Sequence
atgc intronic sequence ATGC exonic sequencegtacagtttcgcatcgtagtccgagttcgttgtactctttttcagctagtggcatgtgacatcaatatatgagagctttttcattttttcagATTAGGATCTGTGATGTGCCTGGGTGTTACAGCTGGTGCCTATGTCCTCACTCTGTTTGCA
Basic information
species | Oryza sativa |
transcript | LOC_Os05g10740.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g10740.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM5G813363_T01 (Zea mays), 3'ss of exon 4
--------gtacagtttcgcatcgtagtccgagttcgttgtactctttttc-----agctagtggcatgtgacatcaatatatgagagctttttca---ttttttcagATTAGGATCTGTGATGTGCCTGGGTGTTACAGCTGGTGCCTATGTCCTCACTCTGTTTGCA
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gtactgtgttgtggcatggcattgtagtcctaatgcatggcttcttcattcttgaaagctactcattcggtaaccccatggatctgattttagtcacacttcattcagTTTAGGATCTGTGATGTGCCTTGGTGTCACCGCTGGTGCGTATGTTCTCACTCTCTTTGCG
upper sequence: LOC_Os05g10740.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA20G36650.1 (Glycine max), 3'ss of exon 4
------gtacagtttcgcatcgt--agtccgagttcgttgtactctttttcagctagtggcatgtgacatcaatatatgagagctttttcattttttcagATTAGGATCTGTGATGTGCCTGGGTGTTACAGCTGGTGCCTATGTCCTCACTCTGTTTGCA
|||| ||| || | | || |||| | | | ||| || || | || || || |||| || | || ||||| ||||||| ||||||||||| |||||||||||||| || ||
tattgaatacacttttagattactgaaacaagcctctttgtctttgatattcttacttggaataggattttaaccattgtccaaaaccctcttaaatcagGCTAAGGGAGGTTCTGTGCTTGGGTGTAACAGCTGGTGCTTATGTCCTCACTCTATTAGCT
upper sequence: LOC_Os05g10740.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA10G30270.2 (Glycine max), 3'ss of exon 4
------------gtacagtttcgcat-cgtagtccgagttcgttgtactctttttcagctagtggcatgtgacatcaatatatgagagctttttcattttttcagATTAGGATCTGTGATGTGCCTGGGTGTTACAGCTGGTGCCTATGTCCTCACTCTGTTTGCA
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atttgttattgaatacaattttagattcctaaaacaagcctctttgatattcttacttggaataggatttta-accattttccaaaaccctcttaaatt----agGCTAAGGGAGGTTCTGTGCTTGGGTGTAACAGCTGGTGCTTATGTCCTCACTCTATTTGCTMapped 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|29643622|gb|CB648629.1|CB648629EST: TCTGTAGAGGATCTCGCCGATCAGGTTGCGGATGTGCTCGATTTCTTCGG ATTAGGATCTGTGATGTGCCTGGGTGTTACAGCTGGTGCCTATGTCCTCAC
genomic: TCTGTAGAGGATCTCGCCGATCAGGTTGCGGATGTGCTCGATTTCTTCGGgtacagtttc ... attttttcagATTAGGATCTGTGATGTGCCTGGGTGTTACAGCTGGTGCCTATGTCCTCAC
EST:
gi|33797484|gb|CF324602.1|CF324602EST: TCTGTAGAGGATCTCGCCGATCAGGTTGCGGATGTGCTCGATTTCTTCGG ATTAGGATCTGTGATGTGCCTGGGTGTTACAGCTGGTGCCTATGTCCTCAC
genomic: TCTGTAGAGGATCTCGCCGATCAGGTTGCGGATGTGCTCGATTTCTTCGGgtacagtttc ... attttttcagATTAGGATCTGTGATGTGCCTGGGTGTTACAGCTGGTGCCTATGTCCTCAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttttcagctagtggcatgtgacatcaatatatgagagctttttcattttttcagATTAGGATCTGTGATGTGCCTGGGTGTTACAGCTGGTGCCTATGTCCTCACTCTGTTTGCA
ctttttcattttttc CT-rich tract
tttttcattttttca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacagtttcgcatcgtagtccgagttcgttgtactctttttcagctagtggcatgtgacatcaatatatgagagctttttcattttttcagATTAGGATCTGTGATGTGCCTGGGTGTTACAGCTGGTGCCTATGTCCTCACTCTGTTTGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG