Sequence
atgc intronic sequence ATGC exonic sequence...tcaaaatttttgcatctgaatattcttatatatgccaatgtccattatctgtcatatgtccatggccttcggtgttaaataatgtatttcttttctctagATTATCCTGTCTATCACACTGCTTTCGATTCCTATAACTGGATGACAAAGTTTGGAGATCCATTCTTTCAGCGCCATGAAGCTG
Basic information
species | Glycine max |
transcript | GLYMA10G11100.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G11100.1 (Glycine max), 3'ss of exon 6
lower sequence: AT3G54720.1 (Arabidopsis thaliana), 3'ss of exon 5
-----tcaaaatttttgcatctgaatattcttatatatgccaatgtccattatctgtcatatgtccatggccttcggtgttaaataatgtatttcttttctct-agATTATCCTGTCTATCACACTGCTTTCGATTCCTATAACTGGATGACAAAGTTTGGAGATCCATTCTTTCAGCGCCATGAAGCTG
| | || | | | | || | |||| | | | | | | | || | || ||| || ||| | || ||||| | |||||||||||||||||||||||| || || |||||| | ||||||| | | ||||||||| ||||| || |||| |||
gtcaatgagaacatgattccttaagtcttgcaaaatattctataatgtgatgttt-taatgcaagtaataccaataatgt---atgttgtttatcctttctttcagATTATCCTGTCTATCACACTGCATTTGACTCCTATGATTGGATGATCCACAACGCAGATCCATTGTTTCACCGTCATGTTGCTA
upper sequence: GLYMA10G11100.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv00s0319g00060.t01 (Vitis vinifera), 3'ss of exon 4
-tcaaaatttttgcatctgaatattcttatatatgccaatgtccattatctgtcatatgtccatggccttcggtgttaaataatgtatttcttttctct---agATTATCCTGTCTATCACACTGCTTTCGATTCCTATAACTGGATGACAAAGTTTGGAGATCCATTCTTTCAGCGCCATGAAGCTG
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gtcaataatgtta-gtagtaaaatttacatcacaattaagatttcatgctaatca---atttggtaaaatagaacttcaactttctttttcttttgtccttgagATTTTCCAGTCTATCACACTGCTTTTGACTCCTATAACTGGATGACAAACCATGGGGATCCATTGTTTCAACGTCACGTGGCTG
upper sequence: GLYMA10G11100.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv08s0032g00670.t01 (Vitis vinifera), 3'ss of exon 5
-tcaaaatttttgcatctgaatattcttatatatgccaatgtccattatctgtca-tatgtccatggccttcggtgttaaataatgtatttctttt---ctctagATTATCCTGTCTATCACACTGCTTTCGATTCCTATAACTGGATGACAAAGTTTGGAGATCCATTCTTTCAGCGCCATGAAGCTG
|||| | | || | ||| || || || |||| ||| || | | | | | || || | | |||||||| || ||||| ||| ||||||||||||||||| || |||||| ||||||||||||| ||| |||||||| ||||| || |||| ||||
gtcaataatgttag----tagtataatt-tacatcacaattaagatttcatgctaatcaatttggtaaaatagaacttcaactttctttttcttttgtccttcagATTTTCCAGTCTATCACACTGCTTTTGACTCCTATGACTGGATGACAAACCATGGGGATCCATTGTTTCAACGTCATGTGGCTG
upper sequence: GLYMA10G11100.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv00s0285g00060.t01 (Vitis vinifera), 3'ss of exon 5
-tcaaaatttttgcatctgaatattcttatatatgccaatgtccattatctgtcatatgtccatggccttcggtgttaaataatgtatttctttt---ctctagATTATCCTGTCTATCACACTGCTTTCGATTCCTATAACTGGATGACAAAGTTTGGAGATCCATTCTTTCAGCGCCATGAAGCTG
|||| | | || | || ||| || || | | ||| | | | || || | | |||||||| || || || ||| ||||||||||||||||| || |||||||||||||||||||| ||| |||||||| ||||| || |||| ||||
gtcaataatgtta-gtagtaaaatttacatcacaattaagatttcatgctaatca---atttggtaaaatagaacttcaactttctttttcttttgtccttcagTTTTTCCAGTCTATCACACTGCTTTTGACTCCTATAACTGGATGACAAACCATGGGGATCCATTGTTTCAACGTCATGTGGCTG
upper sequence: GLYMA10G11100.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv00s0327g00020.t01 (Vitis vinifera), 3'ss of exon 4
-tcaaaatttttgcatctgaatattcttatatatgccaatgtccattatctgtcatatgtccatggccttcggtgttaaataatgtatttctttt---ctctagATTATCCTGTCTATCACACTGCTTTCGATTCCTATAACTGGATGACAAAGTTTGGAGATCCATTCTTTCAGCGCCATGAAGCTG
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gtcaataatgtta-gtagtaaaatttacatcacaattaagatttcatgctaatca---atttggtaaaatagaacttcaactttctttttcttttgtccttcagATTTTCCAGTCTATCACACTGCTTTTGACTCCTATAACTGGATGACAAACCATGGGGATCCATTGTTTCAACGTCACGTGGCTG
upper sequence: GLYMA10G11100.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv00s0352g00020.t01 (Vitis vinifera), 3'ss of exon 5
tcaaaatttttgcatctgaatattcttatatatgccaatgtccattatctgtcatatgtccatggccttcggtgttaaataatgtatttctttt---ctctagATTATCCTGTCTATCACACTGCTTTCGATTCCTATAACTGGATGACAAAGTTTGGAGATCCATTCTTTCAGCGCCATGAAGCTG
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---nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnaatagaacttcaactttcttttttttttgtccttcagATTTTCCAGTCTATCACACTGCTTTTGACTCCTATAACTGGATGACAAACCATGGGGATCCATTGTTTCAACGTCACGTGGCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatctgtcatatgtccatggccttcggtgttaaataatgtatttcttttctctagATTATCCTGTCTATCACACTGCTTTCGATTCCTATAACTGGATGACAAAGTTTGGAGATCCATTCTTTCAGCGCCATGAAGCTG
tgtatttcttttctct CT-rich tract
tgttaaataatgtatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcaaaatttttgcatctgaatattcttatatatgccaatgtccattatctgtcatatgtccatggccttcggtgttaaataatgtatttcttttctctagATTATCCTGTCTATCACACTGCTTTCGATTCCTATAACTGGATGACAAAGTTTGGAGATCCATTCTTTCAGCGCCATGAAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - -gcatctg
- - - - - - - - - - - - - - - tatgcca
- - - - - - - - - - - - - - - - - - - - - - - -tctgtca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - tccatgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggtgtta