Sequence
atgc intronic sequence ATGC exonic sequencegtaagaaaattcatactgaatttgagctatatattagtatccatcttactgttccaaaatatcatcacttacatttgtttaccttctttctgcactgataattggcatgacaaatatgttgcagGTAGGTATGTAGCTCCAGAAGTCCTGCGAAATGAAGAATATGATACTAAAGTGGATGTCTTCTCATTTGCTTTGATACTTCAAGAG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g54480.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g54480.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G045366_T01 (Zea mays), 3'ss of exon 8
gtaagaaaattcatactgaatttgagctatatattagtatccatcttactgttccaaaatatcatcacttacatttgtttaccttctttctgcactgataattggcatgacaaatatgttgcagGTAGGTATGTAGCTCCAGAAGTCCTGCGAAATGAAGAATATGATACTAAAGTGGATGTCTTCTCATTTGCTTTGATACTTCAAGAG
||||| | | || || || ||| |||| | | || ||| |||| | || || |||| || ||| |||| | | |||| ||||| | | ||| | |||||| ||||| |||||||||||||||||||||||||| |||||||| |||||||||||||||||||| ||| |||||||||| |||
gtaagtggactt-tattgt-ttgccactaaatatgtg---ctatattaatgtt----gacattttcccttaacttcttttgcctttcgtatcaactggcaattgtta------aaatgatacagGTAAATATGTGGCTCCAGAAGTCCTGCGAAATGAAGAGTATGATACCAAAGTGGATGTCTTCTCATTCGCTCTGATACTTCAGGAG
upper sequence: LOC_Os01g54480.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA15G09490.2 (Glycine max), 3'ss of exon 8
------------------------------------------------------------------gtaagaaaattcatactgaatttgagctatatattagtatccatcttactgttccaaaatatcat-cacttacat-ttgtttaccttctttctgcactgataattggca---tgacaaatatgtt-gcagGTAGGTATGTAGCTCCAGAAGTCCTGCGAAATGAAGAATATGATACTAAAGTGGATGTCTTCTCATTTGCTTTGATACTTCAAGAG
||| | || | || | ||||| || | | || || | | | | || ||| || || ||| | |||| | | || | | | |||| ||| | ||||| ||||| ||||| | || | ||||||||||| |||||||||||||| || |||||||| | || || ||||||
gtgggtgctgcttttcttcagaactatcattatgcacacttgaaatacctaaatatctgaaatgctgtattttcttattcgttgggcataagaga-atattgtcattattgtgacattttccatgtgctggacttttgcatgctgattcatggttttattttctgaaactgggaaattttttgtttttgtttatagGCCGCTATGTGGCTCCTGAAGTTTTCAGACAAGAAGAATATGACACTAAAGTGGATGTATTTTCATTTGCACTAATTCTGCAAGAG
upper sequence: LOC_Os01g54480.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA13G29520.1 (Glycine max), 3'ss of exon 8
------------------------------------------------------gtaagaaaattcatactgaatt-----tgagctatatattagtatccatcttactgttcca----aaatatcat---cacttacat--ttgtttaccttct----ttctgca-ctgataattggcatgacaaatatgttgcagGTAGGTATGTAGCTCCAGAAGTCCTGCGAAATGAAGAATATGATACTAAAGTGGATGTCTTCTCATTTGCTTTGATACTTCAAGAG
| |||| | || | || | | ||| || ||| ||| ||| || || | | | |||||| | || | | | ||||| | ||| |||| | | | || ||| | ||||| ||||| ||||| | || |||||||||| |||||||||||||| || |||||||| | || || ||||||
gtgggtgctgcttttcttcagaactatcattatgctcacttgaaatatctaaatatctgaaattctgtattttcttattcacggggcataagataatattgtcattattgtgacattttgcatgtgctggacttttacatgctgattcatggtttaattttctgaaactgggaattttttttgtttttgt-ttatagGCCGCTATGTGGCTCCTGAAGTTTTCAGAC---AAGAATATGACACTAAAGTGGATGTATTTTCATTTGCACTAATTCTGCAAGAGMapped 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|86495208|gb|CI137841.1|CI137841EST: AAGCTGTAACTTCTCCAGGCAATGCAT GTAGGTATGTAGCTCCAGAAGTCCTGCGAAATGAAGAATATGATACTAAAG
genomic: AAGCTGTAACTTCTCCAGGCAATGCATgtaagaaaat ... tatgttgcagGTAGGTATGTAGCTCCAGAAGTCCTGCGAAATGAAGAATATGATACTAAAG
EST:
gi|86498118|gb|CI140751.1|CI140751EST: AACTTCTCCAGGCAATGCAT GTAGGTATGTAGCTCCAGAAGTCCTGCGAAATGAAGAATATGATACTAAAG
genomic: AACTTCTCCAGGCAATGCATgtaagaaaat ... tatgttgcagGTAGGTATGTAGCTCCAGAAGTCCTGCGAAATGAAGAATATGATACTAAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tacatttgtttaccttctttctgcactgataattggcatgacaaatatgttgcagGTAGGTATGTAGCTCCAGAAGTCCTGCGAAATGAAGAATATGATACTAAAGTGGATGTCTTCTCATTTGCTTTGATACTTCAAGAG
aaatatgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagaaaattcatactgaatttgagctatatattagtatccatcttactgttccaaaatatcatcacttacatttgtttaccttctttctgcactgataattggcatgacaaatatgttgcagGTAGGTATGTAGCTCCAGAAGTCCTGCGAAATGAAGAATATGATACTAAAGTGGATGTCTTCTCATTTGCTTTGATACTTCAAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA