Sequence
atgc intronic sequence ATGC exonic sequencegtactaagactaagctcagaaactcatcatgcctaatgatgcaatgcctgtcactgactgatgaacactttgttactgcagAGGCAAACCTCCTGTTCCTGGAATCACCTGCCGGAGTTGGCTTTTCATACTCCAACACCACCTCTGATCTCAAGACATCTGGTGATGAGAGGACAG
Basic information
species | Oryza sativa |
transcript | LOC_Os02g55130.3 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g55130.5 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM5G879749_T02 (Zea mays), 3'ss of exon 2
-----gtactaagactaagctcagaaactcatcatgcctaatgatgcaatgcctgtcactgactgatgaacactttgttactgcagAGGCAAACCTCCTGTTCCTGGAATCACCTGCCGGAGTTGGCTTTTCATACTCCAACACCACCTCTGATCTCAAGACATCTGGTGATGAGAGGACAG
|| |||| | | ||| | | | || | || ||| ||| ||||| | |||| ||||||||||||||| |||||||| || || || || ||||| ||||| || ||| ||||||||||||| || |||||||| || || || |||||||| |
gtgagaaacaaagaaagaaagaaaaaaacccttaaaactcttaat-taatcaacatcaacgactgcccgttcccttgt-gttgcagAGGCAAACCTTCTGTTCCTCGAGTCGCCCGCGGGAGTCGGCTTCTCCTACGCCAACACCACCTCGGACCTCAAGACGTCGGGCGACGAGAGGACCG
upper sequence: LOC_Os02g55130.5 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ35996 (Selaginella moellendorffii), 3'ss of exon 3
-------------------gtactaagactaagctcagaaactcatcatgcctaatgatgcaatgcctgtcactgactgatgaacactttgttact-gcagAGGCAAACCTCCTGTTCCTGGAATCACCTGCCGGAGTTGGCTTTTCATACTCCAACACCACCTCTGATCTCAAGACATCTGGTGATGAGAGGACAG
| | | || | || | || || | | || | | | | | ||||| | |||| ||| || | || ||||||||||| |||||||| ||||||| ||||| ||||| |||||| |||| | ||| ||| || | || |
cgcctcacgcttgtctctcttttttctctttagtttcttttggtattagctctcattct-ctttggtttttttcgcgttttttttttgttgttgtttgcagTGGCGAATTTGCTCTTCCTGGAATCTCCTGCCGGTGTTGGCTACTCATATTCCAATACCACCACTGACACAGACGCATTTGGCGACACTCGAACTG
upper sequence: LOC_Os02g55130.5 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ36223 (Selaginella moellendorffii), 3'ss of exon 3
-------------gtactaagactaagctcagaaactcatcatgcctaatgatgcaatgcctgtcactgactgatgaacactttgttactg-------cagAGGCAAACCTCCTGTTCCTGGAATCACCTGCCGGAGTTGGCTTTTCATACTCCAACACCACCTCTGATCTCAAGACATCTGGTGATGAGAGGACAG
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tcgcctcacgcttgt-ctctcttttttctctttagttccttttggtattagctctcattctctttggtttttttcgcgtttttttttgttgttgtttgcagTGGCGAATTTGCTCTTCCTGGAATCTCCTGCCGGTGTTGGCTACTCATATTCCAATACCACCACTGACACAGACGCATTTGGCGACACTCGAACTGMapped 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|58655220|gb|CK043900.1|CK043900EST: TAAGACAAACGGGACAGGGCTCTATCTGAACAAGTACTCATGGAACAGAG AGGCAAACCTCCTGTTCCTGGAATCACCTGCCGGAGTTGGCTTTTCATACT
genomic: TAAGACAAACGGGACAGGGCTCTATCTGAACAAGTACTCATGGAACAGAGgtactaagac ... gttactgcagAGGCAAACCTCCTGTTCCTGGAATCACCTGCCGGAGTTGGCTTTTCATACT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcatgcctaatgatgcaatgcctgtcactgactgatgaacactttgttactgcagAGGCAAACCTCCTGTTCCTGGAATCACCTGCCGGAGTTGGCTTTTCATACTCCAACACCACCTCTGATCTCAAGACATCTGGTGATGAGAGGACAG
ctttgtt CT-rich tract
taatgat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtactaagactaagctcagaaactcatcatgcctaatgatgcaatgcctgtcactgactgatgaacactttgttactgcagAGGCAAACCTCCTGTTCCTGGAATCACCTGCCGGAGTTGGCTTTTCATACTCCAACACCACCTCTGATCTCAAGACATCTGGTGATGAGAGGACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA