Sequence
atgc intronic sequence ATGC exonic sequence...cactgcccagccataggcagagttttcctccatgaaccgtgcctacaacataccaacattgttttacatagtgttaagggattaccatctgccttttcagATTCGTCCAGATCGCCAAACATTATATTGGAGTGCTACTTGGCCAAAGGAAGTTGAACAGCTAGCAAGGAACTTTCTTTTCGACCCATACAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g10050.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g10050.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G143246_T01 (Zea mays), 3'ss of exon 5
----cactgcccagccataggcagagttttcctccatgaaccgtgcc-tacaacataccaacattgttttacatagtgttaagggattaccatctgccttttcagATTCGTCCAGATCGCCAAACATTATATTGGAGTGCTACTTGGCCAAAGGAAGTTGAACAGCTAGCAAGGAACTTTCTTTTCGACCCATACAAG
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ttagtggtctacattgatatgcc-agttactttcattaatctgtgcaatataaattttgattattgttttacgtgatgccaaa----ccttatctgttagttcagATTCGTCCAGATCGCCAAACACTTTACTGGAGTGCTACCTGGCCGAAGGAAGTTGAGCAGCTAGCAAGGAATTTCCTTTTTGACCCATACAAG
upper sequence: LOC_Os01g10050.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA07G01260.1 (Glycine max), 3'ss of exon 5
cactgcccagccataggcagagttttcctccatgaaccgtgcctacaacataccaacattgttttacatag--tgttaagggattaccatctgcc----ttttcagATTCGTCCAGATCGCCAAACATTATATTGGAGTGCTACTTGGCCAAAGGAAGTTGAACAGCTAGCAAGGAACTTTCTTTTCGACCCATACAAG
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----aattaatccaaatcg--atttagaaatacagattgctgaagctgcattttaaagtttctttattctgcttgtcatatgatcactgttttttgtttttcttagATTCGTCCAGATCGTCAAACTTTGTATTGGAGTGCTACCTGGCCAAAGGAGGTCGAACAATTGGCAAGGAAGTTCCTTTATAACCCATACAAA
upper sequence: LOC_Os01g10050.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA07G11880.1 (Glycine max), 3'ss of exon 5
cactgcccagccataggcagagttttcctccatgaaccgtgcctacaacataccaacattgttttacatag--tgttaagggattaccatctgcc----ttttcagATTCGTCCAGATCGCCAAACATTATATTGGAGTGCTACTTGGCCAAAGGAAGTTGAACAGCTAGCAAGGAACTTTCTTTTCGACCCATACAAG
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----aattaatccaaatca--atctagaaatacagattgctgaagctgcattttaaagtttctttattctgcttgtcatatgatcactgttttttgtttttcttagATTCGTCCAGATCGTCAAACTTTGTATTGGAGTGCTACCTGGCCAAAGGAGGTCGAACAATTGGCAAGGAAGTTCCTTTATAACCCATACAAA
upper sequence: LOC_Os01g10050.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA08G20670.1 (Glycine max), 3'ss of exon 5
--cactgcccagccataggcagagttttcctccatgaaccgtgcctacaacataccaacattgttttacatagtgttaagggattaccatctgcctt-ttcagATTCGTCCAGATCGCCAAACATTATATTGGAGTGCTACTTGGCCAAAGGAAGTTGAACAGCTAGCAAGGAACTTTCTTTTCGACCCATACAAG
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attaatccaattcgatttagaaagacagattgctgaagttgcattt-taaaatttctttattctgctggtcatc--tgatcactttttttttgttttacttagATTCGTCCAGATCGTCAAACTTTGTATTGGAGTGCTACCTGGCCAAAGGAGGTTGAACAATTGGCAAGGAAGTTCCTTTATAACCCATACAAA
upper sequence: LOC_Os01g10050.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv09s0002g02100.t01 (Vitis vinifera), 3'ss of exon 5
cactgcccagccataggcagagttttcctccatg-aaccgtgcctacaacataccaacattgtttt---acatagtgttaagggattaccatctgcctttt-cagATTCGTCCAGATCGCCAAACATTATATTGGAGTGCTACTTGGCCAAAGGAAGTTGAACAGCTAGCAAGGAACTTTCTTTTCGACCCATACAAG
|| || | || ||| || || || || || | ||| | | | || ||| | | ||| || | |||||||||| ||||| ||||| | |||||||||||||| ||||| ||||| || ||||| || || ||||| || |||| | |||||| ||
----atccggcttacctttctcctctcttccttgtaattgtatctgttgaattctg-cataatctggagatatcaggttcctatttattggtttgctttatgtagATTCGTCCTGATCGTCAAACCCTCTATTGGAGTGCTACATGGCCCAAGGAGGTGGAACAACTTGCTAGGAAGTTCCTTTACAACCCATGTAAAMapped 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|218490551|gb|FG953048.1|FG953048EST: GGATGCTGGATATGGGCTTTGAACCTCAGATTAAGAAAATTGTTTCTCAG ATTCGTCCAGATCGCCAAACATTATATTGGAGTGCTACTTGGCCAAAGGAA
genomic: GGATGCTGGATATGGGCTTTGAACCTCAGATTAAGAAAATTGTTTCTCAGgtatgcctct ... gccttttcagATTCGTCCAGATCGCCAAACATTATATTGGAGTGCTACTTGGCCAAAGGAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caacataccaacattgttttacatagtgttaagggattaccatctgccttttcagATTCGTCCAGATCGCCAAACATTATATTGGAGTGCTACTTGGCCAAAGGAAGTTGAACAGCTAGCAAGGAACTTTCTTTTCGACCCATACAAG
ccatctgccttttc CT-rich tract
attgtttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cactgcccagccataggcagagttttcctccatgaaccgtgcctacaacataccaacattgttttacatagtgttaagggattaccatctgccttttcagATTCGTCCAGATCGCCAAACATTATATTGGAGTGCTACTTGGCCAAAGGAAGTTGAACAGCTAGCAAGGAACTTTCTTTTCGACCCATACAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- -tgcccag
- - - - - - - - - - - - - - - catgaac
- - - - - - - - - - - - - - - - - - - gtgccta
- - - - - - - - - - - - - - - - - - - - - - -caacata