Sequence
atgc intronic sequence ATGC exonic sequencegtatgtatccattgcactcaagctgtcaaaaaggaaatatcattggtagttgctaggaaagatctaatcatacgccgttccatcctgtgcttgagcctttcaaaacaaacaattcaagataacactactagacttacatcttggagtttaagtagctcttttcttgcatttgactaccagGTGAACTATGGAAATTTCATGCATGGATTGATGAAGGAGAACATCCAGCTCAACCGGAAGGTGCTCTCAGAGCTTTCTATGCATGAGCCCTACAGCTTCA
Basic information
species | Oryza sativa |
transcript | LOC_Os01g53280.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g53280.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G028547_T01 (Zea mays), 3'ss of exon 1
gtatgtatccattgcactcaagctgtcaaaaaggaaatatcattggtagttgctaggaaagatctaatcatacgccgttccatcctgtgcttgagcctttcaaaacaaacaattcaagataacactactagacttacatcttggagtttaagtagctcttttcttgcatttgactaccagGTGAACTATGGAAATTTCATGCATGGATTGATGAAGGAGAACATCCAGCTCAACCGGAAGGTGCTCTCAGAGCTTTCTATGCATGAGCCCTACAGCTTCA
||| |||||| | | |||| | ||| |||||| || ||||||| | || | | | || || || | | ||| | || | || | | || | | || | | || | |||||||||||||||| |||||||| ||||| || || || |||||||| ||||||||||||||||| |||||| ||||||||||||||||||| || |||||||| || |||||||| |
--------------------gtatgtgaaaaagaatggaattttggcatttgttaggaac-atataatcatgc------taattttatacc---atctaataataccagcctctca---ttttaccgttggaagtgc-tcatagctttcctgcatctgtattcttgcatttgactatcagGTGAATTATGGCAACTTTATCCATGGATTAATGAAGGAGAACATCCAACTCAACAGGAAGGTGCTCTCAGAGCTGTCGATGCATGAACCTTACAGCTTTA
upper sequence: LOC_Os01g53280.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT1G16740.1 (Arabidopsis thaliana), 3'ss of exon 1
gtatgtatccattgcactcaagctgtcaaaaaggaaatatcattggtagttgctaggaaagatctaatcatacgccgttcca-tcctgtgcttgagcctttcaaaacaaacaattcaagataacactactagacttacatcttggagtttaagtagctcttttcttgcatttgactaccagGTGAACTATGGAAATTTCATGCATGGATTGATGAAGGAGAACATCCAGCTCAACCGGAAGGTGCTCTCAGAGCTTTCTATGCATGAGCCCTACAGCTTCA
| || | |||| ||| || || | | || || || |||| || | | | | || ||| | | || | ||| | | ||| | |||| | ||||||||||| || || ||||| |||||| |||||||||||||||||||||| ||||| || || ||||| ||| | ||||||||||| || ||||| ||||
-------------------------------------------------------gtaacaagctaaatatatgctattataatactctgttt----cttttgaataaga----tggaaatgaca-tgtttgattggaatcctaacatctaaa---------------acttga--aacagGTGAACTACGGGAACTTCATCCATGGACTGATGAAGGAGAACATCCAGCTGAACCGCAAAGTCCTCTCTGAGTTATCTATGCATGAACCTTACAGTTTCA
upper sequence: LOC_Os01g53280.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv03s0017g01790.t01 (Vitis vinifera), 3'ss of exon 2
gtatgtatccattgcactcaagctgtcaaaaaggaaatatcattggtagttgctaggaaagatctaatcatacgccgttccatcctgtgcttgagcctttcaaaacaaacaattcaagataacactactagacttacatcttggagtttaagtagctcttt-tcttgcatttgactaccagGTGAACTATGGAAATTTCATGCATGGATTGATGAAGGAGAACATCCAGCTCAACCGGAAGGTGCTCTCAGAGCTTTCTATGCATGAGCCCTACAGCTTCA
|||| | ||| ||||| || || || ||| ||||| || | | |||| | | | | | |||| ||| || ||||| || || || || || ||||| ||||||||||||||||||||||| ||| |||| || ||||||||||| ||||||||||| || |||| |||||
----------------------------------------------------------------------------gttctgaaa-atataggaggctttcct--tcaataa--cagtatacgtaagctagaatttgacttatttgtttccttcgttttctaccttggtcttgtctcacagGTTAATTACAATAACTTTATACATGGGTTGATGAAGGAGAACATCCAGCTGAACAGGAAAGTTCTCTCAGAGCTGTCTATGCATGAACCTTACACCTTCA
upper sequence: LOC_Os01g53280.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S152_64V6.1 (Physcomitrella patens), 3'ss of exon 1
gtatgtatccattgcactcaagctgtcaaaaaggaaatatcattggtagttgctaggaaagatctaatcatacgccgttccatcctgtgcttgagcctttcaaaacaaacaattcaagataacactactagacttacatcttggagtttaagtagctcttttcttgcatttgactaccagGTGAACTATGGAAATTTCATGCATGGATTGATGAAGGAGAACATCCAGCTCAACCGGAAGGTGCTCTCAGAGCTTTCTATGCATGAGCCCTACAGCTTCA
|| || || | | | | | | | || || |||| | || || | | || | |||| |||| ||| ||||| || |||| ||| | || | |||||||| || | || |||||||||||||| ||||||||| ||||||| || || ||||||||||
-----------------------------------------------------------------cgctgcttagaattagattctaatcgtaggtttcttcacgagactaactc----caacattgaatttgttctggtttacgctgaataaagttgttttggtgca-----------gGTTAACTACGGGGATTTTATGAACGGGCTTTCCAAGGAGAATATTGACCTGAACCGGAAGGTGCTGTCAGAGCTTGCTATGCACGAACCTTACAGCTTCAMapped 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|88574531|gb|CI666300.1|CI666300EST: TGCGATCCCTTTGGATAGAGCGTATCAATGCTGGTACACGATTGCATGGG GTGAACTATGGAAATTTCATGCATGGATTGATGAAGGAGAACATCCAGCTC
genomic: TGCGATCCCTTTGGATAGAGCGTATCAATGCTGGTACACGATTGCATGGGgtatgtatcc ... tgactaccagGTGAACTATGGAAATTTCATGCATGGATTGATGAAGGAGAACATCCAGCTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tactagacttacatcttggagtttaagtagctcttttcttgcatttgactaccagGTGAACTATGGAAATTTCATGCATGGATTGATGAAGGAGAACATCCAGCTCAACCGGAAGGTGCTCTCAGAGCTTTCTATGCATGAGCCCTACAGCTTCA
ctcttttcttgcattt CT-rich tract
tttaagta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtatccattgcactcaagctgtcaaaaaggaaatatcattggtagttgctaggaaagatctaatcatacgccgttccatcctgtgcttgagcctttcaaaacaaacaattcaagataacactactagacttacatcttggagtttaagtagctcttttcttgcatttgactaccagGTGAACTATGGAAATTTCATGCATGGATTGATGAAGGAGAACATCCAGCTCAACCGGAAGGTGCTCTCAGAGCTTTCTATGCATGAGCCCTACAGCTTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT