Sequence
atgc intronic sequence ATGC exonic sequence...atggcatgacaaataacactatctgttttatgaatactcaatgaaaatatgttgcaactttatcatgaatagattgtaattttccattccatcatcacagTCTTCTGCAAGCAGCAATTGGTGCATTTTCAACTGTTTTTCCTGACTATCAGGAGAGAATTGCTAGGCATGAAGCTGCTCATTTTTTGG
Basic information
species | Oryza sativa |
transcript | LOC_Os04g54640.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g54640.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G004352_T01 (Zea mays), 3'ss of exon 5
--atggcatgacaaataacactatctgttttatgaatactcaatgaaaatatgttgcaactttatcatgaatagattgtaattttccattccatcatcacagTCTTCTGCAAGCAGCAATTGGTGCATTTTCAACTGTTTTTCCTGACTATCAGGAGAGAATTGCTAGGCATGAAGCTGCTCATTTTTTGG
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tgatgctcattcttttgggacagagaaattt--gcacgctccatgtaaaaatgttgcatattaattgtcaaaccatgttaattatgcataccatcattgcagTCTTCTGCAAGCAGCAATCGGAGCGTTCTCTACAGTCTTTCCTGACTACCAGGAGAGGATTGCTAGGCATGAAGCTGCTCATTTCCTAG
upper sequence: LOC_Os04g54640.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA05G31720.1 (Glycine max), 3'ss of exon 5
atggcatgacaaataacactatctgtttt---atgaatactcaatgaaaatatgttgcaactttatcatgaatagattgtaattttccattccatcatcacagTCTTCTGCAAGCAGCAATTGGTGCATTTTCAACTGTTTTTCCTGACTATCAGGAGAGAATTGCTAGGCATGAAGCTGCTCATTTTTTGG
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---gtaagaagaatagtgtttgccatgtagcaatggataccccgcttcag--tgttaaatgttaattttctttacat--taatgctccaagttgctagtgcagGCTTCTCCAAGCTGCTATTGGCAGCTTTTCAACACTTTTTCCTGATTATCAAGAAAGGATTGCCAGGCATGAAGCAGCTCACTTTTTGA
upper sequence: LOC_Os04g54640.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA08G14970.1 (Glycine max), 3'ss of exon 5
atggcatgacaaataacactatctgtttta---tgaatactcaatgaaaatat--gttgcaactttatcatgaatagattgtaattttccattccatcatcacagTCTTCTGCAAGCAGCAATTGGTGCATTTTCAACTGTTTTTCCTGACTATCAGGAGAGAATTGCTAGGCATGAAGCTGCTCATTTTTTGG
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---gtaagaagaattgtgtttgccatgtagcattggatacccctcttaagtgttaaatgttaatttgttttgcat------taatgctccaagttgctagtgtagGCTTCTCCAAGCTGCTATTGGCAGCTTTTCAACACTTTTTCCTGATTATCAAGAAAGGATTGCCAGGCATGAAGCTGCTCACTTTTTGA
upper sequence: LOC_Os04g54640.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv07s0031g01560.t01 (Vitis vinifera), 3'ss of exon 5
---------------------------------------------atggcatga-caaataacactatctgttttatgaatactcaatgaaaatatgttgcaactttatcat-gaatagattgtaattttccattccatcatcacagTCTTCTGCAAGCAGCAATTGGTGCATTTTCAACTGTTTTTCCTGACTATCAGGAGAGAATTGCTAGGCATGAAGCTGCTCATTTTTTGG
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gtaagcgttaaatctgtccatgatacaagttacatttagaggattgtgttaggatcatgttaagttgcatatccaataattgagagac-agagtgtagagaagattaacctcagaactcactgacactctttatctgctc--tgtagGCTTCTTCAGGTTGCCATTGGAGGATTTTCATCATTTTTTCCTGATTATCAGGAGAGGATTGCTAGACATGAAGCAGCCCATTTTTTAGMapped 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|38476935|gb|CF961068.1|CF961068EST: GGCTATCGGAAGTATTTCTCCCGG TCTTCTGCAAGCAGCAATTGGTGCATTTTCAACTGTTTTTCCTGACTATCA
genomic: GGCTATCGGAAGTATTTCTCCCGGgtatgtgttt ... atcatcacagTCTTCTGCAAGCAGCAATTGGTGCATTTTCAACTGTTTTTCCTGACTATCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatatgttgcaactttatcatgaatagattgtaattttccattccatcatcacagTCTTCTGCAAGCAGCAATTGGTGCATTTTCAACTGTTTTTCCTGACTATCAGGAGAGAATTGCTAGGCATGAAGCTGCTCATTTTTTGG
ttttccattccatc CT-rich tract
aatagattgtaatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atggcatgacaaataacactatctgttttatgaatactcaatgaaaatatgttgcaactttatcatgaatagattgtaattttccattccatcatcacagTCTTCTGCAAGCAGCAATTGGTGCATTTTCAACTGTTTTTCCTGACTATCAGGAGAGAATTGCTAGGCATGAAGCTGCTCATTTTTTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT