Sequence
atgc intronic sequence ATGC exonic sequencegtaacgcacgagctttgatgttccttcctttacattgatgcaacgatgtgggattgtgattactgatgcggctttgaaaccgatgtagTCTGCCGAGAGGACTCTGGATGCACCGGACCTCGTCGACGATTACTATCTCAACCTGCTGGACTGGGGAAGCAAGAACGTGCTGTCCATTGCGCTGGGCG
Basic information
species | Oryza sativa |
transcript | LOC_Os02g47180.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g47180.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G085375_T01 (Zea mays), 3'ss of exon 1
---------gtaacgcacgagctttgatgtt---ccttcctttacattgatgcaacg--atgtgggattgt--gattactgatgcggct---ttgaaaccgatgtagTCTGCCGAGAGGACTCTGGATGCACCGGACCTCGTCGACGATTACTATCTCAACCTGCTGGACTGGGGAAGCAAGAACGTGCTGTCCATTGCGCTGGGCG
|| | | | || | | | || | | || || | | ||||| | || ||| ||| |||||| | | ||| | |||||||||||||||| || | ||||| || || || || || ||||| ||||||||||| |||||||| ||||| |||||| |||||||| | ||||
gtacgtgtaatagctcttctgattccacatctagcaatcttatgcaacagtgtagtggcatgtgaaaatggtggatcactaatgcggttgagtcaaaatatgtacagTCTGCCGAGAGGACCCTAAACGCACCAGAACTTGTTGATGACTACTACCTCAACCTGCTTGACTGGGGGAGCAACAACGTGTTGTCCATTTCTTTGGGAA
upper sequence: LOC_Os02g47180.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G085908_T01 (Zea mays), 3'ss of exon 2
---------------------------------------------------------------------------------gtaacgcacgagctttgatgtt---ccttcctttacattgatgcaacg--atgtgggattgt--gattactgatgcggct---ttgaaaccgatgtagTCTGCCGAGAGGACTCTGGATGCACCGGACCTCGTCGACGATTACTATCTCAACCTGCTGGACTGGGGAAGCAAGAACGTGCTGTCCATTGCGCTGGGCG
|| | | | || | | | || | | || | || | | || || | || ||| ||||||| || | | ||| | |||||||||||||||| | | ||||| || || || || || ||||| ||||||||||| |||||||| ||||| |||||| |||||||||| | ||
gtgtctatcaccaatgtcgcttcctccaacctgtaggccgagccggccaagcagcggcgccacattccctaggtacgtgtaatagctcttctgattccacatctagcaatcttatgcaacggtgtagtggcatatgaaaatggtggatcactgatgtggttgagtcaaaatatgtacagTCTGCCGAGAGGACCGTAAACGCACCAGAGCTTGTTGATGACTACTACCTCAACCTGCTTGACTGGGGGAGCAACAACGTGATGTCCATTGCTTTAGGAA
upper sequence: LOC_Os02g47180.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT4G33260.1 (Arabidopsis thaliana), 3'ss of exon 2
---------------gtaacgcacgagctttgatgttccttcctttacattgatgcaacgatgtgggattgtgattactgatgcggctttgaaaccgat--gtagTCTGCCGAGAGGACTCTGGATGCACCGGACCTCGTCGACGATTACTATCTCAACCTGCTGGACTGGGGAAGCAAGAACGTGCTGTCCATTGCGCTGGGCG
| || || | || | | || | | ||| |||| || | |||| | || | || ||| || || | ||||| || |||||||||| ||| | || ||||||| ||| |||||| |||||||||||||||| || || | |||| ||| ||| |
gtatgtactgtatttattgcgtttgatccttaaagctcacttactgg--ttgctgcattagagttgtattg-atctgttgctaaactttctgttgtgattaacagACTTCTGAGAGAACCTTGGATGCACCTGACATTGTTGACGATTTCTACCTCAACTTGCTGGACTGGGGAAGTGCAAATGTCTTAGCCATAGCGTTGGACC
upper sequence: LOC_Os02g47180.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT4G33270.1 (Arabidopsis thaliana), 3'ss of exon 2
-------------gtaacgcac--gagctttgatgttccttcctttacattgatgcaacgatgtgggattgtgattactgatgcggctttgaaaccgat--gtagTCTGCCGAGAGGACTCTGGATGCACCGGACCTCGTCGACGATTACTATCTCAACCTGCTGGACTGGGGAAGCAAGAACGTGCTGTCCATTGCGCTGGGCG
||| || || | || | | || | | ||| ||| || | |||| | || | || ||| || || | |||||||| |||||||||| ||| | || ||||||| ||| |||||| |||||||||||||||| || || | |||| ||| ||| |
gtatgtactgtatttaatgcgtttgatccttaaagctcacttactgg--ttgctgcttttgagttgtattg-atctgttgctaaactttctgttgtgattaacagACTTCTGAGAGGACCTTGGATGCACCTGACATTGTTGACGATTTCTACCTCAACTTGCTGGACTGGGGAAGTGCAAATGTCTTAGCCATAGCGTTGGACCMapped 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|58682281|gb|CK070968.1|CK070968EST: CTTCTACCCACCAGGCCAAGCCGGCCAAGCAGCGGCGCTACATTCCCCAG TCTGCCGAGAGGACTCTGGATGCACCGGACCTCGTCGACGATTACTATCTC
genomic: CTTCTACCCACCAGGCCAAGCCGGCCAAGCAGCGGCGCTACATTCCCCAGgtaacgcacg ... accgatgtagTCTGCCGAGAGGACTCTGGATGCACCGGACCTCGTCGACGATTACTATCTC
EST:
gi|58673539|gb|CK062225.1|CK062225EST: CTTCTACCCACCAGGCCAAGCCGGCCAAGCAGCGGCGCTACATTCCCCAG TCTGCCGAGAGGACTCTGGATGCACCGGACCTCGTCGACGATTACTATCTC
genomic: CTTCTACCCACCAGGCCAAGCCGGCCAAGCAGCGGCGCTACATTCCCCAGgtaacgcacg ... accgatgtagTCTGCCGAGAGGACTCTGGATGCACCGGACCTCGTCGACGATTACTATCTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attgatgcaacgatgtgggattgtgattactgatgcggctttgaaaccgatgtagTCTGCCGAGAGGACTCTGGATGCACCGGACCTCGTCGACGATTACTATCTCAACCTGCTGGACTGGGGAAGCAAGAACGTGCTGTCCATTGCGCTGGGCG
tactgat putative branch site (score: 2)
tttgaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaacgcacgagctttgatgttccttcctttacattgatgcaacgatgtgggattgtgattactgatgcggctttgaaaccgatgtagTCTGCCGAGAGGACTCTGGATGCACCGGACCTCGTCGACGATTACTATCTCAACCTGCTGGACTGGGGAAGCAAGAACGTGCTGTCCATTGCGCTGGGCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC