Sequence
atgc intronic sequence ATGC exonic sequencegtatcactgaaaatctttacttgttaattttttgtttcatgcatatcttattgccatttctgtacatcacatactatgcaacacatacgcagGTTATAAAAAACTCAAATGGGTGCAACCTAGCTGTTGACATATGGAGTTTGGGATGCACTGTCCTGGAGATGGCTACATCGAAACCGCCATGGAGCCAGT
Basic information
species | Oryza sativa |
transcript | LOC_Os04g47240.3 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g47240.3 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G175504_T01 (Zea mays), 3'ss of exon 7
-------------gtatcactgaaaatctttacttgttaattttttgtttcatgcatatcttattgccatttctgtacatcacatacta----tgcaacacatacgcagGTTATAAAAAACTCAAATGGGTGCAACCTAGCTGTTGACATATGGAGTTTGGGATGCACTGTCCTGGAGATGGCTACATCGAAACCGCCATGGAGCCAGT
| | | | | || || || ||||| || ||| ||| ||| |||||||| | | |||||| |||| |||| | ||||||||||||||| || ||||| |||||||| | ||||||||||||||||| || |||||||||||||| |||||||| || || || |||||||||||||
gtactgaaatgaagctcttcctttagtttgtatttttt--tttttaattcaatgtgcatcacattataatttctgttaacaaaatactaaccatgcagcacaaatgcagGTTATAAAAAATTCTAATGGATGCAACCTTGTGGTTGACATATGGAGTTTAGGTTGCACTGTCCTGGAAATGGCTACCTCAAAGCCACCATGGAGCCAGT
upper sequence: LOC_Os04g47240.3 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA20G30100.2 (Glycine max), 3'ss of exon 2
gtatcactgaaaatcttta---cttgttaattttttgtttcatgcatatcttattgccatttctgtacatcacatactatgcaacacatacgcagGTTATAAAAAACTCAAATGGGTGCAACCTAGCTGTTGACATATGGAGTTTGGGATGCACTGTCCTGGAGATGGCTACATCGAAACCGCCATGGAGCCAGT
|| | | | |||||| ||| || |||| | ||| | ||||| | | || |||| | || | | | |||||||||||||| || ||||| |||||||| || || || ||||||||| | |||||||| || |||| ||||||||| | ||||| || ||| ||||
gttctaat-attttctttaaaccttttttcttttatattttgattgtgtcttagatctgtggctcagtatcat-tgctttctgatg---attcagGTTATAAAAAATTCTAATGGATGCAACCTTGCGGTGGATATATGGAGTCTTGGATGCACAGTTTTGGAAATGGCTACAACCAAACCTCCTTGGTTTCAGT
upper sequence: LOC_Os04g47240.3 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA08G01880.1 (Glycine max), 3'ss of exon 7
gtatcactgaaaatctttacttgtt-aattttttgtttcatgcatatcttat-tgccatttctgtacatcacatactatgcaacacatacgcagGTTATAAAAAACTCAAATGGGTGCAACCTAGCTGTTGACATATGGAGTTTGGGATGCACTGTCCTGGAGATGGCTACATCGAAACCGCCATGGAGCCAGT
|| | ||| ||| | || || ||| | | || || | || | | | ||| | ||| || ||| ||||||||||||| |||||||| || || || || ||||| ||||||||| | ||||||||||| |||||||||| ||| | ||||| || |||||||| |
gtcagaatgatt-tctacatccattcaacactttttgttgcagatgctttgtctgtagtatattcttatctttgtcactgcctcaattacatagGTTATAAAAAATTCAAATGGTTGTAATCTTGCGGTTGATATATGGAGTCTAGGATGCACTGTTTTGGAGATGGCAACAACAAAACCTCCTTGGAGCCAAT
upper sequence: LOC_Os04g47240.3 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA16G30030.2 (Glycine max), 3'ss of exon 8
gtatcactgaaaatctttacttgttaattttt-tgtttcatgcat---atcttattgccatttctgtacatcacatactatgcaacaca--tacgcagGTTATAAAAAACTCAAATGGGTGCAACCTAGCTGTTGACATATGGAGTTTGGGATGCACTGTCCTGGAGATGGCTACATCGAAACCGCCATGGAGCCAGT
|| || ||| ||||| |||| | || || || || || ||| || | | | || ||| | ||||||||||||||||| ||||| ||||||||||||||||| |||||||| | |||||||| || |||| ||||||||| | ||||| || ||||| ||||
-----gttgtaatattttctctgttagttttggtcctttatagattcaattacatcttggttttgtgactttata-gctttgctttctgatttttcagGTTATAAAAAACTCTAATGGTTGCAACCTAGCTGTTGATATATGGAGCCTTGGATGCACAGTTTTGGAAATGGCTACAACTAAACCTCCTTGGAGTCAGT
upper sequence: LOC_Os04g47240.3 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA10G37730.1 (Glycine max), 3'ss of exon 9
gtatcactgaaaatctttacttgttaattttttgtttcatgcatatctt-attgccatttctgtacatcacatactatgcaacacat-------acgcagGTTATAAAAAACTCAAATGGGTGCAACCTAGCTGTTGACATATGGAGTTTGGGATGCACTGTCCTGGAGATGGCTACATCGAAACCGCCATGGAGCCAGT
| ||| ||| ||| ||| ||| ||| || |||| || ||||| || | | | | ||| || | | | ||||||||||| ||||| ||||| |||||||| || || || ||||||||| | |||||||| || |||| |||||||| | ||||| || ||| ||||
------gttctaatattttctt--taaaccttttttttatatatattttgattgcatcttagatctgtgattcagtat-cattgctttctgatgattcagGTTATAAAGAACTCTAATGGATGCAACCTTGCAGTGGATATATGGAGTCTTGGATGCACGGTTTTGGAAATGGCTACTACCAAACCTCCTTGGTTTCAGT
upper sequence: LOC_Os04g47240.3 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA09G24970.2 (Glycine max), 3'ss of exon 7
gtatcactgaaaatctttacttgttaattttttgtttcatgcatatcttattgc----catttctgtacatcacatactatgcaacaca--tacgcagGTTATAAAAAACTCAAATGGGTGCAACCTAGCTGTTGACATATGGAGTTTGGGATGCACTGTCCTGGAGATGGCTACATCGAAACCGCCATGGAGCCAGT
|| || ||| ||||| ||| ||| | | || ||| | || ||| | || |||| | ||||||||||||||||| ||||| ||||||||||||||||| |||||||| | |||||||| || |||| ||||||||| | ||||| || ||||| ||||
-----gttgtaatattttctctgtta-ctttcagttctttatagattcaattacatattggttttgtgacttgatagctttgcattctgatttttcagGTTATAAAAAACTCTAATGGTTGCAACCTAGCTGTTGATATATGGAGCCTTGGATGCACAGTTTTGGAAATGGCTACAACTAAACCTCCTTGGAGTCAGT
upper sequence: LOC_Os04g47240.3 (Oryza sativa), 3'ss of exon 8
lower sequence: AT1G63700.1 (Arabidopsis thaliana), 3'ss of exon 7
gtatcactgaaaatctttacttgttaattttttgtttcatgcatatcttattgccatttctgtacatcacatactatgcaacacatacg-cagGTTATAAAAAACTCAAATGGGTGCAACCTAGCTGTTGACATATGGAGTTTGGGATGCACTGTCCTGGAGATGGCTACATCGAAACCGCCATGGAGCCAGT
| | | | | | | | ||||||| || || || || || || ||| | | ||||| ||||| || |||||||| | ||||| || || |||||||||||| | ||||| ||||| | || ||||||||| ||||||| |||||||||||||
--------gtcagtatgctgctacaacctgtctgtttca-----atgttgacaggcgttatgctgatgctttattatcttgcttggatttcagGTGATAAAGAATTCAAATGGCAGTAACCTTGCGGTCGACATATGGAGTCTTGGATGTACTGTTTTAGAAATGGCTACAACGAAACCTCCATGGAGCCAGTMapped 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|58677676|gb|CK066363.1|CK066363EST: AGCAGTGTCCTTTCTCCTTTAAGGGTAGTCCATATTGGATGGCTCCAGAG GTTATAAAAAACTCAAATGGGTGCA
genomic: AGCAGTGTCCTTTCTCCTTTAAGGGTAGTCCATATTGGATGGCTCCAGAGgtatcactga ... acatacgcagGTTATAAAAAACTCAAATGGGTGCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catgcatatcttattgccatttctgtacatcacatactatgcaacacatacgcagGTTATAAAAAACTCAAATGGGTGCAACCTAGCTGTTGACATATGGAGTTTGGGATGCACTGTCCTGGAGATGGCTACATCGAAACCGCCATGGAGCCAGT
atatcttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatcactgaaaatctttacttgttaattttttgtttcatgcatatcttattgccatttctgtacatcacatactatgcaacacatacgcagGTTATAAAAAACTCAAATGGGTGCAACCTAGCTGTTGACATATGGAGTTTGGGATGCACTGTCCTGGAGATGGCTACATCGAAACCGCCATGGAGCCAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA