Sequence
atgc intronic sequence ATGC exonic sequencegtatcctcttgttcaccctcacactttaaatgtcctttatgattatttagatcttgaatcccattgaatttagtttggatgtaaattctgttgtgtgctgatggctagcctcatgtcaattgccaacagTGTAGCATTGATGCATTATTGGAAAAGACCATTAAGCACATGGTTTTCTTGCAAAGTGTGACGAAGCATGCAGACAACCTCAAGGATTCTAACGAATCAA
Basic information
species | Oryza sativa |
transcript | LOC_Os12g06335.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os12g06330.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G069408_T01 (Zea mays), 3'ss of exon 6
gtatcctcttgttc-accctcacactttaaatgtcctttatgattatttagatcttgaat--cccattgaatttagtttggatgtaaattctgttgtgtgctgatggctagcctcatgtcaatt---gccaacagTGTAGCATTGATGCATTATTGGAAAAGACCATTAAGCACATGGTTTTCTTGCAAAGTGTGACGAAGCATGCAGACAACCTCAAGGATTCTAACGAATCAA
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gtatcctcttcttctactcacgcatttcaaacgtgttttagtaatttagggttatttaatgttcaattgcactt-gtttcaaacttcatacacttgtacgatgactgttagtctcacagcattttttgtcaacagTGTAGTATTGATGCATTACTGGAGAAGACCATTAAGCACATGCTTTTCTTGCAAAGTGTGACAAAGCATGCAGATAACCTCAAGGACTCAAACAAATCTG
upper sequence: LOC_Os12g06330.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G031656_T02 (Zea mays), 3'ss of exon 7
gtatcctcttgttc-accctcacactttaaatgtcctttatgattatttagatc--ttgaatcccattgaatttagtttggatgtaaattctgttgtgtgctgatggcta-gcctcatgtcaatt---gccaacagTGTAGCATTGATGCATTATTGGAAAAGACCATTAAGCACATGGTTTTCTTGCAAAGTGTGACGAAGCATGCAGACAACCTCAAGGATTCTAACGAATCAA--
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gtatcctcttcttctacttgtgcatttcaaatgtgtgttaggaat-ttaggattatttaaggttcaatggcacttgtttgaaacttcatatgcttgtgcaatgactgttaagcctcataacattttttgtcaacagtgtagCATTGATGCCTTGTTGGAGAAGACCATTAAGCACATGGTTTTCTTGCAAAGTGTGACAAAGCATGCAGATAACCTCAAGGACTCAAATGAATCTAAG
upper sequence: LOC_Os12g06330.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G031656_T01 (Zea mays), 3'ss of exon 6
gtatcctcttgttc-accctcacactttaaatgtcctttatgattatttagatc--ttgaatcccattgaatttagtttggatgtaaattctgttgtgtgctgatggcta-gcctcatgtcaatt---gccaacagTGTAGCATTGATGCATTATTGGAAAAGACCATTAAGCACATGGTTTTCTTGCAAAGTGTGACGAAGCATGCAGACAACCTCAAGGATTCTAACGAATCAA
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gtatcctcttcttctacttgtgcatttcaaatgtgtgttaggaat-ttaggattatttaaggttcaatggcacttgtttgaaacttcatatgcttgtgcaatgactgttaagcctcataacattttttgtcaacagTGTAGCATTGATGCCTTGTTGGAGAAGACCATTAAGCACATGGTTTTCTTGCAAAGTGTGACAAAGCATGCAGATAACCTCAAGGACTCAAATGAATCTA
upper sequence: LOC_Os12g06330.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA12G09990.1 (Glycine max), 3'ss of exon 1
gtatcctcttgttcaccctcacactttaaatgtcctttatgattatttagatcttgaatcccattgaatttagtttggatgtaaattctgttgtgtgctgatggctagcctcatgtcaattgccaacagTGTAGCATTGATGCATTATTGGAAAAGACCATTAAGCACATGGTTTTCTTGCAAAGTGTGACGAAGCATGCAGACAACCTCAAGGATTCTAACGAATCAA
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----------------------gtatgtagcctttcttgtgctttcctatatctcagtcctgaac--atatatttcacattgggatactgactttattttct--ttaatctcttattacaattcaacagTGTAGCATAGATGCACTTCTGGAAAAGACCATCAAGCATATGCTTTTCCTGCAAAGTGTAACAAAGCATGCTGACAAGCTGAAACAGACAGGGGAATCTA
upper sequence: LOC_Os12g06330.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA11G18290.1 (Glycine max), 3'ss of exon 7
gtatcctcttgttcaccctcacactttaaatgtcctttatgattatttagatcttgaatcc-cattgaatttagtttggatgtaaattctgttgtgtgctgatggctagcctcatgtcaattgccaacagTGTAGCATTGATGCATTATTGGAAAAGACCATTAAGCACATGGTTTTCTTGCAAAGTGTGACGAAGCATGCAGACAACCTCAAGGATTCTAACGAATCAA
| |||| ||| |||| || | || |||| ||| || |||| || || | | || | || ||| ||| | |||||||||||||| |||||| | ||||||||||||| ||||| ||| ||||| |||||||||| || |||||||| ||||| || || | | || || |
---------------gtatatagcttttcttgtgcttttcctacatctcagtcctgaacttatatttaac---atttgaatactaactattttct----------ttaatctcttgttacaattcaacagTGTAGCATAGATGCACTTCTGGAAAAGACCATCAAGCATATGCTTTTCCTGCAAAGTGTAACAAAGCATGCTGACAAGCTGAAACAGACAGGGGAGTCTA
upper sequence: LOC_Os12g06330.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA12G31460.2 (Glycine max), 3'ss of exon 9
gtatcctcttgttcaccctcacactttaaatgtcctttatgattatttagatcttgaatcccattgaatttagtttggatgtaaattctgttgtgtgctgatggctagcctcatgtcaattgccaacagTGTAGCATTGATGCATTATTGGAAAAGACCATTAAGCACATGGTTTTCTTGCAAAGTGTGACGAAGCATGCAGACAACCTCAAGGATTCTAACGAATCAA
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gtatttccttgtttattctttcattcctaat----tttttggtaatttaaatatcttgttctgtc--actgagtt---------gtttttttttct-ttgatctct----ttttatgacttg---acagTGTAGCATAGATGCACTTTTGGAACGGACCATTAAGCATATGCTTTTCTTACAAAGTGTGACAAAGCATGCTGACAAGCTGAAACAAACAGGGGAGTCTA
upper sequence: LOC_Os12g06330.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv06s0009g00440.t01 (Vitis vinifera), 3'ss of exon 6
gtatcctcttgttcaccctcacactttaaatgtcctttatgattatttagatcttgaatcccattgaatttagtttggatgtaaattctgttgtgtgctgatggctagcctcatgtcaattgccaacagTGTAGCATTGATGCATTATTGGAAAAGACCATTAAGCACATGGTTTTCTTGCAAAGTGTGACGAAGCATGCAGACAACCTCAAGGATTCTAACGAATCAA
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--------------------gtaactcatctttcttcctttcttcctcacttttttgaggacattttactatattgagatactgattatgtcct---ctaat--cta--ctgatgtggttt---aacagTGTAGCATTGATGCACTGCTTGAACGCACCATCAAGCATATGCTTTTCTTGCAAAGTGTCATGAAGCATGCAGACAAGCTAAAGCAAACTGGAGAGTCTAMapped 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|44672670|gb|CR286104.1|CR286104EST: TTCAAGGTCGTATAAAGGAGCTGCGGGAACTAGTACCTAATGGGGCAAAG TGTAGCATTGATGCATTATTGGAAAAGACCATTAAGCGCATGGTTTTCTTG
genomic: TTCAAGATCGTATAAAGGAGCTGCGGGAACTAGTACCTAATGGGGCAAAGgtatcctctt ... ttgccaacagTGTAGCATTGATGCATTATTGGAAAAGACCATTAAGCACATGGTTTTCTTG
EST:
gi|58602076|gb|CK012604.1|CK012604EST: TTCAAGATCGTATAAAGGAGCTGCGGGAACTAGTACCTAATGGGGCAAAG TGTAGCATTGATGCATTATTGGAAAAGACCATTAAGCACATGGTTTTCTTG
genomic: TTCAAGATCGTATAAAGGAGCTGCGGGAACTAGTACCTAATGGGGCAAAGgtatcctctt ... ttgccaacagTGTAGCATTGATGCATTATTGGAAAAGACCATTAAGCACATGGTTTTCTTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttggatgtaaattctgttgtgtgctgatggctagcctcatgtcaattgccaacagTGTAGCATTGATGCATTATTGGAAAAGACCATTAAGCACATGGTTTTCTTGCAAAGTGTGACGAAGCATGCAGACAACCTCAAGGATTCTAACGAATCAA
tgctgat putative branch site (score: 3)
tgtaaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatcctcttgttcaccctcacactttaaatgtcctttatgattatttagatcttgaatcccattgaatttagtttggatgtaaattctgttgtgtgctgatggctagcctcatgtcaattgccaacagTGTAGCATTGATGCATTATTGGAAAAGACCATTAAGCACATGGTTTTCTTGCAAAGTGTGACGAAGCATGCAGACAACCTCAAGGATTCTAACGAATCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG