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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggtggatctctaattccatagcactttagttctacactgatgtaaccttctcacaaaatttttccaactgcagCTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTTGTGTCAAGGTTGCTGCAGTACTCGCCAAATTTGCGTTGCACAGCT

Basic information

species Oryza sativa
transcript LOC_Os10g37740.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g37740.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G109624_T01 (Zea mays), 3'ss of exon 10
gttggtggatctctaat-tccatagcactttagtt-------ctacactgatgtaaccttctcacaaaatttt--tccaactgcagCTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTTGTGTCAAGGTTGCTGCAGTACTCGCCAAATTTGCGTTGCACAGCT
||| | ||||||||||| ||  | |   |||  |        ||  | |||  | ||   |||||  || |||  | |   || |||||||||||||||||||||||||||||||||||||||| ||||||||| | || |||||||| |||||  |||| ||||| |||
gttag-ggatctctaatctctgtggtgtttttttcatttcagctgtaatgagttgacaagctcacctaagtttgattctcgtgtagCTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTCGTGTCAAGGCTACTTCAGTACTCACCAAACCTGCGCTGCACTGCT

upper sequence: LOC_Os10g37740.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G131853_T01 (Zea mays), 3'ss of exon 10
gttggtggatctctaattccatag----------cactttagttctacactgatgtaaccttctcac---aaaatttttccaactgcagCTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTTGTGTCAAGGTTGCTGCAGTACTCGCCAAATTTGCGTTGCACAGCT
||| | |||||||||||  |  ||          || || || | ||  | | || ||||  |||||   ||  |   |     || ||||||||||||||||||||||||| || ||||| ||||| ||||||||| |||| |||||||| || ||  |||| ||||| |||
gttag-ggatctctaatctccaaggtgtttttttcatttgagctgtagccagttgaaaccagctcaccctaagttcgatttccgtgtagCTTTTTGGTAAGCGCATGCCACCCGAGGCTGTCGATCTCGTGTCAAGGCTGCTCCAGTACTCACCGAACCTGCGCTGCACTGCT

upper sequence: LOC_Os10g37740.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA07G08320.1 (Glycine max), 3'ss of exon 10
-------------------gttggtggatctctaattccatagcactttagttctacactgatgtaaccttctcacaaaatttttcc---aactg-----cagCTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTTGTGTCAAGGTTGCTGCAGTACTCGCCAAATTTGCGTTGCACAGCT
                   | || |   |    || |       | | || | |   | ||||  |  ||||     | |  |  |    |||||     ||| |||||   ||| | ||||| |||||||| || ||||||||||||||| ||||||| || || |||||| | |||||||| |||
gttagcagttctttcttctgctgctatctgctaaagtattatataatataatccataaatgataaatacttccattcagacctgactgaaaactggcttccagGTTTTTCACAAGAGAATGCCGCCTGAAGCCGTGGATCTTGTGTCAAGGCTGCTGCAATATTCACCAAATCTACGTTGCACCGCT

upper sequence: LOC_Os10g37740.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA03G01850.1 (Glycine max), 3'ss of exon 10
-------------------gttggtggat-ctctaattccata-gcactttagttctacactgatgtaaccttctcacaaaatttttcc---aactg-----cagCTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTTGTGTCAAGGTTGCTGCAGTACTCGCCAAATTTGCGTTGCACAGCT
                   | || |   | ||  | |   ||| | | | || | |   | ||||  |  ||||     | |  |  |    |||||     ||| |||||   ||| | ||||||||||||||||| |||||||| |||||| |||| || || || |||||| | |||||||| |||
gttagcagttctttcctctgctgctacctgctaaagtattatatgtaatataatccataaatgataaatacttccattcagacctgactgaaaactggcttccagGTTTTTCACAAGAGAATGCCACCTGAAGCTGTGGATCTTGTATCAAGGCTGCTTCAATATTCACCAAATCTACGTTGCACTGCT

upper sequence: LOC_Os10g37740.1 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv15s0048g02010.t01 (Vitis vinifera), 3'ss of exon 10
---------------------gttggtgg-atctctaattccatagcactttagttctacac-tgatgtaaccttctcacaaaatttttccaa--------ctgcagCTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTTGTGTCAAGGTTGCTGCAGTACTCGCCAAATTTGCGTTGCACAGCT
                     || | |   ||||      | | | ||||    ||  | |  | || |  |  |  |  |||  || |  ||         | ||||||||   |||||| ||||| || |||||||| |||||||| |||||| |||| ||||| |||||||||||| | ||||| || 
gtttgtcaacaattctaaagggtagatcatatctgctgcccgacatcactgatatttgataaattatatttctatagccaaaagcttatttaagttttgttttccagCTTTTCCATAAGCGAATGCCCCCAGAAGCTGTGGATCTTGTATCAAGGCTGCTTCAGTATTCGCCAAATTTGAGATGCACCGCC

upper sequence: LOC_Os10g37740.1 (Oryza sativa), 3'ss of exon 10
lower sequence: PP1S306_62V6.1 (Physcomitrella patens), 3'ss of exon 8
--------------------------------------------------------------------------------------------------gttggtggatctctaattccatagcactttagttctacactgatgtaaccttctcacaaaat------ttttccaactgcagCTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTTGTGTCAAGGTTGCTGCAGTACTCGCCAAATTTGCGTTGCACAGCT
                                                                                                    | | |    ||    |   | | |  || | | |  ||    ||||||  |       ||      | |   || ||||| ||||    || ||||||||||||||||| |||||  | ||||||||| | || |||||||| |||||| |||| ||||  |||
gtatgttttttgtgcgaatgctatgatgtcatcctgggtgttgcggttgtagtgcggtagtggatgtgggtcagcctttctcgtgtagcggcattgttagttgcgtgcgtcgtggtttgttggatgttgggttttgacgacggtaaccggcgtttggtatggccgatgtgggaattgcagGTTTTCCACAAACGCATGCCACCTGAAGCAGTTGACTTGGTGTCAAGGCTCCTTCAGTACTCTCCAAATCTGCGGTGCAACGCT

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|88580059|gb|CI692059.1|CI692059
EST:     ACTATTCTGAATTCAAATTCCCTCAGATAAAAGCTCATCCATGGCACAAG                         CTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTTGTGT
genomic: ACTATTCTGAATTCAAATTCCCTCAGATAAAAGCTCATCCATGGCACAAGgttggtggat ... ccaactgcagCTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTTGTGT
EST: gi|88361945|gb|CI682122.1|CI682122
EST:     ACTATTCTGAATTCAAATTCCCTCAGATAAAAGCTCATCCATGGCACAAG                         CTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTTGTGTCAAGGTTG
genomic: ACTATTCTGAATTCAAATTCCCTCAGATAAAAGCTCATCCATGGCACAAGgttggtggat ... ccaactgcagCTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTTGTGTCAAGGTTG
EST: gi|29666991|gb|CB663266.1|CB663266
EST:     ACTATTCTGAATTCAAATTCCCTCAGATAAAAGCTCATCCATGGCACAAG                         CTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTTGTGTCAAGGTTG
genomic: ACTATTCTGAATTCAAATTCCCTCAGATAAAAGCTCATCCATGGCACAAGgttggtggat ... ccaactgcagCTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTTGTGTCAAGGTTG
EST: gi|426398|gb|D22261.1|D22261
EST:     ACTATTCTGAATTCAAATTCCCTCAGATAAAAGCTCATCCATGGCACAAG                         CTTTTTGGGAAGC
genomic: ACTATTCTGAATTCAAATTCCCTCAGATAAAAGCTCATCCATGGCACAAGgttggtggat ... ccaactgcagCTTTTTGGTAAGC
EST: gi|58679635|gb|CK068322.1|CK068322
EST:     ACTATTCTGAATTCAAATTCCCTCAGATAAAAGCTCATCCATGGCACAAG                         CTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTTGTGTCAAGGTTG
genomic: ACTATTCTGAATTCAAATTCCCTCAGATAAAAGCTCATCCATGGCACAAGgttggtggat ... ccaactgcagCTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTTGTGTCAAGGTTG

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: 60 (upstream exon), 75 (downstream exon)
Score: 25

ATTTTGGGTACACCAACTAGAGAAGAAATCAGGTGCATGAATCCAAACTATTCTGAATTCAAATTCCCTCAGATAAAAGCTCATCCATGGCACAAGgttggtggat ... ccaactgcagCTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTTGTGTCAAGGTTGCTGCAGTACTCGCCAAATTTGCGTTGCACAGCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagcactttagttctacactgatgtaaccttctcacaaaatttttccaactgcagCTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTTGTGTCAAGGTTGCTGCAGTACTCGCCAAATTTGCGTTGCACAGCT
                             ttctcac  putative branch site (score: 25)
                                        tttttcc  putative PPT
                                  acaaaattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggtggatctctaattccatagcactttagttctacactgatgtaaccttctcacaaaatttttccaactgcagCTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTTGTGTCAAGGTTGCTGCAGTACTCGCCAAATTTGCGTTGCACAGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG