Sequence
atgc intronic sequence ATGC exonic sequence...tactttatacttcattattcaatttatttatattagaatgttttgacttttagatccatttttttaacttaagtgtgcaataatttttgtggtaaattagGTCCAGGATGTTCATCAGTGGCATATGGAGCATCTGAAGAGATTGGCCCATTTAGAATAAACAAAACAGCTTCTGGGCTATACATTAACAAGTTTTCGTG
Basic information
species | Glycine max |
transcript | GLYMA18G50170.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G50170.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os02g55130.4 (Oryza sativa), 3'ss of exon 1
-----------------------------------------------------------tactttatacttcattattc-aatttatttatattagaatgtt--ttgacttttagatccatttt---tttaa-------cttaagtg--tgcaataatttttg-tggtaaatt---agGTCCAGGATGTTCATCAGTGGCATATGGAGCATCTGAAGAGATTGGCCCATTTAGAATAAACAAAACAGCTTCTGGGCTATACATTAACAAGTTTTCGTG
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gtaaatagcaactgtaacatgaagatagcagtagtgcttactgttttactactagtatctctctgatagtctgatgttctaatcactttggattggattgctaattatcttttaaagttactgtagctgtagaaacatccttatttaactccagtaatatttgctgataatttcccagGTCCTGGATGCTCATCGATTGCGTATGGAGCATCTGAAGAGATTGGCCCATTTAGGATTAAGACAAACGGGACAGGGCTCTATCTGAACAAGTACTCATG
upper sequence: GLYMA18G50170.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os02g55130.1 (Oryza sativa), 3'ss of exon 1
-----tactttatacttcattattcaatttatttatattagaatgttttgacttttagatccatttttttaacttaagtgtgcaataatttttg-tggtaaatt---agGTCCAGGATGTTCATCAGTGGCATATGGAGCATCTGAAGAGATTGGCCCATTTAGAATAAACAAAACAGCTTCTGGGCTATACATTAACAAGTTTTCGTG
||||| | | ||| | | | | ||| || | | | | | |||| ||| || | |||| | || |||| |||| || ||| || |||||| ||||| ||||| | || |||||||||||||||||||||||||||||||| || || | || | | ||||| || | ||||||| || ||
ctaatcactttggattggattgctaattatcttt----taaagttactgtagctgtagaaacatcctt---atttaactc--cagtaatatttgctgataatttcccagGTCCTGGATGCTCATCGATTGCGTATGGAGCATCTGAAGAGATTGGCCCATTTAGGATTAAGACAAACGGGACAGGGCTCTATCTGAACAAGTACTCATG
upper sequence: GLYMA18G50170.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv14s0068g00260.t01 (Vitis vinifera), 3'ss of exon 1
tactttatacttcattattcaattt--atttatat-tagaatgttttgacttttagatccatttttttaacttaagtgtgcaataatttttgtggtaaatt---agGTCCAGGATGTTCATCAGTGGCATATGGAGCATCTGAAGAGATTGGCCCATTTAGAATAAACAAAACAGCTTCTGGGCTATACATTAACAAGTTTTCGTG
|| | | |||| || ||| |||| ||| | | | | || || | | | | | ||| | |||||| |||| || |||||| || || || || ||||| ||||| ||||||||||| || ||||||||||| || ||||| || ||||| || || ||| |||||||||| || ||
------gctttttaaaaatcaagttggattaatatataggacccgtctcataatgtatatatatatagtatctgatggtgagacttgttttgttgtaacttgtaagGTCCTGGTTGCTCTTCTGTGGCGTATGGGGCATCTGAAGAAATAGGCCCATTTAGGATCAACAAGACTGCTTCAGGCCTGTACCTTAACAAGTTCTCATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acttttagatccatttttttaacttaagtgtgcaataatttttgtggtaaattagGTCCAGGATGTTCATCAGTGGCATATGGAGCATCTGAAGAGATTGGCCCATTTAGAATAAACAAAACAGCTTCTGGGCTATACATTAACAAGTTTTCGTG
ttttaac putative branch site (score: 2)
aataatttttgtggta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tactttatacttcattattcaatttatttatattagaatgttttgacttttagatccatttttttaacttaagtgtgcaataatttttgtggtaaattagGTCCAGGATGTTCATCAGTGGCATATGGAGCATCTGAAGAGATTGGCCCATTTAGAATAAACAAAACAGCTTCTGGGCTATACATTAACAAGTTTTCGTG
- - - - -cttcatt
- - - - - - - - - - - - - - - - - - - tgttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgtgca