Sequence
atgc intronic sequence ATGC exonic sequence...catgctgatgcatgcctcattctacccatcctaagtgatttgagcttatgacttcattggaatactgtgaattgatggcttcttcaattgtctggtgtagCATCGTATAACTTTGTGATGAAGAGAAAGAAGGAAGGTAGAAAAACAAAGGCACTCCCTCCTTCCAAAAGACTTCGCCTAGAGGCGCAGAGGGTGCTCAA
Basic information
species | Oryza sativa |
transcript | LOC_Os07g31440.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g31440.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM5G871936_T01 (Zea mays), 3'ss of exon 2
----catg-ctgatgcatgcctca--ttctacccat---cctaagtgatttgagct---tatgacttcattggaatactgtgaattgatggcttcttcaattgtctggtgtagCATCGTATAACTTTGTGATGAAGAGAAAGAAGGAAGGTAGAAAAACAAAGGCACTCCCTCCTTCCAAAAGACTTCGCCTAGAGGCGCAGAGGGTGCTCAA
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tattcatgatttatttaatattaaacttttggccactggccttaccgacatgtattctttttatttttattggaataacatgtattgaatgcttactcagTTGTTTGGTGTAGCATCATTCAACTCCGTGATGAATAAAAAGAAGGGAAATACAAGAACAAAGCCGCTCCCTCCTTCTAAAAGACTTCGCCAAGAAGCAC-------------
upper sequence: LOC_Os07g31440.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM5G871936_T03 (Zea mays), 3'ss of exon 1
catgctgatgcatgcctcattctacccatcctaagtgatttgagct---tatgacttcattggaatactgtgaattgatggcttcttcaattgtctggtgtagCATCGTATAACTTTGTGATGAAGAGAAAGAAGGAAGGTAGAAAAACAAAGGCACTCCCTCCTTCCAAAAGACTTCGCCTAGAGGCGCAGAGGGTGCTCAA
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---tttaatattaaacttttggccactggccttaccgacatgtattctttttatttttattggaataacatgtattgaatgcttactcagttgtttggtgtagCATCATTCAACTCCGTGATGAATAAAAAGAAGGGAAATACAAGAACAAAGCCGCTCCCTCCTTCTAAAAGACTTCGCCAAGAAGCACAGAGGGTCCTGAAMapped 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|89166276|gb|CI103366.1|CI103366EST: TCAACTTTTTCCCAAGAACAATGAACCATCACCACATGTTGAACAGGAAG CATCGTATAACTTTGTGATGAAGAGAAAG
genomic: TCAACTTTTTCCCAAGAACAATGAACCATCACCACATGTTGAACAGGAAGgtaactgttt ... tctggtgtagCATCGTATAACTTTGTGATGAAGAGAAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttatgacttcattggaatactgtgaattgatggcttcttcaattgtctggtgtagCATCGTATAACTTTGTGATGAAGAGAAAGAAGGAAGGTAGAAAAACAAAGGCACTCCCTCCTTCCAAAAGACTTCGCCTAGAGGCGCAGAGGGTGCTCAA
aattgat putative branch site (score: 4)
aattgat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
catgctgatgcatgcctcattctacccatcctaagtgatttgagcttatgacttcattggaatactgtgaattgatggcttcttcaattgtctggtgtagCATCGTATAACTTTGTGATGAAGAGAAAGAAGGAAGGTAGAAAAACAAAGGCACTCCCTCCTTCCAAAAGACTTCGCCTAGAGGCGCAGAGGGTGCTCAA
catgctg
- - - - tgcatgc
- - - - - - - - - - - - cccatcc
- - - - - - - - - - - - - - - - - - - - - -gcttatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgatgg