Sequence
atgc intronic sequence ATGC exonic sequencegtaacttttagcccgctatgagttggtttcacttttgattttgatttttgttctggctagcatgtctaaaggaacttggctgtcaagatttaccttatgcatgtccattatgtttcctttgtttgtagAGATCGAGCTGGTGGATATACAAGACTACTGCGGACTAGGATACGGGTTGGCGATGCTGCACCAATGGCATACATTGA
Basic information
species | Oryza sativa |
transcript | LOC_Os05g38580.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g38580.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G112865_T03 (Zea mays), 3'ss of exon 3
gtaacttttagcccgctatgagttggtttcacttttgattttgatttttgttctggctagcatgtctaaaggaacttggctgtcaagatttaccttatgcatgtccattatgtttcctttgtttgtagAGATCGAGCTGGTGGATATACAAGACTACTGCGGACTAGGATACGGGTTGGCGATGCTGCACCAATGGCATACATTGA
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--------------------------taatggtttgtatgataacacaaatg-tgaaaagta-gaatagaatgccatgtatttggaagcagagtggattggaactaattgtatatttttatattccagAGATCGAGCTGGGGGCTACACAAGAATGTTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGA
upper sequence: LOC_Os05g38580.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT5G09770.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaacttttagcccgctatgagttggtttcacttttgattttgatttttgttctggctagcatgtctaaaggaacttggctgtcaagatttaccttatgcatgtccattatgtttcctttgtttgtagAGATCGAGCTGGTGGATATACAAGACTACTGCGGACTAGGATACGGGTTGGCGATGCTGCACCAATGGCATACATTGA
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----------------------------------gtgagtcttcaaattcttttggc-atcat-tttaacagtccattgcctaagcgctttgcattatctggat-----atatattatttgtt-acagAGATAGAGCTGGTGGATACACAAGACTGCTACGTACTCGCATACGAGTTGGTGATGCTGCTCCTATGGCCTATATCGA
upper sequence: LOC_Os05g38580.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv04s0044g00980.t01 (Vitis vinifera), 3'ss of exon 4
gtaacttttagcccgctatgagttggtttcacttttgattttgatttttgttctggctagcatgtctaaaggaacttggctgtcaagatttaccttatgcatgtccattatgtttcctttgtttgtagAGATCGAGCTGGTGGATATACAAGACTACTGCGGACTAGGATACGGGTTGGCGATGCTGCACCAATGGCATACATTGA
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----------------------------------------------------gtgaatcttaaacctgttgcattttcagttttcttttgtatggttgtaatattggatgggcattctctgttt-cagAGATAGAGCTGGTGGATATACAAGATTACTTCGAACTCGCATACGAGTTGGTGATGCTGCACCAATGGCCTATATTGAMapped 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|27547785|gb|CA766051.2|CA766051EST: GGTGACAATGTTGTTCACAAGTTATTCACAGAGCTCGCCTACCGCTACAA AGATCGAGCTGGTGGATATACAAGACTACTGCGGACTAGGATACGGGTTGG
genomic: GGTGACAATGTTGTTCACAAGTTATTCACAGAACTCGCCTACCGCTACAAgtaactttta ... ttgtttgtagAGATCGAGCTGGTGGATATACAAGACTACTGCGGACTAGGATACGGGTTGG
EST:
gi|86531078|gb|CI171284.1|CI171284EST: GGTGACAATGTTGTTCACAAGTTATTCACAGAACTCGCCTACCGCTACAA AGATCGAGCTGGTGGATATACAAGACTACTGCGGACTAGGATACGGGTTGG
genomic: GGTGACAATGTTGTTCACAAGTTATTCACAGAACTCGCCTACCGCTACAAgtaactttta ... ttgtttgtagAGATCGAGCTGGTGGATATACAAGACTACTGCGGACTAGGATACGGGTTGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acttggctgtcaagatttaccttatgcatgtccattatgtttcctttgtttgtagAGATCGAGCTGGTGGATATACAAGACTACTGCGGACTAGGATACGGGTTGGCGATGCTGCACCAATGGCATACATTGA
tgtttcctttgttt CT-rich tract
attatgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaacttttagcccgctatgagttggtttcacttttgattttgatttttgttctggctagcatgtctaaaggaacttggctgtcaagatttaccttatgcatgtccattatgtttcctttgtttgtagAGATCGAGCTGGTGGATATACAAGACTACTGCGGACTAGGATACGGGTTGGCGATGCTGCACCAATGGCATACATTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC