Sequence
atgc intronic sequence ATGC exonic sequencegtcagatgcttgttcttacaagtacattgttcatggtttcattgtttagctggcaaatgatccccctaaattctgtctgtacttgacagGTACAATTTGCAACTGGAAGGGATCTTACACCTGATCAGCTGAACAATATGATAGATACATTATCTGACTG
Basic information
species | Oryza sativa |
transcript | LOC_Os07g30840.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g30840.4 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G152100_T01 (Zea mays), 3'ss of exon 4
gtcagatgcttgtt-cttacaagtacattgttcatggtttcattgtttagctggcaaatgatccccctaaattctgtctgtacttgac--agGTACAATTTGCAACTGGAAGGGATCTTACACCTGATCAGCTGAACAATATGATAGATACATTATCTGACTG----
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gtaagatgcttgcagcctgtatctgcatcat---------cattatctatctgtccaatgatatttttatctgcatactgcattcgttttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGAGCAGCTAAACAACATGATAGAGATCTTATCTGACTGGTTT
upper sequence: LOC_Os07g30840.4 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G152100_T02 (Zea mays), 3'ss of exon 3
gtcagatgcttgtt-cttacaagtacattgttcatggtttcattgtttagctggcaaatgatccccctaaattctgtctgtacttgac--agGTACAATTTGCAACTGGAAGGGATCTTACACCTGATCAGCTGAACAATATGATAGATACATTATCTGACTG-----------------------------
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gtaagatgcttgcagcctgtatctgcatcat---------cattatctatctgtccaatgatatttttatctgcatactgcattcgttttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGAGCAGCTAAACAACATGATAGAGATCTTATCTGACTGGTTTGTATGCTTATTTAAGAAATTTTCTA
upper sequence: LOC_Os07g30840.4 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G152805_T01 (Zea mays), 3'ss of exon 5
gtcagatgcttgttcttacaagtacattgttcatggtttcattgtttagctggcaaatgatccccctaaattctgtctgtacttgac--agGTACAATTTGCAACTGGAAGGGATCTTACACCTGATCAGCTGAACAATATGATAGATACATTATCTGACTG----
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gtaagatgcttgc-------agc-ctgtatctgcagcatcattatctatctgtccaatgatatttttacctccatactgcattcgttttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAATAACATGATAGAGATCTTATCTGACTGGTTT
upper sequence: LOC_Os07g30840.4 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G171745_T04 (Zea mays), 3'ss of exon 5
gtcagatgcttgtt-cttacaagtacattgttcatggtttcattgtttagctggcaaatgatccccctaaattctgtctgtacttgac--agGTACAATTTGCAACTGGAAGGGATCTTACACCTGATCAGCTGAACAATATGATAGATACATTATCTGACTG
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gcaagatgcttgcggcctgtatctgcagcatc---gttttctctgtctaa-tgataacttttttatgaacattttctctgcattcattttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTG
upper sequence: LOC_Os07g30840.4 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G027551_T01 (Zea mays), 3'ss of exon 3
gtcagatgcttgttcttacaagtacattgttcatggtttcattgtttagctggcaaatgatccccctaaattctgtctgtacttgac--agGTACAATTTGCAACTGGAAGGGATCTTACACCTGATCAGCTGAACAATATGATAGATACATTATCTGACTG-----------------------------
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gtaagatgcttgc-------agc-ctgtatctgcagcatcattatctatctatccaatgatatttttatctgcatactgcattcgttttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTGGTTTGTATGCTTATTTAAGAAATTTTCTA
upper sequence: LOC_Os07g30840.4 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G085670_T04 (Zea mays), 3'ss of exon 5
gtcagatgcttgttcttacaagtacattgttcatggtttcattgtttagctggcaaatgatccccctaaattctgtctgtacttgac--agGTACAATTTGCAACTGGAAGGGATCTTACACCTGATCAGCTGAACAATATGATAGATACATTATCTGACTG
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gtaagatgcttgc-------agc-ctgtatctgcagcttcattatctatctgtccaatgatatttttatatgcatactgcattcgttttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTG
upper sequence: LOC_Os07g30840.4 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G115277_T01 (Zea mays), 3'ss of exon 5
gtcagatgcttgttcttacaagtacattgttcatggtttcattgtttagctggcaaatgatcccc---ctaaattctgtctgtacttgacagGTACAATTTGCAACTGGAAGGGATCTTACACCTGATCAGCTGAACAATATGATAGATACATTATCTGACTG
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gtaagatgcttgc-------agc-ctgtatctgcagcatcattatctatctgtccaatgatattttatctgcatactgcattcgttt--tagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAATAACATGATAG----------------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|86499691|gb|CI142324.1|CI142324EST: GGTATTGTCAGGGCCAAATTGGATCAGCTCCGGAGGTGTTTTGAG GTACAATTTGCAACTGGAAGGGATCTTACACCTGATCAGCTGAACAATATG
genomic: GGTATTGTCAGGGGCAAATTGGATCAGCTGCGGAGGTGTTTTGAGgtcagatgct ... tacttgacagGTACAATTTGCAACTGGAAGGGATCTTACACCTGATCAGCTGAACAATATG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggtttcattgtttagctggcaaatgatccccctaaattctgtctgtacttgacagGTACAATTTGCAACTGGAAGGGATCTTACACCTGATCAGCTGAACAATATGATAGATACATTATCTGACTG
ccctaaa putative branch site (score: 3)
attgttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcagatgcttgttcttacaagtacattgttcatggtttcattgtttagctggcaaatgatccccctaaattctgtctgtacttgacagGTACAATTTGCAACTGGAAGGGATCTTACACCTGATCAGCTGAACAATATGATAGATACATTATCTGACTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA