Sequence
atgc intronic sequence ATGC exonic sequencegtaactctacaatgcttttcatctgtgttactgcagatgtgcatggtctacaaaacagtgagggtgtctttatttgttgcagGGAATATGGGATGAGGTTGGTGAGAGCGATGAGGAGCAAGACAAGATGCTCCTTCAGATAGAGCAAGAGTGTTTGAATGTGTACAAAAGAAAG
Basic information
species | Glycine max |
transcript | GLYMA18G10090.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G10090.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os06g40840.1 (Oryza sativa), 3'ss of exon 2
-------------------------------------------------------------------------------gtaactctacaatgctttt-catctgtgttactgcag---atgtgcatggtctacaaaacagtgagggtgtctttat----ttgttgcagGGAATATGGGATGAGGTTGGTGAGAGCGATGAGGAGCAAGACAAGATGCTCCTTCAGATAGAGCAAGAGTGTTTGAATGTGTACAAAAGAAAG-------
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gtgcctttgtctcttccaatgttcttttgtatgtgtgctttataatgactggaactaaggatagcagcaagccattttagttccctatctacaccatagcatctgtgcaacgaaaagttatatgagtagtgcataggattggacaagtgactgactagtgtcatttcagTTGATATGGGATGAGGTTGGTGAAAGCGATGAAGACCGTGACAAGATGTTACTTCAGCTAGAACAAGAATGCTTGGATGTTTACAGGAGAAAGGTTGATC
upper sequence: GLYMA18G10090.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G112337_T02 (Zea mays), 3'ss of exon 4
---------------gtaactctacaatgcttttcatctgtgttactgcagatgtgcatggtctacaaaacagtgagggtgtctttat---ttgttgcagGGAATATGGGATGAGGTTGGTGAGAGCGATGAGGAGCAAGACAAGATGCTCCTTCAGATAGAGCAAGAGTGTTTGAATGTGTACAAAAGAAAG-------
|| || | | | || | || || || | | || || | || | | | ||| || || ||| ||||||||||||||||| || || ||||| || | ||||||||| | |||||| ||||||||||||| || |||| || | ||||||
aaccattctaacccattatctagattaagagttaagatagcatttctacaagaaagagtagtataggattcacacaagtgattgctatgtgttatttcagCTGATATGGGATGAGGTTGGCGAAAGTGATGAAGATCGTGACAAGATGTTACTTCAGCTAGAGCAAGAGTGCTTAGATGTTTATAGGAGAAAGGTTGATC
upper sequence: GLYMA18G10090.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G55230.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaactct-acaatgcttttcatctgtgttactgcagatgtgcatggtctacaaaacagtgagggtgtctttatttgttgcagGGAATATGGGATGAGGTTGGTGAGAGCGATGAGGAGCAAGACAAGATGCTCCTTCAGATAGAGCAAGAGTGTTTGAATGTGTACAAAAGAAAG-------
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gtaaatcttgctaccatctccacctaagt-attagggctttactctcaatcttgtgtaacgtcaactttttt--ttactaaagGAAATCTGGGATGAAGTTGGTGAGAGTGATGATGAACGAGACAAACTGCTTCTTCAGATAGAGCAAGAGTGTCTTGACGTTTACAAGAGAAAAGTCGAGC
upper sequence: GLYMA18G10090.1 (Glycine max), 3'ss of exon 1
lower sequence: AT4G26760.1 (Arabidopsis thaliana), 3'ss of exon 2
gta-actctacaatgcttttcatctgtgttactgcagatgtgcatggtctacaaaacagtgagggtgtctttatttgttgcagGGAATATGGGATGAGGTTGGTGAGAGCGATGAGGAGCAAGACAAGATGCTCCTTCAGATAGAGCAAGAGTGTTTGAATGTGTACAAAAGAAAG-------
||| | | ||| | || | | | | | || || | || ||||| ||| | ||||| |||| ||| |||||||||||||| ||||| ||||| || | |||||| |||| || ||||| ||| |||||||| ||||||| ||||||| ||
gtagatttcgcaaca-tacacacttatcctttta-atatatg---gttccacaaactca-----atgtacaaacttgttacagGAAATCTGGGATGAGGTTGGGGAGAGTGATGAAGAACGAGACAAACTGCTTCTACAGATTGAGGAAGAGTGTCTGAATGTTTACAAAAAGAAAGTTGAGC
upper sequence: GLYMA18G10090.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv19s0090g01230.t01 (Vitis vinifera), 3'ss of exon 1
---------------gtaactctacaatgcttttcatctgtgttac-tgcagatgtgcatggtctacaaaacagtgagggtg--tctttatttgttgcagGGAATATGGGATGAGGTTGGTGAGAGCGATGAGGAGCAAGACAAGATGCTCCTTCAGATAGAGCAAGAGTGTTTGAATGTGTACAAAAGAAAG-------
|| | | || | | | || | | | || | || || | | | || | | ||| ||||| ||| ||||||||||||||||| ||||||||||| | || || |||||||||||| ||||||||||||| ||| | || || || || |||
gtcattgtttactttgtgatatattagtgttataagtagaccttgcatactgaggaacagggcaaatacgctaaatgctgtaaaccatggtttaatgcagCAAATCTGGGATGAGGTTGGTGAAAGCGATGAGGAACGTGATAAAATGCTCCTTCAGTTAGAGCAAGAGTGCTTGGACGTTTATAAGAGGAAGGTTGATC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttactgcagatgtgcatggtctacaaaacagtgagggtgtctttatttgttgcagGGAATATGGGATGAGGTTGGTGAGAGCGATGAGGAGCAAGACAAGATGCTCCTTCAGATAGAGCAAGAGTGTTTGAATGTGTACAAAAGAAAG
tctttattt CT-rich tract
tttatttgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaactctacaatgcttttcatctgtgttactgcagatgtgcatggtctacaaaacagtgagggtgtctttatttgttgcagGGAATATGGGATGAGGTTGGTGAGAGCGATGAGGAGCAAGACAAGATGCTCCTTCAGATAGAGCAAGAGTGTTTGAATGTGTACAAAAGAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA