Sequence
atgc intronic sequence ATGC exonic sequence...atcattagtttataggtctacttgcatgcttagattgttatttttttcttttattttttattttgtgtatggtttcattatttttcaatacaatctgcagGTAGCTGTTGGTGATGTTATATATGTTGAAGCCAATAGTGGAGCTGTTAAAAGGGTGGGCAGAAGTGATGCTTTTGCTACAGAATTTGACCTTGAGGCGG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv06s0004g02910.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os07g08170.1 (Oryza sativa), 3'ss of exon 4
atcattagtttataggtctacttgcatgcttagattgttatttttttcttttattttttattttg--tgtatggtttcattatttttcaatacaatctgcagGTAGCTGTTGGTGATGTTATATATGTTGAAGCCAATAGTGGAGCTGTTAAAAGGGTGGGCAGAAGTGATGCTTTTGCTACAGAATTTGACCTTGAGGCGG
||| | | | | | | || || ||||| | | || ||| ||||||| | ||| | || ||| | | | || || |||||| | || |||||||||||||| ||||||| |||||||| || || ||||| || || ||| ||||||||||||||||||||| || ||||| || |
atcgtgaagctgattagatgccttgatactgagattcacttctgttacttccattttttgcactagttgtttcattacatcagtgatacatgggat--gcagGTGTCAGTGGGTGATGTTATATACATTGAAGCTAATAGTGGTGCGGTCAAAAGAGTTGGTAGATGTGATGCTTTTGCTACAGAATACGATCTTGAAGCTG
upper sequence: Vv06s0004g02910.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os01g62040.1 (Oryza sativa), 3'ss of exon 4
atcattagtttataggtctacttgcatgcttagattgttatttttttcttttattttttatttt--gtgtatggt-ttcattatttttcaa-tacaatctgcagGTAGCTGTTGGTGATGTTATATATGTTGAAGCCAATAGTGGAGCTGTTAAAAGGGTGGGCAGAAGTGATGCTTTTGCTACAGAATTTGACCTTGAGGCGG
|| | || | || | | || ||||| | | | || ||| ||||| | ||| | | || || || | | ||||||| || || |||||||||||||| ||||||| |||||||| || || ||||| || || ||| ||||| ||||||||||||||| || ||||| || |
---tggagctgattagatccctcg-gtactgagattcatttctgttacttccattttctgcacaagatgtttcatatttatcatcagctatctgtgggatgcagGTGGCAGTGGGTGATGTTATATACATTGAAGCTAATAGTGGTGCAGTGAAAAGAGTTGGTAGATGTGATTCTTTTGCTACAGAATACGATCTTGAAGCTG
upper sequence: Vv06s0004g02910.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os01g62040.3 (Oryza sativa), 3'ss of exon 4
atcattagtttataggtctacttgcatgcttagattgttatttttttcttttattttttattttgtgtatggtttcattatttttcaatacaatctgcagGTAGCTGTTGGTGATGTTATATATGTTGAAGCCAATAGTGGAGCTGTTAAAAGGGTGGGCAGAAGTGATGCTTTTGCTACAGAATTTGACCTTGAGGCGG
|||| || | | ||||| || | || | || || ||| | |||| | | || | || |||||| || || |||||||||||||| ||||||| |||||||| || || ||||| || || ||| ||||| ||||||||||||||| || ||||| ||
-----------------gtactgagattcattt-ctgttacttccattttctgcacaagatgtttcatatt-tatcatcagctatctgtgggat--gcagGTGGCAGTGGGTGATGTTATATACATTGAAGCTAATAGTGGTGCAGTGAAAAGAGTTGGTAGATGTGATTCTTTTGCTACAGAATACGATCTTGAAGCT-
upper sequence: Vv06s0004g02910.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G032267_T02 (Zea mays), 3'ss of exon 4
-atcattagtttataggtctacttgcatgcttagattgttatttttttcttttattttttatt-ttgtgtatggtt--tcattatttttcaatacaatctgcagGTAGCTGTTGGTGATGTTATATATGTTGAAGCCAATAGTGGAGCTGTTAAAAGGGTGGGCAGAAGTGATGCTTTTGCTACAGAATTTGACCTTGAGGCGG
| | ||| | | | | | | | | | || | | ||||| |||| | || ||| | |||| ||||| | | | || | | |||| || || |||||||||||||| ||||||| ||||||||||| || ||||| || || ||| ||||| ||||||||||||||| ||| ||||| || |
gctgagtagctccttaaac-attgagttaccttatctattctgtatttctgttatctgcatttgttgctttaggttactcattgtctgcctatgga---tatagGTGGCAGTGGGTGATGTTATATACATTGAAGCAAATAGTGGAGCAGTGAAAAGAGTTGGTAGATGTGATTCTTTTGCTACAGAATATGATCTTGAAGCTG
upper sequence: Vv06s0004g02910.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G018697_T02 (Zea mays), 3'ss of exon 4
-atcattagtttataggtctacttgcatgcttagattgttatttttttcttttattttttattttgtgtatggtttcattatttttcaataca-atctgcagGTAGCTGTTGGTGATGTTATATATGTTGAAGCCAATAGTGGAGCTGTTAAAAGGGTGGGCAGAAGTGATGCTTTTGCTACAGAATTTGACCTTGAGGCGG
|| | | | | || |||||| || | || | | | | | || | || |||| || | | | | || || | | | |||| || || |||||||||||||| | ||||| ||||||||||| || ||||| || || ||| ||||| ||||||||||||||| || ||||| || |
cattgagaaaatgcac-tatatttgcat-tttgggttactgtatctattttgctatcttcatttgttgctttacgttactcattatctgcatatggatatagGTGGCAGTGGGTGATGTTATATACATCGAAGCAAATAGTGGAGCAGTGAAAAGAGTTGGTAGATGTGATTCTTTTGCTACAGAATACGATCTTGAAGCTG
upper sequence: Vv06s0004g02910.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA07G02170.1 (Glycine max), 3'ss of exon 4
----------------------------------------------------------------------atcattagtttataggtctactt-gcatgcttagattgttatttt-----tttcttttattttttattttgtgtatggtttcattattt----ttcaatacaatctgcagGTAGCTGTTGGTGATGTTATATATGTTGAAGCCAATAGTGGAGCTGTTAAAAGGGTGGGCAGAAGTGATGCTTTTGCTACAGAATTTGACCTTGAGGCGG
| |||| ||| | ||| || | ||| | || | |||| | | | ||||| | | || | | | |||| || |||| | |||||||||||||| ||||| ||||| |||| || |||||||| ||||| ||||||||||| |||| |||||||||||||| || ||||||||||| || |
gtgaggtttctgaaattatttcctcttgttctttgtgtgcttctgtctttacaagttataaatttcttttcttattattttttttttcttttttgtatgatgctgttttagttttaaagctgtgtgatatttgtgtcaacaaatgtgatgttttgatttgggatttctgccaatgtacagGTAGCTGTTGGGGATGTAATATACATTGAGGCAAATAGTGGGGCTGTAAAAAGGGTGGGTCGAAGCGATGCTTTTGCTACCGAGTTTGACCTTGAAGCAG
upper sequence: Vv06s0004g02910.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA08G21830.1 (Glycine max), 3'ss of exon 4
---------------------------------------------------------------------------atcattagtttatagg--tctacttgcatgcttagattgttatttttttcttttattttttattttgtgtatggtttcattatttttcaatacaatctgcagGTAGCTGTTGGTGATGTTATATATGTTGAAGCCAATAGTGGAGCTGTTAAAAGGGTGGGCAGAAGTGATGCTTTTGCTACAGAATTTGACCTTGAGGCGG
|| ||| ||| || | || || | | | |||| | ||| | | | | | ||| |||| || |||||| ||| | ||| |||||||||| ||||||||||| |||| || ||||| || ||||| ||||||||||| ||||||||||||| |||||||| ||||||||||| || |
gtgaggtctctaatttcctcttgttctgtgtgtgctccattgtgtaactaagatattgcaagttataaatttcttttctttattttgtatgaagctgttttagttttgaagttgtgtaatatttgtgtcaacaaatctgatgt-tatgattgggggatttttgccaacatgc--cagATAGCTGTTGGCGATGTTATATACATTGAGGCAAATAGCGGGGCTGTAAAAAGGGTGGGTCGAAGTGATGCTTTCGCTACAGAGTTTGACCTTGAAGCTG
upper sequence: Vv06s0004g02910.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT5G22330.1 (Arabidopsis thaliana), 3'ss of exon 4
------atcattagtttataggtctacttgcatgcttagattgttatttttttcttttattttttattttgtgtatggtttcattatttttcaatacaatctgcagGTAGCTGTTGGTGATGTTATATATGTTGAAGCCAATAGTGGAGCTGTTAAAAGGGTGGGCAGAAGTGATGCTTTTGCTACAGAATTTGACCTTGAGGCGG
| | | | | || | ||| | | ||| | | || |||| || | || || | | ||| || |||| | | ||||||||||| || ||||| || ||| | ||||| || ||||||||||| ||| |||| || ||||||||||||||||| || |||||||| || || || |
tctaacgatgtcattctgtggggacaattgtgta--tgaatt--tgctgattactttgtcattctgattggtttct--ttttatatttttgctgtttgcctctcagGTAGCTGTAGGAGATGTAATCTATATCGAAGCAAACAGTGGAGCTGTCAAACGGGTAGGTAGAAGTGATGCTTTTGCCACTGAATTTGATCTGGAAGCAG
upper sequence: Vv06s0004g02910.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: PP1S4_73V6.1 (Physcomitrella patens), 3'ss of exon 5
------------------------atcattagtttataggtctacttgcatgcttagattgttatttttttcttttattttttattttgtgtatggtttcattatttttcaatacaa--------tctgcagGTAGCTGTTGGTGATGTTATATATGTTGAAGCCAATAGTGGAGCTGTTAAAAGGGTGGGCAGAAGTGATGCTTTTGCTACAGAATTTGACCTTGAGGCGG
| | | | | | |||| | |||| || ||| |||| || || | | | | || ||| || | || |||| ||||||||||| || || |||||||||| || ||||| || || ||||| || ||||||||||| ||||| ||||| |||||| | || || |
gtaagcgttgttctgttcacagtcagaactgaatgagtaggaaacttatcgagaaatattgacatgctttcaagaacggtttttcttcacgtttcaatcccaaacattctaatgtaacgcatggttgtgaagGTGCTGGTTGGTGATGTGATTTACATTGAAGCCAACAGCGGAGCAGTGAAGAGGGTTGGGAGAAGTGATGCCTTTGCCACAGAGTTTGACTTGGAAGCAGMapped 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|71863654|gb|DT012709.1|DT012709EST: AGCAGCTGAAGTTGGACCCAACTATTTATGATGCTTTGATTAAGGAGAAG GTAGCTGTTGGTGATGTTATATATGTTGAAGCCAATAGTGGAGCTGTTAAA
genomic: AGCAGCTGAAATTGGACCCAACTATTTATGATGCTTTGATTAAGGAGAAGgtgaggtctt ... caatctgcagGTAGCTGTTGGTGATGTTATATATGTTGAAGCCAATAGTGGAGCTGTTAAA
EST:
gi|71865178|gb|DT014233.1|DT014233EST: AGCAGCTGAAGTTGGACCCAACTATTTATGATGCTTTGATTAAGGAGAAG GTAGCTGTTGGTGATGTTATATATGTTGAAGCCAATAGTGGAGCTGTTAAA
genomic: AGCAGCTGAAATTGGACCCAACTATTTATGATGCTTTGATTAAGGAGAAGgtgaggtctt ... caatctgcagGTAGCTGTTGGTGATGTTATATATGTTGAAGCCAATAGTGGAGCTGTTAAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcttttattttttattttgtgtatggtttcattatttttcaatacaatctgcagGTAGCTGTTGGTGATGTTATATATGTTGAAGCCAATAGTGGAGCTGTTAAAAGGGTGGGCAGAAGTGATGCTTTTGCTACAGAATTTGACCTTGAGGCGG
ttattttttattttgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atcattagtttataggtctacttgcatgcttagattgttatttttttcttttattttttattttgtgtatggtttcattatttttcaatacaatctgcagGTAGCTGTTGGTGATGTTATATATGTTGAAGCCAATAGTGGAGCTGTTAAAAGGGTGGGCAGAAGTGATGCTTTTGCTACAGAATTTGACCTTGAGGCGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - -gcatgct