Sequence
atgc intronic sequence ATGC exonic sequencegtaagattaatttatcatttcatccctatgttttcaattctgagataattttcttctcccttgcaaatctttgtcagattgattaaatgttatgaatcctattcatcagttgatctttgtagattaagtaaatgtttgtgaattttgatcagTTTCTTCAAGGAGTGCCCGCACCCAGACGACAAGCAGCGCAAGGAGCTGAGCAGGGAGCTGGGTCTTGAACCTCTGCAGGTTAAATTCTGGTTTCAGAAC
Basic information
species | Oryza sativa |
transcript | LOC_Os08g08820.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os08g08820.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G130442_T02 (Zea mays), 3'ss of exon 2
----gtaagattaatttatcatttcatcc-ctatgttttcaat-tctgagataattttcttctcccttgcaaatctttgtcagattgattaaatgttatgaatcctattc-atcagttgatctttgtagattaagtaaatgtttgtgaattttgatcagTTTCTTCAAGGAGTGCCCGCACCCAGACGACAAGCAGCGCAAGGAGCTGAGCAGGGAGCTGGGTCTTGAACCTCTGCAGGTTAAATTCTGGTTTCAGAAC
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gtaagaacgatagcttgagctccccttcctctaagcatgcaccatttgaaaggattcattttcgagatagatagataatttcatttcattca---ttaaaaatcgtgtctgattgtttaattggggacgact--gtgaat---tgtga---ttggtcagGTTCTTCAAGGAGTGCCCGCACCCGGACGACAAGCAGCGGAAGGAGCTGAGCCGGGAGCTCGGCCTCGAGCCGCTGCAGGTCAAGTTTTGGTTCCAGAAC
upper sequence: LOC_Os08g08820.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G118063_T03 (Zea mays), 3'ss of exon 3
gtaagattaatttatcatttcatccctatgttttcaattctgagataattttcttctcccttgcaaatctttgtcagattgattaaatgttatgaatcctattcatca-gttgatctttgtagattaagtaaatgtttgtgaattttgatcagTTTCTTCAAGGAGTGCCCGCACCCAGACGACAAGCAGCGCAAGGAGCTGAGCAGGGAGCTGGGTCTTGAACCTCTGCAGGTTAAATTCTGGTTTCAGAAC
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---------------------------gtaaggacaatgacatgaacactcttcttcttctt-----ccctagctagctttaagcaccatt-taaattctattcatcaaggtcatgtctgaatgtttggatattttgaactgtggttgatcagCTTCTTCAAGGAGTGTCCACACCCGGATGACAAGCAGCGAAAGGAGCTGAGCCGGGAGCTCGGTCTCGAGCCGCTGCAGGTCAAGTTCTGGTTCCAGAAC
upper sequence: LOC_Os08g08820.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ37532 (Selaginella moellendorffii), 3'ss of exon 1
gtaagattaatttatcatttcatccctatgttttcaattctgagataattttcttctcccttgcaaatctttgtcagattgattaaatgttatgaatcctattcatcagttgatctttgtagattaagtaaatgtttgtgaattttgatcagTTTCTTCAAGGAGTGCCCGCACCCAGACGACAAGCAGCGCAAGGAGCTGAGCAGGGAGCTGGGTCTTGAACCTCTGCAGGTTAAATTCTGGTTTCAGAAC
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----------------------------------------------------------------------------------------------------gtaagtactgcaagccgagagcatgatgagaacttatctttcttcgtgccagGTTGTTCAAGGAGTGTCCTCATCCCGACGATAAGCAGCGCCAGGAGCTGAGCCGGGAGCTAGGACTGGAGCCTCGGCAAGTCAAGTTCTGGTTCCAGAAT
upper sequence: LOC_Os08g08820.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ10492 (Selaginella moellendorffii), 3'ss of exon 2
gtaagattaatttatcatttcatccctatgttttcaattctgagataattttcttctcccttgcaaatctttgtcagattgattaaatgttatgaatcctattcatcagttgatctttgtagattaagtaaatgtttgtgaattttgatcagTTTCTTCAAGGAGTGCCCGCACCCAGACGACAAGCAGCGCAAGGAGCTGAGCAGGGAGCTGGGTCTTGAACCTCTGCAGGTTAAATTCTGGTTTCAGAAC
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------------------------------------------------------------------------------gtaagagattggttttggtgttgttctcgattggaagtcctcaaggtggattttttcttcgttttctcgcgcagCTTGTTCAAGGAGTGCCCGCATCCGGATGACAAGCAGCGGCAGGAGCTCAGCCGGGAGCTCGGATTGGAGCCGCGGCAAGTCAAGTTTTGGTTCCAGAAT
upper sequence: LOC_Os08g08820.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ34024 (Selaginella moellendorffii), 3'ss of exon 1
gtaagattaatttatcatttcatccctatgttttcaattctgagataattttcttctcccttgcaaatctttgtcagattgattaaatgttatgaatcctattcatcagttgatctttgtagattaagtaaatgtttgtgaattttgatcagTTTCTTCAAGGAGTGCCCGCACCCAGACGACAAGCAGCGCAAGGAGCTGAGCAGGGAGCTGGGTCTTGAACCTCTGCAGGTTAAATTCTGGTTTCAGAAC
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--------------------------------------------------------------------------------------------------gtaagtacta--caagccgagagcatgatgagaacttatctttcttcgtgccagGTTGTTCAAGGAGTGTCCTCATCCCGACGATAAGCAGCGCCAGGAGCTGAGCCGGGAGCTAGGACTGGAGCCTCGGCAAGTCAAGTTCTGGTTCCAGAATMapped 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|58670718|gb|CK059404.1|CK059404EST: AAGAAGCGTTACCACCGCCATACCCAGCACCAGATCCAAGAGATGGAAGC TTTCTTCAAGGAGTGCCCGCACCCAGACGACAAGCAGCGCAAGGAGCTGAG
genomic: AAGAAGCGTTACCACCGCCATACCCAGCACCAGATCCAAGAGATGGAAGCgtaagattaa ... ttttgatcagTTTCTTCAAGGAGTGCCCGCACCCAGACGACAAGCAGCGCAAGGAGCTGAG
EST:
gi|29667380|gb|CB663655.1|CB663655EST: AAGAAGCGTTACCACCGCCATACCCAGCACCAGATCCAAGAGATGGAAGC TTTCTTCAAGGAGTGCCCGCACCCAGACGACAAGCAGCGCAAGGAGCTGAG
genomic: AAGAAGCGTTACCACCGCCATACCCAGCACCAGATCCAAGAGATGGAAGCgtaagattaa ... ttttgatcagTTTCTTCAAGGAGTGCCCGCACCCAGACGACAAGCAGCGCAAGGAGCTGAG
EST:
gi|29637184|gb|CB642193.1|CB642193EST: AAGAAGCGTTACCACCGCCATACCCAGCACCAGATCCAAGAGATGGAAGC TTTCTTCAAGGAGTGCCCGCACCCAGACGACAAGCAGCGCAAGGAGCTGAG
genomic: AAGAAGCGTTACCACCGCCATACCCAGCACCAGATCCAAGAGATGGAAGCgtaagattaa ... ttttgatcagTTTCTTCAAGGAGTGCCCGCACCCAGACGACAAGCAGCGCAAGGAGCTGAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cctattcatcagttgatctttgtagattaagtaaatgtttgtgaattttgatcagTTTCTTCAAGGAGTGCCCGCACCCAGACGACAAGCAGCGCAAGGAGCTGAGCAGGGAGCTGGGTCTTGAACCTCTGCAGGTTAAATTCTGGTTTCAGAAC
agttgat putative branch site (score: 5)
attaagtaaatgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagattaatttatcatttcatccctatgttttcaattctgagataattttcttctcccttgcaaatctttgtcagattgattaaatgttatgaatcctattcatcagttgatctttgtagattaagtaaatgtttgtgaattttgatcagTTTCTTCAAGGAGTGCCCGCACCCAGACGACAAGCAGCGCAAGGAGCTGAGCAGGGAGCTGGGTCTTGAACCTCTGCAGGTTAAATTCTGGTTTCAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG