Sequence
atgc intronic sequence ATGC exonic sequence...tctggaacaaacacaggagcattatgagattttgatgtgcattgtttgttttagttgatcactagtatatctactgaccataactttttttgtgccacagGTGGGTCTTTCACTTTGCCCATCTTCGCCAACTTGCTGTATTAGTTCCTTACATACCTACAGAGAATCCTCAGCTGAGTGATACAGCTTACGAG
Basic information
species | Oryza sativa |
transcript | LOC_Os04g11880.3 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g11880.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G040247_T01 (Zea mays), 3'ss of exon 8
---------------------------------------------tctggaacaaacacaggagcattatgagattttgatgtgcattgtttgttttagttgatcactagtatatctactgaccataactttttttgtgccacagGTGGGTCTTTCACTTTGCCCATCTTCGCCAACTTGCTGTATTAGTTCCTTACATACCTACAGAGAATCCTCAGCTGAGTGATACAGCTTACGAG
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gttagaaaatatgtggatacacagataccaccttttgttgaatgatctagcataa-caccgatgagttgtgagattttgatggat----ctcaccctatgtgttaattgattcattttttaatcaaaacttt---tatgcgacagATGGGTCTTCCACTTTGCTCATCTCCGCCAACTTCCTGTTTTGGTCCCTTATATTCCTACAGAAAATCCTCAGCTGAGTGATACTGCATATGAG
upper sequence: LOC_Os04g11880.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA11G19660.2 (Glycine max), 3'ss of exon 8
tctggaacaaacacaggagcattatgagattttgatgtgcatt-gtttgttttagt-tgatcactagtatatctactgaccataactttttttgtgccacagGTGGGTCTTTCACTTTGCCCATCTTCGCCAACTTGCTGTATTAGTTCCTTACATACCTACAGAGAATCCTCAGCTGAGTGATACAGCTTACGAG
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---------------------gtacggcatgccattatttattagtctgttatagagttctgatttgtaattgggtgttcaatggactgcttt---caacagATGGGTTTTCCACTTTGCACATCTTCGTCAACTCCCTGTTTTAGTTCCTTACATGCCTACTGAAAACCCCAGACTACGTGATACTGCTTACGAG
upper sequence: LOC_Os04g11880.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA12G08840.1 (Glycine max), 3'ss of exon 8
tctggaacaaacacaggagcattatgagattttgatgtgcatt-gtttgttt-tagttgatcactagtatatctactgaccataactttttttgtgccacagGTGGGTCTTTCACTTTGCCCATCTTCGCCAACTTGCTGTATTAGTTCCTTACATACCTACAGAGAATCCTCAGCTGAGTGATACAGCTTACGAG
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---------------------gtatggcatgccattatttattagtctgttaatgagttctgatttgtaaatgggtgttcagtggactgcttt---caacagATGGGTTTTCCACTTTGCACATCTTCGTCAGCTCCCTGTTTTAGTTCCTTACATGCCTACAGAAAACCCCAGACTACGTGATACTGCTTACGAGMapped 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|58675059|gb|CK063746.1|CK063746EST: CAGGAAGCAGCAATGCAGGTGGACA GTGGGTCTTTCACTTTGCCCATCTTCGCCAACTTGCTGTATTAGTTCCTTA
genomic: CAGGAAGCAGCAATGCAGGTGGACAgtgggctgct ... tgtgccacagGTGGGTCTTTCACTTTGCCCATCTTCGCCAACTTGCTGTATTAGTTCCTTA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgttttagttgatcactagtatatctactgaccataactttttttgtgccacagGTGGGTCTTTCACTTTGCCCATCTTCGCCAACTTGCTGTATTAGTTCCTTACATACCTACAGAGAATCCTCAGCTGAGTGATACAGCTTACGAG
ctttttttgt CT-rich tract
ataactttttttgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tctggaacaaacacaggagcattatgagattttgatgtgcattgtttgttttagttgatcactagtatatctactgaccataactttttttgtgccacagGTGGGTCTTTCACTTTGCCCATCTTCGCCAACTTGCTGTATTAGTTCCTTACATACCTACAGAGAATCCTCAGCTGAGTGATACAGCTTACGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - gaacaaa
- - - - - - -caggagc
- - - - - - - - - - - - - - - - - - gtgcatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctactga