Sequence
atgc intronic sequence ATGC exonic sequencegtgcgctcatcaatacgtttttctgtttatattgtgatcaaatcaaagtgacaactgaccataatgacatcaattgtcttgatgtttcacagGAGCATGCAGATTATGACAGAATTGATCAGGAAGCTGATGAATGGAGGGCTAGGCAAATAGCCAAGGACATGGCGCAGCGCAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g12670.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g12670.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G058366_T01 (Zea mays), 3'ss of exon 2
-------------------------gtgc-gctcatcaatacgtttttc-tgtttatattgtgatcaaatcaaagtgac-----------aactgaccat----aatgacatcaattgtcttgatgtttcacagGAGCATGCAGATTATGACAGAATTGATCAGGAAGCTGATGAATGGAGGGCTAGGCAAATAGCCAAGGACATGGCGCAGCGCAAG
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gtgccactcgtcactgtcaccttttatacagctcat-aatacatttctggttccttcattccaaacagccaaaaaaaacccaaccgtgtgaattgtgaattgtggatgacatctcttgtcttgttgtttcatagGAGCGTGCGGATTATGATAGAGTTGACCGGGAAGCTGATGAATGGAGGGCTAAGCAAATAGCCAAGGACATTGCAAAGCGGAGG
upper sequence: LOC_Os01g12670.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G174489_T01 (Zea mays), 3'ss of exon 1
-----------------------gtgcgctcatcaatacgtttttctgtttatattgtgatcaaatcaaagtgacaactgaccata-----------------atgacatcaattgtcttgatgtttcacagGAGCATGCAGATTATGACAGAATTGATCAGGAAGCTGATGAATGGAGGGCTAGGCAAATAGCCAAGGACATGGCGCAGCGCAAG
| | ||| || |||||| || | | || | | ||| ||||| ||| |||| |||||||| ||||||| |||||| ||| |||||||| ||| |||| ||||||||||||||||||||||||| |||||||||||||||||| || | | | |
gtgccactcgtcgctgtcaccttttatacgtctcattatacatttctggttccttcattccaaacagccaaaaaaaaccaaccatgtgaattgtgaaatgtggatggcatctcttgtcttgttgtttcatagGAGCGTGCGGATTATGATAGAGTTGACCAGGAAGCTGATGAATGGAGGGCTAAGCAAATAGCCAAGGACATTGCAAAACAGAGG
upper sequence: LOC_Os01g12670.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G009438_T01 (Zea mays), 3'ss of exon 1
-----------------------gtgcgctcatcaatacgtttttctgtttatattgtgatcaaatcaaagtgacaactg-----accataa--------tgacatcaattgtcttgatgtttcacagGAGCATGCAGATTATGACAGAATTGATCAGGAAGCTGATGAATGGAGGGCTAGGCAAATAGCCAAGGACATGGCGCAGCGCAAG
| | ||| || |||||| || ||| | || ||| |||| | | | || |||| |||||||| ||||||| |||||| ||| |||||||| ||| |||| ||||||||||||||||||||||||| |||||||||||||||||| || |||| | |
gtgccactcgccgctgtcaccttttatacgtctcattatacatttctggtt-cattccaaacagccaaaaaaaccaaccatgtgaattgtgaaatgtggatggcatctcttgtcttgttgtttcatagGAGCGTGCGGATTATGATAGAGTTGACCAGGAAGCTGATGAATGGAGGGCTAAGCAAATAGCCAAGGACATTGCAAAGCGGAGGMapped 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|29678139|gb|CB674414.1|CB674414EST: AGCGATGGAGAAAGAGAAAAAGAAAGCATGTTGCAGAGCTTTTCCAGAAG GAGCATGCAGATTATGACAGAATTGATCAGGAAGCTGATGAATGGAGGGCT
genomic: AGCGATGGAGAAAGAGAAAAAGAAAGCATGTTGCAGAGCTTTTCCAGAAGgtgcgctcat ... tgtttcacagGAGCATGCAGATTATGACAGAATTGATCAGGAAGCTGATGAATGGAGGGCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcaaatcaaagtgacaactgaccataatgacatcaattgtcttgatgtttcacagGAGCATGCAGATTATGACAGAATTGATCAGGAAGCTGATGAATGGAGGGCTAGGCAAATAGCCAAGGACATGGCGCAGCGCAAG
ataatga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgcgctcatcaatacgtttttctgtttatattgtgatcaaatcaaagtgacaactgaccataatgacatcaattgtcttgatgtttcacagGAGCATGCAGATTATGACAGAATTGATCAGGAAGCTGATGAATGGAGGGCTAGGCAAATAGCCAAGGACATGGCGCAGCGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG