Sequence
atgc intronic sequence ATGC exonic sequence...tagaaagtatgttgcaattatattccaaacattattgtataaattccaagtgagatatttttctatagattcttcattattttagagtgtgtgtgtgcagAGGCTAGTGATCAAAACCAAGAGCGTGGAGTTCATGCCCTTCTTCCTCTCACTCTTTGTGTTCCTCTGTGGTACTTCTTGGTTCATCTACGGGCTACTAG
Basic information
species | Glycine max |
transcript | GLYMA14G27610.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G27610.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g65880.3 (Oryza sativa), 3'ss of exon 3
tagaaagtatgttgcaattatattccaaacattattgtataaattccaagtgagatatttttctatagattc-ttcattattttagagtgtgtg-tgtgcagAGGCTAGTGATCAAAACCAAGAGCGTGGAGTTCATGCCCTTCTTCCTCTCACTCTTTGTGTTCCTCTGTGGTACTTCTTGGTTCATCTACGGGCTACTAG
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tgggaa--atgttagaatgacttacattgtgaaacggagggagtaataactaacaaaattaaccataatctgattcgctgatcaattgactccggtgtgcagAGGCTGGTGATCAAGACGAAGAGCGTGGAGTTCATGCCGTTCCTGCTCTCCCTGTCCGTGTTCCTGTGCGGCACCTCCTGGTTCATCTACGGCCTGCTCG
upper sequence: GLYMA14G27610.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os05g35140.1 (Oryza sativa), 3'ss of exon 4
--tagaaagtatgttgcaatt---atattccaaacattattgtataaattccaagtgagatatttttctatagattcttcattattttagagtgtgtgtgtgcagAGGCTAGTGATCAAAACCAAGAGCGTGGAGTTCATGCCCTTCTTCCTCTCACTCTTTGTGTTCCTCTGTGGTACTTCTTGGTTCATCTACGGGCTACTAG
| || | | | | | |||| | | | | ||| | | || || | |||| | ||| | ||| | |||||||||| |||||||| || ||||||||||||| |||||| ||| | | || || |||||||| || || || || |||||||||||||| | || |
tacggcggctaaactcaactcctaacagcggaaacttcttggattggatttcgtggcgattacttgcttgctgattggt-----tttcatggtgaatcgatgcagAGGCTGGTGATCAAGACGAAGAGCGTGGAGTACATGCCGTTCCTGATGTCGCTGGCCGTGTTCCTGTGCGGCACGTCGTGGTTCATCTACGGCTTGCTCG
upper sequence: GLYMA14G27610.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G21460.1 (Arabidopsis thaliana), 3'ss of exon 4
tagaaagtatgttgcaattatattccaaacattattgtataaattccaagtgagatatttttctatagattcttcattattttagagtgtgtgtgtgcagAGGCTAGTGATCAAAACCAAGAGCGTGGAGTTCATGCCCTTCTTCCTCTCACTCTTTGTGTTCCTCTGTGGTACTTCTTGGTTCATCTACGGGCTACTAG
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--gtaagcaaactcaggattggatctttttaaagttctactctttacttttg-gattcattttgttaaattttgtgt----ttggttcattgatttacagAGATTGGTGGTAAAGACGAAGAGTGTAGAGTTTATGCCATTCTTTTTGTCACTCTTTGTCTTCCTCTGTGGTACTTCGTGGTTCGTCTATGGTCTAATCG
upper sequence: GLYMA14G27610.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv18s0001g15330.t01 (Vitis vinifera), 3'ss of exon 4
tagaaagtatgttgcaattatattccaaacattattgtataaattccaagtgagatatttttctatagattcttcattattttagagtgtgtgtgtgcagAGGCTAGTGATCAAAACCAAGAGCGTGGAGTTCATGCCCTTCTTCCTCTCACTCTTTGTGTTCCTCTGTGGTACTTCTTGGTTCATCTACGGGCTACTAG
| ||| | | | || | || | | | | | ||| ||| || || | | | | | | ||| ||||||| | ||||||||||| ||||| || |||| ||||||||||||| | ||||| || ||||||||||| |||||||| ||||| ||| || ||||| |
--gtaagctcagtttactccctttttctttagtagtctcttgaat--aagacagactggattggatgggattaaactccctgattattatgtaattgcagAGAATGGTGATCAAAACAAAGAGTGTAGAGTACATGCCCTTCTTCTTATCACTGTTCGTGTTCCTCTGCGGTACTTCCTGGTTTGTCTTTGGCCTACTCG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccaagtgagatatttttctatagattcttcattattttagagtgtgtgtgtgcagAGGCTAGTGATCAAAACCAAGAGCGTGGAGTTCATGCCCTTCTTCCTCTCACTCTTTGTGTTCCTCTGTGGTACTTCTTGGTTCATCTACGGGCTACTAG
atatttttctatagat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tagaaagtatgttgcaattatattccaaacattattgtataaattccaagtgagatatttttctatagattcttcattattttagagtgtgtgtgtgcagAGGCTAGTGATCAAAACCAAGAGCGTGGAGTTCATGCCCTTCTTCCTCTCACTCTTTGTGTTCCTCTGTGGTACTTCTTGGTTCATCTACGGGCTACTAG
- - - - -tgttgca
- - - - - - - - - - - - ccaaaca
- - - - - - - - - - - - - - - - - - - - - -ttccaag