Sequence
atgc intronic sequence ATGC exonic sequencegtgtgctttgaaatcttggaactaatttatgtgtagtttacattcgtatacgtatgcagtcacatttgtaaattatacttgtagaatgctaggctatttttatgacatagttctattcttttgtccagAATTTCCTTTTCACAACCAGGGATGAAAATGCTCCCATGAAGTTGATTGATTTTGGTCTCTCTGATTTCATTAGACCAG
Basic information
species | Oryza sativa |
transcript | LOC_Os06g50030.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g50030.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G115518_T02 (Zea mays), 3'ss of exon 4
-----------------------------------------------gtgtgctttgaaatcttggaactaatttatgtgtagtttacattcgtatacgtatgcagtcacatttgta-------aattatacttgta--gaatgctaggctat-ttttatgacatagtt-ctat---tcttttgtccagAATTTCCTTTTCACAACCAGGGATGAAAATGCTCCCATGAAGTTGATTGATTTTGGTCTCTCTGATTTCATTAGACCAG
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gtatgcttgaatcactttgtgtatagtttgtatatatgtacagtctagtatgtgtttga--ctggggttttacttctgc-catcgtatttaactgtacttgtttttttatatttaagtgacagcaataatgcttgttttgaaagctaggctgccttttgtgacacaattgctatatttcattggcacagAATTTTCTCTTCACAACAAGAGATGAAAGCGCTCCTATGAAGTTGATTGACTTTGGTCTGTCAGATTTTATTAGACCAG
upper sequence: LOC_Os06g50030.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA07G05750.1 (Glycine max), 3'ss of exon 4
--gtgtgctttgaaatcttggaacta-atttatgtgtagt--ttacattcgtatacgtatgcagtcacatttgtaaattatacttgtagaatgctaggctatttttatgacatagttctattcttttgtccagAATTTCCTTTTCACAACCAGGGATGAAAATGCTCCCATGAAGTTGATTGATTTTGGTCTCTCTGATTTCATTAGACCAG
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gtttgtgctttaaattatcatccatataataatttgtaatgataacatctagttctgtttttaatattac--gaggattaattatatagaatatcaa-taatgttgattcttttttggagtttgcttttacagAATTTCCTCTACACTTCGAGAAGTGAAGATGCTGACATGAAGTTGATTGATTTTGGTCTTTCTGACTTCATCCGACCAG
upper sequence: LOC_Os06g50030.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA16G02340.1 (Glycine max), 3'ss of exon 5
--gtgtgctttgaa--atcttggaactaatttatgtgtagt--ttacattcgtatacgtatgcagtcacatttgtaaattatacttgtagaatgctaggctatttttatgacatagttctattct-tttgtccagAATTTCCTTTTCACAACCAGGGATGAAAATGCTCCCATGAAGTTGATTGATTTTGGTCTCTCTGATTTCATTAGACCAG
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gtttgtgctttaaatcatcatccatataata-atttgtagtgataacatctagttctttttttaatatcat--gaggattaattatataagaatatcaataatgttgattctttttttggaatttgcttttacagAATTTCCTCTACACTTCCAGAAGTGAAGATGCTGACATGAAGTTGATTGATTTTGGTCTTTCTGACTTCATCCGGCCAG
upper sequence: LOC_Os06g50030.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv16s0098g01140.t01 (Vitis vinifera), 3'ss of exon 4
---------------------gtgtgctttgaaatcttggaactaat-ttatgtgtag------tttacattcgtatacgtatgcagtcacatttgtaaat-tatac--ttgta---gaatgctaggct-atttttatgacatagttctattc--------ttttgtccagAATTTCCTTTTCACAACCAGGGATGAAAATGCTCCCATGAAGTTGATTGATTTTGGTCTCTCTGATTTCATTAGACCAG
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gtatagtctaatgaacataatatatatgttattaatttaactctattgttgtatatggaatgaactgatagtcttctgcttgcacagtcaactgtgtgcttatgtgccattgtgtctaattgtcattcccactttcaacaaattactttatttacttctaattctctgcagAATTTTCTTTTTACCACAAGGGATGAGGATGCTCCGATGAAGGTTATTGATTTTGGTCTTTCTGATTTTATTAGAACAGMapped 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|58670971|gb|CK059657.1|CK059657EST: TAGCCTTCTGTCATCTTCAGGGGGTAGTGCATCGTGATTTGAAGCCAGAG AA-TTCCTTTTCACAACCAGGGATGAAAATGCTCCCATGAAGTTGATTGAT
genomic: TAGCCTTCTGTCATCTTCAGGGGGTAGTGCATCGTGATTTGAAGCCAGAGgtgtgctttg ... ttttgtccagAATTTCCTTTTCACAACCAGGGATGAAAATGCTCCCATGAAGTTGATTGAT
EST:
gi|33676550|gb|CF304789.1|CF304789EST: TAGCCTTCTGTCATCTTCAGGGGGTAGTGCATCGTGATTTGAAGCCAGAG AATTTCCTTTTCACAACCAGGGATGAAAATGCTCCCATGAAGTTGATTGAT
genomic: TAGCCTTCTGTCATCTTCAGGGGGTAGTGCATCGTGATTTGAAGCCAGAGgtgtgctttg ... ttttgtccagAATTTCCTTTTCACAACCAGGGATGAAAATGCTCCCATGAAGTTGATTGAT
EST:
gi|58592232|gb|CF990540.1|CF990540EST: TAGCCTTCTGTCATCTTCAGGGGGTAGTGCATCGTGATTTGAAGCCAGAG AATTTCCTTTTCACAACCAGGGATGAAAATGCTCCCATGAAGTTGATTGAT
genomic: TAGCCTTCTGTCATCTTCAGGGGGTAGTGCATCGTGATTTGAAGCCAGAGgtgtgctttg ... ttttgtccagAATTTCCTTTTCACAACCAGGGATGAAAATGCTCCCATGAAGTTGATTGAT
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:
66 (upstream exon),
73 (downstream exon)
Score:
10ATACACAGAGGAAGATGCCAAAGCGATTGTTGTACAGATTTTGAGCGTAGTAGCCTTCTGTCATCTTCAGGGGGTAGTGCATCGTGATTTGAAGCCAGAGgtgtgctttg ... ttttgtccagAATTTCCTTTTCACAACCAGGGATGAAAATGCTCCCATGAAGTTGATTGATTTTGGTCTCTCTGATTTCATTAGACCAG
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatacttgtagaatgctaggctatttttatgacatagttctattcttttgtccagAATTTCCTTTTCACAACCAGGGATGAAAATGCTCCCATGAAGTTGATTGATTTTGGTCTCTCTGATTTCATTAGACCAG
ttctattcttttgtcc CT-rich tract
tatttttatgacata TA-rich tract