Sequence
atgc intronic sequence ATGC exonic sequencegtaagttttatgtttcttcctatgatttaatacttccagtaatttttggactaaagtaagttttatgttttttcgtctgatttaatacttccaatatttgtatttaccttcccattctaaataatcagGCTCCTACTGGGGAAGCTTGCCTGTGTCAACTTAGAGGGTCTTACCCATCAGCAGAAGCTCGCATTTTGGATAAACATATACAATTCCTGCATGATGAAT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv00s0804g00020.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os09g28850.2 (Oryza sativa), 3'ss of exon 4
gtaagttttat---gtttcttcctatgatttaatacttccagtaatttttggactaaagtaagttttatgttttttcgtctgatttaatacttccaatatttgtatttaccttc--ccattctaaataatcagGCTCCTACTGGGGAAGCTTGCCTGTGTCAACTTAGAGGGTCTTACCCATCAGCAGAAGCTCGCATTTTGGATAAACATATACAATTCCTGCATGATGAAT
|| ||| | || | | | | || | | || ||||| || | || | | | ||| | | ||| || || || || | |||| |||| | | ||| |||| | | || || | ||| || |||||||||||||||| ||||| ||||| ||||| |||||||| ||||||||||||
gtgcgttcttgctagtgcaattttccgttcagttattacaagctcggtttggttgtctgtcgagtaggtggccgcctgacataattagcatcgctgatagaggtggttcatgtctacctggcaaaatctgcagGGCTTTGATCCGGAGGCTTTCATCGGTTGACCTGACGGGGCTCTCCCATCAGCAGAAGCTGGCATTCTGGATCAACATCTACAATTCGTGCATGATGAAT
upper sequence: Vv00s0804g00020.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G066516_T01 (Zea mays), 3'ss of exon 4
gtaagttttatgtttc-ttcctatgatttaatacttccagtaatttttggactaaagtaagttttatgttttttcgtctgatttaatacttccaatatttgtatttaccttcccattctaaataatcagGCTCCTACTGGGGAAGCTTGCCTGTGTCAACTTAGAGGGTCTTACCCATCAGCAGAAGCTCGCATTTTGGATAAACATATACAATTCCTGCATGATGAAT
|| ||| ||| ||| ||| || ||||||| | | ||| | ||| | ||| | | || | | || |||| |||| | | ||| ||| ||| | | || || | | ||| || |||||||||||||||| || || ||||| ||| | ||||||||||||||||||||
gtgagtgagttgtccgattcgtattgccgcgcgct---ggtaatttgggctgcctggcgagtgggtggcggtttggcttgaacacgcgtcgcggacgttgatcggggctgtcaa----caaatctgcagGGCCTTGCTGCGGAGGCTGTCGTCGGTTGACCTGGCGGGGCTCTCCCATCAGCAGAAGCTGGCCTTCTGGATCAACGTCTACAATTCCTGCATGATGAAC
upper sequence: Vv00s0804g00020.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA11G06130.1 (Glycine max), 3'ss of exon 4
gtaagttttatgtttcttcctatgatttaatacttccagtaatttttggactaaagtaagtttta--tgttttttcgtctgat--ttaatacttccaatatttgtatttaccttcccattctaaataatcagGCTCCTACTGGGGAAGCTTGCCTGTGTCAACTTAGAGGGTCTTACCCATCAGCAGAAGCTCGCATTTTGGATAAACATATACAATTCCTGCATGATGAAT
||||||| || | || || ||| | || ||||| | | | | | || | || ||| ||||| | ||||| ||||| ||||||| ||| ||| || ||| |||||| |||||| |||| || |||||||||||||||| ||||||||||||||| |||||
-------------------------------------------------------gtaagttataacaggttattaagctgttggttgatactatgggtgtctatctaaactaacacac-----atattcagGTTTCTACTCGGGAAACTTGCCTCTGTGAACATAAAGGATCTTACTCATCAGGAGAAACTTGCATTTTGGATAAACACTTACAATTCCTGCATGCTGAAT
upper sequence: Vv00s0804g00020.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA17G20320.1 (Glycine max), 3'ss of exon 7
gtaagttttatgtttcttcctatgatttaatacttccagtaatttttggactaaagtaagttttatgttttttcgtctgatttaatacttccaatatttgtatttaccttcccattctaaataat-cagGCTCCTACTGGGGAAGCTTGCCTGTGTCAACTTAGAGGGTCTTACCCATCAGCAGAAGCTCGCATTTTGGATAAACATATACAATTCCTGCATGATGAAT
|||| || | | || || |||| | | ||| | |||| ||| || | |||| || || | | || | ||| |||| ||||||| ||||| || |||| | | ||||| |||||||||| |||||| | || || ||||| |||||||||| |||||||||||||||||||||
----------------------------------gtaagtagttatag--ttatagacagttattaactgttttgattgat--gata------atgtaggtatctatctaatcttgctgacaaattcagGTTCCTACTTGGGAAACTAGCCTCTCTGAACTTGAAGGGTCTTACTCATCAGGAAAAACTTGCATTCTGGATAAACACTTACAATTCCTGCATGATGAATMapped 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|37183652|gb|CF603006.1|CF603006EST: GTTGATCTGAACAGAAAAACAAATGCACTGTTTCTGATCCACAGACTAAA GCTCCTACTGGGGAAGCTTGCCTGTGTCAACTTAGAGGGTCTTACCCATCA
genomic: GTTGATCTGAACAGAAAAACAAATGCACTGTTTCTGATCCACAGACTAAAgtaagtttta ... aaataatcagGCTCCTACTGGGGAAGCTTGCCTGTGTCAACTTAGAGGGTCTTACCCATCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cgtctgatttaatacttccaatatttgtatttaccttcccattctaaataatcagGCTCCTACTGGGGAAGCTTGCCTGTGTCAACTTAGAGGGTCTTACCCATCAGCAGAAGCTCGCATTTTGGATAAACATATACAATTCCTGCATGATGAAT
ttctaaa putative branch site (score: 2)
atttaatacttccaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttttatgtttcttcctatgatttaatacttccagtaatttttggactaaagtaagttttatgttttttcgtctgatttaatacttccaatatttgtatttaccttcccattctaaataatcagGCTCCTACTGGGGAAGCTTGCCTGTGTCAACTTAGAGGGTCTTACCCATCAGCAGAAGCTCGCATTTTGGATAAACATATACAATTCCTGCATGATGAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC