Sequence
atgc intronic sequence ATGC exonic sequence...ggaacagggagagtaacagtttcttgctctgaatttttcaactgttatcttgagctgaattatttactgttttgctaagtgattgttggtgaatttgcagGTGTCATACTCGCTGCTGATCTTCTTCTGCGGGATGTTCATCACGGTGGATGGATTCAACAAGACTGGAATTCCAAACACTCTCTGGGAGCTCGTCGAGC
Basic information
species | Oryza sativa |
transcript | LOC_Os10g31040.4 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os10g31040.4 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G060742_T01 (Zea mays), 3'ss of exon 2
ggaacagggagagtaacagtttcttgctctgaatttttcaactgttatcttgagctgaat-tatttactgttttgctaagtgattgttggtgaatttgcagGTGTCATACTCGCTGCTGATCTTCTTCTGCGGGATGTTCATCACGGTGGATGGATTCAACAAGACTGGAATTCCAAACACTCTCTGGGAGCTCGTCGAGC
||| | | || ||| || || | | || || | | | || | | ||| | |||||||||||||||| ||||||||||||||||||| |||||||| ||||| || || ||||||| ||| || || || || | ||||||||||| ||||| |
------------gtactgtgctgccattggcaacctttt--cttttggccagccatgcatgcacgtgatacactgatgacgacgatttgcttgcgctgcagGTGTCATACTCTTTGCTGATCTTCTTCTGCGGCATGTTCATAACGGTCGACGGCTTCAACAGGACCGGCATACCCAATGCGCTCTGGGAGCTGGTCGAAC
upper sequence: LOC_Os10g31040.4 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G347174_T02 (Zea mays), 3'ss of exon 2
ggaacagggagagtaacagtttcttgctctgaatttttcaactgttatcttgagctgaattatttactgttttgctaagtgattgttggtgaatttgcagGTGTCATACTCGCTGCTGATCTTCTTCTGCGGGATGTTCATCACGGTGGATGGATTCAACAAGACTGGAATTCCAAACACTCTCTGGGAGCTCGTCGAGC
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--------------------gtacggcactgcactcctgcactcctgctctga--tgaatccatgatggtt----tacgttacgac-----acactgcagGTGTCCTACTCTTTGCTCATCTTCTTCTGTGGGATGTTCATAACGGTCGACGGCTTCAACAAGACCGGCATACCCAACGCGCTCTGGGAGCTGGTCGAGC
upper sequence: LOC_Os10g31040.4 (Oryza sativa), 3'ss of exon 2
lower sequence: AT1G02260.1 (Arabidopsis thaliana), 3'ss of exon 2
ggaacagggagagtaacagtttcttgctctgaatttttcaactgttatcttgagctgaattatttactgttttgctaagtgattgttggtgaatttgcagGTGTCATACTCGCTGCTGATCTTCTTCTGCGGGATGTTCATCACGGTGGATGGATTCAACAAGACTGGAATTCCAAACACTCTCTGGGAGCTCGTCGAGC
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--------------------gtgaaaaccaaattttcttaa--actctttagagatacaat-tcaaagatcttatcaaa-----gttgtaacttttgcagGTATCGTATTCGCTTTTGATCTTTTTCTGCGGGATGTTCATAACCGTTGATGGATTCAACAAAACTGGTATCCCTACCGCTCTATGGGACCTAATGGAGC
upper sequence: LOC_Os10g31040.4 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv16s0050g00780.t01 (Vitis vinifera), 3'ss of exon 1
---------ggaacagggagagtaacagtt--tcttgctctga-atttttcaactgttatcttgagctgaattattt---------actgttttgctaagtgattgttggtgaatttg--cagGTGTCATACTCGCTGCTGATCTTCTTCTGCGGGATGTTCATCACGGTGGATGGATTCAACAAGACTGGAATTCCAAACACTCTCTGGGAGCTCGTCGAGC
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gtaaaatcagcaatacaatgcttaacttttattttcatacagagattgatgaatacttgattataatttatttgttggagaaagaaaaaactctaaaaagttctatttctcatctttgatcagGTCTCCTATTCCCTTTTGATTTTCTTCTGCGGAATGTTCATTACAGTTGATGGTTTCAACAAAACTGGAATCCCTAGCGCAGTATGGGACTTAATGGAGC
upper sequence: LOC_Os10g31040.4 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ14419 (Selaginella moellendorffii), 3'ss of exon 2
ggaacagggagagtaacagtttcttgctctgaatttttcaactgtt-atcttgagctgaattatttactg-ttttgctaagtgattgttggtgaatttgcagGTGTCATACTCGCTGCTGATCTTCTTCTGCGGGATGTTCATCACGGTGGATGGATTCAACAAGACTGGAATTCCAAACACTCTCTGGGAGCTCGTCGAGC
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ctctcatctttttctcttccttttttctcgcgttcgcggtactatggagactgtggagactaaagccttgatctcgtcctgtgctctttctttg--ttccagGTCTCTTATTCGCTGCTCGTCTTCTTTTCCGGGATGTTCATCACCGTGGATGGATTTAACAGCACTGGCGCTCCAGGCCAGTTCTGGAACGCTGTTGAGCMapped 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|33680059|gb|CF308298.1|CF308298EST: TCATCCTCCTCGCCCTCGACTTCACTGACGCCCAAGCTTGCCTCGAGAAG GTGTCATACTCGCTGCTGATCTTCTTCTGCGGGATGTTCATCACGGTGGAT
genomic: TCATCCTCCTCGCCCTCGACTTCACTGACGCCCAAGCTTGCCTCGAGAAGgtcaatcaaa ... gaatttgcagGTGTCATACTCGCTGCTGATCTTCTTCTGCGGGATGTTCATCACGGTGGAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatcttgagctgaattatttactgttttgctaagtgattgttggtgaatttgcagGTGTCATACTCGCTGCTGATCTTCTTCTGCGGGATGTTCATCACGGTGGATGGATTCAACAAGACTGGAATTCCAAACACTCTCTGGGAGCTCGTCGAGC
aattatttactgtttt 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 |
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ggaacagggagagtaacagtttcttgctctgaatttttcaactgttatcttgagctgaattatttactgttttgctaagtgattgttggtgaatttgcagGTGTCATACTCGCTGCTGATCTTCTTCTGCGGGATGTTCATCACGGTGGATGGATTCAACAAGACTGGAATTCCAAACACTCTCTGGGAGCTCGTCGAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT