Sequence
atgc intronic sequence ATGC exonic sequence...gttctagtacgcgcaccctatgtttgtatttttcaccagcttgcatcattctgatgttactactaatttatatcagctttgacatatatctttcgtgcagTATTCAGAGATTATCGAGCAAATTGACCGTGATGTGAAGCGCACTCACCCTGACATGCATTTTTTCTGTGGAGACTCATCTTTTGCAAAGTCCAATCAGG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g68010.5 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g68010.5 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G068392_T01 (Zea mays), 3'ss of exon 4
----gttctagtacgcgcaccctatgtttgtattt-ttcaccagcttgcatcattctgatgttactactaatttatatcagctttgacatatatctttcgtgcagTATTCAGAGATTATCGAGCAAATTGACCGTGATGTGAAGCGCACTCACCCTGACATGCATTTTTTCTGTGGAGACTCATCTTTTGCAAAGTCCAATCAGG
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acttatgctgttgggttcgttgcatctatgaactgatttgccctcctctattgctctt---ttattggtaactgatgctg--tctggaatttttcttcctaacagTACTCAGAGATTATGGAGCAGATTGACCGCGATGTAAAGCGCACCCACCCTGACATGCAGTTCTTCTGCGGCGACTCGTCTTTTGCAAAGTCCAATCAG-
upper sequence: LOC_Os01g68010.5 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA08G11760.1 (Glycine max), 3'ss of exon 4
gttctagtacgcgcaccctatgtttgtatttttcaccagcttgcatcattctg----atgttactactaatttatatcagctttgacatatatctttcgtgcagTATTCAGAGATTATCGAGCAAATTGACCGTGATGTGAAGCGCACTCACCCTGACATGCATTTTTTCTGTGGAGACTCATCTTTTGCAAAGTCCAATCAGG
|| | || | | | | | | || | ||| |||| || | || | || | | | || ||| | | | | | || || || ||||||| || || ||||||||||| ||||| ||||||||||| ||||| ||||| ||||||| ||| || || |||||||| || ||||||
--tccattat-tgtatcacaattatataaatctcatgctaatgcactataatactctgtgcaatggctgttgtgaagcaaatttc-cgtctttgcattttgtagGATACAGAGATCATAGATCAAATTGACCGAGATGTAAAGCGCACTCATCCTGATATGCACTTTTTCTCTGGTGATTCCCAATTTGCAAAATCTAATCAG-
upper sequence: LOC_Os01g68010.5 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA05G28660.1 (Glycine max), 3'ss of exon 4
---gttctagtacgcgcaccctatgtttgtatttttcaccagcttgcatcattctgatgttactactaatttatatcagctttgacatatatctttcgtgcagTATTCAGAGATTATCGAGCAAATTGACCGTGATGTGAAGCGCACTCACCCTGACATGCATTTTTTCTGTGGAGACTCATCTTTTGCAAAGTCCAATCAGG
|| | ||| | ||| | | | | | | | | |||| || | || | | | || | | | | | | | || || || ||||||| ||||| ||||||||||| ||||| ||||||||||| ||||| ||||| ||||||| ||| || || |||||||| || ||||||
ttcattattgtatcacaattatataaatct-catgctaatgccctataatactctg-tgcaaaggctgttgtgaagcaaatctc-cttctttgcattttgtagGATACAGAGATCATCGACCAAATTGACCGAGATGTAAAGCGCACTCATCCTGATATGCACTTTTTCTCTGGTGATTCCCAATTTGCAAAATCTAATCAG-
upper sequence: LOC_Os01g68010.5 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv05s0029g01350.t01 (Vitis vinifera), 3'ss of exon 4
---gttctagtacgc----gcaccctatgtttgtatttttcaccagcttgca-tcattc-tgatgttactactaatttatatcagctttgacatatatctttcgtgcagTATTCAGAGATTATCGAGCAAATTGACCGTGATGTGAAGCGCACTCACCCTGACATGCATTTTTTCTGTGGAGACTCATCTTTTGCAAAGTCCAATCAGG
|| || || | || || || ||||| | ||| | || |||| | | |||||| || || |||| | | || | ||||||| || |||||||||||||| ||||| ||||||||||| || |||||| | || |||| ||| ||| | | | |||||| | ||||||
cccatttctttatgctattggactataaattggtattaggagatgatatatggtcactgatggtgttttgaattatttattacaatttgaacattttt---------agGACACAGAGATCATAGAGCAAATTGACCGAGATGTCAAGCGCACTCATCCAGACATGAACTTCTTCTCTGGGGACACGCCATCTGCAAAAACAAATCAG-
upper sequence: LOC_Os01g68010.5 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ15182 (Selaginella moellendorffii), 3'ss of exon 4
gttctagtacgcgcaccctatgtttgtatttttcaccagcttgcatcattctgatgttactactaatttatatcagctttgacatatatctttcgtgcagTATTCAGAGATTATCGAGCAAATTGACCGTGATGTGAAGCGCACTCACCCTGACATGCATTTTTTCTGTGGAGACTCATCTTTTGCAAAGTCCAATCAGG
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--------------------------------------gtttgtttacttcctttgcaatt-ccaatccaaatgga---------atttccacttcgcagGACACGGAACTTTTCGAGCAGATTGATCGTGATGTTAAGCGAACTCATCCTGATATGCAGTTTTTCTGTGGTGATAACGAGCGCGCGCACGAAAACCAG-
upper sequence: LOC_Os01g68010.5 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ09811 (Selaginella moellendorffii), 3'ss of exon 4
gttctagtacgcgcaccctatgtttgtatttttcaccagcttgcatcattctgatgttactactaatttatatcagctttgacatatatctttcgtgcagTATTCAGAGATTATCGAGCAAATTGACCGTGATGTGAAGCGCACTCACCCTGACATGCATTTTTTCTGTGGAGACTCATCTTTTGCAAAGTCCAATCAGG
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--------------------------------------gtttgtttacttcctttgc-atttccaatccaaataga---------atttccacttcgcagGACACGGAACTTTTCGAGCAGATTGATCGTGATGTTAAGCGAACTCATCCTGATATGCAGTTTTTCTGTGGTGATAACGAGCGCGCGCACGAAAACCAG-Mapped 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|58672453|gb|CK061139.1|CK061139EST: AGCACCCATTGAGCCTTGGGAAGACAACTGCATGGAATCAGTTCTTTGAG TATTCAGAGATTATCGAGCAAATTGACCGTGATGTGAAGCGCACTCACCCT
genomic: AGCACCCATTGAGCCTTGGGAAGACAACTGCATGGAATCAGTTCTTTGAGgtgcccactg ... tttcgtgcagTATTCAGAGATTATCGAGCAAATTGACCGTGATGTGAAGCGCACTCACCCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcattctgatgttactactaatttatatcagctttgacatatatctttcgtgcagTATTCAGAGATTATCGAGCAAATTGACCGTGATGTGAAGCGCACTCACCCTGACATGCATTTTTTCTGTGGAGACTCATCTTTTGCAAAGTCCAATCAGG
tatctttc CT-rich tract
ttactactaatttata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttctagtacgcgcaccctatgtttgtatttttcaccagcttgcatcattctgatgttactactaatttatatcagctttgacatatatctttcgtgcagTATTCAGAGATTATCGAGCAAATTGACCGTGATGTGAAGCGCACTCACCCTGACATGCATTTTTTCTGTGGAGACTCATCTTTTGCAAAGTCCAATCAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG