Sequence
atgc intronic sequence ATGC exonic sequenceGTACTGAAAGAAGATGAATCCCCCTGCATTTTTGGTCCAATTGTGAAACAGCGATGGTCTTATGCATGTGCGAAGCAGCTTATTGAGAGGCTTATTTTTGgtgagtgcagtaacttttgttattcatgtcattacctgaacactttgtaaccgtgtgctttttgagctttaaccag
Basic information
species | Oryza sativa |
transcript | LOC_Os01g73790.1 |
intron # | 4 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g73790.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G063949_T01 (Zea mays), 5'ss of exon 4
GTACTGAAAGAAGATGAATCCCCCTGCATTTTTGGTCCAATTGTGAAACAGCGATGGTCTTATGCATGTGCGAAGCAGCTTATTGAGAGGCTTATTTTTGgtgagtgcagtaacttttgttattcatgtcattacctgaacactttgtaaccgtgtgctttttgagcttta--accag----------------------
|| || ||||||||||| || ||||| |||||||||||||| |||||||| ||||||| |||||||| || ||||| ||||||||||||||| | |||||| ||| | || ||| |||||| || || | | | | | || | | | |||| | ||| ||
GTTCTTAAAGAAGATGAGTCGCCCTGTATTTTTGGTCCAATCGTGAAACAAAGATGGTCCTATGCATGCGCAAAGCAACTTATTGAGAGGCTTGTATTTGgttagtaaattagctt--gttatttttgccactgtgt-agctgatggtcttccttctcgttttaattattattgtcatttttttattgaacatccaccag
upper sequence: LOC_Os01g73790.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G167872_T02 (Zea mays), 5'ss of exon 2
GTACTGAAAGAAGATGAATCCCCCTGCATTTTTGGTCCAATTGTGAAACAGCGATGGTCTTATGCATGTGCGAAGCAGCTTATTGAGAGGCTTATTTTTGgtgagtgcagtaacttttgttattcatgtcattacctgaacactttgtaaccgtgtgctttttgagctttaaccag---------------------
|| |||||||||||||| || ||||| |||||||||||||| |||||||| |||||||| ||||| || |||||||| ||||||||||| ||||| |||||| ||| ||||| ||| | | || | | || | |||| |||| | ||| ||
GTTCTGAAAGAAGATGAGTCACCCTGTATTTTTGGTCCAATCGTGAAACAACGATGGTCCTATGCTTGCGCGAAGCAACTTATTGAGAGACTTATATTTGgtcagtagagtaaaattttgcact-gtgccgctga-tggccttcttgttctaacacttcttttatgtttttgtcattttgatttgagtatctgccag
upper sequence: LOC_Os01g73790.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA17G05440.1 (Glycine max), 5'ss of exon 2
GTACTGAAAGAAGATGAATCCCCCTGCATTTTTGGTCCAATTGTGAAACAGCGATGGTCTTATGCATGTGCGAAGCAGCTTATTGAGAGGCTTATTTTTGgtgagtgcagtaacttttgttattcatgtcattacctgaacactttgta-accgtgtgctttttgagctttaaccag------------
||||| || || |||||||| || || ||||||||| |||||| || ||| ||||||| ||||||||||| |||||| | |||||||||||| ||| ||||||| | ||| ||| | | ||| | | || ||| | | || |||| | | |
GTACTTAAGGAGGATGAATCTCCTTGTATTTTTGGTTCAATTGAAAAGCAGAGATGGTCCTATGCATGTGCTAAGCAGTTGATTGAGAGGCTTGTTTATGgtgagctgcttttgtttggtttaattttttattgcatatactgtttccatgtcttgacctttgtctcactgagatgacattgttggcag
upper sequence: LOC_Os01g73790.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA11G19550.1 (Glycine max), 5'ss of exon 4
GTACTGAAAGAAGATGAATCCCCCTGCATTTTTGGTCCAATTGTGAAACAGCGATGGTCTTATGCATGTGCGAAGCAGCTTATTGAGAGGCTTATTTTTGgtgagtgca---gtaacttttgtt---attcatgtcattacctgaacactttg-taaccgtg--tgctttttgagctttaaccag
|| || |||||||| ||||| || |||||||||||| | || | ||| ||| | ||||||||||||||||| || ||| | ||||||||||| ||||||||||||| | ||| ||||||| | |||| || || | |||| ||| | | | | ||| | | |
GTTCTTAAAGAAGACGAATCTCCTTGCATTTTTGGTTCTATCGAGAAGCAGAGGTGGTCTTATGCATGTGCAAAACAGTTGATTGAGAGGCTGATTTTTGgtgagttgatttgtattttttgttttggtgtatgtttttttctttcaattttgataattcttactagtgtgtgatcatcggcag-
upper sequence: LOC_Os01g73790.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA12G08930.1 (Glycine max), 5'ss of exon 4
GTACTGAAAGAAGATGAATCCCCCTGCATTTTTGGTCCAATTGTGAAACAGCGATGGTCTTATGCATGTGCGAAGCAGCTTATTGAGAGGCTTATTTTTGgtgagtgcag--taacttttgttattcatgtcattacctgaacactttgt-aaccgtgtg----ctttttgagctttaaccag------
|| || |||||||| || || || |||||||||||| | |||| |||||| | ||||||||||| |||||||| ||| | ||||||||||| |||| |||||||| | | ||||||| | ||| || | |||| | || ||| || ||| | | | |
GTTCTTAAAGAAGACGAGTCTCCTTGCATTTTTGGTTCTATTGAAAAACAGAGGTGGTCTTATGCCTGTGCGAAACAGTTGATTGAGAGGCTGATTTATGgtgagttttgatttgtttttgtt-taggtgttgtttttttttttctttttcaattttgttaattctcactgatgtgtgattattggcag
upper sequence: LOC_Os01g73790.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA12G30490.2 (Glycine max), 5'ss of exon 4
GTACTGAAAGAAGATGAATCCCCCTGCATTTTTGGTCCAATTGTGAAACAGCGATGGTCTTATGCATGTGCGAAGCAGCTTATTGAGAGGCTTATTTTTGgtgagtgcagtaacttttgttattcatgtcattacctgaacactttgtaaccgtgtgctttttgagctttaaccag---------------------
||||| || || ||||| || || || ||||||||| |||||| || ||| ||||||| ||||| ||||| |||||| | |||||||||||| ||| ||||||| | | ||| ||| | | ||| | | || ||| | | | |||| |||| |
GTACTTAAGGAGGATGAGTCTCCTTGTATTTTTGGTTCAATTGAAAAGCAGAGATGGTCCTATGCCTGTGCTAAGCAGTTGATTGAGAGGCTTGTTTATGgtgagctgattttgtttggtttaattttttattgcgtacactgtttccattttttcatgtcttgacctttgtctcactgagatgacattgttggcag
upper sequence: LOC_Os01g73790.1 (Oryza sativa), 5'ss of exon 4
lower sequence: AT1G08200.1 (Arabidopsis thaliana), 5'ss of exon 4
GTACTGAAAGAAGATGAATCCCCCTGCATTTTTGGTCCAATTGTGAAACAGCGATGGTCTTATGCATGTGCGAAGCAGCTTATTGAGAGGCTTATTTTTGgtgagtgcagtaactttt----------gttattcatgtcattac-ctgaacactttgtaaccgtgtgctttttgagctttaaccag
||||| ||||||||| |||||| ||||| |||||| |||||| ||| ||| | ||||| ||||| ||||| ||||| ||||||||||| ||| ||| ||| || ||| || || || | || || | || | ||| | || |||| | | |
GTACTCAAAGAAGATATATCCCCTTGCATCTTTGGTTCAATTGAGAAGCAGAGGTGGTCATATGCTTGTGCAAAGCAACTTATTGAGAGACTTGTTTACGgt--atgtagttttcttacacgaaagaaattttttgtttctagacacaaaaaagtttctcacgtcacttttttctggttgcag----
upper sequence: LOC_Os01g73790.1 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv06s0061g01120.t01 (Vitis vinifera), 5'ss of exon 4
GTACTGAAAGAAGATGAATCCCCCTGCATTTTTGGTCCAATTGTGAAACAGCGATGGTCTTATGCATGTGCGAAGCAGCTTATTGAGAGGCTTATTTTTGgtgagtg--------cagtaacttttgttattcatgtcattacctgaacactttgtaaccgtgtgctttttgagctttaaccag---------
|| || |||||||||| |||||||||||||||||||| |||| ||| ||| | ||||| ||||| ||||| ||||| | ||||||||| | |||| ||||||||| || | | | ||| | ||| | || | | | || | | | |||| | ||| ||
GTCCTCAAAGAAGATGCCTCCCCCTGCATTTTTGGTCCGATTGAGAAGCAGAGGTGGTCCTATGCCTGTGCAAAGCAATTGATTGAGAGGTTGATTTATGgtgagtgaacttttccatcgatctgtacgtttcttagcat-gcgtgtgtatcatacatccttct-catttttattttttttcattgtttacag
upper sequence: LOC_Os01g73790.1 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv03s0017g00680.t01 (Vitis vinifera), 5'ss of exon 4
GTACTGAAAGAAGATGAATCCCCCTGCATTTTTGGTCCAATTGTGAAACAGCGATGGTCTTATGCATGTGCGAAGCAGCTTATTGAGAGGCTTATTTTTGgtgagtgcagtaacttttgttattcatgtcattacctga-acac-tttgtaaccgtgtgctttttgagctttaaccag----------------
| || |||||||||| |||||||||||||||||| |||||| ||| ||| ||||||| ||||| ||||| ||||| | ||||||||| | |||| |||||||| | | || | | || | || | | | | | | ||| | | |||| | | |||
CTTCTCAAAGAAGATGCCTCCCCCTGCATTTTTGGTTCAATTGAGAAGCAGAGATGGTCCTATGCCTGTGCAAAGCAATTAATTGAGAGGTTGATTTATGgtgagtcaact--tttccatcaatctggatgtttcttaacatgcatctgtctcatagatctttctaattttttttttattattattatttacag
upper sequence: LOC_Os01g73790.1 (Oryza sativa), 5'ss of exon 4
lower sequence: EFJ18978 (Selaginella moellendorffii), 5'ss of exon 4
GTACTGAAAGAAGATGAATCCCCCTGCATTTTTGGTCCAATTGTGAAACAGCGATGGTCTTATGCATGTGCGAAGCAGCTTATTGAGAGGCTTATTTTTGgtgagtgcagtaacttttgttattcatgtcattacctgaacactttgtaaccgtg-tgctttttgagctttaaccag
|| || || || || || || || ||||||||||| || |||| ||| ||||||||||| ||||| ||||| |||||||| || ||| | | || | |||| || ||| || |||| || | | || | ||| ||| || | | | | |||| ||||
GTGCTTAAGGAGGACGAGTCTCCTTGCATTTTTGGCCCGATTGAGAAGCAGCGATGGTCGTATGCTTGTGCAAAGCAGCTGATCGAGCGTGTCATCTATGgtaagcaaagt---ttctgtt-----tgaaagaaactaagt--catgtggttgtggtgttatataatcttt--ccag
upper sequence: LOC_Os01g73790.1 (Oryza sativa), 5'ss of exon 4
lower sequence: EFJ07025 (Selaginella moellendorffii), 5'ss of exon 4
GTACTGAAAGAAGATGAATCCCCCTGCATTTTTGGTCCAATTGTGAAACAGCGATGGTCTTATGCATGTGCGAAGCAGCTTATTGAGAGGCTTATTTTTGgtgagtgcagtaacttttgttattcatgtcattacctgaacactttgtaaccgtg-tgctttttgagctttaaccag
|| || || || || || || || ||||||||||| || |||| ||| ||||||||||| ||||| ||||| |||||||| || ||| | | || | |||| || ||| || |||| || | | || | | ||| ||| || ||| | | |||| ||||
GTCCTTAAGGAGGACGAGTCTCCTTGCATTTTTGGCCCGATTGAGAAGCAGCGATGGTCGTATGCTTGTGCAAAGCAGCTGATCGAGCGTGTCATCTATGgtaagcaaagt---ttctgtt-----tgaaagaaactaagt--tatgtggttgtggtgttttataatcttt--ccagMapped 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|58677005|gb|CK065692.1|CK065692EST: GCGATGGTCTTATGCATGTGCGAAGCAGCTTATTGAGAGGCTTATTTTTG CTGAAGGAGCAGAAAATGGCCTTGAGTTCACAATTGTGAGACCTTTCAATT
genomic: GCGATGGTCTTATGCATGTGCGAAGCAGCTTATTGAGAGGCTTATTTTTGgtgagtgcag ... ctttaaccagCTGAAGGAGCAGAAAATGGCCTTGAGTTCACAATTGTGAGACCTTTCAATT
EST:
gi|58675034|gb|CK063721.1|CK063721EST: GCGATGGTCTTATGCATGTGCGAAGCAGCTTATTGAGAGGCTTATTTTTG CTGAAGGAGCAGAAAATGGCCTTGAGTTCACAATTGTGAGACCTTTCAATT
genomic: GCGATGGTCTTATGCATGTGCGAAGCAGCTTATTGAGAGGCTTATTTTTGgtgagtgcag ... ctttaaccagCTGAAGGAGCAGAAAATGGCCTTGAGTTCACAATTGTGAGACCTTTCAATT
EST:
gi|58587635|gb|CF985943.1|CF985943EST: GCGATGGTCTTATGCATGTGCGAAGCAGCTTATTGAGAGGCTTATTTTTG CTGAAGGAGCAGAAAATGGCCTTGAGTTCACAATTGTGAGACCTTTCAATT
genomic: GCGATGGTCTTATGCATGTGCGAAGCAGCTTATTGAGAGGCTTATTTTTGgtgagtgcag ... ctttaaccagCTGAAGGAGCAGAAAATGGCCTTGAGTTCACAATTGTGAGACCTTTCAATT
EST:
gi|58587411|gb|CF985719.1|CF985719EST: GCGATGGTCTTATGCATGTGCGAAGCAGCTTATTGAGAGGCTTATTTTTG CTGAAGGAGCAGAAAATGGCCTTGAGTTCACAATTGTGAGACCTTTCAATT
genomic: GCGATGGTCTTATGCATGTGCGAAGCAGCTTATTGAGAGGCTTATTTTTGgtgagtgcag ... ctttaaccagCTGAAGGAGCAGAAAATGGCCTTGAGTTCACAATTGTGAGACCTTTCAATT
EST:
gi|58655446|gb|CK044126.1|CK044126EST: GCGATGGTCTTATGCATGTGCGAAGCAGCTTATTGAGAGGCTTATTTTTG CTGAAGGAGCAGAAGAATGGCCTTGAGTTCACAATTGTGAGACCTTTCAAT
genomic: GCGATGGTCTTATGCATGTGCGAAGCAGCTTATTGAGAGGCTTATTTTTGgtgagtgcag ... ctttaaccagCTGAAGGAGCAGAA-AATGGCCTTGAGTTCACAATTGTGAGACCTTTCAAT
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),
64 (downstream exon)
Score:
13GTACTGAAAGAAGATGAATCCCCCTGCATTTTTGGTCCAATTGTGAAACAGCGATGGTCTTATGCATGTGCGAAGCAGCTTATTGAGAGGCTTATTTTTGgtgagtgcag ... ctttaaccagCTGAAGGAGCAGAAAATGGCCTTGAGTTCACAATTGTGAGACCTTTCAATTGGATTGGACCAAGAATGGACTTTATTCCTGGTGTTGATGGTCCTAGTGA
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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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GTACTGAAAGAAGATGAATCCCCCTGCATTTTTGGTCCAATTGTGAAACAGCGATGGTCTTATGCATGTGCGAAGCAGCTTATTGAGAGGCTTATTTTTGgtgagtgcagtaacttttgttattcatgtcattacctgaacactttgtaaccgtgtgctttttgagctttaaccag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG