Sequence
atgc intronic sequence ATGC exonic sequenceAATTTTTTGGAAACCTAATGGATGCAGGTAAATTGTCTATATGTGGAGAGGAAAGTTTTGGGACAGGATCTGATCACATCAGGGAGAAGGATGGCATATGgtaaaatattgtttatacatggatgctttttctattagatatccttactgtcctagtatccagttgttgcctagaaatgccaaaacagagataagtgcatcagaattgctttctatgcatgcttgatagtttgcactcttttcttgagaactgtctgcatggaactagtcacactcccgctaactactgactttcag
Basic information
species | Oryza sativa |
transcript | LOC_Os10g11140.1 |
intron # | 16 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os10g11140.2 (Oryza sativa), 5'ss of exon 16
lower sequence: GRMZM2G025854_T02 (Zea mays), 5'ss of exon 16
AATTTTTTGGAAACCTAATGGATGCAGGTAAATTGTCTATATGTGGAGAGGAAAGTTTTGGGACAGGATCTGATCACATCAGGGAGAAGGATGGCATATGgtaaaatattgtttatacatggatgctttttctattagatatccttactgtcctagtatccagttgttgcctagaaatgccaaaacagagataagtgcatcagaattgctttctatgcatgcttgatagtttgcactcttttcttgagaactgtctgcatggaactagtcacactcccgctaactactgactttcag
|||||||||| ||||||||||||||||| ||||||||||| ||||||||||||||||||||||| ||||||||||||||||| |||||||||||||| |||||| | | ||| ||| || | | | ||| || || || || | | | || | ||||||||| || ||| || |||| || || || || ||| |||||| | |||| || |||| |||| ||||| ||||
AATTTTTTGGCAACCTAATGGATGCAGGAAAATTGTCTATTTGTGGAGAGGAAAGTTTTGGGACTGGATCTGATCACATCAGAGAGAAGGATGGCATCTGgtaagaagtaaattac---------------ttatcagctgtagattttgt-----taatcaattttttctttgtaagttctaaacagaga----------agctttggacatcattcatgttt-------------ctgtttgtgtgaaatgtctgtagacaactt-ccatactcttatcaactcttgactctcag
upper sequence: LOC_Os10g11140.2 (Oryza sativa), 5'ss of exon 16
lower sequence: AT5G51820.1 (Arabidopsis thaliana), 5'ss of exon 16
AATTTTTTGGAAACCTAATGGATGCAGGTAAATTGTCTATATGTGGAGAGGAAAGTTTTGGGACAGGATCTGATCACATCAGGGAGAAGGATGGCATATGgtaaaatattgtttatacatggatgcttttt--ctattagatatccttactgtcctagtatccagttgttgcctagaaatgccaaaacagagataagtgcatcagaattgctttctatgcatgcttgatagtttgcactcttttcttgagaactgtctgcatggaactagtcacactcccgctaactactgactttcag
||||||||||||| || |||||||| || |||||||| || |||||||| || || ||||| ||||| |||||||||||| | ||||||||||| ||||||||| | || ||| | | ||||| | | | |||| | | | | | || | | | || | || | |||||| |
AATTTTTTGGAAATCTTATGGATGCTGGAAAATTGTCAATCTGTGGAGAAGAGAGCTTTGGCACAGGTTCTGATCACATCCGTGAGAAGGATGGAATATGgtaa--tcttccttaaatcta-atgctcactaataactggatacttatgcgata-tgcaacgtttccgtctaatgggattgtatcatcacacataagtttgcga-----------------------------------------------------------------------------------------------
upper sequence: LOC_Os10g11140.2 (Oryza sativa), 5'ss of exon 16
lower sequence: Vv16s0022g02320.t01 (Vitis vinifera), 5'ss of exon 16
AATTTTTTGGAAACCTAATGGATGCAGGTAAATTGTCTATATGTGGAGAGGAAAGTTTTGGGACAGGATCTGATCACATCAGGGAGAAGGATGGCATATGgtaaaatattgtttatacatggatgctttttctattagatatccttactgtcctagtatccagttgttgcctagaa-atgccaaaacagagataagtgcatcagaattgctttctatgcatgcttgatagtttgcactcttttcttgagaactgtctgcatggaactagtcacactcccgctaactactgactttcag
|||||||||| ||||| |||||||| || || |||||||| ||||| || ||||||||||| ||||| ||||||||||| | ||||||||||||||||||||| || | || || | | || ||| || || | | || ||| | || | | ||| || ||| | | | | |||
AATTTTTTGGGAACCTTATGGATGCTGGAAAGTTGTCTATTTGTGGGGAAGAAAGTTTTGGAACAGGTTCTGATCACATTCGTGAGAAGGATGGCATATGgtaa------gtctctaaat-----ttactagtaatagtgcctttttttgcctcaagatt-gtctgtaacttaaagcaattcaacccaacgatgctttaagccccaactctt--------------------------------------------------------------------------------------
upper sequence: LOC_Os10g11140.2 (Oryza sativa), 5'ss of exon 16
lower sequence: EFJ34621 (Selaginella moellendorffii), 5'ss of exon 15
AATTTTTTGGAAACCTAATGGATGCAGGTAAATTGTCTATATGTGGAGAGGAAAGTTTTGGGACAGGATCTGATCACATCAGGGAGAAGGATGGCATATGgtaaaatattgtttatacatggatgctttttctattag--atatccttactgtcctagtatccagttgttgcctagaaatgccaaaacagagataagtgcatcagaattgctttctatgcatgcttgatagtttgcactcttttcttgagaactgtctgcatggaactagtcacactcccgctaactactgactttcag
| |||||||| || || ||||| || || ||| |||| || || ||||||||||||||||| || ||||||||||| || | || |||||||| || |||||| | | | | | |||| | | | | ||| | ||| | | | | ||||
AGTTTTTTGGCAATCTCATGGACGCGGGAAAACTGTCGATTTGCGGAGAGGAAAGTTTTGGAACGGGATCTGATCATATTCGTGAAAAGGATGGAATCTGgtaagcttctatcacttcgcagatgatgtaaccagtagttacatcttgcacggtttttaaaccag--------------------------------------------------------------------------------------------------------------------------------------
upper sequence: LOC_Os10g11140.2 (Oryza sativa), 5'ss of exon 16
lower sequence: EFJ32824 (Selaginella moellendorffii), 5'ss of exon 15
AATTTTTTGGAAACCTAATGGATGCAGGTAAATTGTCTATATGTGGAGAGGAAAGTTTTGGGACAGGATCTGATCACATCAGGGAGAAGGATGGCATATGgtaaaatattgtttatacatggatgctttttctattag--atatccttactgtcctagtatccagttgttgcctagaaatgccaaaacagagataagtgcatcagaattgctttctatgcatgcttgatagtttgcactcttttcttgagaactgtctgcatggaactagtcacactcccgctaactactgactttcag
| |||||||| || || ||||| || || ||| |||| || || ||||||||||||||||| || ||||||||||| || | || |||||||| || ||||| | ||| | | ||| | | | | ||| | ||| | | | | ||||
AGTTTTTTGGCAATCTCATGGACGCGGGAAAACTGTCGATTTGCGGAGAGGAAAGTTTTGGAACGGGATCTGATCATATTCGTGAAAAGGATGGAATCTGgtaggcttctgtcatttcgcaaatgatgtaaccagtagttacatcttgcacggtttttaaaccag--------------------------------------------------------------------------------------------------------------------------------------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|29681951|gb|CB678226.1|CB678226EST: TCAGGGAGAAGGATGGCATATG GGCTGTTCTAGCTTGGCTGTCCATACTTGCACACCGGAACAAGGATAAGAA
genomic: TCAGGGAGAAGGATGGCATATGgtaaaatatt ... tgactttcagGGCTGTTCTAGCTTGGCTGTCCATACTTGCACACCGGAACAAGGATAAGAA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
AATTTTTTGGAAACCTAATGGATGCAGGTAAATTGTCTATATGTGGAGAGGAAAGTTTTGGGACAGGATCTGATCACATCAGGGAGAAGGATGGCATATGgtaaaatattgtttatacatggatgctttttctattagatatccttactgtcctagtatccagttgttgcctagaaatgccaaaacagagataagtgcatcagaattgctttctatgcatgcttgatagtttgcactcttttcttgagaactgtctgcatggaactagtcacactcccgctaactactgactttcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG