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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaactctcaaaaactcttaaatgatgtttttcagttgtgtttacttcccagtgatttcaggccgttattgtacctgcagATGGTTGATCCAACTGGAATTGCAAATTGGTCAGTGACACATGTTGATTGGTCTGAAGGAAAATGGCATCCTAAAGCTTACAGGGCTGTTGACACAAGCT

Basic information

species Oryza sativa
transcript LOC_Os06g48700.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g48700.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G099255_T01 (Zea mays), 3'ss of exon 8
gtaagaactctcaaaaactcttaaatgatgttttt----------cagttgtgtttacttcccag-----------tgatttcaggccgttattgtacctgcagATGGTTGATCCAACTGGAATTGCAAATTGGTCAGTGACACATGTTGATTGGTCTGAAGGAAAATGGCATCCTAAAGCTTACAGGGCTGTTGACACAAGCT
|||||   ||  ||     |     |  |||| |           ||      |||  | || ||           | |  |    | |    |||  | | ||||||||||||| ||||||||  | || ||||| ||||| ||||| || ||||| ||||| || |||||||| ||||  ||||||||||  ||||||||||
gtaagtgttcagaagcttgccccccttttgttctcttcgatcagccaacaacattttttaccgagataaaaaaaactaaactgcatctgcatctgtggccgaagATGGTTGATCCGACTGGAATCTCGAACTGGTCGGTGACGCATGTCGACTGGTCCGAAGGGAAGTGGCATCCCAAAGTCTACAGGGCTGCGGACACAAGCT

upper sequence: LOC_Os06g48700.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G114337_T01 (Zea mays), 3'ss of exon 8
-------------------------------gtaagaactctcaaa---aactcttaaatgatgtttt--tcagttgtgtttacttcccagtgatttcag--gccgtta---ttgtacctgcagATGGTTGATCCAACTGGAATTGCAAATTGGTCAGTGACACATGTTGATTGGTCTGAAGGAAAATGGCATCCTAAAGCTTACAGGGCTGTTGACACAAGCT
                                |  |  ||||   |     |    |||  |  ||||  | ||        ||   | | |||        ||| ||    ||||  || ||||||| ||| || |||||||||||||| ||||||||||| || || |||||||| ||||| ||||||||||| ||||  ||||||||||| || || ||||
gtaagtgttcagaagcttgtagacgacggccttttgttctcttcgaccagccagcaaaacaacattttatttagaaaaaaaaacgaactactgaacaacactgcccttgcatttgtggcttcagATGGCTGACCCGACTGGAATTGCAAACTGGTCAGTGACGCACGTAGATTGGTCCGAAGGGAAATGGCATCCCAAAGTCTACAGGGCTGTGGATACGAGCT

upper sequence: LOC_Os06g48700.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA14G17110.1 (Glycine max), 3'ss of exon 8
gtaagaactctcaaaaactcttaaatgatgtttttcagttg-tgtttacttcccagtgatttcaggccgttattgtacctgcagATGGTTGATCCAACTGGAATTGCAAATTGGTCAGTGACACATGTTGATTGGTCTGAAGGAAAATGGCATCCTAAAGCTTACAGGGCTGTTGACACAAGCT
|| ||  | |  |     |||    | |  |       | |   | ||  || |    |  | |  |  ||  |||   |  ||||| |||||||   |||||| |||||||||||  | ||| ||||||||||||||||||||||||||||||| |   | | ||| |||   || |  |  |
gtcagtgcaccaatctgttctcttttaaattgcaatgataggcatctatctcactcgcagctaactcatttggtgtgtatttagATGCTTGATCCTGGTGGAATCGCAAATTGGTCGATAACATATGTTGATTGGTCTGAAGGAAAATGGCATCCAAGGTCATTCAGAGCTCGGGATATTACAT

upper sequence: LOC_Os06g48700.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA13G00610.1 (Glycine max), 3'ss of exon 8
gtaagaactctcaaaaactcttaaatgatgtttttcagttgtgtttacttcccagtgatttcaggccgttattgtacctgcagATGGTTGATCCAACTGGAATTGCAAATTGGTCAGTGACACATGTTGATTGGTCTGAAGGAAAATGGCATCCTAAAGCTTACAGGGCTGTTGACACAAGCT
|| |||  |   |         |  |  | | ||| |  | | |   | | |   | |||    ||   | |      |  |||||||||||||   ||| ||||||||||||||| | || |||||||| ||||||||  |||||||||| || ||| |||||||||||   ||    |  |
gtgagattttgaattgtaatacagttcttttgttttaactttttcagccttcagctaatt---agcttatgtctcgaatttagATGGTTGATCCTGGTGGCATTGCAAATTGGTCACTAACTCATGTTGACTGGTCTGAGAGAAAATGGCACCCAAAATCTTACAGGGCTCAGGATGTTACTT

upper sequence: LOC_Os06g48700.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA17G29670.1 (Glycine max), 3'ss of exon 8
gtaagaactctcaaaaactct----taaatgatgtttttcagt-tgtgtttacttcccagtgatttcaggccgttattgtacctgcagATGGTTGATCCAACTGGAATTGCAAATTGGTCAGTGACACATGTTGATTGGTCTGAAGGAAAATGGCATCCTAAAGCTTACAGGGCTGTTGACACAAGCT
|| ||  | |  |     |||    |||||     |  |  |  | | | ||  || |||  |  ||     ||    ||   |  ||||| |||||||   |||||| ||||||||||| || ||| ||||||||||||||||||||||||||||||| | | | | ||| |||   || |  |  |
gtcagtccaccaatctgttctcttttaaattgcaatgataggcatttatctatctcacagctaactcgttttgt----gtgtatttagATGCTTGATCCTGGTGGAATCGCAAATTGGTCGGTAACATATGTTGATTGGTCTGAAGGAAAATGGCATCCAAGATCATTCAGAGCTCGGGATATTACTT

upper sequence: LOC_Os06g48700.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA17G06790.4 (Glycine max), 3'ss of exon 7
gtaagaactctcaaaaactcttaaatgatgttttt--cagttgtgtttacttcccagtgatttcaggccgttattgtacctgcagATGGTTGATCCAACTGGAATTGCAAATTGGTCAGTGACACATGTTGATTGGTCTGAAGGAAAATGGCATCCTAAAGCTTACAGGGCTGTTGACACAAGCT
|| |||| |      || ||| | |   |  ||||   |    | || |      ||  | ||   ||  || |      |  |||||||||||||   ||| |||||||| |||||| | || |||||||||||||||||  |||||||||| |||||| | |||||||||   ||    |  |
gtgagaattt----gaattctaatacagttcttttgttaacatttttcagcctttagctaatt--agcttttgtctctgatttagATGGTTGATCCTGGTGGCATTGCAAACTGGTCACTAACTCATGTTGATTGGTCTGAGAGAAAATGGCACCCTAAATCATACAGGGCTCAGGATGTTACTT

upper sequence: LOC_Os06g48700.1 (Oryza sativa), 3'ss of exon 8
lower sequence: AT4G25870.1 (Arabidopsis thaliana), 3'ss of exon 7
gtaag---aactctcaaaaac---tcttaaatgatgtttttcagttgtgtttacttcccagtgatttcaggccgttattgtacctgcagATGGTTGATCCAACTGGAATTGCAAATTGGTCAGTGACACATGTTGATTGGTCTGAAGGAAAATGGCATCCTAAAGCTTACAGGGCTGTTGACACAAGCT
|| ||   |  |||  | | |   ||||  |  || ||||     | |   | ||    |||| ||    | ||    | | | | |||||| ||||||| |  || ||  ||||||||||||||||   |||||||||||||||| |||  |||||||| ||  | ||| | |     || |     |
gtgagtctatttcttcacaccccatcttttacaatcttttaagcctcttgatgctgaaaagtgtttatttgtcg--gctcttctttcagATGATTGATCCCATGGGGATCTCAAATTGGTCAGTGACGTTTGTTGATTGGTCTGAACGAAGGTGGCATCCAAAGACATACGGAGGAAACGAGATTTCAT

upper sequence: LOC_Os06g48700.1 (Oryza sativa), 3'ss of exon 8
lower sequence: AT2G19160.1 (Arabidopsis thaliana), 3'ss of exon 8
----------gtaagaactctcaaaaactcttaaatgat--gtttttcagttgtgtttacttcc-cagtgatttcaggccgttattgtacctgcagATGGTTGATCCAACTGGAATTGCAAATTGGTCAGTGACACATGTTGATTGGTCTGAAGGAAAATGGCATCCTAAAGCTTACAGGGCTGTTGACA-CAAGCT
           |    | ||| || |      ||||| |   ||||| |||  | | |   |||  | |    | | |   | ||       ||||||| ||||||| ||||| ||||| || ||| | |||||| ||||||||||||||||  |||| |||||||| | |   |||| | |||  || | || || 
gtgagaattcattttgattctaaagagaaagaaaatgtttgattttttagtactttctttatccataatatacttatggtctgataaatttcgcagATGCTTGATCCTACTGGCATTGCTAACTGGACTGTGACATATGTTGATTGGTCTGAGAGAAAGTGGCATCCAAGAAAATACATGCCTGAAGATATCACGC-

upper sequence: LOC_Os06g48700.1 (Oryza sativa), 3'ss of exon 8
lower sequence: AT4G31350.2 (Arabidopsis thaliana), 3'ss of exon 8
--------------------gtaagaactctcaaaaactcttaaa---tgatgtttttcagttgtgtttacttcccagtgatttca--ggccgttattg--tacctgcagATGGTTGATCCAACTGGAATTGCAAATTGGTCAGTGACACATGTTGATTGGTCTGAAGGAAAATGGCATCCTAAAGCTTACAGGGCTGTTGACACAAGCT
                    |      |  |  |  || |||||    | | ||  |    ||    | |||||    | || ||   |  | | ||    | | | |||||| ||||||||  |||||| ||||| ||||| || |||||||| |||||||| || || ||||||||||| ||    ||||  ||    ||||  |   
gtcagttgtactgcttgcttgcgtcttccttttattacccttaagccttaaagtactcattttcctctaacttcatcataatctctccgctcatgatctctttctttcagATGATTGATCCAGATGGAATAGCAAACTGGTCGGTCACACATGTAGATTGGTCCGAGGGCAAATGGCATCCGAAGCTGTACAATGCAAGAGACATCACTC

upper sequence: LOC_Os06g48700.1 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv04s0008g02630.t01 (Vitis vinifera), 3'ss of exon 8
--------------------gtaagaactctcaaaaactcttaaatgatgtttttcagttgtgtttacttcccagtgatttcaggccgttattg-tacctgcagATGGTTGATCCAACTGGAATTGCAAATTGGTCAGTGACACATGTTGATTGGTCTGAAGGAAAATGGCATCCTAAAGCTTACAGGGCTGTTGACACAAGCT
                            || || |||  |||   | |     | |  || | |     |  |    |||||   ||  |  || | | | |||||| | ||||| |||||||||||||| ||||| ||||||||||| |||||||| |||||||| |||||||| ||||| ||||||| |   |||   || |
gtcagcacattaaactttgtactctttttcccataaaaccttgtgttaaaccctcctattatttccttgtttccaacatttcttcccactgctgctgctttcagATGATCGATCCTACTGGAATTGCAAACTGGTCTGTGACACATGTAGATTGGTCAGAAGGAAAGTGGCATCCAAAAGCATACAGGGGTCAAGACGTCAGTT

upper sequence: LOC_Os06g48700.1 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv11s0103g00490.t01 (Vitis vinifera), 3'ss of exon 8
gtaagaactctcaaaaact-----cttaa-atgatgtttttcagttgtgttt----------acttcccagtgatttcaggccgttattgtacctg-cagATGGTTGATCCAACTGGAATTGCAAATTGGTCAGTGACACATGTTGATTGGTCTGAAGGAAAATGGCATCCTAAAGCTTACAGGGCTGTTGACACAAGCT
|| |||  | |  |  | |     |||   || || | |||  | | || |           | | || | ||| |   |  | ||  | ||  || |||||  ||||||||  ||| |||||||| |||||||| ||||||||||| |||||||||| ||| |||||||| ||| | |||||||||   ||    |  |
gtgagatatatataccatttgttccttggtattatatcttttggctctgctctagtctcatcattcccaactgaatatggttctttcatctatttgtcagATAATTGATCCAGGTGGCATTGCAAACTGGTCAGTTACACATGTTGACTGGTCTGAAGCAAAGTGGCATCCAAAATCATACAGGGCTCAGGATGTTAATT

upper sequence: LOC_Os06g48700.1 (Oryza sativa), 3'ss of exon 8
lower sequence: PP1S38_381V6.1 (Physcomitrella patens), 3'ss of exon 7
-----------gtaagaactctcaaaaactc---ttaaatgatgtttttcagttgtgtttacttcccagtgatttcagg---ccgttattgtacctgcagATGGTTGATCCAACTGGAATTGCAAATTGGTCAGTGACACATGTTGATTGGTCTGAAGGAAAATGGCATCCTAAAGCTTACAGGGCTGTTGACACAAGCT
            |     |||||     |     ||| || | ||||   |   ||  | |  |   | |||   || |   ||| ||||     | |||||| | ||| |  |     || |||||||| | ||||| |||||||||||||| || || ||||||||||||||  ||||   |     |||||  |   
gcttgtattattttgcttctctcttgcgcgtcaattagattaggtttgggatccgtagtgatatattattgacagcatgtgtccgatattactagttcagATGATGGATGCGGCCCACCTTTCAAATTGGACTGTGACCCATGTTGATTGGTCAGAGGGTAAATGGCATCCTAAGTCTTATGAGAAGACTGACATCACGG

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|9865410|gb|AU101160.1|AU101160
EST:     TAACTGCTATTCTGATGAACACTATTTGCCAACCCTCTTTAAT                         ATGGTTGATCCAACTGGAATTGCAAATTGGTCAGTGACACATGTTGATTGG
genomic: TAACTGCTATTCTGATGAACACTATTTGCCAACCCTCTTTAATgtaagaactc ... gtacctgcagATGGTTGATCCAACTGGAATTGCAAATTGGTCAGTGACACATGTTGATTGG
EST: gi|88995627|gb|CI022950.1|CI022950
EST:     AATGGCATAACTGCTATTCTGATGAACACTATTTGCCAACCCTCTTTAAT                         ATGGTTGATCCAACTGGAATTGCAAATTGGTCAGTGACACATGTTGATTGG
genomic: AATGGCATAACTGCTATTCTGATGAACACTATTTGCCAACCCTCTTTAATgtaagaactc ... gtacctgcagATGGTTGATCCAACTGGAATTGCAAATTGGTCAGTGACACATGTTGATTGG
EST: gi|88837201|gb|CI078561.1|CI078561
EST:     AATGGCATAACTGCTATTCTGATGAACACTATTTGCCAACCCTCTTTAAT                         ATGGTTGATCCAACTGGAATTGCAAATTGGTCAGTGACACATGTTGATTGG
genomic: AATGGCATAACTGCTATTCTGATGAACACTATTTGCCAACCCTCTTTAATgtaagaactc ... gtacctgcagATGGTTGATCCAACTGGAATTGCAAATTGGTCAGTGACACATGTTGATTGG
EST: gi|163926002|gb|EG709678.1|EG709678
EST:     CTATTTGCCAACCCTCTTTAAT                         ATGGTTGATCCAACTGGAATTGCAAATTGGTCAGTGACACATGTTGATTGG
genomic: CTATTTGCCAACCCTCTTTAATgtaagaactc ... gtacctgcagATGGTTGATCCAACTGGAATTGCAAATTGGTCAGTGACACATGTTGATTGG
EST: gi|88833767|gb|CI077248.1|CI077248
EST:     AATGGCATAACTGCTATTCTGATGAACACTATTGGCCAACCCTCTTTAAT                         ATGGTTGATCCAACTGGAATTGCAAATTGGTCAGTGACACATGTTGATTGG
genomic: AATGGCATAACTGCTATTCTGATGAACACTATTTGCCAACCCTCTTTAATgtaagaactc ... gtacctgcagATGGTTGATCCAACTGGAATTGCAAATTGGTCAGTGACACATGTTGATTGG

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: 70 (upstream exon), 73 (downstream exon)
Score: 18

CCGGGAAACGAATGGCATAACTGCTATTCTGATGAACACTATTTGCCAACCCTCTTTAATgtaagaactc ... gtacctgcagATGGTTGATCCAACTGGAATTGCAAATTGGTCAGTGACACATGTTGATTGGTCTGAAGGAAAATGGCATCCTAAAGCTTACAGGGCTGTTGACACAAGCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtttttcagttgtgtttacttcccagtgatttcaggccgttattgtacctgcagATGGTTGATCCAACTGGAATTGCAAATTGGTCAGTGACACATGTTGATTGGTCTGAAGGAAAATGGCATCCTAAAGCTTACAGGGCTGTTGACACAAGCT
                                        ttattgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagaactctcaaaaactcttaaatgatgtttttcagttgtgtttacttcccagtgatttcaggccgttattgtacctgcagATGGTTGATCCAACTGGAATTGCAAATTGGTCAGTGACACATGTTGATTGGTCTGAAGGAAAATGGCATCCTAAAGCTTACAGGGCTGTTGACACAAGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT