Sequence
atgc intronic sequence ATGC exonic sequence...ttaactgaattgagctgaaatgaacctttttaggtaggaattaattggtagtttgaatttgatatatatcattagaaattccaatttgtggttgcattagGCCTTGAGAGATGTGGGAAGAGCTGCAGGCTGAGGTGGATAAACTACCTCAGGCCAGACCTCAAGAGGGGAGCATTCTCACAGGAAGAAGAAGACCTCAT
Basic information
species | Oryza sativa |
transcript | LOC_Os07g44090.3 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g44090.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G150841_T02 (Zea mays), 3'ss of exon 1
ttaactgaattg--agctgaaatgaacctttttaggtaggaattaattggtagtttgaatttgatatatatcattagaaattcca-atttgtggttgcattagGCCTTGAGAGATGTGGGAAGAGCTGCAGGCTGAGGTGGATAAACTACCTCAGGCCAGACCTCAAGAGGGGAGCATTCTCACAGGAAGAAGAAGACCTCAT
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ttgcattggttgctagcagtcgcagagttgaattgatggcaattcgttaatcgtt--atggtgatg-atgctgtttatttttgcatgcttgcgtgtgcattagGTCTAGAGAGGTGTGGGAAGAGCTGCAGGCTGAGGTGGATCAACTACCTCAGGCCGGACCTCAAGAGGGGAGCGTTCTCGCAGGAAGAGGAGGACCTCAT
upper sequence: LOC_Os07g44090.3 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S277_14V6.1 (Physcomitrella patens), 3'ss of exon 1
ttaactgaattgagctgaaatgaacctttttaggt-------aggaattaattggtagtttgaatttgatatatatcattagaaattccaatttgtggttgcattagGCCTTGAGAGATGTGGGAAGAGCTGCAGGCTGAGGTGGATAAACTACCTCAGGCCAGACCTCAAGAGGGGAGCATTCTCACAGGAAGAAGAAGACCTCAT
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-taacatatttaaagtgaaaaaaggttcttttcattgatgtaaggaatctaatcgtgtggagaaattgatgaatgttcctgga-----caatgaatg-ctgcaacagGTCTCCAAAGGTGCGGGAAGAGCTGCAGGTTGCGGTGGATCAACTACCTCCGGCCGGATTTGAAACGAGGCGTATTTTCGGCAGCAGAGGAGAACTTGAT
upper sequence: LOC_Os07g44090.3 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S189_29V6.1 (Physcomitrella patens), 3'ss of exon 1
ttaactgaattgagctgaaatga-acctttttaggtaggaattaattggtagttt-gaatttgatatatatcattagaaattccaatttgtggttgcattagGCCTTGAGAGATGTGGGAAGAGCTGCAGGCTGAGGTGGATAAACTACCTCAGGCCAGACCTCAAGAGGGGAGCATTCTCACAGGAAGAAGAAGACCTCAT
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-tttcctctttgctctaaaaaaagaaaagttcagataccccgttgacaccaatttagaataagagttgtgtcgct-gacgctggtgtgccctggaacaacagGGTTACAGAGATGTGGAAAAAGCTGCAGGTTAAGGTGGATAAACTATCTGAGGCCAGACTTAAAGCGAGGGGTTTTCTCACCAGCAGAGGAGAATCTGAT
upper sequence: LOC_Os07g44090.3 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S24_48V6.1 (Physcomitrella patens), 3'ss of exon 1
ttaactgaattgagctgaaatgaacctttttaggtaggaattaattggtagt-ttgaatttgat-atatatcattagaaattccaatttgtggttgcattagGCCTTGAGAGATGTGGGAAGAGCTGCAGGCTGAGGTGGATAAACTACCTCAGGCCAGACCTCAAGAGGGGAGCATTCTCACAGGAAGAAGAAGACCTCAT
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-tcgcttcatttgttcggaagaagttaaagttgctcctcgcatggcaatagtgttggattgggtgatctagctcttacacttgtgtgctacgga-acaacagGATTACAGCGATGTGGGAAGAGCTGCAGGTTAAGGTGGATAAATTATCTGAGGCCCGACTTAAAGCGAGGTGTCTTCTCTCCAGCGGAGGAGAATCTGAT
upper sequence: LOC_Os07g44090.3 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ38262 (Selaginella moellendorffii), 3'ss of exon 1
ttaactgaattgagctgaaatgaacctttttaggtaggaattaattggtagtttgaatttgatatatatcattagaaattccaatttgtggttgcatt-----agGCCTTGAGAGATGTGGGAAGAGCTGCAGGCTGAGGTGGATAAACTACCTCAGGCCAGACCTCAAGAGGGGAGCATTCTCACAGGAAGAAGAAGACCTCAT
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-----------------------------------gtgagt--atttgta-cctcaatttcaagt-tctcgt--gagctcacaattcttggtggcattgtcacagGCCTCCAAAGATGTGGGAAGAGCTGCAGGCTGAGATGGATCAACTATCTCCGGCCCGACTTGAAAAGGGGCCACTTTTCGCAACAGGAAGAAGAGTTGATMapped 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|58654162|gb|CK042842.1|CK042842EST: CATTGCCAAGTATGGCCATGGCTGCTGGAGCTCCGTCCCCAAGCTTGCAG GCCTTGAGAGATGTGGGAAGAGCTGCAGGCTGAGGTGGATAAACTACCTCA
genomic: CATTGCCAAGTATGGCCATGGCTGCTGGAGCTCCGTCCCCAAGCTTGCAGgtatatacac ... gttgcattagGCCTTGAGAGATGTGGGAAGAGCTGCAGGCTGAGGTGGATAAACTACCTCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggtagtttgaatttgatatatatcattagaaattccaatttgtggttgcattagGCCTTGAGAGATGTGGGAAGAGCTGCAGGCTGAGGTGGATAAACTACCTCAGGCCAGACCTCAAGAGGGGAGCATTCTCACAGGAAGAAGAAGACCTCAT
atttgat putative branch site (score: 5)
tttgaatttgatatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttaactgaattgagctgaaatgaacctttttaggtaggaattaattggtagtttgaatttgatatatatcattagaaattccaatttgtggttgcattagGCCTTGAGAGATGTGGGAAGAGCTGCAGGCTGAGGTGGATAAACTACCTCAGGCCAGACCTCAAGAGGGGAGCATTCTCACAGGAAGAAGAAGACCTCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - agctgaa