Sequence
atgc intronic sequence ATGC exonic sequence...tgattttagtattaaatgcttttaagtattcatatagtattaaatagtggaattgccggaccatgtttcttacttgatggcagaagttgaacaatttaagCAGGCAGACATCGACTTACGGGGGCATGACGACTTTCTCTCTGAACCTGGAGGAATAATGGATTTTGAAGAGGACCGCATCCGACCAAAAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os07g30840.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g30840.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G085670_T04 (Zea mays), 3'ss of exon 7
--tgattttagtattaaatgctttta-agtattca-tatagtattaaatagtggaattgccggaccatgtttcttacttgatggcagaagttgaacaatttaagCAGGCAGACATCGACTTACGGGGGCATGACGACTTTCTCTCTGAACCTGGAGGAATAATGGATTTTGAAGAGGACCGCATCCGACCAAAAAG
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tataattatt-ttttgagtgttcatataatggcaactactgtattaaatagtg---ttgccgaaccatgtttcttacttgatggcagaagttgaacaatttaagCAGGCAGACATCGACATACGAGGGCATGACGACTACCTCTCTGAATCTGTAGGAATAATGGATTTTGAAGAGGACCGTGTCCGACCAAAGAG
upper sequence: LOC_Os07g30840.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G171745_T04 (Zea mays), 3'ss of exon 7
tgattttagtattaaatgcttttaagtattca--tatagtattaaatagtggaattgccggaccatgtttcttacttgatggcagaagttgaacaatttaagCAGGCAGACATCGACTTACGGGGGCATGACGACTTTCTCTCTGAACCTGGAGGAATAATGGATTTTGAAGAGGACCGCATCCGACCAAAAAG
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--ttattatttttcagtgttcatataatggcagctactgtattaaatagtg---ttgccgaaccatgtttcttacttgatggcagaagttaaacaatttaagcagGCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGAGGAATAATGGATTTTGAAGAGGACCGCGTCCGACCAAAAAG
upper sequence: LOC_Os07g30840.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G085670_T01 (Zea mays), 3'ss of exon 7
--------------------------------------------------------------------------------------------------------tgattttagtattaaatg--cttttaagtattcatatagtattaaatagtgga---------attgccggaccatgtttcttacttgatggcagaagttgaacaatttaagCAGGCAGACATCGACTTACGGGGGCATGACGACTTTCTCTCTGAACCTGGAGGAATAATGGATTTTGAAGAGGACCGCATCCGACCAAAAAG
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gtgagctagattaaactgaagcatttgttaggaataaatttgcatctgcttgtgatgagttatgctctgttttcttcattttcctacttctgccttactgcctcatgtttagatatataattattttttgagtgttcatataatggcaactactgtattaaatagtgttgccgaaccatgtttcttacttgatggcagAAGTTGAACAATTTAAGCAGGCAGACATCGACATACGAGGGCATGACGACTACCTCTCTGAATCTGTAGGAATAATGGATTTTGAAGAGGACCGTGTCCG---------
upper sequence: LOC_Os07g30840.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G171745_T05 (Zea mays), 3'ss of exon 6
--------tgattttagtattaaatgcttttaagtattcatatagtattaaatagtgga---------attgccggaccatgtttcttacttgatggcagaagttgaacaatttaagCAGGCAGACATCGACTTACGGGGGCATGACGACTTTCTCTCTGAACCTGGAGGAATAATGGATTTTGAAGAGGACCGCATCCGACCAAAAAG
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ctgccttctgtttagatttattattatttttcagtgttcatataatggcagctactgtattaaatagtgttgccgaaccatgtttcttacttgatggcagAAGTTAAACAATTTAAGCAGGCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGAGGAATAATGGATTTTGAAGAGGACCGCGTCCG---------
upper sequence: LOC_Os07g30840.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G085670_T03 (Zea mays), 3'ss of exon 6
tgattttagtattaaatgctttta-agtattca-tatagtattaaatagtggaattgccggaccatgtttcttacttgatggcagaagttgaacaatttaagCAGGCAGACATCGACTTACGGGGGCATGACGACTTTCTCTCTGAACCTGGAGGAATAATGGATTTTGAAGAGGACCGCATCCGACCAAAAAG
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--aattattttttgagtgttcatataatggcaactactgtattaaatagtg---ttgccgaaccatgtttcttacttgatggcagaagttgaacaatttaagcagGCAGACATCGACATACGAGGGCATGACGACTACCTCTCTGAATCTGTAGGAATAATGGATTTTGAAGAGGACCGTGTCCGACCAAAGAG
upper sequence: LOC_Os07g30840.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G171745_T02 (Zea mays), 3'ss of exon 7
-tgattttagtattaaatgcttttaagtattca--tatagtattaaatagtggaattgccggaccatgtttcttacttgatggcagaagttgaacaatttaagCAGGCAGACATCGACTTACGGGGGCATGACGACTTTCTCTCTGAACCTGGAGGAATAATGGATTTTGAAGAGGACCGCATCCGACCAAAAAG
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ttattattatttttcagtgttcatataatggcagctactgtattaaatagtg---ttgccgaaccatgtttcttacttgatggcagaagttaaacaatttaagCAGGCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGAGGAATAATGGATTTTGAAGAGGACCGCGTCCGACCAAAAAGMapped 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|88219553|gb|CI219113.1|CI219113EST: ACCAGAAAGAGTTCGAAGACAAGGTAGAAGAAGCCAAAAAATCAATCAAG CAGGCAGACATCGACTTACGGGGGCATGACGACTTTCTCTCTGAACCTGGA
genomic: ACCAGAAAGAGTTCGAAGACAAGGTAGAAGAAGCCAAAAAATCAATCAAGgtgagttgga ... acaatttaagCAGGCAGACATCGACTTACGGGGGCATGACGACTTTCTCTCTGAACCTGGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agtggaattgccggaccatgtttcttacttgatggcagaagttgaacaatttaagCAGGCAGACATCGACTTACGGGGGCATGACGACTTTCTCTCTGAACCTGGAGGAATAATGGATTTTGAAGAGGACCGCATCCGACCAAAAAG
aacaatttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgattttagtattaaatgcttttaagtattcatatagtattaaatagtggaattgccggaccatgtttcttacttgatggcagaagttgaacaatttaagCAGGCAGACATCGACTTACGGGGGCATGACGACTTTCTCTCTGAACCTGGAGGAATAATGGATTTTGAAGAGGACCGCATCCGACCAAAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - aatgctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcagaag