Sequence
atgc intronic sequence ATGC exonic sequence...aatcttttatatatggaatatggattgctgaataatgttaatcactgtgtctcatctggtatttattgatttttggttcaatgaattattgtatttgcagGTAGTTGCTGTGAAACAACTTGACCGAAATGGCCTTCAAGGAAATAGAGAATTCTTGGTGGAGGTTCTCATGCTTAGCCTCTTACATCACCCAAACCTTG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv05s0020g01770.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os01g71000.1 (Oryza sativa), 3'ss of exon 2
-------------------------------------------aatcttttatatatggaatatggattgctgaat-aatgttaatcactgtgt---ctcatctggtattta--ttgatttttggttca---atgaattattgtatttgc-agGTAGTTGCTGTGAAACAACTTGACCGAAATGGCCTTCAAGGAAATAGAGAATTCTTGGTGGAGGTTCTCATGCTTAGCCTCTTACATCACCCAAACCTTG
||| || | | | | | | | | | ||| || | | ||| | | || | ||| || || ||| || ||||| ||| | || | ||| ||||||||||| |||||||| || ||||| ||||||||||||||||||||| |||| ||||| |||||||| || || |||||||| | ||||| |
gtcagtctttcttaacctatctagatctattgagattttactaaatacttgaagtttaggttttcagcgatttagttaatattcagtaaaatgttggcagaattgctgttttgctttatccctggagcactaatgaaatataccacttcccagGCTGTTGCTGTGAAGCAACTTGATCGCAATGGTCTTCAAGGAAATAGAGAATTCCTGGTTGAGGTCCTCATGCTCAGTCTTCTACATCACACTAACCTGG
upper sequence: Vv05s0020g01770.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os01g15470.3 (Oryza sativa), 3'ss of exon 2
-----aatcttttatatatggaatatggattgctgaataatgttaatcactgtgtctcatctggtatttattgatttttggttcaatgaattattgtatttgcagGTAGTTGCTGTGAAACAACTTGACCGAAATGGCCTTCAAGGAAATAGAGAATTCTTGGTGGAGGTTCTCATGCTTAGCCTCTTACATCACCCAAACCTTG
||| || ||| || | | | | | || ||||| | | | | | | | || | |||| ||||| | | || || || |||||| ||||| || ||||| ||||| | |||||| ||||| ||||| ||||||||| | ||||||||||||||||| || ||||| ||||| || || | |
atgggaatgcttagactattga-tgttaacaga-aagtattgttatgctatataccctttgtataaatttctaattt--ggttccagcatttgctgcatc-gcagGTTGTTGCAGTTAAACAGCTTGATCTAAATGGGCTTCAGGGAAACAGAGAATTCCTTGTGGAGGTTCTCATGCTCAGTCTCTTGCATCATCCTAATTTAG
upper sequence: Vv05s0020g01770.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os07g47270.1 (Oryza sativa), 3'ss of exon 2
aatcttttatatatggaatatggattgctgaataatgttaatcactgtgtctcatctggtatttattgatttttggt--tcaatgaatta----ttgtat--------ttgcagGTAGTTGCTGTGAAACAACTTGACCGAAATGGCCTTCAAGGAAATAGAGAATTCTTGGTGGAGGTTCTCATGCTTAGCCTCTTACATCACCCAAACCTTG
||| ||| || || | ||||| | | || ||| | | || | | | | || | || | | || ||| || | |||||| |||| ||||| ||||||||| |||||||||| |||||||| ||||||| | ||||||||||||||||| || ||||| || || || || || |
---gtttgctattcctaacattggctgctgtgtgctcttgttcattagctgcaatttagagcatgatttttctgagtgtccgacaccttttcttttgcatatatcatctagcagGTTATTGCCGTGAAGCAACTTGACAGAAATGGCCTACAAGGAAACCGAGAATTTCTCGTGGAGGTTCTCATGCTAAGTCTCTTGCACCATCCTAATCTGG
upper sequence: Vv05s0020g01770.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os05g30870.1 (Oryza sativa), 3'ss of exon 2
aatcttttatatatggaatatggattgctgaataat--gttaatcactgtgtctcatctggtatttattgatttttggttcaatgaa-ttattgtatttgcagGTAGTTGCTGTGAAACAACTTGACCGAAATGGCCTTCAAGGAAATAGAGAATTCTTGGTGGAGGTTCTCATGCTTAGCCTCTTACATCACCCAAACCTTG
|| || | || | | || | || || | || | | || | | || | | | | || |||| ||| || |||||| ||||| ||||| |||||||| || ||||| ||||||||||||||||| || |||| || || || ||||| || || || || || ||||| |
-atggttactgcatttcttttaaccccctatgtgatctgtggagcattagaggagacatgtt--tccttaaagtcttgatcgatgagcttaccaaatatgcagGCTGTTGCAGTGAAGCAACTTGATCGCAATGGACTTCAAGGAAATAGAGAGTTTCTGGTTGAAGTCCTTATGCTCAGTCTATTGCACCATGATAACCTGG
upper sequence: Vv05s0020g01770.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G037585_T01 (Zea mays), 3'ss of exon 2
-----------------------------------------------------------------aatct---tttatatatggaatatgg-attgctgaataatgtta--atcactgtgtctcatctggtatttattgatttttggt-tcaatgaattattgtatttgcagGTAGTTGCTGTGAAACAACTTGACCGAAATGGCCTTCAAGGAAATAGAGAATTCTTGGTGGAGGTTCTCATGCTTAGCCTCTTACATCACCCAAACCTTG
||| || | | || | || ||| || |||| || || || | | | | | ||| | | | || | | || || |||| ||||||||||| |||||||| || |||||||| ||||||||||| ||||| |||| |||||||||||||| || |||||||||||| | ||||| |
gtaagcatatctgaaacatgacgcattgacattttgattgtaaagctaaatcctctcaaatttggcttctgagttgaaacattaagtaaaatgttggtgggaaatgctaacataacgattatacttgcgccctggattagccctggatactaacagagttttac-ttcccagGCTGTTGCTGTGAAGCAACTTGATCGTAATGGCCTCCAAGGAAATAGGGAATTTCTGGTTGAGGTTCTCATGCTCAGTCTCTTACATCACACTAACCTGG
upper sequence: Vv05s0020g01770.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G145709_T01 (Zea mays), 3'ss of exon 2
-----------------------------------------------------------------aatct---tttatatatggaatatgg-attgctgaataatgtta--atcactgtgtctcatctggtatttattgatttttggt-tcaatgaattattgtatttgcagGTAGTTGCTGTGAAACAACTTGACCGAAATGGCCTTCAAGGAAATAGAGAATTCTTGGTGGAGGTTCTCATGCTTAGCCTCTTACATCACCCAAACCTTG
||| || | | || | || |||| |||| || || || | | | | | ||| | | | | || | | || || |||| |||||||||||||||||||| || ||||| || |||||||| || ||||| |||| |||||||||||||| || |||||||||||| | ||||| |
gtaagtatctcttaaacatgatgcatcgacattttatctgtgaagctaaatccttccaaatttggcttctgagttgaaacattaagtaaaatattggaaggaaatgctaacataacgattatacttaagccctggattagtcctggatactaacagagttttac-ttcccagGCTGTTGCTGTGAAACAACTTGATCGTAATGGTCTCCAAGGAAACAGGGAATTTCTGGTTGAGGTTCTCATGCTCAGTCTCTTACATCACACTAACCTGG
upper sequence: Vv05s0020g01770.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G074381_T01 (Zea mays), 3'ss of exon 2
aatcttttatatatggaatatggattgct---gaataatgttaatcactgtgtctcatctggtatttattgatttttggttcaatgaattattgtatttgcagGTAGTTGCTGTGAAACAACTTGACCGAAATGGCCTTCAAGGAAATAGAGAATTCTTGGTGGAGGTTCTCATGCTTAGCCTCTTACATCACCCAAACCTTG
| | | || ||| || || | | || ||| | | | | | | | ||| ||| | | | | || || | || | || |||||| ||||| || ||||||||||| | |||||| |||||||| || ||||||||| | ||||||||||||||||| | |||| | |||||||| || ||||
tcgttgtgctgattgcaatgtgagctgtttcaaactattgtaacttaatttttgttttcta-tatatgtctaatgctgctttagctt-ttgctacatg-gcagGTTGTTGCAGTCAAACAACTTGATCTAAATGGGCTTCAAGGGAACAGAGAATTCCTCGTGGAGGTTCTCATGCTCAACCTCCTGCATCACCCTAATCTTG
upper sequence: Vv05s0020g01770.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G177061_T01 (Zea mays), 3'ss of exon 1
--------------------------------------------aatcttttatatatggaat-atggattgctgaataatgttaatcact---gtgtctcatctggt--atttattgat-ttttggttcaatgaattattgtatttgcagGTAGTTGCTGTGAAACAACTTGACCGAAATGGCCTTCAAGGAAATAGAGAATTCTTGGTGGAGGTTCTCATGCTTAGCCTCTTACATCACCCAAACCTTG
|| || ||||| | | || | || | || | |||| | |||| ||| ||| || ||| || | | |||| |||||||||| |||||||| ||||||| ||||||||||| | |||||| | ||||||||||||||||| || ||||| || || || || || |
gtttgctaacatttgctgattgtgttgtaatttctgtacactgcaaatttggatatagagtctcattaagaagaaaaagggagaagtcccctgagtgttctaattggttgattgcctgacaccttcgtttttcatcttctatcttgcatagGTCATTGCTGTGAAGCAACTTGATAGAAATGGTTTTCAAGGAAATCGTGAATTCCTTGTGGAGGTTCTCATGCTAAGTCTCTTGCACCATCCTAATCTGG
upper sequence: Vv05s0020g01770.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G140590_T06 (Zea mays), 3'ss of exon 1
------------------------------------aatcttttatatatggaata---tggattgctgaataatgttaatcactgtgtctcatctggtatttattgatttttggttcaatgaattattgtatt-tgcagGTAGTTGCTGTGAAACAACTTGACCGAAATGGCCTTCAAGGAAATAGAGAATTCTTGGTGGAGGTTCTCATGCTTAGCCTCTTACATCACCCAAACCTTG
|| ||| ||||| || || ||| ||| ||| || | || | | || | | | | || || | | || ||||||| ||||| ||||| |||||||| || ||||||||||||||||| || || || |||| |||||||| |||||||| || || || || || || |
gtttgtgattcaaaatgctttgatgcttccgtattccatttttcttatattgaccctcttgtattttatgatatggttgatatataggtaagaatacattttcttcagtgtaacacttaaccaa--actacatcgtgcagGTTGTTGCAGTGAAGCAACTTGATCGCAATGGCCTTCAAGGAAACAGGGAGTTTCTGGTTGAGGTTCTAATGCTTAGTCTGTTGCACCATGACAATCTAG
upper sequence: Vv05s0020g01770.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G048210_T02 (Zea mays), 3'ss of exon 2
--------------------------------------------aatcttttatatatggaat-atggattgctgaataatgttaatcact--gtgtctcatctggt--atttattgat-ttttggttcaatgaattattgtatttgcagGTAGTTGCTGTGAAACAACTTGACCGAAATGGCCTTCAAGGAAATAGAGAATTCTTGGTGGAGGTTCTCATGCTTAGCCTCTTACATCACCCAAACCTTG
|| || ||||| | | || | || | | || |||| | |||| ||| ||| || ||| || | | |||| |||||||||| |||||||| ||||||| ||||||||||| | ||||| | ||||||||||||||||| || ||||| || || || || || |
gtttgctaacatttgctgattgtgttgtaatttctgtacactgcaaatttggatataaagtctcattaagaagaaaagggagaagtcccctgagtgttctaattggttgattgcctgacaccttcgtttttcatcttctatcttgcatagGTCATTGCTGTGAAGCAACTTGATAGAAATGGTTTTCAAGGAAATCGTGAATTTCTTGTGGAGGTTCTCATGCTAAGTCTCTTGCACCATCCTAATCTGG
upper sequence: Vv05s0020g01770.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA13G28730.1 (Glycine max), 3'ss of exon 2
-aatcttttatata-tggaatatggattgctgaataatg-ttaatcactgtgtctcatctggtatttattgatttttggttcaatgaattattgtatttgcagGTAGTTGCTGTGAAACAACTTGACCGAAATGGCCTTCAAGGAAATAGAGAATTCTTGGTGGAGGTTCTCATGCTTAGCCTCTTACATCACCCAAACCTTG
| | | | | | | | | || ||| || || | | ||| | ||| | | ||| | |||||| | | ||| ||| | ||||||||||||||||| ||||| |||||||||||||| |||||||||||| |||| || |||||||| ||||| ||||| || ||||| ||||| ||||| ||||
aagttatctgtctgctctcaattttcctgttgattattgctctgttactataactctgcc--tctttcataatttttaatg-atgaaatcattctcgttgcagGTAGTTGCTGTAAAACAGCTTGACCGAAATGGTCTTCAAGGAAATCGAGAGTTTTTGGTGGAAGTTCTTATGCTCAGTCTCTTGCATCATCCAAATCTTG
upper sequence: Vv05s0020g01770.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA15G10360.1 (Glycine max), 3'ss of exon 2
-aatcttttatata-tggaatatggattgctgaataatg-ttaatcactgtgtctcatctggtatttattgatttttggttcaatgaattattgtatttgcagGTAGTTGCTGTGAAACAACTTGACCGAAATGGCCTTCAAGGAAATAGAGAATTCTTGGTGGAGGTTCTCATGCTTAGCCTCTTACATCACCCAAACCTTG
| | ||| | | ||||| | ||| || || | | ||| | || | | ||| | || || || | ||| ||| | || |||||| |||||||| ||||| |||||||||||||| |||||||||||| |||| || |||||||| ||||| ||||| || ||||| ||||| ||||| ||||
aagttatttgtctgctggaaattttcccattgattattgctctgttactataactatgcc--tctttcgtaatcttca-ttaatgaaatcattctcttcgcagGTGGTTGCTGTAAAACAGCTTGACCGAAATGGTCTTCAAGGAAATCGAGAGTTTTTGGTGGAAGTTCTTATGCTCAGTCTCTTGCATCATCCAAATCTTG
upper sequence: Vv05s0020g01770.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: EFJ25419 (Selaginella moellendorffii), 3'ss of exon 2
aatcttttatatatggaatatggattgctgaataatgttaatcactg-tgtctcatctggtatttattgatttttggttcaatgaattattgtatttgcagGTAGTTGCTGTGAAACAACTTGACCGAAATGGCCTTCAAGGAAATAGAGAATTCTTGGTGGAGGTTCTCATGCTTAGCCTCTTACATCACCCAAACCTTG
| || | | || | | | | ||| | |||| ||| || | ||| || | | |||||| || || ||||| || || || |||| || ||||||||||| ||||||||||||||||| ||||| ||||| ||| | | || || ||||| || |
----------gttcggtgttcttgctctcttgcaaaaccagttttttctttcttgtttggt-tttgttc-taacaagttttcctccttccaacact-gcagGTTGTGGCAGTGAAGCAGCTGGATAGAAACGGACTTCAAGGAAACAGAGAATTCTTGGTGGAAGTTCTGATGCTCAGCTTGCTTCACCATCCAAATCTCG
upper sequence: Vv05s0020g01770.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: EFJ23436 (Selaginella moellendorffii), 3'ss of exon 2
aatcttttatatatggaatatggattgctgaataatgttaatcact-gtgtctcatctggtatttattgatttttggttcaatgaattattgtattt--------gcagGTAGTTGCTGTGAAACAACTTGACCGAAATGGCCTTCAAGGAAATAGAGAATTCTTGGTGGAGGTTCTCATGCTTAGCCTCTTACATCACCCAAACCTTG
| | | | || || || | | | | | || || ||||| | || |||| | | || |||||| || || ||||| || || || |||| || ||||||||||| ||||||||||||||||| ||||| ||||| ||| | | || || ||||| || |
--------------------------gttcggtgttcttgctctcttgcaagttttttctttcttgtttggttttg-tctaacaaattttcctccttccaacactgcagGTTGTGGCAGTGAAGCAGCTGGATAGAAACGGACTTCAAGGAAACAGAGAATTCTTGGTGGAAGTTCTGATGCTCAGCTTGCTTCACCATCCAAATCTCGMapped 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|30302616|gb|CB979410.1|CB979410EST: AAGGAGGGTTTGGGCGTGTTTACAAAGGTCGCTTAGAGAGCACTGGACAA GTAGTTGCTGTGAAACAACTTGACCGAAATGGCCTTCAAGGAAATAGAGAA
genomic: AAGGAGGGTTTGGGCGTGTTTACAAAGGTCGCTTAGAGAGCACTGGACAAgtaagctatg ... gtatttgcagGTAGTTGCTGTGAAACAACTTGACCGAAATGGCCTTCAAGGAAATAGAGAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtgtctcatctggtatttattgatttttggttcaatgaattattgtatttgcagGTAGTTGCTGTGAAACAACTTGACCGAAATGGCCTTCAAGGAAATAGAGAATTCTTGGTGGAGGTTCTCATGCTTAGCCTCTTACATCACCCAAACCTTG
tattgat putative branch site (score: 3)
aatgaattattgtatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aatcttttatatatggaatatggattgctgaataatgttaatcactgtgtctcatctggtatttattgatttttggttcaatgaattattgtatttgcagGTAGTTGCTGTGAAACAACTTGACCGAAATGGCCTTCAAGGAAATAGAGAATTCTTGGTGGAGGTTCTCATGCTTAGCCTCTTACATCACCCAAACCTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - -tgctgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caatgaa