Sequence
atgc intronic sequence ATGC exonic sequenceTCAAGAAGATCCGGCTTGAGCAGGAGGATGAGGGTGTCCCCTCCACCGCCATCCGCGAGATCTCGCTCCTCAAGGAGATGCATCACCGCAACATCGTCAGgtcctctctattaaccaaccctctgctgctcttgtttaggactttggattcacttattaggagtagtcatcacggactgattgattcattgattgatgtg...
Basic information
species | Oryza sativa |
transcript | LOC_Os03g01850.1 |
intron # | 3 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g01850.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G143213_T02 (Zea mays), 5'ss of exon 2
TCAAGAAGATCCGGCTTGAGCAGGAGGATGAGGGTGTCCCCTCCACCGCCATCCGCGAGATCTCGCTCCTCAAGGAGATGCATCACCGCAACATCGTCAGgtcctctcta---ttaaccaaccctctgctgctcttgtttaggactttgg---attcacttattaggagtagtcat---cacggac-tgattgattcattgattgatgtg-----------------------------------------------------------------
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TCAAGAAGATCCGCCTCGAGCAGGAGGACGAGGGCGTCCCGTCCACCGCCATCCGCGAGATCTCTCTCCTCAAGGAGATGAACCACGGCAACATCGTCAGgtccgctttggttttatgcaacagcgggtaggtgtcgttttaggatgggattcgtttgctcgatggaaatgatggtgcgtatgtatgcaatcaagtaaaagtcagacgcaattttgatgctgcgatgccctgtagtgttggtacgctgacaagctttatactctcctaagtgcag
upper sequence: LOC_Os03g01850.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G008327_T01 (Zea mays), 5'ss of exon 2
TCAAGAAGATCCGGCTTGAGCAGGAGGATGAGGGTGTCCCCTCCACCGCCATCCGCGAGATCTCGCTCCTCAAGGAGATGCATCACCGCAACATCGTCAGgtcctctctattaac-caaccctctgctgctcttgtttaggactttggatt-cacttattagga-gtagtcatcacggactgattgattcattgattgatgtg
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TCAAGAAGATCCGCCTCGAGCAGGAGGACGAGGGCGTCCCGTCCACCGCCATCCGCGAGATCTCTCTCCTCAAGGAGATGAACCACGGCAACATCGTCAGgtccgctgcgcctgctctgccctcctccattat-attcccccttttgcattgctgttattacgacggatttagggtcgatcgatcggccgacgcatccgcg--
upper sequence: LOC_Os03g01850.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA05G25320.1 (Glycine max), 5'ss of exon 1
TCAAGAAGATCCGGCTTGAGCAGGAGGATGAGGGTGTCCCCTCCACCGCCATCCGCGAGATCTCGCTCCTCAAGGAGATGCATCACCGCAACATCGTCAGgtcctctctattaaccaaccctctgctgctcttgtttaggactttggattcacttattaggagtagtcatcacggactgattgattcat-tgattgatgtg-
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TGAAGAAGATTCGCCTCGAGCAGGAGGATGAGGGGGTTCCCAGCACCGCCATTCGCGAGATTTCTCTCTTGAAAGAAATGCAGCACAGGAACATTGTTAGgtatataatatatctgaagaatgtgttggtcttcaattgtgcaattcatgtgctgagaaagaata-ttat-atggacgtagtggtagaaattagaaaaatag
upper sequence: LOC_Os03g01850.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA15G14390.1 (Glycine max), 5'ss of exon 2
TCAAGAAGATCCGGCTTGAGCAGGAGGATGAGGGTGTCCCCTCCACCGCCATCCGCGAGATCTCGCTCCTCAAGGAGATGCATCACCGCAACATCGTCAGgtcctctctattaaccaaccctctgctgctcttgtttaggactttggattcacttattaggagtagtcatcacggactgattgattcattgattgatgtg--
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TCAAGAAGATTCGCCTCGAGCAGGAGGACGAAGGCGTTCCCAGCACCGCCATTCGCGAGATTTCTCTCCTCAAAGAGATGCAGCATAGGAACATTGTTAGgtatatcatctaattccttctcctttcattggaatgcaatgtgttgttgtcgatgatgaaattggagggttaataat--gttgtcgccgcactctatttgtc
upper sequence: LOC_Os03g01850.1 (Oryza sativa), 5'ss of exon 3
lower sequence: EFJ15022 (Selaginella moellendorffii), 5'ss of exon 2
TCAAGAAGATCCGGCTTGAGCAGGAGGATGAGGGTGTCCCCTCCACCGCCATCCGCGAGATCTCGCTCCTCAAGGAGATGCATCACCGCAACATCGTCAGgtcc-tctctattaaccaaccctctgctgctcttgtttaggactt-tggattcacttattaggagtagtcatcacggactgattgattcattgattgatgtg
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TCAAGAAGATCCGACTGGACCAGGAGGACGAGGGCGTCCCCAGCACGGCGATCCGCGAAATATCGCTCCTCAAGGAAATGCAGCACGGCAACATTGTGAGgtgcgtgtccact--tccattctctggaatggatttctaaaacgaatcgattgggctgcccag---------------------------------------Mapped 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|33678604|gb|CF306843.1|CF306843EST: ATCCGCGAGATCTCTTTCCTCAAGGAGATGCATCACCGCAACATCGTCAG GTTACACGATGTTATCCACAGTGAGAACCGCATAGGTCTTGTCTTTGAGTA
genomic: ATCCGCGAGATCTCGCTCCTCAAGGAGATGCATCACCGCAACATCGTCAGgtcctctcta ... ctgcgtgcagGTTACACGATGTTATCCACAGTGAGAAGCGCATAGGTCTTGTCTTTGAGTA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TCAAGAAGATCCGGCTTGAGCAGGAGGATGAGGGTGTCCCCTCCACCGCCATCCGCGAGATCTCGCTCCTCAAGGAGATGCATCACCGCAACATCGTCAGgtcctctctattaaccaaccctctgctgctcttgtttaggactttggattcacttattaggagtagtcatcacggactgattgattcattgattgatgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccaaccc