Sequence
atgc intronic sequence ATGC exonic sequencegtatgtgttgcatttacggtgagctaggctagttcatagctgaatatgttttgatgttgttaattcatatctgcagAGGCCCTGTCCAGACTATACAATGTAATCAAACATCCCAATGCGTTGGACTTGGATAATGCGATGGCATATGACAATGCTGTTTCTGCTCTTGGGAAAAT
Basic information
species | Oryza sativa |
transcript | LOC_Os03g49420.1 |
intron # | 15 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g49420.1 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM2G033619_T01 (Zea mays), 3'ss of exon 15
gtatgtgttgcatttacggtgagctaggctagttcatagctgaatatgttttgatgttgttaa--------ttcatatctgcagAGGCCCTGTCCAGACTATACAATGTAATCAAACATCCCAATGCGTTGGACTTGGATAATGCGATGGCATATGACAATGCTGTTTCTGCTCTTGGGAAAAT
||||| ||| || || | || | | | | || | | | || |||| |||||| || || ||| |||||||||| |||||| |||||||||||||||||||||| ||||| |||| ||||||||||| ||||| |||||||||||||||||||||||||| |||||
gtatggtttgtatctatgttgtattcgatttatgtatgcatt--tgttattcgatgctgttaacaatcttgtttatttctacagAGGCCCTATCCAGATTATACAATGTAATCAAACATCCTAATGCCCTGGATTTGGATAATGCAATGGCCTATGACAATGCTGTTTCTGCTCTTGGAAAAAT
upper sequence: LOC_Os03g49420.1 (Oryza sativa), 3'ss of exon 15
lower sequence: GLYMA05G28950.1 (Glycine max), 3'ss of exon 18
gtatgtgttgcatttacggtgagctaggctagttcatagctgaatatgttttgatgttgttaattcatatctgcagAGGCCCTGTCCAGACTATACAATGTAATCAAACATCCCAATGCGTTGGACTTGGATAATGCGATGGCATATGACAATGCTGTTTCTGCTCTTGGGAAAAT
||| ||| | ||||| | | || || | | |||||| | | |||||||||| || || || || | ||| ||| | ||||| ||||| | | | ||||||| ||||||||||||||||||||||| ||| | || |||||
gtactgcttgatccattaacaaactaggaaaaagctgtactatattgagtaacaagttgttgttggcttactgcagAGGCTCTTTCGAGGTTAAATGCTGTGATCCAGCATCCTAATGCTCTTCATTCAGATAATGTAATGGCATATGACAATGCTGTTTCCGCTTTGGGAAAAAT
upper sequence: LOC_Os03g49420.1 (Oryza sativa), 3'ss of exon 15
lower sequence: GLYMA16G04400.1 (Glycine max), 3'ss of exon 16
-----gtatgtgttgcatttacggtgagctaggctagttcatagctgaatatgttttgatgttgttaattcatatc----tgcagAGGCCCTGTCCAGACTATACAATGTAATCAAACATCCCAATGCGTTGGACTTGGATAATGCGATGGCATATGACAATGCTGTTTCTGCTCTTGGGAAAAT
| | | || | | | || | | || |||| |||| | | || | | ||||||||| || || || || | ||| || | ||||| ||||| | | | ||||| ||||||||||||||||||||||| |||||||| |||||
gttagttgcacaataccattttcttattttgttgtcgtgccttactatatatattttttggataaatgtttctgttctattgcagAGGCACTTTCAAGGTTAGATGCTGTGATAAGGCATCCAAATGCACTACATTCTGATAACATAATGGCATATGACAATGCTGTTTCAGCTCTTGGAAAAAT
upper sequence: LOC_Os03g49420.1 (Oryza sativa), 3'ss of exon 15
lower sequence: Vv06s0004g00500.t01 (Vitis vinifera), 3'ss of exon 16
gtatgtgttgcatttacggtg--agctaggctagttcatagctgaatatgttttgat-----gttgttaattcatatctgcagAGGCCCTGTCCAGACTATACAATGTAATCAAACATCCCAATGCGTTGGACTTGGATAATGCGATGGCATATGACAATGCTGTTTCTGCTCTTGGGAAAAT
|||||| | | | || || | || | ||| | | | | ||| | ||| ||| || | | ||||||| || || || ||| | ||||| ||||| ||||| || | ||||||| ||||||||||| ||||||||||||||||| || |||||
gtatgttctacttgcacattgttgggaagttaatttcttttgctattgtcctttaactaacagttcttagttgccttgttcagAGGCTCTTTCAAGGCTAAATGTCGTAATACGGCATCCTAATGCACTGCAACCAGATAATGTAATGGCATATGATAATGCTGTTTCTGCTCTAGGAAAAATMapped 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|29681491|gb|CB677766.1|CB677766EST: GCATNTAGGCCTCACACTGGTG AGGCCCTGTCCAGACTATACAATGTAATCAAACATCCCAATGCGTTGGACT
genomic: GCATTTAGGCCTCACACTGGTGgtatgtgttg ... atatctgcagAGGCCCTGTCCAGACTATACAATGTAATCAAACATCCCAATGCGTTGGACT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agctaggctagttcatagctgaatatgttttgatgttgttaattcatatctgcagAGGCCCTGTCCAGACTATACAATGTAATCAAACATCCCAATGCGTTGGACTTGGATAATGCGATGGCATATGACAATGCTGTTTCTGCTCTTGGGAAAAT
tgttaat putative branch site (score: 3)
ttgttaattcatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtgttgcatttacggtgagctaggctagttcatagctgaatatgttttgatgttgttaattcatatctgcagAGGCCCTGTCCAGACTATACAATGTAATCAAACATCCCAATGCGTTGGACTTGGATAATGCGATGGCATATGACAATGCTGTTTCTGCTCTTGGGAAAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT