Sequence
atgc intronic sequence ATGC exonic sequence...ttatcaaaaaaagaatttttttttctagtagatattctttgtaagaggaaacaaaagcaaacaagaaatagatttaaaattgtcactttgtatggtgcagGTTTCATCTCCAACAATCATTGTTGAAAGAGCAGGATCTTATGCCTGGACACACAAAAGCTGGAGAGTTCGAGAAGAGTTTGCTCGGACTGTCACATCAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv07s0005g05010.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os02g40430.1 (Oryza sativa), 3'ss of exon 1
-ttatcaaaaaaagaatttttttttctagtagatattctttgtaagaggaaacaaaagcaaacaagaaatagatttaaaattgtcactttgtatggtg-cagGTTTCATCTCCAACAATCATTGTTGAAAGAGCAGGATCTTATGCCTGGACACACAAAAGCTGGAGAGTTCGAGAAGAGTTTGCTCGGACTGTCACATCAG
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ttttccaatgttaatattcatttatattcttatggacctttatg-gttctgatattattttgcggggtatac-taagctgtttttactctctacattctcagGTTTCATCACCGACAATCATTGTTGAAAGAGCTGGAAGTTATGCATGGACTCACAAGAGCTGGAGGGTGCGGGAAGAATTTGTACGCACTGTTGCAACAG
upper sequence: Vv07s0005g05010.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os04g42840.1 (Oryza sativa), 3'ss of exon 1
--ttatcaaaaaa---agaatttttttttctagtagatattctttgtaagaggaaacaaaagcaaacaagaaatagatttaaaattgtcactttgtatggtgcagGTTTCATCTCCAACAATCATTGTTGAAAGAGCAGGATCTTATGCCTGGACACACAAAAGCTGGAGAGTTCGAGAAGAGTTTGCTCGGACTGTCACATCAG
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attcatcctatgatttgaaaggaccaatccaaacatgtttgtcttattatcagggttttggattattggcagctaaccttttaat-----ctatctgtatctcagGTTTCTTCGCCGACAATCATAGTTGAAAGAGCTGGAAGTTATGCATGGACTCACAAGAGTTGGAGGGTCCGGGAAGAGTTTGTACGTACAGTGGCAACCG
upper sequence: Vv07s0005g05010.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G052078_T01 (Zea mays), 3'ss of exon 1
ttatcaaaaaaagaatttttttttctagtagatattctttgtaagaggaaacaaaagcaaac----aagaaatagatttaaaat--tgtcactttgtatggtgcagGTTTCATCTCCAACAATCATTGTTGAAAGAGCAGGATCTTATGCCTGGACACACAAAAGCTGGAGAGTTCGAGAAGAGTTTGCTCGGACTGTCACATCAG
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------catatgtactttcgtcctttgattatcaaagcattcaagcctagatgtttgcttgttttaaagttatcgtcttgaaatattttgtttttgtccaactcagGTTTCTTCACCAACAATCATAGTTGAAAGAGCTGGTAGTTATGCATGGACTCATAAGAGTTGGAGGGTGCGGGAAGAGTTTGTACGTACGGTGGCAACTG
upper sequence: Vv07s0005g05010.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA19G35460.1 (Glycine max), 3'ss of exon 1
-ttatcaaaaaaagaattttttt-ttctagtagatattctttgtaagaggaaacaaaagcaaacaagaaatagatttaaaattgtcactttgtatggtgcagGTTTCATCTCCAACAATCATTGTTGAAAGAGCAGGATCTTATGCCTGGACACACAAAAGCTGGAGAGTTCGAGAAGAGTTTGCTCGGACTGTCACATCAG
| ||| | | | | | || | | ||| | | || || | | | | || | ||| || ||| |||||||||| ||||| ||||| ||||||||||||||||| || | ||| ||| |||| ||||||||||||||| ||||||||||| | || |||||||| | |
aagagtaaaggtgaagtaaatatgtcctgattgtaattttgaaaatgatacttttttagtaccttgcattttgcattcattttg--gattattattatgcagGTTTCTTCTCCTACAATAATTGTTGAAAGAGCAGGGTCCTTTGCTTGGGCACATAAAAGCTGGAGAGTTAGAGAAGAGTTTACACGAACTGTCACGGCTG
upper sequence: Vv07s0005g05010.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA13G19230.1 (Glycine max), 3'ss of exon 1
-ttatcaaaaaaagaatttttttttctagtagatattctttgtaagaggaaacaaaagcaaacaagaaatagatttaaaattgtcactttgtatggtgcagGTTTCATCTCCAACAATCATTGTTGAAAGAGCAGGATCTTATGCCTGGACACACAAAAGCTGGAGAGTTCGAGAAGAGTTTGCTCGGACTGTCACATCAG
| | || | |||| | | |||| | || || | || | ||| | ||| || ||| | |||||||||||||| ||||| ||||||||||||||||| || | ||| |||||| ||||||||||||||| |||| || ||||| || || |||||||| |
ttcactgtcccctcaagctgattttgttgcagatttaaatttaaattccgggtattgttgaattttctttcattttgagatttattattattatt-tacagGTTTCATCTCCTACAATAATTGTTGAAAGAGCAGGGTCCTTTGCATGGACAAGCAAAAGCTGGAGAGTCAGAGAGGAATTTGCGCGAACAGTCACATCTG
upper sequence: Vv07s0005g05010.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA03G32710.1 (Glycine max), 3'ss of exon 1
---ttatcaaaaaaagaatttttttttctagtagatattctttgtaagaggaaacaaaagcaaacaagaaatagatttaaaattgtcactttgtatggtgcagGTTTCATCTCCAACAATCATTGTTGAAAGAGCAGGATCTTATGCCTGGACACACAAAAGCTGGAGAGTTCGAGAAGAGTTTGCTCGGACTGTCACATCAG
| | | || | | |||| | |||||| ||| || ||| || | ||| ||| ||| | | ||| |||||||||| ||||| ||||| ||||||||||||||||| || | ||| ||| |||| |||||||||||||| |||| |||||| | || |||||| || | |
aagtaaatatgtcctgattgtaattttgaaaatgatatttttt-tagtccttgcgttttgcattcattttggattattattattatcattat-tata-tgcagGTTTCTTCTCCTACAATAATTGTTGAAAGAGCAGGGTCCTTTGCTTGGGCACATAAAAGCTGGAGAGTCAGAGAGGAGTTTACACGAACTGTCGCAGCTG
upper sequence: Vv07s0005g05010.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA10G04850.1 (Glycine max), 3'ss of exon 1
ttatcaaaaaaagaatttttttttctagtagatattctttgtaagaggaaacaaaagcaaacaagaaatagatttaaaattgtcactttgtatggt--gcagGTTTCATCTCCAACAATCATTGTTGAAAGAGCAGGATCTTATGCCTGGACACACAAAAGCTGGAGAGTTCGAGAAGAGTTTGCTCGGACTGTCACATCAG
| | | | |||| | |||| | || || | || | || | ||| | ||| ||| | |||||||||||||| ||||| ||||||||||||||||| || | ||| |||||| || |||||||||||| |||| || ||||| || || |||||||| |
ctgttttcttggggctggttttgct--gcagatttaaatttaaattctggctattgttgaatttcctttcatttggagattttttttttttattatttacagGTTTCATCTCCTACAATAATTGTTGAAAGAGCAGGGTCCTTTGCTTGGACAAGCAGAAGCTGGAGAGTCAGAGAGGAATTTGCACGAACAGTCACATCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aggaaacaaaagcaaacaagaaatagatttaaaattgtcactttgtatggtgcagGTTTCATCTCCAACAATCATTGTTGAAAGAGCAGGATCTTATGCCTGGACACACAAAAGCTGGAGAGTTCGAGAAGAGTTTGCTCGGACTGTCACATCAG
aaacaagaaatagatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttatcaaaaaaagaatttttttttctagtagatattctttgtaagaggaaacaaaagcaaacaagaaatagatttaaaattgtcactttgtatggtgcagGTTTCATCTCCAACAATCATTGTTGAAAGAGCAGGATCTTATGCCTGGACACACAAAAGCTGGAGAGTTCGAGAAGAGTTTGCTCGGACTGTCACATCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - -aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - aaacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - gcaaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaataga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaattg