Sequence
atgc intronic sequence ATGC exonic sequencegtaagaactctcaaaaactcttaaatgatgtttttcagttgtgtttacttcccagtgatttcaggccgttattgtacctgcagATGGTTGATCCAACTGGAATTGCAAATTGGTCAGTGACACATGTTGATTGGTCTGAAGGAAAATGGCATCCTAAAGCTTACAGGGCTGTTGACACAAGCT
Basic information
species | Oryza sativa |
transcript | LOC_Os06g48700.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g48700.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G099255_T01 (Zea mays), 3'ss of exon 8
gtaagaactctcaaaaactcttaaatgatgttttt----------cagttgtgtttacttcccag-----------tgatttcaggccgttattgtacctgcagATGGTTGATCCAACTGGAATTGCAAATTGGTCAGTGACACATGTTGATTGGTCTGAAGGAAAATGGCATCCTAAAGCTTACAGGGCTGTTGACACAAGCT
||||| || || | | |||| | || ||| | || || | | | | | ||| | | ||||||||||||| |||||||| | || ||||| ||||| ||||| || ||||| ||||| || |||||||| |||| |||||||||| ||||||||||
gtaagtgttcagaagcttgccccccttttgttctcttcgatcagccaacaacattttttaccgagataaaaaaaactaaactgcatctgcatctgtggccgaagATGGTTGATCCGACTGGAATCTCGAACTGGTCGGTGACGCATGTCGACTGGTCCGAAGGGAAGTGGCATCCCAAAGTCTACAGGGCTGCGGACACAAGCT
upper sequence: LOC_Os06g48700.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G114337_T01 (Zea mays), 3'ss of exon 8
-------------------------------gtaagaactctcaaa---aactcttaaatgatgtttt--tcagttgtgtttacttcccagtgatttcag--gccgtta---ttgtacctgcagATGGTTGATCCAACTGGAATTGCAAATTGGTCAGTGACACATGTTGATTGGTCTGAAGGAAAATGGCATCCTAAAGCTTACAGGGCTGTTGACACAAGCT
| | |||| | | ||| | |||| | || || | | ||| ||| || |||| || ||||||| ||| || |||||||||||||| ||||||||||| || || |||||||| ||||| ||||||||||| |||| ||||||||||| || || ||||
gtaagtgttcagaagcttgtagacgacggccttttgttctcttcgaccagccagcaaaacaacattttatttagaaaaaaaaacgaactactgaacaacactgcccttgcatttgtggcttcagATGGCTGACCCGACTGGAATTGCAAACTGGTCAGTGACGCACGTAGATTGGTCCGAAGGGAAATGGCATCCCAAAGTCTACAGGGCTGTGGATACGAGCT
upper sequence: LOC_Os06g48700.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA14G17110.1 (Glycine max), 3'ss of exon 8
gtaagaactctcaaaaactcttaaatgatgtttttcagttg-tgtttacttcccagtgatttcaggccgttattgtacctgcagATGGTTGATCCAACTGGAATTGCAAATTGGTCAGTGACACATGTTGATTGGTCTGAAGGAAAATGGCATCCTAAAGCTTACAGGGCTGTTGACACAAGCT
|| || | | | ||| | | | | | | || || | | | | | || ||| | ||||| ||||||| |||||| ||||||||||| | ||| ||||||||||||||||||||||||||||||| | | | ||| ||| || | | |
gtcagtgcaccaatctgttctcttttaaattgcaatgataggcatctatctcactcgcagctaactcatttggtgtgtatttagATGCTTGATCCTGGTGGAATCGCAAATTGGTCGATAACATATGTTGATTGGTCTGAAGGAAAATGGCATCCAAGGTCATTCAGAGCTCGGGATATTACAT
upper sequence: LOC_Os06g48700.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA13G00610.1 (Glycine max), 3'ss of exon 8
gtaagaactctcaaaaactcttaaatgatgtttttcagttgtgtttacttcccagtgatttcaggccgttattgtacctgcagATGGTTGATCCAACTGGAATTGCAAATTGGTCAGTGACACATGTTGATTGGTCTGAAGGAAAATGGCATCCTAAAGCTTACAGGGCTGTTGACACAAGCT
|| ||| | | | | | | ||| | | | | | | | | ||| || | | | ||||||||||||| ||| ||||||||||||||| | || |||||||| |||||||| |||||||||| || ||| ||||||||||| || | |
gtgagattttgaattgtaatacagttcttttgttttaactttttcagccttcagctaatt---agcttatgtctcgaatttagATGGTTGATCCTGGTGGCATTGCAAATTGGTCACTAACTCATGTTGACTGGTCTGAGAGAAAATGGCACCCAAAATCTTACAGGGCTCAGGATGTTACTT
upper sequence: LOC_Os06g48700.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA17G29670.1 (Glycine max), 3'ss of exon 8
gtaagaactctcaaaaactct----taaatgatgtttttcagt-tgtgtttacttcccagtgatttcaggccgttattgtacctgcagATGGTTGATCCAACTGGAATTGCAAATTGGTCAGTGACACATGTTGATTGGTCTGAAGGAAAATGGCATCCTAAAGCTTACAGGGCTGTTGACACAAGCT
|| || | | | ||| ||||| | | | | | | || || ||| | || || || | ||||| ||||||| |||||| ||||||||||| || ||| ||||||||||||||||||||||||||||||| | | | | ||| ||| || | | |
gtcagtccaccaatctgttctcttttaaattgcaatgataggcatttatctatctcacagctaactcgttttgt----gtgtatttagATGCTTGATCCTGGTGGAATCGCAAATTGGTCGGTAACATATGTTGATTGGTCTGAAGGAAAATGGCATCCAAGATCATTCAGAGCTCGGGATATTACTT
upper sequence: LOC_Os06g48700.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA17G06790.4 (Glycine max), 3'ss of exon 7
gtaagaactctcaaaaactcttaaatgatgttttt--cagttgtgtttacttcccagtgatttcaggccgttattgtacctgcagATGGTTGATCCAACTGGAATTGCAAATTGGTCAGTGACACATGTTGATTGGTCTGAAGGAAAATGGCATCCTAAAGCTTACAGGGCTGTTGACACAAGCT
|| |||| | || ||| | | | |||| | | || | || | || || || | | ||||||||||||| ||| |||||||| |||||| | || ||||||||||||||||| |||||||||| |||||| | ||||||||| || | |
gtgagaattt----gaattctaatacagttcttttgttaacatttttcagcctttagctaatt--agcttttgtctctgatttagATGGTTGATCCTGGTGGCATTGCAAACTGGTCACTAACTCATGTTGATTGGTCTGAGAGAAAATGGCACCCTAAATCATACAGGGCTCAGGATGTTACTT
upper sequence: LOC_Os06g48700.1 (Oryza sativa), 3'ss of exon 8
lower sequence: AT4G25870.1 (Arabidopsis thaliana), 3'ss of exon 7
gtaag---aactctcaaaaac---tcttaaatgatgtttttcagttgtgtttacttcccagtgatttcaggccgttattgtacctgcagATGGTTGATCCAACTGGAATTGCAAATTGGTCAGTGACACATGTTGATTGGTCTGAAGGAAAATGGCATCCTAAAGCTTACAGGGCTGTTGACACAAGCT
|| || | ||| | | | |||| | || |||| | | | || |||| || | || | | | | |||||| ||||||| | || || |||||||||||||||| |||||||||||||||| ||| |||||||| || | ||| | | || | |
gtgagtctatttcttcacaccccatcttttacaatcttttaagcctcttgatgctgaaaagtgtttatttgtcg--gctcttctttcagATGATTGATCCCATGGGGATCTCAAATTGGTCAGTGACGTTTGTTGATTGGTCTGAACGAAGGTGGCATCCAAAGACATACGGAGGAAACGAGATTTCAT
upper sequence: LOC_Os06g48700.1 (Oryza sativa), 3'ss of exon 8
lower sequence: AT2G19160.1 (Arabidopsis thaliana), 3'ss of exon 8
----------gtaagaactctcaaaaactcttaaatgat--gtttttcagttgtgtttacttcc-cagtgatttcaggccgttattgtacctgcagATGGTTGATCCAACTGGAATTGCAAATTGGTCAGTGACACATGTTGATTGGTCTGAAGGAAAATGGCATCCTAAAGCTTACAGGGCTGTTGACA-CAAGCT
| | ||| || | ||||| | ||||| ||| | | | ||| | | | | | | || ||||||| ||||||| ||||| ||||| || ||| | |||||| |||||||||||||||| |||| |||||||| | | |||| | ||| || | || ||
gtgagaattcattttgattctaaagagaaagaaaatgtttgattttttagtactttctttatccataatatacttatggtctgataaatttcgcagATGCTTGATCCTACTGGCATTGCTAACTGGACTGTGACATATGTTGATTGGTCTGAGAGAAAGTGGCATCCAAGAAAATACATGCCTGAAGATATCACGC-
upper sequence: LOC_Os06g48700.1 (Oryza sativa), 3'ss of exon 8
lower sequence: AT4G31350.2 (Arabidopsis thaliana), 3'ss of exon 8
--------------------gtaagaactctcaaaaactcttaaa---tgatgtttttcagttgtgtttacttcccagtgatttca--ggccgttattg--tacctgcagATGGTTGATCCAACTGGAATTGCAAATTGGTCAGTGACACATGTTGATTGGTCTGAAGGAAAATGGCATCCTAAAGCTTACAGGGCTGTTGACACAAGCT
| | | | || ||||| | | || | || | ||||| | || || | | | || | | | |||||| |||||||| |||||| ||||| ||||| || |||||||| |||||||| || || ||||||||||| || |||| || |||| |
gtcagttgtactgcttgcttgcgtcttccttttattacccttaagccttaaagtactcattttcctctaacttcatcataatctctccgctcatgatctctttctttcagATGATTGATCCAGATGGAATAGCAAACTGGTCGGTCACACATGTAGATTGGTCCGAGGGCAAATGGCATCCGAAGCTGTACAATGCAAGAGACATCACTC
upper sequence: LOC_Os06g48700.1 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv04s0008g02630.t01 (Vitis vinifera), 3'ss of exon 8
--------------------gtaagaactctcaaaaactcttaaatgatgtttttcagttgtgtttacttcccagtgatttcaggccgttattg-tacctgcagATGGTTGATCCAACTGGAATTGCAAATTGGTCAGTGACACATGTTGATTGGTCTGAAGGAAAATGGCATCCTAAAGCTTACAGGGCTGTTGACACAAGCT
|| || ||| ||| | | | | || | | | | ||||| || | || | | | |||||| | ||||| |||||||||||||| ||||| ||||||||||| |||||||| |||||||| |||||||| ||||| ||||||| | ||| || |
gtcagcacattaaactttgtactctttttcccataaaaccttgtgttaaaccctcctattatttccttgtttccaacatttcttcccactgctgctgctttcagATGATCGATCCTACTGGAATTGCAAACTGGTCTGTGACACATGTAGATTGGTCAGAAGGAAAGTGGCATCCAAAAGCATACAGGGGTCAAGACGTCAGTT
upper sequence: LOC_Os06g48700.1 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv11s0103g00490.t01 (Vitis vinifera), 3'ss of exon 8
gtaagaactctcaaaaact-----cttaa-atgatgtttttcagttgtgttt----------acttcccagtgatttcaggccgttattgtacctg-cagATGGTTGATCCAACTGGAATTGCAAATTGGTCAGTGACACATGTTGATTGGTCTGAAGGAAAATGGCATCCTAAAGCTTACAGGGCTGTTGACACAAGCT
|| ||| | | | | | ||| || || | ||| | | || | | | || | ||| | | | || | || || ||||| |||||||| ||| |||||||| |||||||| ||||||||||| |||||||||| ||| |||||||| ||| | ||||||||| || | |
gtgagatatatataccatttgttccttggtattatatcttttggctctgctctagtctcatcattcccaactgaatatggttctttcatctatttgtcagATAATTGATCCAGGTGGCATTGCAAACTGGTCAGTTACACATGTTGACTGGTCTGAAGCAAAGTGGCATCCAAAATCATACAGGGCTCAGGATGTTAATT
upper sequence: LOC_Os06g48700.1 (Oryza sativa), 3'ss of exon 8
lower sequence: PP1S38_381V6.1 (Physcomitrella patens), 3'ss of exon 7
-----------gtaagaactctcaaaaactc---ttaaatgatgtttttcagttgtgtttacttcccagtgatttcagg---ccgttattgtacctgcagATGGTTGATCCAACTGGAATTGCAAATTGGTCAGTGACACATGTTGATTGGTCTGAAGGAAAATGGCATCCTAAAGCTTACAGGGCTGTTGACACAAGCT
| ||||| | ||| || | |||| | || | | | | ||| || | ||| |||| | |||||| | ||| | | || |||||||| | ||||| |||||||||||||| || || |||||||||||||| |||| | ||||| |
gcttgtattattttgcttctctcttgcgcgtcaattagattaggtttgggatccgtagtgatatattattgacagcatgtgtccgatattactagttcagATGATGGATGCGGCCCACCTTTCAAATTGGACTGTGACCCATGTTGATTGGTCAGAGGGTAAATGGCATCCTAAGTCTTATGAGAAGACTGACATCACGGMapped 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|9865410|gb|AU101160.1|AU101160EST: TAACTGCTATTCTGATGAACACTATTTGCCAACCCTCTTTAAT ATGGTTGATCCAACTGGAATTGCAAATTGGTCAGTGACACATGTTGATTGG
genomic: TAACTGCTATTCTGATGAACACTATTTGCCAACCCTCTTTAATgtaagaactc ... gtacctgcagATGGTTGATCCAACTGGAATTGCAAATTGGTCAGTGACACATGTTGATTGG
EST:
gi|88995627|gb|CI022950.1|CI022950EST: AATGGCATAACTGCTATTCTGATGAACACTATTTGCCAACCCTCTTTAAT ATGGTTGATCCAACTGGAATTGCAAATTGGTCAGTGACACATGTTGATTGG
genomic: AATGGCATAACTGCTATTCTGATGAACACTATTTGCCAACCCTCTTTAATgtaagaactc ... gtacctgcagATGGTTGATCCAACTGGAATTGCAAATTGGTCAGTGACACATGTTGATTGG
EST:
gi|88837201|gb|CI078561.1|CI078561EST: AATGGCATAACTGCTATTCTGATGAACACTATTTGCCAACCCTCTTTAAT ATGGTTGATCCAACTGGAATTGCAAATTGGTCAGTGACACATGTTGATTGG
genomic: AATGGCATAACTGCTATTCTGATGAACACTATTTGCCAACCCTCTTTAATgtaagaactc ... gtacctgcagATGGTTGATCCAACTGGAATTGCAAATTGGTCAGTGACACATGTTGATTGG
EST:
gi|163926002|gb|EG709678.1|EG709678EST: CTATTTGCCAACCCTCTTTAAT ATGGTTGATCCAACTGGAATTGCAAATTGGTCAGTGACACATGTTGATTGG
genomic: CTATTTGCCAACCCTCTTTAATgtaagaactc ... gtacctgcagATGGTTGATCCAACTGGAATTGCAAATTGGTCAGTGACACATGTTGATTGG
EST:
gi|88833767|gb|CI077248.1|CI077248EST: AATGGCATAACTGCTATTCTGATGAACACTATTGGCCAACCCTCTTTAAT ATGGTTGATCCAACTGGAATTGCAAATTGGTCAGTGACACATGTTGATTGG
genomic: AATGGCATAACTGCTATTCTGATGAACACTATTTGCCAACCCTCTTTAATgtaagaactc ... gtacctgcagATGGTTGATCCAACTGGAATTGCAAATTGGTCAGTGACACATGTTGATTGG
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),
73 (downstream exon)
Score:
18CCGGGAAACGAATGGCATAACTGCTATTCTGATGAACACTATTTGCCAACCCTCTTTAATgtaagaactc ... gtacctgcagATGGTTGATCCAACTGGAATTGCAAATTGGTCAGTGACACATGTTGATTGGTCTGAAGGAAAATGGCATCCTAAAGCTTACAGGGCTGTTGACACAAGCT
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtttttcagttgtgtttacttcccagtgatttcaggccgttattgtacctgcagATGGTTGATCCAACTGGAATTGCAAATTGGTCAGTGACACATGTTGATTGGTCTGAAGGAAAATGGCATCCTAAAGCTTACAGGGCTGTTGACACAAGCT
ttattgta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagaactctcaaaaactcttaaatgatgtttttcagttgtgtttacttcccagtgatttcaggccgttattgtacctgcagATGGTTGATCCAACTGGAATTGCAAATTGGTCAGTGACACATGTTGATTGGTCTGAAGGAAAATGGCATCCTAAAGCTTACAGGGCTGTTGACACAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT