Sequence
atgc intronic sequence ATGC exonic sequencegtgctcatactttgcatggattcctcatatatgattcttataattcttttttggtagatttttttttactgataagaatttactgattgatcgatttctttttgcttgcttgatgatatataaaagcatatgttttgcagGAATTTTCCTCAAGGAACAATAAGTGACATGGTTAGCGATGCTTCTGATGGGATTTCATTTGTTTGTGAGACTGTTGGTGCCTATGGAGGAGATCCTAAT
Basic information
species | Oryza sativa |
transcript | LOC_Os05g50170.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g50170.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G325504_T01 (Zea mays), 3'ss of exon 1
gtgctcatactttgcatggattcctcatatatgattcttataattcttttttggtagatttttttttactgataagaatttactgattgatcgatttctttttgcttgcttgatgatatataaaagcatatgttttgcagGAATTTTCCTCAAGGAACAATAAGTGACATGGTTAGCGATGCTTCTGATGGGATTTCATTTGTTTGTGAGACTGTTGGTGCCTATGGAGGAGATCCTAAT
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-------------------------------tcaccattatg-ttttcaacctgtacctttttaattaattttgaa----tattgactaaatgatttatttttgcttcatcggcaaaatttaa----atatggatggcagAAATTTCCCTCAAGGAACAATAAGCGACATGGTCAGTGATGCTTCTGAGGCGATATCATTCATTTGTAACAATGTTGTTAGCTTTGGAGGGGATCCTAAT
upper sequence: LOC_Os05g50170.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM5G854930_T01 (Zea mays), 3'ss of exon 5
gtgctcatactttgcatggattcctcatatatgattcttataattcttttttggtagatttttttttactgataagaatttactgattgatcgatttctttttgcttgcttgatgatatataaaagcatatgttttgcagGAATTTTCCTCAAGGAACAATAAGTGACATGGTTAGCGATGCTTCTGATGGGATTTCATTTGTTTGTGAGACTGTTGGTGCCTATGGAGGAGATCCTAAT
| | |||| || | ||| ||||| ||| | | || || ||| ||| ||||| ||||||||| | | || ||| ||||| | |||| ||||| ||||||||||||||||| |||||||| || ||||||||||| | ||| ||||| ||||| | | ||||| | || |||||| |||||||||
-------------------------------tcaccattatg-ttttcaacctgtacctttttaattaattttgag----tattgactgaatgatttatttttgcttcatcagcaaaatttaa----atatggatggcagAAATTTCCCTCAAGGAACAATAAGCGACATGGTCAGTGATGCTTCTGAGGCGATATCATTCATTTGTAACAATGTTGTTAGCTTTGGAGGGGATCCTAAT
upper sequence: LOC_Os05g50170.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM5G854930_T01 (Zea mays), 3'ss of exon 7
gtgctcatactttgcatggattcctcatatatgattcttataattcttttttgg-tagatttttttttactgataagaatttactgattgatcgatttctttttgcttgcttgatgatatataaaagcatatgttttgcagGAATTTTCCTCAAGGAACAATAAGTGACATGGTTAGCGATGCTTCTGATGGGATTTCATTTGTTTGTGAGACTGTTGGTGCCTATGGAGGAGATCCTAAT
| | ||| | ||| | || |||||| | | || ||| ||| ||||| ||||||||| | | || ||| ||||| | |||| ||||| ||||||||||||||||| |||||||| || ||||||||||| | ||| ||||| ||||| | | ||||| | || |||||| |||||||||
-------------------------------------tcaccattatgtttaaaacaaatacctttttaattaattttgagtattgactgaatgatttatttttgcttcatcagcaaaatttaa----atatggatggcagAAATTTCCCTCAAGGAACAATAAGCGACATGGTCAGTGATGCTTCTGAGGCGATATCATTCATTTGTAACAATGTTGTTAGCTTTGGAGGGGATCCTAAT
upper sequence: LOC_Os05g50170.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G427351_T01 (Zea mays), 3'ss of exon 6
gtgctcatactttgcatggattcctcatatatgattcttataattcttttttggtagatttttttttactgataagaatttactgattgatcgatttctttttgcttgcttgatgatatataaaagcatatgttttgcagGAATTTTCCTCAAGGAACAATAAGTGACATGGTTAGCGATGCTTCTGATGGGATTTCATTTGTTTGTGAGACTGTTGGTGCCTATGGAGGAGATCCTAAT
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-------------------------------tcaccattatgtttccaacctg-tacctttttaattaattttgag----tattgactaaatgatttatttttgcttcattggcaaaatttaa----atatggatggcagAAATTTCCCTCAAGGAACAATAAGCGACATGGTCAGTGATGCTTCTGAGGCGATATCATTCATTTGTAACAATGTTGTTAGCTTTGGAGGGGATCCTAAT
upper sequence: LOC_Os05g50170.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G437845_T01 (Zea mays), 3'ss of exon 5
gtgctcatactttgcatggattcctcatatatg------attcttataattc-----ttttttggtagatttttttttactgataagaatt---tactgattgatcgatttctttttgcttgcttgatgatatataaaagcatatgttttgcagGAATTTTCCTCAAGGAACAATAAGTGACATGGTTAGCGATGCTTCTGATGGGATTTCATTTGTTTGTGAGACTGTTGGTGCCTATGGAGGAGATCCTAAT
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gtgctgatgccttaaagaattttgtgatgtatacaccacatatgtgtagttcaccattatgttttcaacctgtacctttttaattaattttgagtactgactgaatgatttatttttgcttcatcggcaaaatttaa----atatggatggcagAAATTTCCCTCAAGGAACAATAAGCGACATGGTCAGTGATGCTTCTGAGGTGATATCATTCATTTGTAACAATGTTGTTAGCTTTGGAGGGGATCCTAAT
upper sequence: LOC_Os05g50170.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G406177_T01 (Zea mays), 3'ss of exon 4
gtgctcatactttgcatggattcctcatatatgattcttataattcttttttggtagatttttttttactgataagaatttactgattgatcgatttctttttgcttgcttgatgatatataaaagcatatgttttgcagGAATTTTCCTCAAGGAACAATAAGTGACATGGTTAGCGATGCTTCTGATGGGATTTCATTTGTTTGTGAGACTGTTGGTGCCTATGGAGGAGATCCTAAT
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-------------------------------tcaccattatg-ttttcaacctgtacctttttaattaattttgag----tattgactgaatgatttatttttgcttcatcggcaaaatttaa----atatggatggcagAAATTTCCCTCAAGGAACAATAAGCGACATGGTCAGTGATGCTTCTGAGGCGATATCATTCATTTGTAACAATGTTGTTAGCTTTGGAGGGGATCCTAAT
upper sequence: LOC_Os05g50170.1 (Oryza sativa), 3'ss of exon 5
lower sequence: AT1G26120.1 (Arabidopsis thaliana), 3'ss of exon 5
gtgc-tcatactttgcatggattcctcatatatgattcttataattcttttttggtagatttttttttactgataagaatttactgattgatcgatttctttttgcttgcttgatgatatataaaagcatatgttttgcagGAATTTTCCTCAAGGAACAATAAGTGACATGGTTAGCGATGCTTCTGATGGGATTTCATTTGTTTGTGAGACTGTTGGTGCCTATGGAGGAGATCCTAAT
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gtaagttatgcgtgctttgagttttttttctttg-ttctggcacattgaatgtggtgggttcctctc-----atcctccttcagtattcatttagagtttctcaatctcattggcaatatct-------cctcttacacagGAATTTTCCGCAAGGATCTATTAGTGACATGGTCAAGGATGCTTCTTCTGGCATCTCATTTGTTTGCAATCATATTGCTGAGTATGGAGGTGATCCAGATMapped 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|66926863|gb|CX113711.1|CX113711EST: GGAATTATAGTTGCATGCATTGATTACAG GAATTTTCCTCAAGGAACAATAAGTGACATGGTTAGCGATGCTTCTGATGG
genomic: GGAATTATAGTTGCATGCATTGATTACAGgtgctcatac ... tgttttgcagGAATTTTCCTCAAGGAACAATAAGTGACATGGTTAGCGATGCTTCTGATGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attgatcgatttctttttgcttgcttgatgatatataaaagcatatgttttgcagGAATTTTCCTCAAGGAACAATAAGTGACATGGTTAGCGATGCTTCTGATGGGATTTCATTTGTTTGTGAGACTGTTGGTGCCTATGGAGGAGATCCTAAT
atatataaaagcatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgctcatactttgcatggattcctcatatatgattcttataattcttttttggtagatttttttttactgataagaatttactgattgatcgatttctttttgcttgcttgatgatatataaaagcatatgttttgcagGAATTTTCCTCAAGGAACAATAAGTGACATGGTTAGCGATGCTTCTGATGGGATTTCATTTGTTTGTGAGACTGTTGGTGCCTATGGAGGAGATCCTAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC