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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagagcatgatatttttattagtttctgcaaaatgataatttggattgatgggagtgtctggtgatgtatgtgttcacattttgtaaacccttatgcagATATTTGTTATGTGGCTTGATTTTGTCACATATTTGCACCATCATGGCCATGAGGACAAGCTTCCTTGGTACCGTGGAAAG

Basic information

species Oryza sativa
transcript LOC_Os03g18070.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g18070.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G128971_T03 (Zea mays), 3'ss of exon 1
gtaagagcatgatatttttatt--------agtttctgcaaaat--gataatttggattgatgggagtgtctggtgatgtatgtgttcacattttgtaaacccttatgcagATATTTGTTATGTGGCTTGATTTTGTCACATATTTGCACCATCATGGCCATGAGGACAAGCTTCCTTGGTACCGTGGAAAG
||||||||   ||    |  |         |  ||||||||||   ||||||||| || | |||  || | ||||| ||||  | |       |  |       | ||||| ||||||||   ||||| ||| | |||||||| ||||||||||||||||| || ||||||||||| |||||||||||||||
gtaagagcggcatgccctcctcttcggcccaacttctgcaaaaaaagataatttgaatgggtggt-gtctgtggtgctgtaaatttatgttcctgctgg---tgtgtgcagGTATTTGTTGCTTGGCTGGATATGGTCACATACTTGCACCATCATGGCCACGAAGACAAGCTTCCCTGGTACCGTGGAAAG

upper sequence: LOC_Os03g18070.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G074401_T01 (Zea mays), 3'ss of exon 5
gtaagagc-atgatatttttatt-------agtttctgcaaaatgataatttggattgatgggagtgtctggtgatgtatgtgttcacattttgtaaacccttatgcagATATTTGTTATGTGGCTTGATTTTGTCACATATTTGCACCATCATGGCCATGAGGACAAGCTTCCTTGGTACCGTGGAAAG
|||||||| |   |  || | ||       |  |||||||||| |||||| || ||   |||  || | ||||| || |  |         |  |       | ||||| ||||||||   ||||| ||| | || ||||| ||||||||||||||||| || ||||||||||| |||||||||||| ||
gtaagagccacattccttctcttcagtcccaacttctgcaaaaagataatctgaatgtgtggt-gtctgtggtgctggaaattgatgtggctgctgcttgtgtgtgcagGTATTTGTTGCTTGGCTGGATATGGTTACATACTTGCACCATCATGGCCACGAAGACAAGCTTCCCTGGTACCGTGGACAG

upper sequence: LOC_Os03g18070.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA01G29630.1 (Glycine max), 3'ss of exon 5
gtaagagcatgatatttttattagtttctgcaaaatgataatttggattgatgggagtgtc-tggtgatgtatgtgttcacattttgtaaacccttatgcagATATTTGTTATGTGGCTTGATTTTGTCACATATTTGCACCATCATGGCCATGAGGACAAGCTTCCTTGGTACCGTGGAAAG
||||   |    | |||| |||||   ||   || |  ||||  |  ||  |   ||  ||    | | ||     ||    ||||||||       || |||| |||||||||||| | ||||| || || |||||||| || ||||||||||| |||||| | |||||||| |||||| ||
gtaaattccacctcttttgattagacactt--aattagtaatgagtctttcttttagaatcacaatcaagtcctaatttgacttttgtaat------tgaagATTTTTGTTATGTGGTTGGATTTGGTGACTTATTTGCATCACCATGGCCATGAAGACAAGTTACCTTGGTATCGTGGAGAG

upper sequence: LOC_Os03g18070.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA03G07570.1 (Glycine max), 3'ss of exon 5
gtaagagcatgatattttt---attagtttctgcaaaatga---taatttggattgatgggagtgtctggtgatgtatgtgttcacattttgtaaacc--cttatgca------gATATTTGTTATGTGGCTTGATTTTGTCACATATTTGCACCATCATGGCCATGAGGACAAGCTTCCTTGGTACCGTGGAAAG
||||   |    | |||||   | ||  |  |  ||| | |   ||||| | ||||         | | |      || |  |   |  |  |||     ||| || |      ||| |||||||||||| | ||||| || || |||||||| || ||||||||||| |||||  | |||||||| |||||| ||
gtaaattccatctctttttctaactacgtattagaaacttaatataattagtattggatctttctttttgaatcaaatctagttctaactcctaatttgtcttttgtaattgaagATTTTTGTTATGTGGTTGGATTTGGTGACTTATTTGCATCACCATGGCCATGAAGACAAATTACCTTGGTATCGTGGAGAG

upper sequence: LOC_Os03g18070.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA07G18350.1 (Glycine max), 3'ss of exon 5
gtaagagcatgatatttttattagtttctgcaaaatgataatttggattgatgggagtgtctggtgatgtatgtgttcacattttgtaaacccttatgcagATATTTGTTATGTGGCTTGATTTTGTCACATATTTGCACCATCATGGCCATGAGGACAAGCTTCCTTGGTACCGTGGAAAG
     ||  |  |    || |   |   | |||  || |  ||    ||||    |   |    ||| ||     ||    |||  | ||      || ||||||| || |||||| | ||||| || || ||||||||||||||||||||||| | |||  | |||||||| |||||||||
--gtaagtttcttccccttttccatcatttcaa--tggttcttctttttgaataaaaaatg-aatgaagttctcatttgactttcttgaaat----tgaagATATTCGTCATGTGGTTGGATTTGGTGACTTATTTGCACCATCATGGCCATGAAGGCAAATTGCCTTGGTATCGTGGAAAG

upper sequence: LOC_Os03g18070.1 (Oryza sativa), 3'ss of exon 5
lower sequence: AT5G05580.1 (Arabidopsis thaliana), 3'ss of exon 5
gtaagagca--tgatatttttattagtttctgcaaaatgataatttggattgatgggagtgtctggtgatgtatgtgttcac---attttgtaaaccc---ttatgcagATATTTGTTATGTGGCTTGATTTTGTCACATATTTGCACCATCATGGCCATGAGGACAAGCTTCCTTGGTACCGTGGAAAG
|||    |   |  | |   | |  ||||| |  |||    | | || |||  |  |        |   || | ||||| |    | |||  |||| |   | |||||||||||||| |||||| | || || ||||| || |||||||| ||||| ||||| |||||||| |||||||| |||||||||
gtatcctctacttctgtacctctccgtttcagacaaacttgattatgtattcctttgttgcctcagatgtgaaggtgtttattggaattttcaaacacaattaatgcagATATTTGTAATGTGGTTGGACTTCGTCACTTACTTGCACCACCATGGACATGAAGACAAGCTCCCTTGGTATCGTGGAAAG

upper sequence: LOC_Os03g18070.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv08s0105g00430.t01 (Vitis vinifera), 3'ss of exon 5
gtaagagcatgatatt----tttattagtttctgca------aaatgataatttggattgatgggagtgtc-tggtgatgt-atgtgtt-cacatt----ttg--taaacccttatgcagATATTTGTTATGTGGCTTGATTTTGTCACATATTTGCACCATCATGGCCATGAGGACAAGCTTCCTTGGTACCGTGGAAAG
|||| | |||  |  |    |  ||   ||||| ||       ||||| ||||    ||| |     |  | |  | |  | || |||| || |||    |||  |     |||   ||||| |||||||||||||| |||||||| || ||| |||| || ||||| ||||| || || ||||||||||| |||||||||
gtaa-atcatatttctcccctccatatatttctacacttgaggaatga-aattcatcttgctttttcttccctaatcacatcatatgtttcatattgactttggctgtttgctttgtcagATTTTTGTTATGTGGCTGGATTTTGTGACTTATCTGCATCACCATGGTCATGATGATAAACTTCCTTGGTATCGTGGAAAG

upper sequence: LOC_Os03g18070.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv13s0067g01120.t01 (Vitis vinifera), 3'ss of exon 5
gtaagagcatgatatttttattagtttctgcaaaatgataatttggattgatgggagtgtctggtgatgtatgtgttcacattttgtaaaccctt---atgcagATATTTGTTATGTGGCTTGATTTTGTCACATATTTGCACCATCATGGCCATGAGGACAAGCTTCCTTGGTACCGTGGAAAG
|| || |||       ||| ||||||| ||     |  |  | | |  || || |    | | | | | ||       |   |||| ||   |     |||||||| || || |||||| | ||||| || || || ||||| || ||||||||||| || |||||||||||||| |||||||||
gtcagtgcag------tttcttagtttttg-----ttgttttcttggctgttgagttcatgttg-gttttactcagctaagctttgaaacttccatgaatgcagATTTTCGTCATGTGGTTGGATTTAGTGACTTACTTGCATCACCATGGCCATGAAGAGAAGCTTCCTTGGTATCGTGGAAAG

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|58587962|gb|CF986270.1|CF986270
EST:     TTGTGATGGGGCCCCTCAAAATGTTAAAGCTCTATGCTGTTCCATACGTG                         ATATTTGTCATGTGGCTTGATTT-GTCACATACTTGCACCATCATG
genomic: TTGTGATGGGGCCCCTCAAAATGTTAAAGCTCTATGCTGTTCCATACGTGgtaagagcat ... ccttatgcagATATTTGTTATGTGGCTTGATTTTGTCACATATTTGCACCATCATG
EST: gi|29684208|gb|CB680483.1|CB680483
EST:     TTGTGATGGGGCCCCTCAAAATGTTAAAGCTCTATGCTGTTCCATACGTG                         ATATTTGTTATGTGGCTTGATTTTGTCACATATTTGCACCATCATGGCCAT
genomic: TTGTGATGGGGCCCCTCAAAATGTTAAAGCTCTATGCTGTTCCATACGTGgtaagagcat ... ccttatgcagATATTTGTTATGTGGCTTGATTTTGTCACATATTTGCACCATCATGGCCAT
EST: gi|29618634|gb|CB623646.1|CB623646
EST:     TTGTGATGGGGCCCCTCAAAATGTTAAAGCTCTATGCTGTTCCATACGTG                         ATATTTGTTATGTGGCTTGATTTTGTCACATACTTGCACCATCATGGCCAT
genomic: TTGTGATGGGGCCCCTCAAAATGTTAAAGCTCTATGCTGTTCCATACGTGgtaagagcat ... ccttatgcagATATTTGTTATGTGGCTTGATTTTGTCACATATTTGCACCATCATGGCCAT
EST: gi|89195878|gb|CI007297.1|CI007297
EST:     TTAAAGCTCTATGCTGTTCCATACGTG                         ATATTTGTTATGTGGCTTGATTTTGTCACATATTTGCACCATCATGGCCAT
genomic: TTAAAGCTCTATGCTGTTCCATACGTGgtaagagcat ... ccttatgcagATATTTGTTATGTGGCTTGATTTTGTCACATATTTGCACCATCATGGCCAT

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), 67 (downstream exon)
Score: 46

ATCAACTGCATCCTGGCTGGCAATGGTTGGGATTCTTGCTGGTCTGACCTTTGTGATGGGGCCCCTCAAAATGTTAAAGCTCTATGCTGTTCCATACGTGgtaagagcat ... ccttatgcagATATTTGTTATGTGGCTTGATTTTGTCACATATTTGCACCATCATGGCCATGAGGACAAGCTTCCTTGGTACCGTGGAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgatgggagtgtctggtgatgtatgtgttcacattttgtaaacccttatgcagATATTTGTTATGTGGCTTGATTTTGTCACATATTTGCACCATCATGGCCATGAGGACAAGCTTCCTTGGTACCGTGGAAAG
 gattgat  putative branch site (score: 46)
                                            cccttat  putative PPT
                                  attttgtaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagagcatgatatttttattagtttctgcaaaatgataatttggattgatgggagtgtctggtgatgtatgtgttcacattttgtaaacccttatgcagATATTTGTTATGTGGCTTGATTTTGTCACATATTTGCACCATCATGGCCATGAGGACAAGCTTCCTTGGTACCGTGGAAAG

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