Sequence
atgc intronic sequence ATGC exonic sequence...tctttgcctaaataaccagcaatgcaacaatttactgcatattttcgttgagctattctctattgttggttaaatctaattaattattagcgcattccagGTCAAATATCTCTGGCTTCTTTTTGATTTAGCTGCAGGCCCTGATAATATTGTTGAAAATGGGCCATATAA
Basic information
species | Oryza sativa |
transcript | LOC_Os01g56670.4 |
intron # | 14 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g56670.2 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM2G173868_T02 (Zea mays), 3'ss of exon 13
---------tctttgcctaaataaccagcaatgcaacaatttactgcatattttcgttgagctattctctattgttggttaaatctaattaattattagcgcattccagGTCAAATATCTCTGGCTTCTTTTTGATTTAGCTGCAGGCCCTGATAATATTGTTGAAAATGGGCCATATAA
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atctagaagtgcactcttttttgggacagagggcgtaaataca-tgc-cattttcctttatttatcctctattgctg---aaatctaactacct----gcacataccagGTCAAGTATCTCTGGCTTCTTTTTGATTTAGCTGCTGGCCCTGACAATATTGTTGAAAATGGACCATATAA
upper sequence: LOC_Os01g56670.2 (Oryza sativa), 3'ss of exon 14
lower sequence: GLYMA10G32320.1 (Glycine max), 3'ss of exon 13
tctttgcctaaataaccagcaatgcaacaatttactgcatattttcgttgagctattctctatt-gttggttaaatctaattaattattagcgcatt--ccagGTCAAATATCTCTGGCTTCTTTTTGATTTAGCTGCAGGCCCTGATAATATTGTTGAAAATGGGCCATATAA
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--ctaccattaacatttgtcttgcctttcatattttgtct-tttccccccctctattatttatttaaaagaaaaatgctgctactaacctatgctacaattagGTCAAGTATCTGTGGCTTCTGTTTGATTTGGCTGTGGGTCCTGACAATCTTGTGGAAAATGGGCCTTACAA
upper sequence: LOC_Os01g56670.2 (Oryza sativa), 3'ss of exon 14
lower sequence: Vv05s0020g04650.t01 (Vitis vinifera), 3'ss of exon 15
tctttgcctaaataaccagcaatgcaacaattta--ctgcatat-tttcgttgagctattctctattgttggttaaatctaattaattattagcgcattccagGTCAAATATCTCTGGCTTCTTTTTGATTTAGCTGCAGGCCCTGATAATATTGTTGAAAATGGGCCATATAA
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tgtctttctag-catttgttttttgattggcttgtgctccttttatttccttatgttatctttttccttttcattgat-tattgaactatccacat-tattagGTCAAGTATTTGTGGCTTCTTTTTGATTTGGCTGCGGGTTCGGACAACCTTGTTGAAAATGGGCCATACAAMapped 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|58654851|gb|CK043531.1|CK043531EST: AAACCCACCAGCAGGATGACCACATGGAGAGTTTTTTCCTTGCAGAAACA GTCAAATATCTCTGGCTTCTTTTTGATTTAGCTGCAGGCCCTGATAATATT
genomic: AAACCCACCAGCAGGATGACCACATGGAGAGTTTTTTCCTTGCAGAAACAgtgagtttat ... cgcattccagGTCAAATATCTCTGGCTTCTTTTTGATTTAGCTGCAGGCCCTGATAATATT
EST:
gi|29667977|gb|CB664252.1|CB664252EST: ACCACATGGAGAGTTTTTTCCTTGCAGAAACA GTCAAATATCTCTGGCTTCTTTTTGATTTAGCTGCAGGCCCTGATAATATT
genomic: ACCACATGGAGAGTTTTTTCCTTGCAGAAACAgtgagtttat ... cgcattccagGTCAAATATCTCTGGCTTCTTTTTGATTTAGCTGCAGGCCCTGATAATATT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cgttgagctattctctattgttggttaaatctaattaattattagcgcattccagGTCAAATATCTCTGGCTTCTTTTTGATTTAGCTGCAGGCCCTGATAATATTGTTGAAAATGGGCCATATAA
aattaat putative branch site (score: 3)
tattgttggttaaatc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tctttgcctaaataaccagcaatgcaacaatttactgcatattttcgttgagctattctctattgttggttaaatctaattaattattagcgcattccagGTCAAATATCTCTGGCTTCTTTTTGATTTAGCTGCAGGCCCTGATAATATTGTTGAAAATGGGCCATATAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG