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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttaagaagatctataaaactgtgttgcaccattcagaactgtcaaaattctcttgttccattgaacaatttagtacttacttaaatccattatctcagGCTGTGCGCCGGCGCTTTGATAAACGTATTTACATTCCACTACCCGACCTGAAAGCAAGGCAACATATGTTTAAG

Basic information

species Oryza sativa
transcript LOC_Os01g04814.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g04814.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G088834_T01 (Zea mays), 3'ss of exon 4
gtttaagaagatctataaaactgtgttgcaccattcagaactgtcaaaattctcttgttccattgaaca--atttagtacttacttaaatccattatctcagGCTGTGCGCCGGCGCTTTGATAAACGTATTTACATTCCACTACCCGACCTGAAAGCAAGGCAACATATGTTTAAG
|  ||      |  |   ||      | | |||   | ||  || |     |  || |    |  ||||   ||| || |||      || |||| |  ||||||||||| ||  | ||||| || ||||| |||||||| ||||| ||| |||||||||||||||| |||||||||
gagtacagttttgcaccgaatacaacttcgccaa--aaaaaagtaacgtccccattatcttgtgaaacactgtttggttctttgactgattcattgttgcagGCTGTGCGGCGAAGATTTGACAAGCGTATCTACATTCCGCTACCTGACTTGAAAGCAAGGCAACACATGTTTAAG

upper sequence: LOC_Os01g04814.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G126860_T01 (Zea mays), 3'ss of exon 4
-----------------------gtttaagaagatctataaaactgtgttgcaccattcagaactgtcaaaattctcttgttccattgaacaatttagtacttacttaaatccattatctcagGCTGTGCGCCGGCGCTTTGATAAACGTATTTACATTCCACTACCCGACCTGAAAGCAAGGCAACATATGTTTAAG
                        |||   |   | |||| |  ||      || |    | | ||||   ||| ||||||   |    ||  |||||| |||    | || |||| |  ||||||||||| ||  | ||||| || ||||| |||||||| ||||| |||  |||||||||||| ||||||||||||
gttacaaaaaaaaaccacgtaccattttgcattgtatatagatttgcaa-aaacaaaaagggaatgtccccattatcttgtgaaac---actgtttagttctttggcatattcattgttgcagGCTGTGCGGCGAAGATTTGACAAGCGTATCTACATTCCGCTACCTGACACGAAAGCAAGGCAGCATATGTTTAAG

upper sequence: LOC_Os01g04814.3 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ25940 (Selaginella moellendorffii), 3'ss of exon 4
gtttaagaagatctataaaactgtgttgcaccattcagaactgtcaaaattctcttgttccattgaacaatttagtact--tacttaaatccattatctcagGCTGTGCGCCGGCGCTTTGATAAACGTATTTACATTCCACTACCCGACCTGAAAGCAAGGCAACATATGTTTAAG
                                  | || |   |    |||   |||| | || || |  |  |    |   ||||||||| |   || |||||||| ||| |||| |||||||| || ||||||||||| ||||||||| |||||||||||||||||||||| |||
---------------------------------gtgagtagaatttggatt---ttgtgcgatagagctttccatccttgtcacttaaatc-acgctcgcagGCTGTTCGCAGGCGATTTGATAAGCGCATTTACATTCCTCTACCCGACTTGAAAGCAAGGCAACATATGTTCAAG

upper sequence: LOC_Os01g04814.3 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ10867 (Selaginella moellendorffii), 3'ss of exon 4
gtttaagaagatctataaaactgtgttgcaccattcagaactgtcaaaattctcttgttccattgaacaatttagtact--tacttaaatccattatctcagGCTGTGCGCCGGCGCTTTGATAAACGTATTTACATTCCACTACCCGACCTGAAAGCAAGGCAACATATGTTTAAG
                                  | || |   |    |||   ||||   || || |  |  |    |   ||||||||| |   || |||||||| ||| |||| |||||||| || ||||||||||| ||||||||| |||||||||||||||||||||| |||
---------------------------------gtgagtagaatttggatt---ttgtgggatagagctttccatccttgtcacttaaatc-acgctcgcagGCTGTTCGCAGGCGATTTGATAAGCGCATTTACATTCCTCTACCCGACTTGAAAGCAAGGCAACATATGTTCAAG

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|29642909|gb|CB647916.1|CB647916
EST:     ACAAAGTACTGGTTCTTGCTGCTACAAACACGCCATATGCTCTAGACCAG                         GCTGTGCGCCGGCGCTTTGATAAACGTATTTACATTCCACTACCCGACCTG
genomic: ACAAAGTACTGGTTCTTGCTGCTACAAACACGCCATATGCTCTAGACCAGgtttaagaag ... attatctcagGCTGTGCGCCGGCGCTTTGATAAACGTATTTACATTCCACTACCCGACCTG
EST: gi|29660448|gb|CB656723.1|CB656723
EST:     ACAAAGTACTGGTTCTTGCTGCTACAAACACGCCATATGCTCTAGACCAG                         GCTGTGCGCCGGCGCTTTGATAAACGTATTTACATTCCACTACCCGACCTG
genomic: ACAAAGTACTGGTTCTTGCTGCTACAAACACGCCATATGCTCTAGACCAGgtttaagaag ... attatctcagGCTGTGCGCCGGCGCTTTGATAAACGTATTTACATTCCACTACCCGACCTG
EST: gi|29619358|gb|CB624370.1|CB624370
EST:     ACAAAGTACTGGTTCTTGCTGCTACAAACACGCCATATGCTCTAGACCAG                         GCTGTGCGCCGGCGCTTTGATAAACGTATTTACATTCCGCTACCCGACCTG
genomic: ACAAAGTACTGGTTCTTGCTGCTACAAACACGCCATATGCTCTAGACCAGgtttaagaag ... attatctcagGCTGTGCGCCGGCGCTTTGATAAACGTATTTACATTCCACTACCCGACCTG
EST: gi|29619357|gb|CB624369.1|CB624369
EST:     CACGCCATATGCTCTAGACCAG                         GCTGTGCGCCGGCGCTTTGATAAACGTATTTACATTCCGCTACCCGACCTG
genomic: CACGCCATATGCTCTAGACCAGgtttaagaag ... attatctcagGCTGTGCGCCGGCGCTTTGATAAACGTATTTACATTCCACTACCCGACCTG
EST: gi|300215967|gb|HO088593.1|HO088593
EST:     ACAAAGTACTGGTTCTTGCTGCTACAAACACGCCATATGCTCTAGACCAG                         GCTGTGCGCCGGCGCTTTGATAAACGTATTTACATTCCGCTACCCGACCTG
genomic: ACAAAGTACTGGTTCTTGCTGCTACAAACACGCCATATGCTCTAGACCAGgtttaagaag ... attatctcagGCTGTGCGCCGGCGCTTTGATAAACGTATTTACATTCCACTACCCGACCTG
EST: gi|29625991|gb|CB631002.1|CB631002
EST:     ACAAAGTACTGGTTCTTGCTGCTACAAACACGCCATATGCTCTAGACCAG                         GCTGTGCGCCGGCGCTTTGATAAACGTATTTACATTCCGCTACCCGACCTG
genomic: ACAAAGTACTGGTTCTTGCTGCTACAAACACGCCATATGCTCTAGACCAGgtttaagaag ... attatctcagGCTGTGCGCCGGCGCTTTGATAAACGTATTTACATTCCACTACCCGACCTG
EST: gi|29627907|gb|CB632918.1|CB632918
EST:     ACAAAGTACTGGTTCTTGCTGCTACAAACACGCCATATGCTCTAGACCAG                         GCTGTGCGCCGGCGCTTTGATAAACGTATTTACATTCCGCTACCCGACCTG
genomic: ACAAAGTACTGGTTCTTGCTGCTACAAACACGCCATATGCTCTAGACCAGgtttaagaag ... attatctcagGCTGTGCGCCGGCGCTTTGATAAACGTATTTACATTCCACTACCCGACCTG
EST: gi|29640679|gb|CB645688.1|CB645688
EST:     ACAAAGTACTGGTTCTTGCTGCTACAAACACGCCATATGCTCTAGACCAG                         GCTGTGCGCCGGCGCTTTGATAAACGTATTTACATTCCACTACCCGACCTG
genomic: ACAAAGTACTGGTTCTTGCTGCTACAAACACGCCATATGCTCTAGACCAGgtttaagaag ... attatctcagGCTGTGCGCCGGCGCTTTGATAAACGTATTTACATTCCACTACCCGACCTG
EST: gi|29643243|gb|CB648250.1|CB648250
EST:     ACAAAGTACTGGTTCTTGCTGCTACAAACACGCCATATGCTCTAGACCAG                         GCTGTGCGCCGGCGCTTTGATAAACGTATTTACATTCCACTACCCGACCTG
genomic: ACAAAGTACTGGTTCTTGCTGCTACAAACACGCCATATGCTCTAGACCAGgtttaagaag ... attatctcagGCTGTGCGCCGGCGCTTTGATAAACGTATTTACATTCCACTACCCGACCTG
EST: gi|29676832|gb|CB673107.1|CB673107
EST:     ACAAAGTACTGGTTCTTGCTGCTACAAACACGCCATATGCTCTAGACCAG                         GCTGTGCGCCGGCGCTTTGATAAACGTATTTACATTCCACTACCCGACCTG
genomic: ACAAAGTACTGGTTCTTGCTGCTACAAACACGCCATATGCTCTAGACCAGgtttaagaag ... attatctcagGCTGTGCGCCGGCGCTTTGATAAACGTATTTACATTCCACTACCCGACCTG
EST: gi|396941489|gb|HO188698.1|HO188698
EST:     ACAAAGTACTGGTTCTTGCTGCTACAAACACGCCATATGCTCTAGACCAG                         GCTGTGCGCCGGCGCTTTGATAAACGTATTTACATTCCACTACCCGACCTG
genomic: ACAAAGTACTGGTTCTTGCTGCTACAAACACGCCATATGCTCTAGACCAGgtttaagaag ... attatctcagGCTGTGCGCCGGCGCTTTGATAAACGTATTTACATTCCACTACCCGACCTG
EST: gi|58588110|gb|CF986418.1|CF986418
EST:     ACAAAGTACTGGTTCTTGCTGCTACAAACACGCCATATGCTCTAGACCAG                         GCTGTGGGCCGGCGCTTTGATAAACGTATTTACATTCCGCTACCCGACCTG
genomic: ACAAAGTACTGGTTCTTGCTGCTACAAACACGCCATATGCTCTAGACCAGgtttaagaag ... attatctcagGCTGTGCGCCGGCGCTTTGATAAACGTATTTACATTCCACTACCCGACCTG
EST: gi|33381146|gb|CF196489.1|CF196489
EST:     ACAAAGTACTGGTTCTTGCTGCTACAAACACGCCATATGCTCTNNNCCAG                         GCTGTGCGCCGGCGCTTTGATAA-CGTAT
genomic: ACAAAGTACTGGTTCTTGCTGCTACAAACACGCCATATGCTCTAGACCAGgtttaagaag ... attatctcagGCTGTGCGCCGGCGCTTTGATAAACGTAT
EST: gi|313080751|gb|HO213548.1|HO213548
EST:     ACTGGTTCTTGCTGCTACAAACACGCCATATGCTCTAGACCAG                         GCTGTGCGCCGGCGCTTTGATAAACGTATTTACATTCCGCTACCCGACCTG
genomic: ACTGGTTCTTGCTGCTACAAACACGCCATATGCTCTAGACCAGgtttaagaag ... attatctcagGCTGTGCGCCGGCGCTTTGATAAACGTATTTACATTCCACTACCCGACCTG

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: 75 (upstream exon), 69 (downstream exon)
Score: 61

GGTGTTGGCCATAATGATGACAAAGTACTGGTTCTTGCTGCTACAAACACGCCATATGCTCTAGACCAGgtttaagaag ... attatctcagGCTGTGCGCCGGCGCTTTGATAAACGTATTTACATTCCACTACCCGACCTGAAAGCAAGGCAACATATGTTTAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaattctcttgttccattgaacaatttagtacttacttaaatccattatctcagGCTGTGCGCCGGCGCTTTGATAAACGTATTTACATTCCACTACCCGACCTGAAAGCAAGGCAACATATGTTTAAG
                              tacttac  putative branch site (score: 61)
                                              ttatctc  putative PPT
                                 ttacttaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttaagaagatctataaaactgtgttgcaccattcagaactgtcaaaattctcttgttccattgaacaatttagtacttacttaaatccattatctcagGCTGTGCGCCGGCGCTTTGATAAACGTATTTACATTCCACTACCCGACCTGAAAGCAAGGCAACATATGTTTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG