Sequence
atgc intronic sequence ATGC exonic sequencegtaagtgaaattcatccattttgtagccttacatttatcttttctattacatctgctttcgtgagtgcatacttaattctatttaataaatgcagAAAATTGGCTATGACAATGCTGCAGCTGTTGCTAAGAAAGCACACAAAGAAGGAAGCACATTGAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os03g21950.1 |
intron # | 15 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g21950.1 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM2G010823_T01 (Zea mays), 3'ss of exon 15
gtaagtgaaattcatccattttgtagccttacatttatcttttctattacatctgctttcgtgagtgcatacttaattctatttaataaatgcagAAAATTGGCTATGACAATGCTGCAGCTGTTGCTAAGAAAGCACACAAAGAAGGAAGCACATTGAAG
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gtaagtaaaatgaaa--atttaccttttttaaatatctgtttgtggttgtaaaaagta--gtgagc-catgcttactttt--tgaacgattgcagAAAATTGGCTATGACAATGCTGCAGCTGTTGCTAAGAAAGCCCACAAAGAAGGAACCACGTTGAAG
upper sequence: LOC_Os03g21950.1 (Oryza sativa), 3'ss of exon 15
lower sequence: GLYMA10G02040.1 (Glycine max), 3'ss of exon 15
gtaagtgaaattcatccattttgtagccttacatttatcttttctattacatctgctttcgtgagtgcatacttaattctatttaataaatgcagAAAATTGGCTATGACAATGCTGCAGCTGTTGCTAAGAAAGCACACAAAGAAGGAAGCACATTGAAG
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------gtaagtgtcctcttgtctacttttgtaacttgctaattt-tcacattttttt--------aaaaactgaatttaatttgtctgttccagAAAATTGGTTATGACAAGGCAGCAGCAGTTGCCAAGACAGCCCACAAAGAGGGGTGTACTCTTAAG
upper sequence: LOC_Os03g21950.1 (Oryza sativa), 3'ss of exon 15
lower sequence: GLYMA10G02040.2 (Glycine max), 3'ss of exon 15
gtaagtgaaattcatccattttgtagccttacatttatcttttctattacatctgctttcgtgagtgcatacttaattctatttaataaatgcagAAAATTGGCTATGACAATGCTGCAGCTGTTGCTAAGAAAGCACACAAAGAAGGAAGCACATTGAAG----------------------------------
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------gtaagtgtcctcttgtctacttttgtaacttgctaattt-tcacattttttt--------aaaaactgaatttaatttgtctgttccagAAAATTGGTTATGACAAGGCAGCAGCAGTTGCCAAGACAGCCCACAAAGAGGGGTGTACTCTTAAGGTGATGATGCCATGTTATACTTGTTTTTCCGTTT
upper sequence: LOC_Os03g21950.1 (Oryza sativa), 3'ss of exon 15
lower sequence: GLYMA02G01920.1 (Glycine max), 3'ss of exon 15
gtaagtgaaattcatccattttgtagccttacatttatcttttctattacatctgctttcgtgagtgcatacttaattctatttaataaatgcagAAAATTGGCTATGACAATGCTGCAGCTGTTGCTAAGAAAGCACACAAAGAAGGAAGCACATTGAAG
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gtaagtg--------tcctcttgtcttctc-cggtaacttgctaattttcacatattttt-------taaacggaattgaatttgcctgtttcagAAAATTGGTTATGACAAGGCAGCAGCAGTTGCCAAGACAGCCCACAAAGAGGGGTGTACTCTTAAG
upper sequence: LOC_Os03g21950.1 (Oryza sativa), 3'ss of exon 15
lower sequence: AT2G47510.1 (Arabidopsis thaliana), 3'ss of exon 16
-----------gtaagtgaaattcatccattttgtagcc----ttacatttatcttttctattacatctgctttcgtgagtgcatacttaattctatttaataaatgc-agAAAATTGGCTATGACAATGCTGCAGCTGTTGCTAAGAAAGCACACAAAGAAGGAAGCACATTGAAG
| |||| | | | ||| || | |||| ||| || ||| | || | |||| || || | | | || | | | | | ||||||| || ||||||||||||||||| ||||| |||||||| |||||||||||| | |||||||||
gtaagtctctaaatattgaactccgcctttttagtcatccgttttaccattaggattactaatgaatgtactttgatgc-tgagttttggaatccttatcctctttaccagAAAATCGGGTATGACAATGCTGCAGCAGTTGCCAAGAAAGCTCACAAAGAAGGATGTACATTGAAG
upper sequence: LOC_Os03g21950.1 (Oryza sativa), 3'ss of exon 15
lower sequence: AT5G50950.1 (Arabidopsis thaliana), 3'ss of exon 15
gtaagt-----gaaattcatccattttgt--agccttacat-ttatcttttctattacatctgctttcgtgagtgcatacttaattctatttaataaatgcagAAAATTGGCTATGACAATGCTGCAGCTGTTGCTAAGAAAGCACACAAAGAAGGAAGCACATTGAAG----------------------------------
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gtaagtctctaaatattaaacttctttgtcaagtcatccatattctcattatgattacaaatgaatttacc--tcaatgctaattcctcctttac-----cagAAAATTGGCTATGACAATGCTGCAGCAGTAGCCAAAAGAGCTCACAAAGAAGGATGCACATTAAAGGTAAACAATAAACTATTAACGTTTTCATCACTAA
upper sequence: LOC_Os03g21950.1 (Oryza sativa), 3'ss of exon 15
lower sequence: AT5G50950.2 (Arabidopsis thaliana), 3'ss of exon 15
gtaagt-----gaaattcatccattttgt--agccttacat-ttatcttttctattacatctgctttcgtgagtgcatacttaattctatttaataaatgcagAAAATTGGCTATGACAATGCTGCAGCTGTTGCTAAGAAAGCACACAAAGAAGGAAGCACATTGAAG
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gtaagtctctaaatattaaacttctttgtcaagtcatccatattctcattatgattacaaatgaatttacc--tcaatgctaattcctcctttac-----cagAAAATTGGCTATGACAATGCTGCAGCAGTAGCCAAAAGAGCTCACAAAGAAGGATGCACATTAAAG
upper sequence: LOC_Os03g21950.1 (Oryza sativa), 3'ss of exon 15
lower sequence: Vv14s0060g01700.t01 (Vitis vinifera), 3'ss of exon 13
--------------------------------gtaag--tgaaattca-tccattttgtagccttacatttatcttttctat-tacatctgct---ttcgtgagtgcatacttaa-----ttctatttaataaatgcagAAAATTGGCTATGACAATGCTGCAGCTGTTGCTAAGAAAGCACACAAAGAAGGAAGCACATTGAAG
| | | | ||||| |||||||| | ||| |||| ||| ||| ||| | || | | | | || || | | || || || || || |||||||| |||||||| ||||||||||| ||||| |||||||| ||||| || |||| ||| | |||
gtgagtgtttttcctccgccatcatttgtttaatcatcttaagattcagtccattttat--ttttaaattttccttctctgcctacttgtgttggatgtggcaatggattttgatcgactttttacttcatgaac-cagAAAATCGGCTATGATAATGCTGCAGCGGTTGCCAAGAAAGCTCACAAGGAGGGAACCACTCTTAAG
upper sequence: LOC_Os03g21950.1 (Oryza sativa), 3'ss of exon 15
lower sequence: PP1S49_154V6.1 (Physcomitrella patens), 3'ss of exon 15
----------------------------------------------------------gtaagtgaaattcatccattttgtagccttacatttatcttttctattacatctgc--------------------tttcgtgagtg-catacttaattctatttaataaatgcagAAAATTGGCTATGACAATGCTGCAGCTGTTGCTAAGAAAGCACACAAAGAAGGAAGCACATTGAAG
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gtaagttcacttgccttctttttgtgcgtttaattaagttggacggctgctattattttgaaaggagattttattgctctatgcgtttggggttgtcttgatgagtacaattgtgtgctgagtgtggacattctctccggaagtggcattgctgatttcattcttgttgggcagAAAATTGGTTATGACAAAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAAGGGACTACATTGAAGMapped 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|3761301|gb|C98549.1|C98549EST: TCTTTGATGTTGGTGACATCTTTGANCCCT AAAATTGGCTATGACAATNCTGCAGCTGTTGCTAAGAAANCACACAAAGAA
genomic: TCTTTGATGTTGGTGACATCTTTGAACCCTgtaagtgaaa ... ataaatgcagAAAATTGGCTATGACAATGCTGCAGCTGTTGCTAAGAAAGCACACAAAGAA
EST:
gi|27548701|gb|CA767533.2|CA767533EST: TCTTTGATGTTGGTGACATCTTTGAACCCT AAAATTGGCTATGACAATGCTGCAGCTGTTGCTAAGAAAGCACACAAAGAA
genomic: TCTTTGATGTTGGTGACATCTTTGAACCCTgtaagtgaaa ... ataaatgcagAAAATTGGCTATGACAATGCTGCAGCTGTTGCTAAGAAAGCACACAAAGAA
EST:
gi|86527905|gb|CI168111.1|CI168111EST: TCTTTGATGTTGGTGACATCTTTGAACCCT AAAATTGGCTATGACAATGCTGCAGCTGTTGCTAAGAAAGCACACAAAGAA
genomic: TCTTTGATGTTGGTGACATCTTTGAACCCTgtaagtgaaa ... ataaatgcagAAAATTGGCTATGACAATGCTGCAGCTGTTGCTAAGAAAGCACACAAAGAA
EST:
gi|33793415|gb|CF322587.1|CF322587EST: TCTTTGATGTTGGTGACATCTTTGAACCCT AAAATTGGCTATGACAATGCTGCAGCTGTTGCTAAGAAAGCACACAAAGAA
genomic: TCTTTGATGTTGGTGACATCTTTGAACCCTgtaagtgaaa ... ataaatgcagAAAATTGGCTATGACAATGCTGCAGCTGTTGCTAAGAAAGCACACAAAGAA
EST:
gi|66913561|gb|CX100409.1|CX100409EST: TCTTTGATGTTGGTGACATCTTTGAACCCT AAAATTGGCTATGACAATGCTGCAGCTGTTGCTAAGAAAGCACACAAAGAA
genomic: TCTTTGATGTTGGTGACATCTTTGAACCCTgtaagtgaaa ... ataaatgcagAAAATTGGCTATGACAATGCTGCAGCTGTTGCTAAGAAAGCACACAAAGAA
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:
73 (upstream exon),
65 (downstream exon)
Score:
26TCTTTGATGTTGGTGACATCTTTGAACCCTgtaagtgaaa ... ataaatgcagAAAATTGGCTATGACAATGCTGCAGCTGTTGCTAAGAAAGCACACAAAGAAGGAAGCACATTGAAG
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttctattacatctgctttcgtgagtgcatacttaattctatttaataaatgcagAAAATTGGCTATGACAATGCTGCAGCTGTTGCTAAGAAAGCACACAAAGAAGGAAGCACATTGAAG
atttaat putative branch site (score: 26)
atacttaattctattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtgaaattcatccattttgtagccttacatttatcttttctattacatctgctttcgtgagtgcatacttaattctatttaataaatgcagAAAATTGGCTATGACAATGCTGCAGCTGTTGCTAAGAAAGCACACAAAGAAGGAAGCACATTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG