGCAAAAATTGAAACAGAGAAAATGCTTATTGCCATGGTTGAGACTGAA
genomic: CCATCCAGGAGCAACTTTTGCTTGAAAGAGATCCTCATGGAAATGTTCAGgtaaacagtt ... ttgtttttagGTTGCAAAAATTGAAACAGAGAAAATGCTTATTGCCATGGTTGAGACTGAA
EST: gi|88578785|gb|CI687736.1|CI687736
EST:     CCATCCAGGAGCAACTTTTGCTTGAAAGAGATCCTCATGGAAATGTTCAG                         GTTGCAAAAATTGAAACAGAGAAAATGCTTATTGCCATGGTTGAGACTGAA
genomic: CCATCCAGGAGCAACTTTTGCTTGAAAGAGATCCTCATGGAAATGTTCAGgtaaacagtt ... ttgtttttagGTTGCAAAAATTGAAACAGAGAAAATGCTTATTGCCATGGTTGAGACTGAA
EST: gi|88197484|gb|CI197186.1|CI197186
EST:     TCCTCATGGAAATGTTCAG                         GTGGCAAAAATTGAAACAGAGAAAATGCTTATTGCCATGGTTGAGACTGAA
genomic: TCCTCATGGAAATGTTCAGgtaaacagtt ... ttgtttttagGTTGCAAAAATTGAAACAGAGAAAATGCTTATTGCCATGGTTGAGACTGAA
EST: gi|88432901|gb|CI690757.1|CI690757
EST:     CCATCCAGGAGCAACTTTTGCTTGAAAGAGATCCTCATGGAAATGTTCAG                         GTTGCAAAAATTGAAACAGAGAAAATGCTTATTGCCATGGTTGAGACTGAA
genomic: CCATCCAGGAGCAACTTTTGCTTGAAAGAGATCCTCATGGAAATGTTCAGgtaaacagtt ... ttgtttttagGTTGCAAAAATTGAAACAGAGAAAATGCTTATTGCCATGGTTGAGACTGAA
EST: gi|3106670|gb|D42390.1|D42390
EST:     CCATCCAGGAGCAACTTTTGCTTGAAAGAGATCCTCATGGAAATGTTCAG                         GTTGCAAAAATTGAAACAGAGAAAATGCTTATTGCCATGGTTGAGACTGAA
genomic: CCATCCAGGAGCAACTTTTGCTTGAAAGAGATCCTCATGGAAATGTTCAGgtaaacagtt ... ttgtttttagGTTGCAAAAATTGAAACAGAGAAAATGCTTATTGCCATGGTTGAGACTGAA
EST: gi|2312262|gb|C28417.1|C28417
EST:     CCATCCAGGAGCAACTTTTGCTTGAAAGAGATCCTCATGGAAATGTTCAG                         GTTGCAAAAATTGAAACAGAGAAAATGCTTATTGCCATGGTTGAGACTGAA
genomic: CCATCCAGGAGCAACTTTTGCTTGAAAGAGATCCTCATGGAAATGTTCAGgtaaacagtt ... ttgtttttagGTTGCAAAAATTGAAACAGAGAAAATGCTTATTGCCATGGTTGAGACTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgaagagttggtcatactaagtccctaactggtgttggaaatttttgtttttagGTTGCAAAAATTGAAACAGAGAAAATGCTTATTGCCATGGTTGAGACTGAATTGGAGAAGAGAAAAGCTGAGGGGAAGTACCCCGCACATTTCAGAGGCC
                       ccctaac  putative branch site (score: 2)
                                          tttttgttttt  putative PPT
                                       aaatttttgttttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaacagttatagtcctcccttcgctgacatgactttttgctgaagagttggtcatactaagtccctaactggtgttggaaatttttgtttttagGTTGCAAAAATTGAAACAGAGAAAATGCTTATTGCCATGGTTGAGACTGAATTGGAGAAGAGAAAAGCTGAGGGGAAGTACCCCGCACATTTCAGAGGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA