Sequence
atgc intronic sequence ATGC exonic sequencegtaatatctgcaccttttcttcatgccggtagtctcgtcttgcctgtcattttacaaattacatattcagGCATGTTTCCAAATCACATTCCAAATCCTGAGGACAAAACTGCAATGAAAGCCATTACACAAGCTGTGGCCGATAACAAGGCAGACTTGGGCATCATATT
Basic information
species | Oryza sativa |
transcript | LOC_Os07g26610.2 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g26610.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G069676_T03 (Zea mays), 3'ss of exon 9
gtaatatctgcaccttttcttcatgc-----cggtagtctcgtcttgcctgtcattt--tacaaattacatattcagGCATGTTTCCAAATCACATTCCAAATCCTGAGGACAAAACTGCAATGAAAGCCATTACACAAGCTGTGGCCGATAACAAGGCAGACTTGGGCATCATATT
|||||| || |||||||||||| || | ||| || ||||| || | | ||||||| ||| ||||||| ||||||||||| || |||||||||||||| |||||||| ||||||||||| || ||||||||||||||||| |||||||||||
gtaatagcttgttgttttcttcatgcaattataataccttttgcttttctcccatttcttatacaccacatatttagGTTTGTTTCCCAATCACATTCCCAACCCTGAGGACAAAACCGCAATGAAGTTTATTACACAAGCAGTTCTTGATAACAAGGCAGACTTAGGCATCATATT
upper sequence: LOC_Os07g26610.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA20G32030.1 (Glycine max), 3'ss of exon 8
------gtaatatctgcaccttttcttcatgccggtagtctcgtcttgcctgtcattttacaaattaca-----------tattcagGCATGTTTCCAAATCACATTCCAAATCCTGAGGACAAAACTGCAATGAAAGCCATTACACAAGCTGTGGCCGATAACAAGGCAGACTTGGGCATCATATT
|| || | | || | || | | | | || | ||| | | | ||| ||||||||| ||||||||||||| || ||||||||||||||||| || ||||||||||| || || ||||| || |||||||| | || | || || || ||
gtaattactatgcttggaggaatgatttcaactgggtatggcaaatggactttaattctttgagtaacaaatggcttttctattcagGCTTGTTTCCAAATCATATCCCAAATCCTGAGGACAAGACAGCAATGAAAGCTATAACCCAAGCAGTCCTTGATAACAAAGTTGATCTTGGAATTATTTT
upper sequence: LOC_Os07g26610.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA10G35490.2 (Glycine max), 3'ss of exon 8
gtaatatctgcacctt------ttcttcatgccggtagtctcgtcttgcctgtcattttacaaattaca-----------tattcagGCATGTTTCCAAATCACATTCCAAATCCTGAGGACAAAACTGCAATGAAAGCCATTACACAAGCTGTGGCCGATAACAAGGCAGACTTGGGCATCATATT
|||||| || | | || || || | | | || | ||| | | | ||| ||||||||| ||||||||||||| || |||||||||||||||||||| ||||||||||| || || ||||| || |||||||| || || | || || || ||
gtaataactatgcttggaggaattatttgaattgggtatggtaaatggactttgattctttgagtaacaaatggctgttgtattcagGCTTGTTTCCAAATCATATCCCAAATCCTGAGGACAAAACAGCAATGAAAGCTATAACCCAAGCAGTCCTTGATAACAAAGCTGATCTTGGAATTATCTT
upper sequence: LOC_Os07g26610.1 (Oryza sativa), 3'ss of exon 9
lower sequence: EFJ15375 (Selaginella moellendorffii), 3'ss of exon 7
gtaatatctgcaccttttcttcatgccggtagtctcgtcttgcctgtcattttacaaattacatattcagGCATGTTTCCAAATCACATTCCAAATCCTGAGGACAAAACTGCAATGAAAGCCATTACACAAGCTGTGGCCGATAACAAGGCAGACTTGGGCATCATATT
| | | || | || | | ||| | | | | | | ||| ||||||||||||| ||||| ||||| |||||||||||||| | |||||| ||||| | ||| ||||| | | ||||||| |||||||| ||||||||
-----gtacgaaactctgtttgagaaatgaagtttttaccttctgg--actttgg------------cagGCATGTTTCCGAATCATATTCCCAATCCTGAGGACAAGAAAGCAATGGAAGCCGTGACAAGTGCTGTTCTCAAGCACAAGGCGGACTTGGGGATCATATT
upper sequence: LOC_Os07g26610.1 (Oryza sativa), 3'ss of exon 9
lower sequence: EFJ24972 (Selaginella moellendorffii), 3'ss of exon 7
gtaatatctgcaccttttcttcatgccggtagtctcgtcttgcctgtcat-tttacaaatt---acatattcagGCATGTTTCCAAATCACATTCCAAATCCTGAGGACAAAACTGCAATGAAAGCCATTACACAAGCTGTGGCCGATAACAAGGCAGACTTGGGCATCATATT
| | | || | | | ||| | || || | ||||||||||||| ||||| ||||| |||||||||||||| | |||||| ||||| | ||| ||||| | | ||||||| |||||||| ||||||||
------------------------gtacgaaactctgtttgagaaatgaagtttgtacatctggactttggcagGCATGTTTCCGAATCATATTCCCAATCCTGAGGACAAGAAAGCAATGGAAGCCGTGACAAGTGCTGTTCTCAAGCACAAGGCGGACTTGGGGATCATATTMapped 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|29613465|gb|CB618478.1|CB618478EST: CAAGCCGTTAGGCGCTATTACTACTGGGAGCCAATTCCTAGAGCCTGATG GCATGTTTCCAAATCACATTCCAAACCCTGAGGACAAAACTGCAATGAAAG
genomic: CAAGCCGTTAGGCGCTATTACTACTGGGAGCCAATTCCTAGAGCCTGATGgtaatatctg ... acatattcagGCATGTTTCCAAATCACATTCCAAATCCTGAGGACAAAACTGCAATGAAAG
EST:
gi|29660678|gb|CB656953.1|CB656953EST: CAAGCCGTTAGGCGCTATTACTACTGGGAGCCAATTCCTAGAGCCTGATG GCATGTTTCCCAATCACATTCCAA
genomic: CAAGCCGTTAGGCGCTATTACTACTGGGAGCCAATTCCTAGAGCCTGATGgtaatatctg ... acatattcagGCATGTTTCCAAATCACATTCCAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttcttcatgccggtagtctcgtcttgcctgtcattttacaaattacatattcagGCATGTTTCCAAATCACATTCCAAATCCTGAGGACAAAACTGCAATGAAAGCCATTACACAAGCTGTGGCCGATAACAAGGCAGACTTGGGCATCATATT
tcattttacaaattac 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatatctgcaccttttcttcatgccggtagtctcgtcttgcctgtcattttacaaattacatattcagGCATGTTTCCAAATCACATTCCAAATCCTGAGGACAAAACTGCAATGAAAGCCATTACACAAGCTGTGGCCGATAACAAGGCAGACTTGGGCATCATATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG