Sequence
atgc intronic sequence ATGC exonic sequencegtactttgttattgtctattgcttaatcctgcttgattgtatttgaactgcaaacaagaatatcttattaattccccattgaaaatgattttgtgttgtttaatttttttttcctggctggccttatacatgatatcttcaacagatatgctgatgatgtcctatccttgtttcaatctgttgtagGATGCTTGTGTATGAGTATGTAAATAATGGGAATTTGGAGCAGTGGCTTCATGGTGATGTAGGGCCTCGAAGTCCTCTTACTTGGGAGATTCGAATGAAT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv07s0031g00480.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os04g35080.1 (Oryza sativa), 3'ss of exon 2
gtactttgttattgtctattgcttaatcctgcttgattgtatttgaactgcaaacaagaatatcttattaattccccattgaaaatgattttgtgttgtttaatttttttttcctggctggccttatacatgatatcttcaacagatatgctgatgatgtcctatcctt---gtttcaatctgttgtagGATGCTTGTGTATGAGTATGTAAATAATGGGAATTTGGAGCAGTGGCTTCATGGTGATGTAGGGCCTCGAAGTCCTCTTACTTGGGAGATTCGAATGAAT
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-----------------------------------------------------------------------------------------------------------------gtaccttgaa--atcaatggattctatgactgagtagcttgcaatgtataatattttctgtacgaatccttttcagGATGCTTGTGTACGAGTATGTCAATAATGGAAACTTAGAGCAATGGCTCCATGGTGATGTTGGTCCCGTAAGCCCTCTCACATGGGATATGAGAATGAAG
upper sequence: Vv07s0031g00480.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os05g36050.1 (Oryza sativa), 3'ss of exon 2
gtactttgttattgtctattgcttaatcctgcttgattgtatttgaactgcaaacaagaatatcttattaattccccattgaaaatgattttgtgttgtttaatttttttttcctggctggccttatacatgatatcttcaacagatatgctgatgatgtcctatccttgtttcaatctg-ttgtagGATGCTTGTGTATGAGTATGTAAATAATGGGAATTTGGAGCAGTGGCTTCATGGTGATGTAGGGCCTCGAAGTCCTCTTACTTGGGAGATTCGAATGAAT
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------------------------------------------gtacactacacacaccacgcaattgccaaatcgccgcc--------ttct---tttttttctttcctttttttggctgttctcttaccagatcattcctacctacctactc-cgat--cctaccatttcttgcctgtgatctcagGATACTTGTGTATGAGTACGTGGACAATGGCAACTTGGAGCAGTGGCTTCATGGCGACGTTGGACCGGTTAGCCCTCTGTCTTGGGACATCAGGATGAAC
upper sequence: Vv07s0031g00480.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G050861_T01 (Zea mays), 3'ss of exon 2
gtactttgttattgtctattgcttaatcctgcttgattgtatttgaactgcaaacaagaatatcttattaattccccattgaaaatgattttgtgttgtttaatttttttttcctggctggccttatacatgatatcttcaacagatatgctgatgatgtcctatccttgtttcaatctgttgtagGATGCTTGTGTATGAGTATGTAAATAATGGGAATTTGGAGCAGTGGCTTCATGGTGATGTAGGGCCTCGAAGTCCTCTTACTTGGGAGATTCGAATGAAT
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-----------------------------------------------------------gtatcttcttg------tatggacaatagctttagcttat---attgtgaaattatag--aaccaaggagtttgtagctttatcataaat-ttcattgtatatggttctttt------ccattccagGATGCTTGTGTATGAGTACGTTAATAATGGAAACTTGGAGCAATGGCTCCATGGGGATGTTGGCCCTGTGAGCCCTCTTACATGGGATATCAGAATGAAG
upper sequence: Vv07s0031g00480.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA11G05830.1 (Glycine max), 3'ss of exon 2
gtactttgttattgtctattgcttaatcctgcttgattgtatttgaactgcaaacaagaatatcttattaattccccattgaaaatgattttgtgttgtttaatttttttttcctggctggccttatacatgatatcttcaacagatatgctgatgatgtcctatccttgtttcaatctgttgtagGATGCTTGTGTATGAGTATGTAAATAATGGGAATTTGGAGCAGTGGCTTCATGGTGATGTAGGGCCTCGAAGTCCTCTTACTTGGGAGATTCGAATGAAT
| || ||| || | || || | || ||| || ||||||||| | | | || | |||| | || ||| ||| | | | | | || || || | | || || |||||||| |||||||| || | ||||| ||||| ||||||||||| ||||| ||||| |||||| | |||||||| |||||||| |||||||||||
-------------------------------------------------------------gtattcttactttcttctttaa--ttatccaaaattgcttcttttttttttttttgtag--tatagatatgaacttttgaactgatgaggtttt--tttttaattattattattcac-gctgcagAATGCTTGTTTATGAGTACGTGGACAATGGTAATTTAGAGCAGTGGCTGCATGGGGATGTTGGGCCTTGCAGTCCTCTAACTTGGGAAATTCGAATGAAC
upper sequence: Vv07s0031g00480.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA01G39420.1 (Glycine max), 3'ss of exon 3
gtactttgttattgtctattgcttaatcctgcttgattgtatttgaactgcaaacaagaatatcttattaattccccattgaaaatgattttgtgttgtttaattttt-ttttcctggctggccttatacatgatatcttcaacagatatgctgatgatgtcctatccttgtttcaatctgttgtagGATGCTTGTGTATGAGTATGTAAATAATGGGAATTTGGAGCAGTGGCTTCATGGTGATGTAGGGCCTCGAAGTCCTCTTACTTGGGAGATTCGAATGAAT
|| | || | || || |||||| | ||| || || |||| | | |||| ||| ||| | | || || |||||||| |||||||| || | ||||| ||||| ||||||||||| ||||| ||||| |||||| | |||||||| |||||||| |||||||||||
--------------------------------------------------------------------------------------------gtactcttcatttcttactttcctctttaa--ttaaccaaaattgcttccttttttttttctttgat----tattattggtcc-------tgcagAATGCTTGTTTATGAGTACGTTGACAATGGTAATTTAGAGCAGTGGCTGCATGGGGATGTTGGGCCTTGCAGTCCTCTAACTTGGGAAATTCGAATGAAC
upper sequence: Vv07s0031g00480.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: PP1S568_2V6.1 (Physcomitrella patens), 3'ss of exon 3
gtactttgttattgtctattgcttaatcctgcttgattgtatttgaactgcaaacaagaatatcttattaattccccattgaaaatgattttgtgttgtttaatttttttttcctggctggc-cttatacatgatatcttcaacagatatgctgatgatgtcctatccttgtttca---atctgttgtagGATGCTTGTGTATGAGTATGTAAATAATGGGAATTTGGAGCAGTGGCTTCATGGTGATGTAGGGCCTCGAAGTCCTCTTACTTGGGAGATTCGAATGAAT
|| |||| || |||| |||| || | || | | ||| | | || | ||| | | || || || |||||||||||||||||| ||||| || | ||||||||| ||||||||||||| ||||| | | | || | ||| | ||||| ||| |||
-----------------------------------------------------------------------------------------------gtgaagcatttattcttcccacctggagtttttgtgtgccagca-caattctcttacacgtgcaatgctaacttcgtctctcgtggcttttgtagGATGCTTGTGTACGAGTACGTGGACAATGGGAATCTGGAGCAGTGGCTACATGGACCTCTGTCACAAACAAACACACTTCCATGGGAAGCTCGCATGCGG
upper sequence: Vv07s0031g00480.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: PP1S358_6V6.1 (Physcomitrella patens), 3'ss of exon 2
gtactttgttattgtctattgcttaatcctgcttgattgtatttgaactgcaaacaagaatatcttattaattccccattgaaaatgattttgtgttgtttaatttttttttcctggctggccttatacatgatatcttcaacagatatgctgatgatgtcc--tatccttgtttcaat---ctgttgtagGATGCTTGTGTATGAGTATGTAAATAATGGGAATTTGGAGCAGTGGCTTCATGGTGATGTAGGGCCTCGAAGTCCTCTTACTTGGGAGATTCGAATGAAT
||| | | || || |||||| | | | | || | | ||| | ||||| | | | ||| ||||| |||||| |||||||||||||| ||||| || ||||||| || |||||||||||||| ||||| | | | || | | ||| | ||||| || |||
--------------------------------------------------------------------------------------------gtga-atgtcatcccttcttcctgcccagtttgttgtgtggtggc----gcagctcc-ttgatgttctttgttgacctcgtttctggtggctgttgcagGATGCTTGTGTACGAGTACGTGGATAATGGAAACTTGGAGCAGTGGCTGCATGGACCTCTGTCCCAAACAAATACACTTCCATGGGAAGCCCGCATGCGG
upper sequence: Vv07s0031g00480.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: EFJ27863 (Selaginella moellendorffii), 3'ss of exon 3
gtactttgttattgtctattgcttaatcctgcttgattgtatttgaactgcaaacaagaatatcttattaattccccattgaaaatgattttgtgttgtttaatttttttttcctggctggccttatacatgatatcttcaacagatatgctgatgatgtcctatccttgtttcaatctgttgtagGATGCTTGTGTATGAGTATGTAAATAATGGGAATTTGGAGCAGTGGCTTCATGGTGATGTAGGGCCTCGAAGTCCTCTTACTTGGGAGATTCGAATGAAT
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------------------------------------------------------------------------------------------------------------------------------------gtacgtcgaattctcatgaaagagtttttcactttggatgacgaacttctacagGATGCTGGTATATGAGTACGTAGACAATGGTAATCTGGAGCAGTGGCTTCACGGCCCAGCCTCCATTCTCAACTCTCCAACATGGGAGGTTAGGATGAAA
upper sequence: Vv07s0031g00480.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: EFJ36811 (Selaginella moellendorffii), 3'ss of exon 3
gtactttgttattgtctattgcttaatcctgcttgattgtatttgaactgcaaacaagaatatcttattaattccccattgaaaatgattttgtgttgtttaatttttttttcctggctggccttatacatgatatcttcaacagatatgctgatgatgtcctatccttgtttcaatctgttgtagGATGCTTGTGTATGAGTATGTAAATAATGGGAATTTGGAGCAGTGGCTTCATGGTGATGTAGGGCCTCGAAGTCCTCTTACTTGGGAGATTCGAATGAAT
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-----------------------------------------------------------------------------------------------------------------------------gtacgtcgaattctcgtgaaagatttt-------ttcactttggatgacgaacttctacagGATGCTGGTATATGAGTACGTAGACAATGGTAATCTGGAGCAGTGGCTTCACGGCCCAGCCTCCATTCTCAACTCTCCAACATGGGAAGTTCGGATGAAAMapped 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|294965685|gb|GW839140.1|GW839140EST: CATAAAAATTTAGTGAGATTGCTTGGTTACTGTGCGGAAGGAGCTCATAG GATGCTTGTGTATGAGTATGTAAATAATGGGAATTTGGAGCAGTGGCTTCA
genomic: CATAAAAATTTAGTGAGATTGCTTGGTTACTGTGCGGAAGGAGCTCATAGgtactttgtt ... tctgttgtagGATGCTTGTGTATGAGTATGTAAATAATGGGAATTTGGAGCAGTGGCTTCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatatcttcaacagatatgctgatgatgtcctatccttgtttcaatctgttgtagGATGCTTGTGTATGAGTATGTAAATAATGGGAATTTGGAGCAGTGGCTTCATGGTGATGTAGGGCCTCGAAGTCCTCTTACTTGGGAGATTCGAATGAAT
tgctgat putative branch site (score: 3)
tttcaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtactttgttattgtctattgcttaatcctgcttgattgtatttgaactgcaaacaagaatatcttattaattccccattgaaaatgattttgtgttgtttaatttttttttcctggctggccttatacatgatatcttcaacagatatgctgatgatgtcctatccttgtttcaatctgttgtagGATGCTTGTGTATGAGTATGTAAATAATGGGAATTTGGAGCAGTGGCTTCATGGTGATGTAGGGCCTCGAAGTCCTCTTACTTGGGAGATTCGAATGAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT