Sequence
atgc intronic sequence ATGC exonic sequencegtacttttgtcagtgaattgcatgtgcatgatttgtttgcaaaatagtcaataggccatggcttctagaagaacagctaagacaatatggtcactttgcagGTACCAACAGGATGGAAATTTTTTGGAAACCTAATGGATGCAGGTAAATTGTCTATATGTGGAGAGGAAAGTTTTGGGACAGGATCTGATCACATCAGGG
Basic information
species | Oryza sativa |
transcript | LOC_Os10g11140.1 |
intron # | 15 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os10g11140.1 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM2G025854_T02 (Zea mays), 3'ss of exon 15
gtacttttgtcagtgaattgca-tgtgcatgatt-tgtttgcaaaatagtcaa------taggcc-atggcttctagaagaacagctaagacaatatggtcactttgcagGTACCAACAGGATGGAAATTTTTTGGAAACCTAATGGATGCAGGTAAATTGTCTATATGTGGAGAGGAAAGTTTTGGGACAGGATCTGATCACATCAGGG
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gtaccattgccatagagcttcactgttcattgtcatatatacaaactgacaaagtgttgtaaacctgtaatttctacttgatcatctaagactaagatgccacttcttagGTTCCAACAGGCTGGAAATTTTTTGGCAACCTAATGGATGCAGGAAAATTGTCTATTTGTGGAGAGGAAAGTTTTGGGACTGGATCTGATCACATCAGAG
upper sequence: LOC_Os10g11140.1 (Oryza sativa), 3'ss of exon 15
lower sequence: AT5G51820.1 (Arabidopsis thaliana), 3'ss of exon 15
--gtacttttgtcagtgaattgcatgtgcatgatttgtttgcaaaatagtcaataggccatggcttctagaagaacagctaagacaatatggtcactttgcagGTACCAACAGGATGGAAATTTTTTGGAAACCTAATGGATGCAGGTAAATTGTCTATATGTGGAGAGGAAAGTTTTGGGACAGGATCTGATCACATCAGGG
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gttcaccctttttagtcaacag-atgtattttctaggtttgcaac----cagataaaattaggaggataaactttttgacaaagcaacttg--tatgttttagGTTCCCACTGGATGGAAATTTTTTGGAAATCTTATGGATGCTGGAAAATTGTCAATCTGTGGAGAAGAGAGCTTTGGCACAGGTTCTGATCACATCCGTG
upper sequence: LOC_Os10g11140.1 (Oryza sativa), 3'ss of exon 15
lower sequence: Vv16s0022g02320.t01 (Vitis vinifera), 3'ss of exon 15
-------------gtact--tttgtcagtgaattgcatgtgca--tgatttgtttgcaa---aatagtcaataggccatggc----ttctagaagaacag-ctaagacaata----tggtcact-----ttgcagGTACCAACAGGATGGAAATTTTTTGGAAACCTAATGGATGCAGGTAAATTGTCTATATGTGGAGAGGAAAGTTTTGGGACAGGATCTGATCACATCAGGG
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gtgaagcccttctgtactaatttgtc-gtgattaacatggaaaactgtcttgcttaaaatggaaaggtttatatccattgacatacttctctcctaacaaactatgtccttaacaatgactattcttggtttcagGTCCCCACTGGATGGAAATTTTTTGGGAACCTTATGGATGCTGGAAAGTTGTCTATTTGTGGGGAAGAAAGTTTTGGAACAGGTTCTGATCACATTCGTG
upper sequence: LOC_Os10g11140.1 (Oryza sativa), 3'ss of exon 15
lower sequence: EFJ34621 (Selaginella moellendorffii), 3'ss of exon 14
gtacttttgtcagtgaattgcatgtgcatgatttgtttgcaaaatagtcaataggccatggcttctagaag-aacagctaagacaatatggtcactttgcagGTACCAACAGGATGGAAATTTTTTGGAAACCTAATGGATGCAGGTAAATTGTCTATATGTGGAGAGGAAAGTTTTGGGACAGGATCTGATCACATCAGGG
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---------------------------------------------gtacgggacgctaccgactttatgagcaatggttcacacagcaaaattg--ttgaagGTTCCAACTGGCTGGAAGTTTTTTGGCAATCTCATGGACGCGGGAAAACTGTCGATTTGCGGAGAGGAAAGTTTTGGAACGGGATCTGATCATATTCGTG
upper sequence: LOC_Os10g11140.1 (Oryza sativa), 3'ss of exon 15
lower sequence: EFJ32824 (Selaginella moellendorffii), 3'ss of exon 14
gtacttttgtcagtgaattgcatgtgcatgatttgtttgcaaaatagtcaataggccatggcttctagaag-aacagctaagacaatatggtcactttgcagGTACCAACAGGATGGAAATTTTTTGGAAACCTAATGGATGCAGGTAAATTGTCTATATGTGGAGAGGAAAGTTTTGGGACAGGATCTGATCACATCAGGG
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---------------------------------------------gtacgggacgctaccgactttatgagcgatggctcacacagcaaaattg--ttgaagGTTCCAACTGGCTGGAAGTTTTTTGGCAATCTCATGGACGCGGGAAAACTGTCGATTTGCGGAGAGGAAAGTTTTGGAACGGGATCTGATCATATTCGTGMapped 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|58676489|gb|CK065176.1|CK065176EST: GTGGTGCTCTTGATCGTGTAGCTGATAAATTGAATGTTCCGTTCTTTGAG GTACCAACAGGATGGAAATTTTTTGGAAACCTAATGGATGCAGGTAAATTG
genomic: GTGGTGCTCTTGATCGTGTAGCTGATAAATTGAATGTTCCGTTCTTTGAGgtacttttgt ... cactttgcagGTACCAACAGGATGGAAATTTTTTGGAAACCTAATGGATGCAGGTAAATTG
EST:
gi|33796171|gb|CF323951.1|CF323951EST: GTGGTGCTCTTGATCGTGTAGCTGATAAATTGAATGTTCCGTTCTTTGAG GTACCAACAGGATGGAAATTTTTTGGAAACCTAATGGATGCAGGTAAATTG
genomic: GTGGTGCTCTTGATCGTGTAGCTGATAAATTGAATGTTCCGTTCTTTGAGgtacttttgt ... cactttgcagGTACCAACAGGATGGAAATTTTTTGGAAACCTAATGGATGCAGGTAAATTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtcaataggccatggcttctagaagaacagctaagacaatatggtcactttgcagGTACCAACAGGATGGAAATTTTTTGGAAACCTAATGGATGCAGGTAAATTGTCTATATGTGGAGAGGAAAGTTTTGGGACAGGATCTGATCACATCAGGG
tcacttt CT-rich tract
acaatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacttttgtcagtgaattgcatgtgcatgatttgtttgcaaaatagtcaataggccatggcttctagaagaacagctaagacaatatggtcactttgcagGTACCAACAGGATGGAAATTTTTTGGAAACCTAATGGATGCAGGTAAATTGTCTATATGTGGAGAGGAAAGTTTTGGGACAGGATCTGATCACATCAGGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA