Sequence
atgc intronic sequence ATGC exonic sequenceGAGAGCTTCACCAAGGTGAAGAAGTACGGCCTCACGATGCTGCTGACGCAGGACGAAGGGGTGAAGACCTTCATCGCCAACCTCAACACCCAGCTCTCAGgtcgtctggcctcactcaccggatcactagcctgcctgtctccatttggtttcttttttctttttcttttgctgctgctgattgatcttgcctgtgtttcctgcgttgccgcgcgcag
Basic information
species | Oryza sativa |
transcript | LOC_Os04g40940.2 |
intron # | 2 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g40940.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G047143_T03 (Zea mays), 5'ss of exon 3
GAGAGCTTCACCAAGGTGAAGAAGTACGGCCTCACGATGCTGCTGACGCAGGACGAAGGGGTGAAGACCTTCATCGCCAACCTCAACACCCAGCTCTCAGgtcgtctggcctcactcaccggatcactagcctgcctgtctccatttggtttcttttttctttttcttttgctgctgctgattgatcttgcctgtgtttcctgcgttgccgcgcgcag
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GAGAGCTTCAGCAAGGTGAAGAAGTACGGGCTTACCATGCTGCTCACGCAGGACGAGGGCGTGAAGAACTTCATCGCCAGCCTCACCTCCCAGCTCTCAGgtcggttttcctcacac-cactacctgaggccgatctctccttcctcgagtgctcgcgaatgtctctgaaaaactcactgtcgcag--------------------------------
upper sequence: LOC_Os04g40940.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G112072_T03 (Zea mays), 5'ss of exon 2
---GAGAGCTTCACCAAGGTGAAGAAGTACGGCCTCACGATGCTGCTGACGCAGGACGAAGGGGTGAAGACCTTCATCGCCAACCTCAACACCCAGCTCTCAGgtcgtctggcctcactcaccggatcactagcctgcctgtctccatttggtttcttttttctttttcttttgctgctgctgattgatcttgcctgtgtttcctgcgttgccgcgcgcag
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GGGGAGAGCTTCGCCAAGGTGAAGAAGTACGGGCTCACCATGCCGCTCACGCAGGACGAGTGGGTTAA---CTTCATCACTAGCGCCACCTCCAAGAACTCAGgt-gctta---tctcccacccaggcac--------ccaccatagatcgatgtatctctccttcctgaggtctttcggtcattggattttg----tgtatctgaaactgaatggtgcagMapped 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|163920022|gb|EG709828.1|EG709828EST: GGACGAAGGGGTGAAGACCTTCATCGCCAACCTCAACACCCAGCTCTCAG AGTGGCTGGAGGCCGGGAAGCTGCAGAGGATCGTGCTGGTGATCATGAGCA
genomic: GGACGAAGGGGTGAAGACCTTCATCGCCAACCTCAACACCCAGCTCTCAGgtcgtctggc ... ccgcgcgcagAGTGGCTGGAGGCCGGGAAGCTGCAGAGGATCGTGCTGGTGATCATGAGCA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GAGAGCTTCACCAAGGTGAAGAAGTACGGCCTCACGATGCTGCTGACGCAGGACGAAGGGGTGAAGACCTTCATCGCCAACCTCAACACCCAGCTCTCAGgtcgtctggcctcactcaccggatcactagcctgcctgtctccatttggtttcttttttctttttcttttgctgctgctgattgatcttgcctgtgtttcctgcgttgccgcgcgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC