Sequence
atgc intronic sequence ATGC exonic sequenceGTTTGTGCATGGTGATGTGAAACCAGAGAACTTTCTGCTTGGCCAGCCTGGATCACCTGACGAGAAGAAGCTTTATCTTATTGATCTTGGTTTAGgtaagctattaatagtttgtttcatttcaccacattttcatggcatacactaggactaaaatcttatgctttatacacttgtatttccaattgttgttgcccctattagttttcaagtattttttgtatgatatggcattgtccaaattgtacag
Basic information
species | Oryza sativa |
transcript | LOC_Os07g07560.2 |
intron # | 8 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g07560.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G037923_T02 (Zea mays), 5'ss of exon 8
GTTTGTGCATGGTGATGTGAAACCAGAGAACTTTCTGCTTGGCCAGCCTGGATCACCTGACGAGAAGAAGCTTTATCTTATTGATCTTGGTTTAGgtaagctattaatagtttgtttcatttcaccacattttcatggcatac-actaggactaaaatcttatgctttatacacttgtatttccaattgttgttgcccctattagttttcaagtatttt-ttgta--tgatatggcattgtccaaattgtacag
|||||||||||||||||||||||||||||| ||||||||||| ||||||||||| ||||| || ||||||||||| ||||| |||||||||||||||| || || | ||| ||| || | || || ||| | || | | | | ||| ||| | || | | | | || ||| |||| || | | ||| |||| ||||||| | |||||||||||
GTTTGTGCATGGTGATGTGAAACCAGAGAATTTTCTGCTTGGTCAGCCTGGATCGCCTGAAGATAAGAAGCTTTACCTTATAGATCTTGGTTTAGgtatgcatttgtcaattttttttatccaagtgt-ttactattccatgccacctttgtttc--tttgaaacttcatagattt----tcttagtgttatttttcccaattatcttcccccttctttgttgttgttgatatgtggcacccaaaattgtacag
upper sequence: LOC_Os07g07560.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G458035_T01 (Zea mays), 5'ss of exon 6
GTTTGTGCATGGTGATGTGAAACCAGAGAACTTTCTGCTTGGCCAGCCTGGATCACCTGACGAGAAGAAGCTTTATCTTATTGATCTTGGTTTAGgtaagctattaatagtttgtttcatttcaccacattttcatggcatac-actaggactaaaatcttatgctttatacacttgtatttccaattgttgttgcccctattagttttcaagtattttttgta--tgatatggcattgtccaaattgtacag
|||||||||||||||||||||||||||||| ||||||||||| ||||||||||| ||||| | ||||||||||| |||| |||||||||||||||| || || | ||| ||| || | || || ||| | || | | | | ||| ||| | | ||| | |||| || ||| |||| | | | ||| |||| ||||||| | ||||||||||
GTTTGTGCATGGTGATGTGAAACCAGAGAATTTTCTGCTTGGTCAGCCTGGATCGCCTGAATATAAGAAGCTTTACCTTACAGATCTTGGTTTAGgtatgcatttgtcaattt-ttttatccaagtgt-ttactattccatgccacctttgtttc--tttgaaacttcatagatt-----ttcttagtgttattttcccaattatctcccccttctttgttgttgttgatatgtggcacccaaaattgtacaa
upper sequence: LOC_Os07g07560.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G082099_T01 (Zea mays), 5'ss of exon 2
GTTTGTGCATGGTGATGTGAAACCAGAGAACTTTCTGCTTGGCCAGCCTGGATCACCTGACGAGAAGAAGCTTTATCTTATTGATCTTGGTTTAGgtaagctattaatagtttgtttcatttcaccacattttcatggcatac-actaggactaaaatcttatgctttatacacttgtatttccaattgttgttgcccctattagttttcaagtattttttgta--tgatatggcattgtccaaattgtacag
|||||||||||||||||||||||||||||| ||||||||||| ||||||||||| ||||| || ||||||||||| |||| |||||||||||||||| || || | ||| ||| || | || || ||| | || | | | | ||| ||| | | ||| | |||| || ||| |||| | | | ||| |||| ||||||| | ||||||||||
GTTTGTGCATGGTGATGTGAAACCAGAGAATTTTCTGCTTGGTCAGCCTGGATCGCCTGAAGATAAGAAGCTTTACCTTACAGATCTTGGTTTAGgtatgcatttgtcaattt-ttttatccaagtgt-ttactattccatgccacctttgtttc--tttgaaacttcatagatt-----ttcttagtgttattttcccaattatctcccccttctttgttgttgttgatatgtggcacccaaaattgtacaa
upper sequence: LOC_Os07g07560.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G110085_T01 (Zea mays), 5'ss of exon 3
-----GTTTGTGCATGGTGATGTGAAACCAGAGAACTTTCTGCTTGGCCAGCCTGGATCACCTGACGAGAAGAAGCTTTATCTTATTGATCTTGGTTTAGgtaagctattaatagtttgtttcatttcaccacattttcatggcatac-actaggactaaaatcttatgctttatacacttgtatttccaattgttgttgcccctattagttttcaagtatttt-ttgta--tgatatggcattgtccaaattgtacag
|||||||||||||||||||||||||||||| ||||||||||| ||||||||||| ||||| || ||||||||||| ||||| |||||||||||||||| || || | ||| ||| || | || || ||| | || | | | | ||| ||| | | ||| | |||| || ||| |||| | | | ||| |||| ||||||| | ||||||||||
GCCAGGTTTGTGCATGGTGATGTGAAACCAGAGAATTTTCTGCTTGGTCAGCCTGGATCGCCTGAAGATAAGAAGCTTTACCTTATAGATCTTGGTTTAGgtatgcatttgtcaattt-ttttatccaagtgt-ttactattccatgccacctttgtttc--tttgaaacttcatagatt-----ttcttagtgttattttcccaattatctccccccttctttgttgttgttgatatgtggcacccaaaattgtacaa
upper sequence: LOC_Os07g07560.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G164265_T03 (Zea mays), 5'ss of exon 8
GTTTGTGCATGGTGATGTGAAACCAGAGAACTTTCTGCTTGGCCAGCCTGGATCACCTGACGAGAAGAAGCTTTATCTTATTGATCTTGGTTTAGgtaagctattaatagtttgtttcatttcac-cacattttcatggcata-cactaggactaaaatcttatgctttatacacttgtatttccaattgttgttgcccctattagttttcaagtattttttgtatgatatggcattgtccaaattgtacag
|||||||||||||||||||||||||||||| ||||||||||| ||||||||||| |||||||| ||||| ||||| ||||| ||||| |||||||||| || || | | |||| | | | || || |||| |||| | | | |||||| | || | | | || ||| ||| || || |||| ||||||| | |||||||||||||
GTTTGTGCATGGTGATGTGAAACCAGAGAATTTTCTGCTTGGTCAGCCTGGATCGCCTGACGATAAGAAACTTTACCTTATAGATCTCGGTTTAGgtatgcatttgtcaaatagtttttatctatgtattttactattccatatcactgtagtttctttgaaactatttatattttcttagtgctattttcccacttgcctcccccctttgttgttgttgttgt-tgatatg-tggtacccaaattgtacag
upper sequence: LOC_Os07g07560.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA16G04580.1 (Glycine max), 5'ss of exon 8
GTTTGTGCATGGTGATGTGAAACCAGAGAACTTTCTGCTTGGCCAGCCTGGATCACCTGACGAGAAGAAGCTTTATCTTATTGATCTTGGTTTAGgtaagctattaatagtttgtttcatttcaccacattttcatggcatacactaggactaaaatcttatgctttatacacttgtatttccaattgttgttgcccctattagttttcaagtattttttgtatgatatggcattgtccaaattgtacag
|||||||||||| ||||||||||| || |||||| ||||||| || ||||||||| |||| || |||||| | |||||||||||||||||| | |||| | | | || ||| || | | | || | | ||| || ||| | | | ||| | ||| | | | ||||| | | || |||| ||| ||||||| |
GTTTGTGCATGGAGATGTGAAACCTGAAAACTTTTTGCTTGGTCAACCTGGATCAGCTGAAGATAAGAAGTTATATCTTATTGATCTTGGTCTGGgtatgttgtccat--------tcaaaccag-------ttgttgtttatgttgcgtttaa--ctttctgcctcaccacttggtacatgatattttcatgact--tattaatgtcca-----------tatggcatg-cattgtcttcag-------
upper sequence: LOC_Os07g07560.1 (Oryza sativa), 5'ss of exon 8
lower sequence: AT3G03940.1 (Arabidopsis thaliana), 5'ss of exon 8
GTTTGTGCATGGTGATGTGAAACCAGAGAACTTTCTGCTTGGCCAGCCTGGATCACCTGACGAGAAGAAGCTTTATCTTATTGATCTTGGTTTAGgtaagctattaatagtttgtttcatttcaccacattttcatggcatacactaggactaaaatcttatgctttatacacttgtatttccaattgttgttgcccctattagttttcaagtattttttgtatgatatggcattgtccaaattgtacag
|||||||||||| |||||||||||||| |||||| ||||||| ||||||||| || | ||||||||||| || || ||||| ||||||||| ||||| || | || | || || | |||||| | | || | ||| | | || |
GTTTGTGCATGGAGATGTGAAACCAGAAAACTTTTTGCTTGGTCAGCCTGGAACAGCAGACGAGAAGAAACTATACCTTATCGATCTTGGTCTAGgtgagtatctgttaaatatttacaatcgttttatttttca------aaatcttaacatatatcatctatttcag---------------------------------------------------------------------------------
upper sequence: LOC_Os07g07560.1 (Oryza sativa), 5'ss of exon 8
lower sequence: Vv08s0007g07420.t01 (Vitis vinifera), 5'ss of exon 8
GTTTGTGCATGGTGATGTGAAACCAGAGAACTTTCTGCTTGGCCAGCCTGGATCACCTGACGAGAAGAAGCTTTATCTTATTGATCTTGGTTTAGgtaagctattaatagtttgtttcatttcaccacattttcatggcatacactaggactaaaatcttatgctttatacacttgtatttccaattgttgttgcccctattagttttcaagtattttttgtatgatatggcattgtccaaattgtacag
|||||||||||| |||||||| |||||||||||| | ||||| || |||||| | |||| ||||||||||| | |||||||||||||||||| |||| || || || | | | ||| | || || ||| || | | | || ||| |||| | ||| || || |||
GTTTGTGCATGGAGATGTGAAGCCAGAGAACTTTTTACTTGGTCAACCTGGAACTGCTGATGAGAAGAAGCTATTTCTTATTGATCTTGGTTTGGgtatgccatc-----cttcctcaagtctttcac-ctgtcgtgtcatgtcctctgcgtgg-----tgtgaaccatagtattgtttcaccatgtgaaacaatgtgcatgagtg--------------------------------------------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|58659496|gb|CK048176.1|CK048176EST: GCCTGGATCACCTGACGAGAAGAAGCTTTATCTTATTGATCTTGGTTTAG CATCGAAATGGAGGGAGTCATCAGGGCAACATGTTGATTATGACCAAAGGC
genomic: GCCTGGATCACCTGACGAGAAGAAGCTTTATCTTATTGATCTTGGTTTAGgtaagctatt ... aattgtacagCATCGAAATGGAGGGAGTCATCAGGGCAACATGTTGATTATGACCAAAGGC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GTTTGTGCATGGTGATGTGAAACCAGAGAACTTTCTGCTTGGCCAGCCTGGATCACCTGACGAGAAGAAGCTTTATCTTATTGATCTTGGTTTAGgtaagctattaatagtttgtttcatttcaccacattttcatggcatacactaggactaaaatcttatgctttatacacttgtatttccaattgttgttgcccctattagttttcaagtattttttgtatgatatggcattgtccaaattgtacag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC