Sequence
atgc intronic sequence ATGC exonic sequence...tgaatcaaaacggacaatatctacacagtttttattttataaggtgttcgggttttatatgtttatggtctcatgccatgatatgtcatgtatgatatagATGAGCAACTACTCTTCCATGGATGGAGTCTTGTACTGCAAGCCTCATTTTGAGCAACTCTTCAGGGAATCTGGCAGTTTGAGTAAGAAGTTCCAATCAT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv02s0025g03980.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os02g42820.1 (Oryza sativa), 3'ss of exon 1
-------tgaatcaaaacggacaatatctacacagttttta--ttttataaggtgttcgggttttatatgtttatggtctcatgccatgatatgtcatgtatgatatagATGAGCAACTACTCTTCCATGGATGGAGTCTTGTACTGCAAGCCTCATTTTGAGCAACTCTTCAGGGAATCTGGCAGTTTGAGTAAGAAGTTCCAATCAT
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gtatgtatatatggcatcgatcggc-cctgcaacatgttcagtttttattaggtaattaaatcaactat---cacatttttcgttcaaaacat-ttacgcatc-tgcagATGTGTAACTACTCTTCGATGGATGGTGTCCTGTACTGCAAGACGCACTTTGAGCAGCTCTTCAAAGAGACGGGGAGCTTCTCAAAGAAATTCTCGCAAG
upper sequence: Vv02s0025g03980.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G170034_T02 (Zea mays), 3'ss of exon 1
----------------------------------------------------------------------------------tgaatcaaaacggac-aatatctacacagtttttattttataaggtgttcgggt---tttatatgtttatggtctcatgccatgatatgt---catgtatgatatagATGAGCAACTACTCTTCCATGGATGGAGTCTTGTACTGCAAGCCTCATTTTGAGCAACTCTTCAGGGAATCTGGCAGTTTGAGTAAGAAGTTCCAATCAT
|| ||| ||| || || | | || | || | | | | | | || || |||||||| | || | | || | | |||| |||| ||||||||||||||| || ||| ||||||||||| | || ||||| || ||||||| ||| | || | || ||||| || |||
gtatgcatgcgtggcctgagctcaactccgcatgcgcattcgccctgcttgcgatgtgtgcggcaatgcgctaatgctcatttgcatcgaaagaaacgaagctttgtttgattcggttcagatcatctcgacagatgaacatgtagaaatacggtctcattttttcatttctgcatgcgtctcctccagATTAGCAGCTACTCTTCCATGGACGGCGTCCTGTACTGCAAGACGCACTTTGAACAGCTCTTCAAGGAGACAGGGACCTTCTCAAAGAACTTTCAAGGTA
upper sequence: Vv02s0025g03980.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G170034_T01 (Zea mays), 3'ss of exon 1
----------------------------------------------------------------------------------tgaatcaaaacggac-aatatctacacagtttttattttataaggtgttcgggt---tttatatgtttatggtctcatgccatgatatgt---catgtatgatatagATGAGCAACTACTCTTCCATGGATGGAGTCTTGTACTGCAAGCCTCATTTTGAGCAACTCTTCAGGGAATCTGGCAGTTTGAGTAAGAAGTTCCAATCAT
|| ||| ||| || || | | || | || | | | | | | || || |||||||| | || | | || | | |||| |||| ||||||||||||||| || ||| ||||||||||| | || ||||| || ||||||| ||| | || | || ||||| || |||
gtatgcatgcgtggcctgagctcaactccgcatgcgcattcgccctgcttgcgatgtgtgcggcaatgcgctaatgctcatttgcatcgaaagaaacgaagctttgtttgattcggttcagatcatctcgacagatgaacatgtagaaatacggtctcattttttcatttctgcatgcgtctcctccagATTAGCAGCTACTCTTCCATGGACGGCGTCCTGTACTGCAAGACGCACTTTGAACAGCTCTTCAAGGAGACAGGGACCTTCTCAAAGAACTTTCAAG--- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttcgggttttatatgtttatggtctcatgccatgatatgtcatgtatgatatagATGAGCAACTACTCTTCCATGGATGGAGTCTTGTACTGCAAGCCTCATTTTGAGCAACTCTTCAGGGAATCTGGCAGTTTGAGTAAGAAGTTCCAATCAT
ttttatatgtttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgaatcaaaacggacaatatctacacagtttttattttataaggtgttcgggttttatatgtttatggtctcatgccatgatatgtcatgtatgatatagATGAGCAACTACTCTTCCATGGATGGAGTCTTGTACTGCAAGCCTCATTTTGAGCAACTCTTCAGGGAATCTGGCAGTTTGAGTAAGAAGTTCCAATCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- aatcaaa
- - - - - - - - - - ctacaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcatgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtcatg