Sequence
atgc intronic sequence ATGC exonic sequencegtaaccaaccacaactaattttccatcaaagatcatgccaatctattttgctgatcgaaatggatgggaatcaatggaacgattttgcagAGGAGGTACGGGTGCCGCGCGATGATGCTGGAGACGGTGGCGGCGGTGCCGGGGATGGTGGGCGGCATGCTGCTGCACCTCCGGTCGCTCCGCCGCTTCG
Basic information
species | Oryza sativa |
transcript | LOC_Os02g47200.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g47200.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AC233960.1_FGT002 (Zea mays), 3'ss of exon 2
---------------------------------------gtaaccaa--ccacaactaattttccatcaaagatcatgcc----aatctattttgctgatcgaaatggatgggaatcaatggaacgatt-ttgcagAGGAGGTACGGGTGCCGCGCGATGATGCTGGAGACGGTGGCGGCGGTGCCGGGGATGGTGGGCGGCATGCTGCTGCACCTCCGGTCGCTCCGCCGCTTCG
|| |||| | |||| || | | | ||| ||| ||| | ||| || | | | ||| | |||||||||||||| ||||| || ||||||||||| || |||||||||||||||||||||||||||||||||||||| ||||| || ||||||||||||||||
gtgatccctgctcgccccaaccatttccctgaacatccagtctccaagactccaacaaaacggggcagagtcaccctgctgaagaattggattttccgattactattttgctaacatgacgagttaattgtctcagAGGAGGTACGGCTGCCGTGCTATGATGCTGGAAACAGTGGCGGCGGTGCCGGGGATGGTGGGCGGCATGCTGCTTCACCTGCGCTCGCTCCGCCGCTTCG
upper sequence: LOC_Os02g47200.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT1G32350.1 (Arabidopsis thaliana), 3'ss of exon 1
gtaacc-aaccacaactaattttccatcaaagatcatgccaatctattttgc-tgatcgaaatggatgggaa--tcaatggaacgatttt-----gcagAGGAGGTACGGGTGCCGCGCGATGATGCTGGAGACGGTGGCGGCGGTGCCGGGGATGGTGGGCGGCATGCTGCTGCACCTCCGGTCGCTCCGCCGCTTCG
|||| || || || | | | || | | | | | ||| | |||| | | || | ||| |||||| |||||| | || ||||| |||||| |||| ||||||||||| ||||||||||| ||||| || || ||||| ||||| | || ||||| | ||||
gtaatttaatcagaaattttaaatcttcttcatttgttcttttatttttaacatgattttgttttttcaaaaattgaataatttgatttttgagtatagAGGAAGCACATGTGCCATGCGATGTTGCTAGAGACGGTGGCTGCGGTGCCGGGAATGGTCGGGGGGATGCTTTTGCACTTGAAATCTCTCCGGAGGTTCG
upper sequence: LOC_Os02g47200.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv02s0033g01380.t01 (Vitis vinifera), 3'ss of exon 2
-----------gtaaccaaccaca-actaattttccatcaaagatcatgccaatct--attttgctgatcgaaatggatgggaatcaatggaacgatttt-----gcagAGGAGGTACGGGTGCCGCGCGATGATGCTGGAGACGGTGGCGGCGGTGCCGGGGATGGTGGGCGGCATGCTGCTGCACCTCCGGTCGCTCCGCCGCTTCG
| | | | || || |||| | | | |||| | |||| | | | || | ||| | ||||| | | || ||||| || ||| |||||||||||||||| |||||||| || ||||| || || |||||| ||||| || ||| | | || ||||
gtaccttttattcacacgatcccacgctgctttttctgaatgggtcatattttttctagcgttgccattttcccccatttaaatataagaattccattcttaatgacagAGAAAGCACATGTGCCATGCCATGCTGCTGGAGACGGTGGCAGCGGTGCCAGGCATGGTCGGGGGAATGCTGTTGCACTGCCAGTCCCCGAGGCGGTTCG
upper sequence: LOC_Os02g47200.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S183_11V6.1 (Physcomitrella patens), 3'ss of exon 3
------gtaaccaaccacaactaattttccatcaaagatcatgccaatctattttgctg--atcgaaat--ggatgggaatcaatggaacgattttgcagAGGAGGTACGGGTGCCGCGCGATGATGCTGGAGACGGTGGCGGCGGTGCCGGGGATGGTGGGCGGCATGCTGCTGCACCTCCGGTCGCTCCGCCGCTTCG
|||| || | | || | | | | | | ||| || || | ||| ||| || || | | | ||||| | |||| | || || |||||||||||||| |||||||| || || || ||||| ||||| |||||||| || | || | || ||
taggctataactggtacaaagttcgtcgggattagttttgtctcgagtgcagtttattgtcattggaattaggaatctcatgtattatttgctctcgcagAAGCGGTATGATGTTCGTGCAATGATGCTGGAGACCGTGGCGGCTGTTCCTGGAATGGTCGGCGGAATGCTGCTCCATTGCAAATCATTGCGTAAATTTC
upper sequence: LOC_Os02g47200.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ27318 (Selaginella moellendorffii), 3'ss of exon 2
---------------------------------------------------------------------------------------------gtaaccaaccacaactaattttccatcaaagatcatgccaatctat--tttgctgatcgaaatggatgggaatcaatggaacgattttgcagAGGAGGTACGGGTGCCGCGCGATGATGCTGGAGACGGTGGCGGCGGTGCCGGGGATGGTGGGCGGCATGCTGCTGCACCTCCGGTCGCTCCGCCGCTTCG
| || | | || || | ||||| | | | | | |||||| || | | | | | || | |||||||| | | ||||| ||||| ||||||||||| ||||| || || ||||| ||||||||||| || || |||||||||||| ||| ||||| ||||| ||||
gtgaaagcgatgcgtttgcccacagacattttcttccaggcaagatatctttctttctttctttctatcttttgaatatgaatgagcatgtttatgttgaatccttgcgaagttcc---tggggatcaaacgagtttttagtttgctagtctta-taaacttggactgattttat--ttttgcagCGACGATACGGCTGCCGAGCGATGATGCTCGAGACTGTCGCTGCGGTCCCGGGGATGGTCGGGGGGATGCTGCTGCACTGCCGCTCGCTTCGCCGGTTCG
upper sequence: LOC_Os02g47200.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ26025 (Selaginella moellendorffii), 3'ss of exon 3
gtaaccaaccacaactaattttccatcaaagatcatgccaatctattttgctgatcgaaatggatgggaatcaatggaacgattttgcagAGGAGGTACGGGTGCCGCGCGATGATGCTGGAGACGGTGGCGGCGGTGCCGGGGATGGTGGGCGGCATGCTGCTGCACCTCCGGTCGCTCCGCCGCTTCG
| |||| | | | |||| | || | | ||||| | || || | |||||||||| || ||||| || |||||||||||||| ||||| | || || ||||||||||| |||||||| ||||| | || | ||||| ||||
------------------------gtatgctcgcatggcgaatt-ttttttttctcttagttgatggt--ttgatctt-tgaatccaaagAGGAGGTATGGATGCCGGGCTATGATGCTGGAGACTGTGGCTGGAGTTCCCGGGATGGTGGGTGGCATGCTCTTGCACTGCAAATCCTTGCGCCGATTCG
upper sequence: LOC_Os02g47200.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ35306 (Selaginella moellendorffii), 3'ss of exon 2
-----------------------------------------------------------------------------------------gtaaccaaccacaactaattttccatcaaagatcatgccaatctat--tttgctgatcgaaatggatgggaatcaatggaacgattttgcagAGGAGGTACGGGTGCCGCGCGATGATGCTGGAGACGGTGGCGGCGGTGCCGGGGATGGTGGGCGGCATGCTGCTGCACCTCCGGTCGCTCCGCCGCTTCG
| || | | || | | ||||| | | | | | |||||| || | | | | | | | |||||||| | | ||||| ||||| ||||||||||| ||||| || || ||||| ||||||||||| || || |
gtgaaagcgatgcgtttgcccacagacattttcttccaggcaagatatctttctctctttctatcctttgaatatgaatgagcatgtttatgttgaatccttgcgaagctcc---tggggatcaaacgagtttttagtttgctagTCTTA-TAAACTTGGACTGGTTTTAT--TTTTGCAGCGACGATACGGCTGCCGAGCGATGATGCTCGAGACTGTCGCTGCGGTCCCGGGGATGGTCGGGGGGA---------------------------------
upper sequence: LOC_Os02g47200.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ14430 (Selaginella moellendorffii), 3'ss of exon 2
gtaaccaaccacaactaattttccatcaaagatcatgccaatctattttgctgatcgaaatggatgggaatcaatggaacgattttgcagAGGAGGTACGGGTGCCGCGCGATGATGCTGGAGACGGTGGCGGCGGTGCCGGGGATGGTGGGCGGCATGCTGCTGCACCTCCGGTCGCTCCGCCGCTTCG
| |||| | | | |||| | || | | ||||| | || || | ||||||||||||| ||||| || |||||||||||||| ||||| | || || ||||||||||| |||||||| ||||| | || | ||||| ||||
------------------------gtatgctcgcatggcgaaattttttttttctcttagttgatggt--ttgatctt-tgaatccaaagAGGAGGTACGGATGCCGGGCTATGATGCTGGAGACTGTGGCTGGAGTTCCCGGGATGGTGGGTGGCATGCTCTTGCACTGCAAATCCTTGCGCCGATTCGMapped 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|33682633|gb|CF310872.1|CF310872EST: CCTACTGGACCGTCAAGGCGCTGCGCGTGCCCACTGACATCTTCTTCCAG AGGAGGTACGGGTGCCGCGCGATGATGCTGGAGACGGTGGCGGCGGTGCCG
genomic: CCTACTGGACCGTCAAGGCGCTGCGCGTGCCCACTGACATCTTCTTCCAGgtaaccaacc ... gattttgcagAGGAGGTACGGGTGCCGCGCGATGATGCTGGAGACGGTGGCGGCGGTGCCG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgccaatctattttgctgatcgaaatggatgggaatcaatggaacgattttgcagAGGAGGTACGGGTGCCGCGCGATGATGCTGGAGACGGTGGCGGCGGTGCCGGGGATGGTGGGCGGCATGCTGCTGCACCTCCGGTCGCTCCGCCGCTTCG
tgctgat putative branch site (score: 3)
atctatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaccaaccacaactaattttccatcaaagatcatgccaatctattttgctgatcgaaatggatgggaatcaatggaacgattttgcagAGGAGGTACGGGTGCCGCGCGATGATGCTGGAGACGGTGGCGGCGGTGCCGGGGATGGTGGGCGGCATGCTGCTGCACCTCCGGTCGCTCCGCCGCTTCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC