Sequence
atgc intronic sequence ATGC exonic sequenceGAAGGCCAAGGAGGCAGCAGGTGGGGAGCCACCAGCTGGGTACATTCATGTGAGGGCAAGGAGAGGCCAAGCAACAGACAGCCACAGCCTTGCTGAGAGGgtcactcactcaccagtcttttgttctcttatctgaatcgttgttatcttaattagtagtaacagctgtttgttagtgcccttcacttaactacaggagtagtaacatctgttgatttgttacttatag
Basic information
species | Oryza sativa |
transcript | LOC_Os05g01256.2 |
intron # | 2 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g01256.2 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv01s0244g00010.t01 (Vitis vinifera), 5'ss of exon 2
GAAGGCCAAGGAGGCAGCAGGTGGGGAGCCACCAGCTGGGTACATTCATGTGAGGGCAAGGAGAGGCCAAGCAACAGACAGCCACAGCCTTGCTGAGAGGgtcactcactcaccagtcttttgttctctta--tctgaatcgttgttatcttaattagtagtaacagctgtttgttagtgcccttcacttaactacaggagtagtaacatctgttgatttgttacttatag
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GAAGAGGAAGAAGAAAGTGGTGAAAGAGGTCCCAAGTGGGTTTGTTCATGTGAGAGCAAGGAGGGGTGAAGCAACAGACAGTCACAGCCTTGCTGAAAGGgtattttagttgttatactacaaattaattaactttggaaaatgaccattcaaataaatt----cagcttttcatt--tactttt------gctgggtgggtttcactttccag-----------------
upper sequence: LOC_Os05g01256.2 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv17s0000g00430.t01 (Vitis vinifera), 5'ss of exon 2
GAAGGCCAAGGAGGCAGCAGGTGGGGAGCCACCAGCTGGGTACATTCATGTGAGGGCAAGGAGAGGCCAAGCAACAGACAGCCACAGCCTTGCTGAGAGGgt-cactcactcaccagtctt--ttgtt-----ctctta----tctgaatcgttgttatcttaattagtagtaacagctgtttgttagtgcccttcacttaactacaggagtagtaacatctgttgatttgttacttatag-------------------------------------------------------------
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GAAGGATCAGAAGAAAGCCTCTGAAGAGCCTCCAACCGGCTACATTCATGTAAGAGCAAGGAGGGGCCAAGCAACAGACAGCCACAGCCTTGCAGAGAGGgtactactgttcactaatattaattattaaaagcccatggaacccagtgtctttgttacatttattaa-ggcattagtttcccataataccccaacaacaaatcacagagttttcaatgttttggtacctaccaga-atagtttctaaaagaatttctcaccctattcttacaactattcattttcttcaaatgggttccagMapped 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|58674551|gb|CK063238.1|CK063238EST: TGAGGGCAAGGAGAGGCCAAGCAACAGACAGCCACAGCCTTGCTGAGAGG GTGAGAAGGGAGAAGATCAGTGAGAGGATGAAGATGCTGCAAAGCCTGGTT
genomic: TGAGGGCAAGGAGAGGCCAAGCAACAGACAGCCACAGCCTTGCTGAGAGGgtcactcact ... ttacttatagGTGAGAAGGGAGAAGATCAGTGAGAGGATGAAGATGCTGCAAAGCCTGGTT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GAAGGCCAAGGAGGCAGCAGGTGGGGAGCCACCAGCTGGGTACATTCATGTGAGGGCAAGGAGAGGCCAAGCAACAGACAGCCACAGCCTTGCTGAGAGGgtcactcactcaccagtcttttgttctcttatctgaatcgttgttatcttaattagtagtaacagctgtttgttagtgcccttcacttaactacaggagtagtaacatctgttgatttgttacttatag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG