Sequence
atgc intronic sequence ATGC exonic sequencegtatgtatttccatctcgaacttggtaattattaggataccattttgtgttgcacggttgaaaattattcatttttatacctgtagGTGTACAAAAAGCTCAGTGAAAGTATTAAGGACATTGATGGTGCAAGGATGGAAGATAACAAATTCTGTGTGTCCGTTCATTACCGCAATGTAGCACCAC
Basic information
species | Oryza sativa |
transcript | LOC_Os10g40555.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os10g40550.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G178546_T01 (Zea mays), 3'ss of exon 6
gtatgtatttccatctcgaacttggtaattattaggataccattttgtgttgcacggttgaaaattattcatttttatacctgt-agGTGTACAAAAAGCTCAGTGAAAGTATTAAGGACATTGATGGTGCAAGGATGGAAGATAACAAATTCTGTGTGTCCGTTCATTACCGCAATGTAGCACCAC
|||||| | || | |||| | | ||| | | |||| || ||| | ||||| | | | | | | ||| || ||||||| |||| || |||| ||| ||||||||||||||||||||||||||||||| ||||| |||||||| || || |||||||| ||||| || |
gtatgttgtaccggcct---cttg--agt--ttaagttgccatcttatgtcatatggttgg--acttctgagtggtgtacatgccagGTGTATGAAAAACTTGGTGAGAGTGTTAAGGACATTGATGGTGCAAGGATGGAAGACAACAAGTTCTGTGTATCTGTGCATTACCGTAATGTGGCGGAAG
upper sequence: LOC_Os10g40550.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA06G47630.2 (Glycine max), 3'ss of exon 5
--gtatgtatttc------catctcgaacttggtaattattaggataccattttgtgttgcacggttgaaaattattcatttt-tatacctgtagGTGTACAAAAAGCTCAGTGAAAGTATTAAGGACATTGATGGTGCAAGGATGGAAGATAACAAATTCTGTGTGTCCGTTCATTACCGCAATGTAGCACCAC-
| | ||||| || | | | | | || ||||| || | |||| | | ||| | | | |||| ||||| || |||| || || || || || |||| | || | |||||||| |||||||| || |||||||||||||||| | |
gcatgtatattttgaaaaatattttacaatgaatctcttttcaatcttttatttgtactggaaagttggatgctgatcaactaatctttgaacagGTACGTGGGTTGCTCAAGGAGTGTATAAAAGATATAGAAGGAGCAACAGTTGAGAACAACAAATTTTGTGTGTCTGTGCATTACCGCAATGTAG-ATGAGG
upper sequence: LOC_Os10g40550.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA06G47630.1 (Glycine max), 3'ss of exon 6
gtatgtatttc----catctcgaacttggtaattattaggataccattttgtgttgcacggttgaaaattattcatttt-tatacctgtagGTGTACAAAAAGCTCAGTGAAAGTATTAAGGACATTGATGGTGCAAGGATGGAAGATAACAAATTCTGTGTGTCCGTTCATTACCGCAATGTAGCACCAC---
|||| | || || | | | | | || ||||| || | |||| | | ||| | | | |||| ||||| || |||| || || || || || |||| | || | |||||||| |||||||| || |||||||||||||||| | |
gtatattttgaaaaatattttacaatgaatctcttttcaatcttttatttgtactggaaagttggatgctgatcaactaatctttgaacaggtacgtgggttgctcaaggagtgtataaaagATATAGAAGGAGCAACAGTTGAGAACAACAAATTTTGTGTGTCTGTGCATTACCGCAATGTAG-ATGAGGAG
upper sequence: LOC_Os10g40550.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA04G13880.1 (Glycine max), 3'ss of exon 6
--gtatgtatttccatctcgaacttg--gtaattattaggataccat-tttgtgttgcacggttgaaaattattcatttt-tatacctgtagGTGTACAAAAAGCTCAGTGAAAGTATTAAGGACATTGATGGTGCAAGGATGGAAGATAACAAATTCTGTGTGTCCGTTCATTACCGCAATGTAGCACCAC-
| | ||||| | | || | | | | || | | ||| ||| | ||| | | ||| | | | | |||| ||||| || | | | || ||||| || |||| | || | |||||||| |||||||| || |||||||||||||||| | |
gcatgtatattttgaaaattactttacaatgaatctctcaatcttttatctgtattggaaagttttatgctgatcaactaatgtttcaacagGTACTTGGGTTGCTCATGGAGTGCACAGAAGATATTGAAGGAGCAACAGTTGAGAACAACAAATTTTGTGTGTCTGTGCATTACCGCAATGTAG-ATGAGGMapped 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|58607388|gb|CK035421.1|CK035421EST: AGGTCAACCTCTTCCAACCTGCAAGTGAGTTTTTACCTATGATCAGCGAG GTGTACAAAAAGCTCAGTGAAAGTATTAAGGACATTGATGGTGCAAGGATG
genomic: AGGTCAACCTCTTCCAACCTGCAAGTGAGTTTTTACCTATGATTAGCGAGgtatgtattt ... atacctgtagGTGTACAAAAAGCTCAGTGAAAGTATTAAGGACATTGATGGTGCAAGGATG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaggataccattttgtgttgcacggttgaaaattattcatttttatacctgtagGTGTACAAAAAGCTCAGTGAAAGTATTAAGGACATTGATGGTGCAAGGATGGAAGATAACAAATTCTGTGTGTCCGTTCATTACCGCAATGTAGCACCAC
tttttat CT-rich tract
ttgaaaattattcatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtatttccatctcgaacttggtaattattaggataccattttgtgttgcacggttgaaaattattcatttttatacctgtagGTGTACAAAAAGCTCAGTGAAAGTATTAAGGACATTGATGGTGCAAGGATGGAAGATAACAAATTCTGTGTGTCCGTTCATTACCGCAATGTAGCACCAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA