Sequence
atgc intronic sequence ATGC exonic sequenceGTCACCACGATGTATCACTTGGATCGCCCTATGTACTTGTTGGGATATCTAGCGAATCAAAGCCGAGTTTATCTTATTGACAAGGAATTCAAgtgtgttttcttgataatactgcctgcttattgtctggtgttgaattcttgaactaacatatttttcttgttgcag
Basic information
species | Oryza sativa |
transcript | LOC_Os06g05180.1 |
intron # | 16 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g05180.1 (Oryza sativa), 5'ss of exon 16
lower sequence: GRMZM2G086015_T01 (Zea mays), 5'ss of exon 1
--------GTCACCACGATGTATCACTTGGATCGCCCTATGTACTTGTTGGGATATCTAGCGAATCAAAGCCGAGTTTATCTTATTGACAAGGAATTCAAgtgtgttttcttgataatactgcctgcttattgtc-tgg----tgttgaattcttgaactaacatatttttcttgttgcag
||||| || |||||||| |||||||||||||||||| ||||||||||| | ||||| ||||| ||||||||||||||||||||||| || |||| |||||||| || || | ||| | ||| | | | |||| | |||| ||||||| || |||| | |||
ACTTACAGGTCACTACAATGTATCATTTGGATCGCCCTATGTACCTGTTGGGATATATTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTGAAgtatgttttctcgaaaacaatgcttcctttcctttgtagcatctgttaatttctctgactaacaaata--gcttggtacag
upper sequence: LOC_Os06g05180.1 (Oryza sativa), 5'ss of exon 16
lower sequence: GRMZM2G000645_T01 (Zea mays), 5'ss of exon 16
GTCACCACGATGTATCACTTGGATCGCCCTATGTACTTGTTGGGATATCTAGCGAATCAAAGCCGAGTTTATCTTATTGACAAGGAATTCAAgtgtgttttcttgataatactgcctgcttattgtc-tgg----tgttgaattcttgaactaacatatttttcttgttgcag
||||| || |||||||| |||||||||||||||||||||||||||||| | ||||| ||||| ||||||||||||||||||||||| || |||| |||||||| || || | ||| | ||| | | | |||| | |||| ||||||| || |||| | |||
GTCACTACAATGTATCATTTGGATCGCCCTATGTACTTGTTGGGATATATTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTGAAgtatgttttctcgaaaacaatgcttcctttcctttgtagcatctgttaatttctctgactaacaaata--gcttggtacag
upper sequence: LOC_Os06g05180.1 (Oryza sativa), 5'ss of exon 16
lower sequence: GRMZM2G095348_T01 (Zea mays), 5'ss of exon 16
GTCACCACGATGTATCACTTGGATCGCCCTATGTACTTGTTGGGATATCTAGCGAATCAAAGCCGAGTTTATCTTATTGACAAGGAATTCAAgtgtgttttcttgataatactgcctgcttatt--------gtctggtgttgaattcttgaactaacatatttttcttgttgcag
||||| || |||||||| |||||||||||||||||| | ||||||||||| ||||| ||||| ||||||||||||||||||||||| || ||||| | ||||| | || | || | ||| | |||| |||| | |||| |||||||||| |||| | |||
GTCACTACAATGTATCATTTGGATCGCCCTATGTACCTATTGGGATATCTTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTTAAgtgcgctttctctaaaacaatgtttcctttcttttgtaacatctgctgttaatttctgtgactaacatataag-cttgatacag
upper sequence: LOC_Os06g05180.1 (Oryza sativa), 5'ss of exon 16
lower sequence: GRMZM2G448913_T01 (Zea mays), 5'ss of exon 5
GTCACCACGATGTATCACTTGGATCGCCCTATGTACTTGTTGGGATATCTAGCGAATCAAAGCCGAGTTTATCTTATTGACAAGGAATTCAAgtgtgttttcttgataatactgcctgcttattgtc-tgg----tgttgaattcttgaactaacatatttttcttgttgcag
||||||||||||||| ||||||||||| | ||||| ||||| ||||||||||||||||||||||| || |||| |||||||| || || | ||| | ||| | | | | || | |||| ||||||| || |||| | |||
---------------------GATCGCCCTATGTACCTGTTGGGATATATTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTGAAgtatgttttctcgaaaacaatgcttcctttcctttgtagcatctattaatttctctgactaacaaata--gcttggtacag
upper sequence: LOC_Os06g05180.1 (Oryza sativa), 5'ss of exon 16
lower sequence: GLYMA15G01680.1 (Glycine max), 5'ss of exon 16
GTCACCACGATGTATCACTTGGATCGCCCTATGTACTTGTTGGGATATCTAGCGAATCAAAGCCGAGTTTATCTTATTGACAAGGAATTCAAgtgtgttttcttgataatactgcctgcttattgtctggtgttgaattct--tgaactaacatatttttcttgttgcag--------------
|| || ||||||| ||| ||||| |||||||||||||||||||||||||| || || ||||| || |||||| | |||||||| || || |||| || || | | |||| || | | || || |||| | | || ||||||||| ||
GTAACTACGATGTTTCATTTGGACCGCCCTATGTACTTGTTGGGATATCTTGCAAACCAAAGTCGTGTTTATTTGATTGACAAAGAGTTTAAgtaagt------gaaacttctgcttggattattcaaagttttaaattgcaataatcttgactatttttctgtttatcaattgtttttctcag
upper sequence: LOC_Os06g05180.1 (Oryza sativa), 5'ss of exon 16
lower sequence: GLYMA08G22140.1 (Glycine max), 5'ss of exon 16
GTCACCACGATGTATCACTTGGATCGCCCTATGTACTTGTTGGGATATCTAGCGAATCAAAGCCGAGTTTATCTTATTGACAAGGAATTCAAgtgtgttttcttgataatactgcctgcttat--tgtct-ggtgttgaattcttgaac-taacatatttttcttgttgcag
|| || || |||| ||| ||||| || ||||||||||||||||||||||| || | ||||| || ||| | || ||||| |||||||||| || | || | | | | | ||| || | | || ||| | || | | || | |||
GTTACTACAATGTTTCATTTGGACCGTCCTATGTACTTGTTGGGATATCTTGCCAGCCAAAGTAAGGTCTATTTGATGGACAAAGAATTCAAgtaagtgga-tcaatggtttgcattattcaaaatatctcaatgcagtaatcctgattattttttaactgttttact-cag
upper sequence: LOC_Os06g05180.1 (Oryza sativa), 5'ss of exon 16
lower sequence: GLYMA07G03890.2 (Glycine max), 5'ss of exon 5
GTCACCACGATGTATCACTTGGATCGCCCTATGTACTTGTTGGGATATCTAGCGAATCAAAGCCGAGTTTATCTTATTGACAAGGAATTCAAgtgtgttttcttgataatactgcctgcttattgtct---ggtgttgaattcttgaactaacatatttttctt--gttgcag-------
|| || || |||| ||| ||||| || ||||||||||||||||||||||| || | ||||| || ||| | || ||||| |||||||||| || | || | | | | ||| || | || ||| | | || || || ||
GTTACTACAATGTTTCATTTGGACCGTCCTATGTACTTGTTGGGATATCTTGCCAGCCAAAGTAAGGTCTATTTGATAGACAAAGAATTCAAgtaagtgga-tcaatggtttgcattattcaaaatctctcaatgcagtggtcctgattttttttcttcttttttaactgtgttactcag
upper sequence: LOC_Os06g05180.1 (Oryza sativa), 5'ss of exon 16
lower sequence: GLYMA13G43680.2 (Glycine max), 5'ss of exon 16
GTCACCACGATGTATCACTTGGATCGCCCTATGTACTTGTTGGGATATCTAGCGAATCAAAGCCGAGTTTATCTTATTGACAAGGAATTCAAgtgtgttttcttgataatactgcctgcttattgtctggtgttgaattct--tgaactaacatatttttcttgttgcag--------------
|| || ||||||| ||| ||||| ||||| |||||||||||||||||||| || || ||||| || |||||| | |||||||| || || |||| || || | | |||| || | | || || |||| | | || || |||||| ||
GTAACTACGATGTTTCATTTGGACCGCCCCATGTACTTGTTGGGATATCTTGCAAACCAAAGTCGTGTTTATTTGATTGACAAAGAGTTTAAgtaagt------gaaacttctgcttggattattcaaagttttaaattgcagtaatcttgactacttttctgtttatcaattttttttctcag
upper sequence: LOC_Os06g05180.1 (Oryza sativa), 5'ss of exon 16
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 5'ss of exon 20
GTCACCACGATGTATCACTTGGATCGCCCTATGTACTTGTTGGGATATCTAGCGAATCAAAGCCGAGTTTATCTTATTGACAAGGAATTCAAgtgtgtt--ttcttgataatactgcctgcttattgtctggtgttgaattcttgaactaacatatt---tttcttgttgcag
|| || || |||||||| |||| || ||||||||||||||||| ||||| || ||||||||| | |||||| | |||||||| || ||||||| | | || | | || |||| | | | ||| || | ||| | | ||| | || |||
GTAACTACAATGTATCATCTGGACCGTCCTATGTACTTGTTGGGTTATCTCGCTAATCAAAGCAGGGTTTATTTGATTGACAAAGAGTTCAAgtaagcagatgttttactgttatgattgctaacaatgttttgt--aacttactgacttctgtgtccactttatgattacag
upper sequence: LOC_Os06g05180.1 (Oryza sativa), 5'ss of exon 16
lower sequence: AT1G52360.2 (Arabidopsis thaliana), 5'ss of exon 16
GTCACCACGATGTATCACTTGGATCGCCCTATGTACTTGTTGGGATATCTAGCGAATCAAAGCCGAGTTTATCTTATTGACAAGGAATTCAAgtgtgttttcttgataatactgcctgcttatt---gtctggtgttgaa-ttcttgaactaacatatttttcttgt---tgcag
|| ||||| |||||||| ||||| ||||| ||||| |||||||||||||| || | |||||| || |||| | | ||||| |||||||||| || | | ||| || | || | | || | | ||| || ||| | | |||| |||||
GTAACCACAATGTATCATTTGGACCGCCCAATGTATTTGTTGGGATATCTTGCAAGTCAAAGTCGGGTTTTCTTGGTAGACAAAGAATTCAAgtaagtgct-tagatttgtgtgtttatataattgagattgttctagaagtttctgatgctgttcccctgttttgtggatgcag
upper sequence: LOC_Os06g05180.1 (Oryza sativa), 5'ss of exon 16
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 16
GTCACCACGATGTATCACTTGGATCGCCCTATGTACTTGTTGGGATATCTAGCGAATCAAAGCCGAGTTTATCTTATTGACAAGGAATTCAAgtgtgttttctt------------gataatactgcctgcttattgt----ctggtgt-tgaattcttgaactaacatatttttcttgttgcag
|| ||||| |||| ||| ||||| || |||||||| ||||||||||||||||| ||||||||||| || ||||| || ||||| || |||||||| || ||| | | | | || || |||| || | | ||| || | | | | || | |||||
GTAACCACAATGTTTCATTTGGACCGGCCTATGTATTTGTTGGGATATCTAGCTAATCAAAGCCGGGTGTATCTCATAGACAAAGAGTTCAAgtgagtggacttttggcagaaagggggagtggagggtggttgttgtattgctaacatctttattattaagttggtttttccttttcaatgcag
upper sequence: LOC_Os06g05180.1 (Oryza sativa), 5'ss of exon 16
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 5'ss of exon 16
GTCACCACGATGTATCACTTGGATCGCCCTATGTACTTGTTGGGATATCTAGCGAATCAAAGCCGAGTTTATCTTATTGACAAGGAATTCAAgtgtgttttcttgataa------tactgcctgcttattg--tctggtgttg-aatt--cttgaactaacatatttttcttgttgcag
|| ||||| |||| ||||||||| || |||||||| ||||| |||||||| || | |||||| || ||||||||||| ||||| || || ||||| | |||| | | |||| || | || | || | ||| |||| | || | | ||| || | |||||
GTAACCACCATGTTTCACTTGGACCGGCCTATGTATTTGTTAGGATATCTTGCCAGTCAAAGTCGCGTTTATCTTATAGACAAAGAGTTTAAgtgagggagcttgggagctgcacttctgcaatctgactgcttttgttcttgtaattgatctaaatttatttatgttatcttatgcag
upper sequence: LOC_Os06g05180.1 (Oryza sativa), 5'ss of exon 16
lower sequence: EFJ36319 (Selaginella moellendorffii), 5'ss of exon 11
GTCACCACGATGTATCACTTGGATCGCCCTATGTACTTGTTGGGATATCTAGCGAATCAAAGCCGAGTTTATCTTATTGACAAGGAATTCAAgtgtgttttcttgataatactgcctgcttattg--tctggtgttgaattcttgaactaacatatttttcttgttgcag
|| || || ||||||||| |||| || ||||| ||| | || ||||| || |||||||||||||| ||||| || |||||||| ||||||| || || | || || || | | | || ||| |||| |
GTAACTACTATGTATCACCTGGACAAGCCAATGTATTTGCTTGGCTATCTGGCAAATCAAAGCCGAGTGTATCTGATCGACAAGGAGTTCAAgtaagtgttttcgacgatcatgaacgatggctaatcctcctgtgaaattacag-------------------------
upper sequence: LOC_Os06g05180.1 (Oryza sativa), 5'ss of exon 16
lower sequence: EFJ09529 (Selaginella moellendorffii), 5'ss of exon 11
GTCACCACGATGTATCACTTGGATCGCCCTATGTACTTGTTGGGATATCTAGCGAATCAAAGCCGAGTTTATCTTATTGACAAGGAATTCAAgtgtgttttcttgataatactgcctgcttattgtctggtgttgaattcttgaactaacatatttttcttgttgcag
|| || || ||||||||| |||| || ||||| ||| | || ||||| || |||||||||||||| ||||| || |||||||| ||||||| || || || | | ||| | || | | || ||| || || ||
GTAACTACTATGTATCACCTGGACAAGCCAATGTATTTGCTTGGCTATCTGGCAAATCAAAGCCGAGTGTATCTGATCGACAAGGAGTTCAAgtaagtgttttttac----ttttctgatcat-gaacgatggctaatcctcctgtgaaattacag------------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|58690875|gb|CK079562.1|CK079562EST: GGATATCTAGCGAATCAAAGCCGAGTTTATCTTATTGACAAGGAATTCAA TGTCATGGGGTACACATTACTTCTTAGTTTGATTGAGTACAAGACACTTGT
genomic: GGATATCTAGCGAATCAAAGCCGAGTTTATCTTATTGACAAGGAATTCAAgtgtgttttc ... cttgttgcagTGTCATGGGGTACACATTACTTCTTAGTTTGATTGAGTACAAGACACTTGT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GTCACCACGATGTATCACTTGGATCGCCCTATGTACTTGTTGGGATATCTAGCGAATCAAAGCCGAGTTTATCTTATTGACAAGGAATTCAAgtgtgttttcttgataatactgcctgcttattgtctggtgttgaattcttgaactaacatatttttcttgttgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA