Sequence
atgc intronic sequence ATGC exonic sequencegtaatgtgggcatgccctttgtactaccgatattattaagctgtaaaaaatatcgattttctagttaatgcgatctattattctttttgggcagTTCTTATGTTGTTCATGGTACTGAACTCACACCAGATGTCTCCGAACTTTTTG
Basic information
species | Oryza sativa |
transcript | LOC_Os03g16570.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g16570.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G337425_T01 (Zea mays), 3'ss of exon 3
gtaatgtgggcatgccctttgtactaccgatattattaagctgtaaaaaatatcgattttctagttaatgcgatctattattctttttgggcagTTCTTATGTTGTTCATGGTACTGAACTCACACCAGATGTCTCCGAACTTTTTG
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gtaatccgtttgcgcc-tgtctattaacgatactgttgagctgctaaaga---ctattcttcggttaac----tttgtgttttttgttgggcagTTCTTGTTTTGTTCATGGTACTGAACTCGCACCAGATCTCTCCCAATCTTCTG
upper sequence: LOC_Os03g16570.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G492252_T01 (Zea mays), 3'ss of exon 3
gtaatgtgggcatgccctttgtactaccgatattattaagctgtaaaaaatatcgattttctagttaatgcgatctattattctttttgggcagTTCTTATGTTGTTCATGGTACTGAACTCACACCAGATGTCTCCGAACTTTTTG
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gtaattgggtcg---cctatctattaccgacactgttgagctgctaaagat---tattctttggttaacgttgtgt----tttttgttgggcagTTTTTGTTTTGTTCATGGTACTGAACTCACACCAGATGTCTCCCAATCTTTTG
upper sequence: LOC_Os03g16570.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G337425_T03 (Zea mays), 3'ss of exon 3
gtaatgtgggcatgccctttgtactaccgatattattaagctgtaaaaaatatcgattttctagttaatgcgatctattattctttttgggcagTTCTTATGTTGTTCATGGTACTGAACTCACACCAGATGTCTCCGAACTTTTTG-----------------------------------------------
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gtaatccgtttgcgcc-tgtctattaacgatactgttgagctgctaaaga---ctattcttcggttaac----tttgtgttttttgttgggcagTTCTTGTTTTGTTCATGGTACTGAACTCGCACCAGATCTCTCCCAATCTTCTGGTAAGTTTTCGTGCTCAGTGGTCAGTGCGAGGTGTCCACGAGTCAAT
upper sequence: LOC_Os03g16570.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA11G34130.2 (Glycine max), 3'ss of exon 3
----------------gtaatgtgggcat-----gccctttgtactaccgatattattaagctgtaaaaaatat-cgattttctagttaat-gcgatctattattctttttgggcagTTCTTATGTTGTTCATGGTACTGAACTCACACCAGATGTCTCCGAACTTTTTG
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gtattaatgtactcatattatgtttgtttttatcactttttgtgaatatgttttttctttcccttatattgcatgcaatgtccctcccatttacgccttactgcttgtatgtttcagTTCTTCTGTTATTCATGATACTGAACTCTCACCAGATGTCCCCAAACTTTCTG
upper sequence: LOC_Os03g16570.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA18G04160.1 (Glycine max), 3'ss of exon 4
----gtaatgtgggcatgccct--ttgtactaccgatattattaagctgtaaaaaatatcgattttcta----gttaatg--cgatcta----ttattctttttggg---cagTTCTTATGTTGTTCATGGTACTGAACTCACACCAGATGTCTCCGAACTTTTTG
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ggtattaatgttctcatattatgcttgttttaaccacattttgtgaatgtgttttttccttcctttatattgcatcaaggtcccatttacgccttactgcttatatgtttcaGTTCTTCTGTTATTCATGATACTGAACTCTCACCAGATGTCCCCAAACTTTCT-
upper sequence: LOC_Os03g16570.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv13s0019g01960.t01 (Vitis vinifera), 3'ss of exon 2
------------------------------------gtaatgtgggcatgccctttgtactaccgatatta---ttaagctgtaaaaaata--tcgattttctagttaa-tgcgatctatt----attctttttg--------ggcagTTCTTATGTTGTTCATGGTACTGAACTCACACCAGATGTCTCCGAACTTTTTG
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gtctttttaatatttaatttttaaagttatatcttttttatgttctctctcctttttttatttttattttaatttttaatttttacaagtggtttgagtttctaacaaaatgcattctaatccacattttacttgtctgattcaacagTTCTTTTGCTGTTCATGATACTAAACTCACACCAGATGTCACCTAACTTTCTGMapped 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|218484447|gb|FG955624.1|FG955624EST: TCATGCGGGTGGTCGGCCGGTGAACAGCAACCTGGCTTTTCTTGTCACTG TTCTTATGTTGTTCATGGTACTGAACTCACACCAGATGTCTCCGAACTTTT
genomic: TCATGCGGGTGGTCGGCCGGTGAACAGCAACCTGGCTTTTCTTGTCACTGgtaatgtggg ... ttttgggcagTTCTTATGTTGTTCATGGTACTGAACTCACACCAGATGTCTCCGAACTTTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gctgtaaaaaatatcgattttctagttaatgcgatctattattctttttgggcagTTCTTATGTTGTTCATGGTACTGAACTCACACCAGATGTCTCCGAACTTTTTG
agttaat putative branch site (score: 4)
tctattattcttttt putative PPT
aaaaaatatcgatttt 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
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gtaatgtgggcatgccctttgtactaccgatattattaagctgtaaaaaatatcgattttctagttaatgcgatctattattctttttgggcagTTCTTATGTTGTTCATGGTACTGAACTCACACCAGATGTCTCCGAACTTTTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG