Sequence
atgc intronic sequence ATGC exonic sequencegtatgttgatccctgctataaatggacatttcatatcttttcaaagtggttaaatcaatggcttatatgcaaatatggtacagGTCAGTGAGTTGCTTGGTTCCTTTGGTGATAATGAACTTTCTCCCGAGTGTCTAGATGGTGCTCAGAGATTCTTGAAGCCAGATGGGATTTCTATTCCTT
Basic information
species | Oryza sativa |
transcript | LOC_Os02g04660.2 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g04660.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G011456_T03 (Zea mays), 3'ss of exon 15
-----gt-atgttgatccctgctataaatggacatttcatatcttttcaaagtggttaaatcaatggct--tatatgcaaatatggtacagGTCAGTGAGTTGCTTGGTTCCTTTGGTGATAATGAACTTTCTCCCGAGTGTCTAGATGGTGCTCAGAGATTCTTGAAGCCAGATGGGATTTCTATTCCTT
|| || || | | | |||||| ||| | | | |||| ||| | | | | || || || || | | ||| | ||||| ||||| |||||||| |||||||| || |||||||| ||||| |||||||| ||||||||||| ||||||||||||| ||||||||||| |||||||
gtacggtgatatttcttttttttggaaatggtcatgttaaacctttccaacccgttgatgttaaaaactcttacatacctacatgattcagGTAAGTGAATTGCTTGGGTCCTTTGGGGACAATGAACTATCTCCGGAGTGTCTGGATGGTGCTCAACGATTCTTGAAGCCTGATGGGATTTCCATTCCTT
upper sequence: LOC_Os02g04660.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G169927_T03 (Zea mays), 3'ss of exon 15
gtatgttgat----ccctgctataaatggacatttcatatcttttcaaagtggttaaatc----aatggcttatatgcaaatatggtacagGTCAGTGAGTTGCTTGGTTCCTTTGGTGATAATGAACTTTCTCCCGAGTGTCTAGATGGTGCTCAGAGATTCTTGAAGCCAGATGGGATTTCTATTCCTT
||| | |||| | | | |||||| ||| ||| |||| ||| || | | | || |||| | | ||||| ||||||||||| |||||||| ||||||||||| |||||||| ||||| |||||||| |||||||||||||||||||||||||| ||||||||||| |||||||
gtacggtgatatttctttcttggaaatggtcatgctatacctttccaacctgttagattttaaaaacctcttacaaacctatatgaatcagGTCAGTGAATTGCTTGGGTCCTTTGGTGACAATGAACTATCTCCTGAGTGTCTTGATGGTGCTCAGAGATTCTTGAAGCCTGATGGGATTTCCATTCCTT
upper sequence: LOC_Os02g04660.2 (Oryza sativa), 3'ss of exon 10
lower sequence: AT4G31120.2 (Arabidopsis thaliana), 3'ss of exon 16
------gtatgttgatccctgctataaatggacatttcatatcttttcaaagtggttaaatcaatggcttatatgcaaatatggtacagGTCAGTGAGTTGCTTGGTTCCTTTGGTGATAATGAACTTTCTCCCGAGTGTCTAGATGGTGCTCAGAGATTCTTGAAGCCAGATGGGATTTCTATTCCTT
| | ||| || ||| ||| | | || | | ||| | ||| || | ||| | | ||||| || || |||| ||||| ||||| || |||||||||||||| |||||||| ||||| || || || || |||||||||| || ||||| || || |
gtcagtatgtacagatttttgtagctaatactcatgc--tgacattatata-cagttcatctaatt-ctcgtttgcctcttctatgcagGTTAGCGAACTGCTGGGTTCTTTTGGAGACAATGAACTTTCTCCTGAGTGTCTTGATGGAGCCCAAAGGTTTCTGAAGCCAGACGGAATTTCAATACCAT
upper sequence: LOC_Os02g04660.2 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv04s0008g03120.t01 (Vitis vinifera), 3'ss of exon 16
gtatgttgatc--cctgctataaatggacatttcatatcttttcaaagtggttaaatcaatggcttatatgcaaatatggtac-agGTCAGTGAGTTGCTTGGTTCCTTTGGTGATAATGAACTTTCTCCCGAGTGTCTAGATGGTGCTCAGAGATTCTTGAAGCCAGATGGGATTTCTATTCCTT
|||||| | | | || | ||| ||||| | | ||| || ||| || ||| | | |||| | |||| ||||||||||| ||||| |||||||| ||||| || ||||| |||||||| ||||| ||||| ||||| ||||||| |||||| ||||| || || |
gtatgtgggttttcttgtggtgaat--acattctttcttacttctttgttgtt---tcttatgctcctctctaaattgaattttagGTTAGTGAGTTGCTGGGTTCTTTTGGTGACAATGAGCTGTCTCCTGAGTGTCTTGATGGAGCTCAAAGATTTTTGAAGCAAGATGGAATTTCAATACCATMapped 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|58682054|gb|CK070741.1|CK070741EST: TTTCAAGTGACATGCGGTGCTGGGAAGCCCCTGAGAAAGCAGATATTTNG GTCAGTGAGTTGCTTGGTTTCTTTGGTGATAATGAACTTTCTCCCGAGTGT
genomic: TTTCAAGTGACATGCGGTGCTGGGAAGCCCCTGAGAAAGCAGATATTTTGgtatgttgat ... tatggtacagGTCAGTGAGTTGCTTGGTTCCTTTGGTGATAATGAACTTTCTCCCGAGTGT
EST:
gi|58659401|gb|CK048081.1|CK048081EST: TTTCAAGTGACATGCGGTGCTGGGAAGCCCCTGAGAAAGCAGATATTTTG GTCAGTGAGTTGCTTGGTTCCTTTGGTGATAATGAACTTTCTCCCGAGTGT
genomic: TTTCAAGTGACATGCGGTGCTGGGAAGCCCCTGAGAAAGCAGATATTTTGgtatgttgat ... tatggtacagGTCAGTGAGTTGCTTGGTTCCTTTGGTGATAATGAACTTTCTCCCGAGTGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttcatatcttttcaaagtggttaaatcaatggcttatatgcaaatatggtacagGTCAGTGAGTTGCTTGGTTCCTTTGGTGATAATGAACTTTCTCCCGAGTGTCTAGATGGTGCTCAGAGATTCTTGAAGCCAGATGGGATTTCTATTCCTT
ttatatgcaaatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgttgatccctgctataaatggacatttcatatcttttcaaagtggttaaatcaatggcttatatgcaaatatggtacagGTCAGTGAGTTGCTTGGTTCCTTTGGTGATAATGAACTTTCTCCCGAGTGTCTAGATGGTGCTCAGAGATTCTTGAAGCCAGATGGGATTTCTATTCCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG