Sequence
atgc intronic sequence ATGC exonic sequence...cttttgatgctatataaacaattttgccttatttctatgtgggtaagctcattttgttgttacgtaacttatatttgctgcaaacaatatatgaatacagGTTCAGGAGCCAGACTTAGTTGGTGTAAGCCATTTACTAGTTGATGAAATTCATGAACGTGGCATGAATGAAGATTTTCTCATCATAATTCTTCGCGACC
Basic information
species | Oryza sativa |
transcript | LOC_Os10g33275.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os10g33275.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G381470_T01 (Zea mays), 3'ss of exon 5
-------------------------------------------------------------cttttgatgctatataa-acaatt--ttgccttatttctatgtgggtaagctcattttgttgttacgtaacttatatttgctgcaaacaatatatgaat-acagGTTCAGGAGCCAGACTTAGTTGGTGTAAGCCATTTACTAGTTGATGAAATTCATGAACGTGGCATGAATGAAGATTTTCTCATCATAATTCTTCGCGACC
| |||||| || ||| || | ||| | ||| | | || | | | | || | | || |||| ||| ||||| ||||| ||| |||||||| ||||| |||||| |||| || || ||||||||||||| |||||||||||||| |||||||||||||||||||||||||||| || || ||||
gtatcctcctttttagccaaccttgttgacatattttgctcacttcagcctaccttaacacttgctgatgcaatttaatgcacctgattgtttattttttgtatgcttgaatgcttccattttagttgcattttgaatttactg-aaacattatataaattgcagGTTCAAGAGCCTGACTTAATTGGGGTGAGTCATTTACTAGTTGGCGAAATTCATGAACGCTGCATGAATGAAGATTTTCTCATCATAATACTGCGTGACC
upper sequence: LOC_Os10g33275.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM5G863698_T01 (Zea mays), 3'ss of exon 1
--cttttgatgctatataaacaattttgccttatttctatgtgggtaagctcattttgttgttacgtaacttatatttgctgcaaacaatatatgaat-acagGTTCAGGAGCCAGACTTAGTTGGTGTAAGCCATTTACTAGTTGATGAAATTCATGAACGTGGCATGAATGAAGATTTTCTCATCATAATTCTTCGCGACC
| || || || | ||| | || ||| |||| | | ||| || | ||| ||| || |||| ||| ||| | ||||| ||| |||||||| ||||| |||||| |||| || || ||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||| || || ||||
ctgatgcaatttaatgcaaccgattgtttattttttgtatgcttgaatgcttccattttagttgcgt--tttgaatttactg-aaatagtatataaattgcagGTTCAAGAGCCTGACTTAATTGGGGTGAGTCATTTACTAGTTGATGAAATTCATGAACGCGGCATGAATGAAGATTTTCTCATCATAATACTACGTGACC
upper sequence: LOC_Os10g33275.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G399212_T01 (Zea mays), 3'ss of exon 8
--cttttgatgctatataaacaattttgccttatttctatgtgggtaagctcattttgttgttacgtaacttatatttgctgcaaacaatatatgaat-acagGTTCAGGAGCCAGACTTAGTTGGTGTAAGCCATTTACTAGTTGATGAAATTCATGAACGTGGCATGAATGAAGATTTTCTCATCATAATTCTTCGCGACC
| || || | | ||| | || ||| |||| | | ||| || | ||| | | || |||| ||| ||||| ||||| ||| |||||||| ||||| |||||| |||| || || |||||||||||||| |||||||||||||| ||||||||||||||||||||||||||||| || || ||||
ctgatgcaatttaatgcacccgattgtttattttttgtatgcttgaatgcttccattttagttgcat--tttgaatttactg-aaacagtatataaattgcagGTTCAAGAGCCTGACTTAATTGGGGTGAGTCATTTACTAGTTGACGAAATTCATGAACGCGGCATGAATGAAGATTTTCTCATCATAATACTGCGTGACC
upper sequence: LOC_Os10g33275.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA02G35240.1 (Glycine max), 3'ss of exon 8
cttttgatgctatataaacaattttgccttatttctatgtggg-taagctcattttgttgttacgtaacttatat-----ttgctgcaaacaatatatgaatacagGTTCAGGAGCCAGACTTAGTTGGTGTAAGCCATTTACTAGTTGATGAAATTCATGAACGTGGCATGAATGAAGATTTTCTCATCATAATTCTTCGCGACC
| |||||| | | || | ||| |||| | || || || || || | |||| | || | | | | | | | |||| || || |||||||| |||||| || ||||| || || ||||||||||||||| | |||||||||||||| ||| | || |||||| | || ||||
-----aaaaatatatagttgagaattttgcatctttatatgggatgttcttatattcttccta-gcaactagtggccttgtttttactgtctttgttgttaaatagGTACAAGACCCAGACTTGACTGGTGTTAGTCATTTGCTGGTGGATGAAATTCATGAAAGAGGCATGAATGAAGACTTTTTAATTATAATTTTACGTGACC
upper sequence: LOC_Os10g33275.1 (Oryza sativa), 3'ss of exon 7
lower sequence: AT2G35920.1 (Arabidopsis thaliana), 3'ss of exon 6
-----cttttgatgctata-taaacaattttgccttatttctatgtgggtaagctcattttgttgttacgtaacttatatttgctgcaaacaatatatgaatacagGTTCAGGAGCCAGACTTAGTTGGTGTAAGCCATTTACTAGTTGATGAAATTCATGAACGTGGCATGAATGAAGATTTTCTCATCATAATTCTTCGCGACC
| | | || || ||| | | | | | || || | ||||| | | | | |||| | || | | | | | ||| ||| || |||| || | || | ||||||||||| || || ||||| ||||| ||| | |||||||||||||||||||| | || || || ||||| |
gtaagatacaactattctactactcaactactcatcacatgtagttgaagtatgatattttaa-gcttctttactttgaaatgtcgaatcaattgttgaaatgcagATTGAGGATCCTAATCTAACTAACGTAAGCCATTTGCTCGTGGATGAGATTCACGAAAGAGGCATGAATGAAGATTTTCTACTAATCATACTACGCGATC
upper sequence: LOC_Os10g33275.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv08s0032g01230.t01 (Vitis vinifera), 3'ss of exon 6
cttttgatgctatataaacaatt--ttgccttat-----ttctatgtgggtaagctcattttgttgttacgtaacttatatttgctgcaaacaatatat-gaatacagGTTCAGGAGCCAGACTTAGTTGGTGTAAGCCATTTACTAGTTGATGAAATTCATGAACGTGGCATGAATGAAGATTTTCTCATCATAATTCTTCGCGACC
|| || | || ||| ||| ||| | || | || | | |||| || |||| | || | | | | || | ||||||||||||||| ||||| || ||||||||||||||| ||||| ||||||||||||||| | ||||||||||| || || || | |||||| | | ||||
-------tgtcatttgaaggattagttgttgtataagcatactgggatggcacacacattctgatgttttcttttccat-tctcttatgattttgatgttaaatacagGTTCAGGACCCAGATCTAACTGGTGTAAGCCATTTGCTAGTGGATGAAATTCATGAAAGAGGCATGAATGAGGACTTCCTTTTAATAATTTTGCATGACC
upper sequence: LOC_Os10g33275.1 (Oryza sativa), 3'ss of exon 7
lower sequence: PP1S36_206V6.1 (Physcomitrella patens), 3'ss of exon 7
-----------------------------------------------------cttttgatgctatataaacaattt---tgccttatttctatg-tgggtaagc-tcattttgttgttacgtaacttatatttgctgcaaacaatatatgaatacagGTTCAGGAGCCAGACTTAGTTGGTGTAAGCCATTTACTAGTTGATGAAATTCATGAACGTGGCATGAATGAAGATTTTCTCATCATAATTCTTCGCGACC
| | | || | | | || ||| | || ||| | |||| | || || || || | | ||| || | | | |||| || ||||| ||||| |||||| || ||| | | ||||| |||||||||||||| ||||||||||||||||| | | || ||| | || || |
gtacgttctgtgccttatattacgaacttggagattctttttcattgtatgattgtctagtacttggcagaaatttgcagtgcagaagatcaatggtaggtaggaaccacttcgtcatttgccagtactaacttgttggcat--gtggggttgcatagGTCCAAGAGCCTGACTTGAATGGTGTGAGTCATGTCATGGTTGACGAAATTCATGAACGCGGCATGAATGAAGATTTCTTATTGATCATTTTACGAGATCMapped 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|33678639|gb|CF306878.1|CF306878EST: CACAAACCAGACTGCTATTCTGCACCACAGGAGTTCTACTTAGAAGATTG GTTCAGGAGCCAGACTTAGTTGGTGTAAGCCATTTACTAGTTGATGAAATT
genomic: CACAAACCAGACTGCTATTCTGCACCACAGGAGTTCTACTTAGAAGATTGgtatgcctat ... atgaatacagGTTCAGGAGCCAGACTTAGTTGGTGTAAGCCATTTACTAGTTGATGAAATT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agctcattttgttgttacgtaacttatatttgctgcaaacaatatatgaatacagGTTCAGGAGCCAGACTTAGTTGGTGTAAGCCATTTACTAGTTGATGAAATTCATGAACGTGGCATGAATGAAGATTTTCTCATCATAATTCTTCGCGACC
acgtaac putative branch site (score: 3)
aaacaatatatgaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cttttgatgctatataaacaattttgccttatttctatgtgggtaagctcattttgttgttacgtaacttatatttgctgcaaacaatatatgaatacagGTTCAGGAGCCAGACTTAGTTGGTGTAAGCCATTTACTAGTTGATGAAATTCATGAACGTGGCATGAATGAAGATTTTCTCATCATAATTCTTCGCGACC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA