Sequence
atgc intronic sequence ATGC exonic sequenceGTAGATCCCCTGGGCAAGGTTGATCCAGAAGTGGAAGATTTGCTTTTGGAGATTGCTGATGACTTCATTGATTCGgtaatgtgtttgttgtttgtaaatcatgcttttacagcacacttgctcttagtgaatttctatttggttgaaaaatgtgattccgtgtgattcagaatctgagtaccttgagcttctgattttgcttcttttatctgatggacaaaacttgtatcaactgaccttttttatttgttactag
Basic information
species | Oryza sativa |
transcript | LOC_Os01g62820.2 |
intron # | 4 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g62820.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G149230_T02 (Zea mays), 5'ss of exon 4
GTAGATCCCCTGGGCAAGGTTGATCCAGAAGTGGAAGATTTGCTTTTGGAGATTGCTGATGACTTCATTGATTCGgtaatgtgtttgttgtttgtaaatcatgcttttacagcacacttgctcttagtgaatttctatttggttgaaaaatgtgattccgtgtgattcagaatctgagtaccttgagcttctgattttgcttcttttatctgatggacaaaacttgtatcaactgaccttttttatttgttactag
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GTAGATCCCTTAGGCAAGGTTGACCCAGAAGTGGAGGATTTACTTCTAGAAATCGCTGATGACTTCATTGGCTCGgtaatg---ttgttgctt-tgctacttgttcatagagtataatt--tcttatccaattcaga----atttgagcatcttcctct-tctaattta---tctgtggagat--atcttgtgattcagctgacatgggtttgtggttag------------------------------------
upper sequence: LOC_Os01g62820.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G002276_T01 (Zea mays), 5'ss of exon 4
GTAGATCCCCTGGGCAAGGTTGATCCAGAAGTGGAAGATTTGCTTTTGGAGATTGCTGATGACTTCATTGATTCGgtaatgtgtttgttgtttgtaaatcatgcttttacagcacacttgctcttagtgaatttctatttggttgaaaaatgtgattccgtgt--gattcagaatctgagtaccttgagcttctgattttgct-tcttttatctgatggacaaaacttgta--tcaactgaccttttttatttgttactag
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GTAGACCCCCTAGGCAAGGTTGACCCTGAAGTGGAGGATTTACTTCTAGAAATCGCCGATGACTTCATTGACTCGgtaatgt---tgttgctt---------------------------------------tgctgtttgtttagagagtataatttcctatcaaatttagaattttagcatcttcctcttctaagtttgaaatatgttatctg-tggagatatcttgtgattcatctgacacgg---gtttgcgattag
upper sequence: LOC_Os01g62820.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA07G04200.1 (Glycine max), 5'ss of exon 4
GTAGATCCCCTGGGCAAGGTTGATCCAGAAGTGGAAGATTTGCTTTTGGAGATTGCTGATGACTTCATTGATTCGgtaatgtgtttgttgtttgtaaatcatgcttttacagcacacttgctcttagtgaatttctatttggttgaaaaatgt-gattccgtgtgattcagaatctgagtaccttgagcttctgattttgcttcttttatctgatggacaaaacttgtatcaactgaccttttttatttgttactag
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GTGGATCCACAAGGTAGGCTGGACCCCGAAGTTATAGATCTTCTTTTAGAGCTTGCTGATGACTTCATTGATTCTgtaagaa--ttcttacatgtt--ttat-ctttttccccaga-tcatgataaatgtgtatatagtgcatgccaaactgttgatattgtgccttacacatcttgttta----------------------------------------------------------------------------
upper sequence: LOC_Os01g62820.2 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv09s0002g01420.t01 (Vitis vinifera), 5'ss of exon 4
GTAGATCCCCTGGGCAAGGTTGATCCAGAAGTGGAAGATTTGCTTTTGGAGATTGCTGATGACTTCATTGATTCGgtaatgtgtttg-ttgtttgtaaatcatgcttttacagcacacttgctcttagtgaatttctatttggttgaaaaatgtgattccgtgtgattcagaatctgagtaccttgagcttctgattttgcttcttttatctgatggacaaaacttgtatcaactgaccttttttatttgttactag
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GTGGATTCACAAGGAAAGCTGGACCCTGAAGTTGAAGATCTTCTTTTGGAGATTGCTGATGACTTCATTGATTCGgtaa-gtatgtgcttgcatatgaacattatacagatgtgactcctacccctactgcccatacatgtgcacacctattgt--ttccatgc--tccgtgatagagat-----------------------------------------------------------------------------Mapped 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|29624357|gb|CB629368.1|CB629368EST: GATTTGCTTTTGGAGATTGCTGATGACTTCATTGATTCG GTGACTGCATTTGCGTGTACCCTTGCGAAGCATAGGAAATCATCAGTCCTG
genomic: GATTTGCTTTTGGAGATTGCTGATGACTTCATTGATTCGgtaatgtgtt ... ttgttactagGTGACTGCATTTGCGTGTACCCTTGCGAAGCATAGGAAATCATCAGTCCTG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GTAGATCCCCTGGGCAAGGTTGATCCAGAAGTGGAAGATTTGCTTTTGGAGATTGCTGATGACTTCATTGATTCGgtaatgtgtttgttgtttgtaaatcatgcttttacagcacacttgctcttagtgaatttctatttggttgaaaaatgtgattccgtgtgattcagaatctgagtaccttgagcttctgattttgcttcttttatctgatggacaaaacttgtatcaactgaccttttttatttgttactag
- - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT