Sequence
atgc intronic sequence ATGC exonic sequence...caatgacacccctagtatcctgtctactttctcagcccactttttaaaacattgactgaatttgtcaagcatattaatgaaagattaccattttgtttagGAAGAAGAATATCTTTAAGTTGGCACAAGGCGAGTACATTGCTCCTGAGAAGATTGAAAATGTATACGCCAAATGCAAATTTGTGGCGCAGTGCTTTGTA
Basic information
species | Glycine max |
transcript | GLYMA10G39540.1 |
intron # | 18 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G39540.1 (Glycine max), 3'ss of exon 18
lower sequence: LOC_Os11g04980.1 (Oryza sativa), 3'ss of exon 18
--caatgacacccctagtatcctgtctactttctcagcccactttttaaaacattgactgaatttgtcaagcatattaatgaaagattaccattttgtttagGAAGAAGAATATCTTTAAGTTGGCACAAGGCGAGTACATTGCTCCTGAGAAGATTGAAAATGTATACGCCAAATGCAAATTTGTGGCGCAGTGCTTTGTA
| | | | | | || | | | | || ||| | ||| || | || | | | ||| | | |||| | ||||| ||||| || || ||||| || ||||| || ||||| ||||| ||||||||||| ||||| || || || ||||| ||| | |||||||||||| ||
attttttaggctatctat-tttaatttattcccctggaactctgtttcgtctgattacttttcttattaaattt-taattgatgcaattttcttttctcaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATA
upper sequence: GLYMA10G39540.1 (Glycine max), 3'ss of exon 18
lower sequence: GRMZM2G176546_T01 (Zea mays), 3'ss of exon 9
------------------------------------------------caatgacacccctagtatcctgtctactttctcagcccacttttta---aaacattgactgaatttgtcaagcatattaatgaaagattaccattttg--------------tttagGAAGAAGAATATCTTTAAGTTGGCACAAGGCGAGTACATTGCTCCTGAGAAGATTGAAAATGTATACGCCAAATGCAAATTTGTGGCGCAGTGCTTTGTA
|| | | | | || ||| || | || |||| | | || ||| | | | || | | |||| || |||||||| ||||| || || ||||| || ||||| || ||||| ||||| ||||||||||||||||| || ||||||||||| || | || || || ||| ||
gtaaaaacgtgcactgttttatattttatccattcagaacttgtgttcttgcagaacactt--ttccttggctatattgttgatttacattttccctaggcgctgtttgatctcaccgtttttcttcctatattattaatgccttaaatttctcctggattttagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAAAATGTCTATGCCAAATGCAAGTTCATTGCCCAATGTTTTATA
upper sequence: GLYMA10G39540.1 (Glycine max), 3'ss of exon 18
lower sequence: AT3G05970.1 (Arabidopsis thaliana), 3'ss of exon 18
---caatg-acacccctagtatcctgtctactttctcagcccactttttaaaacattgactgaatttgtcaagcatattaatgaaagattaccat--tttgtttagGAAGAAGAATATCTTTAAGTTGGCACAAGGCGAGTACATTGCTCCTGAGAAGATTGAAAATGTATACGCCAAATGCAAATTTGTGGCGCAGTGCTTTGTA
| || | | | ||||| | || ||| || | | |||| || | || ||||| | || ||| | | ||||| || || |||| ||| |||||||| ||||| || ||||| || || ||||| || ||||| ||||| |||||||| || || ||||||||||||||||||| |||||||| ||
agggagtgcaaagctctagtcttgggt-tacattttggg--gacttgttggtatctt--ttgaatc-gcgaatcatctgagtgaaattttctgatcctttgaatagAAAGAAGAACATCTTCAAATTGGCGCAGGGGGAGTATATAGCTCCAGAGAAAATTGAAAACGTCTATGCCAAATGCAAATTTGTGGGCCAGTGCTTCATA
upper sequence: GLYMA10G39540.1 (Glycine max), 3'ss of exon 18
lower sequence: Vv05s0020g03080.t01 (Vitis vinifera), 3'ss of exon 18
---------------------------------------------------------------------------------------------caatgacacccctagtatcctgtctactttctcagccc--actttttaaaacattgactgaatttgtcaagcatattaatgaaagattaccattttgtttagGAAGAAGAATATCTTTAAGTTGGCACAAGGCGAGTACATTGCTCCTGAGAAGATTGAAAATGTATACGCCAAATGCAAATTTGTGGCGCAGTGCTTTGTA
|| | | | | | | | | || | | | || |||| ||| | || | | || ||| || || | ||||||||||| || ||||||||||||||||| |||||||| ||||| ||||| ||||| |||||||| || |||||||||||||| || ||||||||||||
gtaaagaccatatcatttttgttgacagttcttagacgaattaataatgactcctctctagttttggatgactcaattgactgtatgttcatatcttggtcctgtgattttgttattgatataatcgactataattacatacttcattacctgtgcatttcttagctttgtattaaaagttgttatatgac--agGAAGAAGAACATTTTTAAGTTGGCACAAGGAGAGTACATAGCTCCAGAGAAAATTGAGAATGTATATGCTAAATGCAAATTTGTTGCCCAGTGCTTTGTA
upper sequence: GLYMA10G39540.1 (Glycine max), 3'ss of exon 18
lower sequence: PP1S408_23V6.1 (Physcomitrella patens), 3'ss of exon 20
--caatgacacccctagtatcctgtctactttctcagcccactttttaaaacattgactgaatttgtcaagcatattaatgaaagattaccattttgtttagGAAGAAGAATATCTTTAAGTTGGCACAAGGCGAGTACATTGCTCCTGAGAAGATTGAAAATGTATACGCCAAATGCAAATTTGTGGCGCAGTGCTTTGTA
||| | | | | |||||| |||| || || | | || || | | || | | | | || | |||||||||||||||||||||||||| ||||| ||||||||||| || |||||||| || ||||| ||| | || | | ||||| | ||
tgtcgtgagtggatcaatttagcttttactttttcaggaatgttcacaagtagtatgttctgttcttcgtgtttgttgagtcat--tcatcacacattgcagGAAGAAGAATATCTTTAAGTTGGCTCAAGGAGAGTACATTGCCCCGGAGAAGATCGAGAATGTCTACCTTCGCAGTCGTTTCATAACACAGTGTTACATA
upper sequence: GLYMA10G39540.1 (Glycine max), 3'ss of exon 18
lower sequence: PP1S33_126V6.1 (Physcomitrella patens), 3'ss of exon 21
--------------------------------------------------------------------------caatgacacccctagtatcctgtctactttctca--gcccactttttaaaacattgactgaatttgtcaagcatattaatgaa----agattaccattttgttta-----gGAAGAAGAATATCTTTAAGTTGGCACAAGGCGAGTACATTGCTCCTGAGAAGATTGAAAATGTATACGCCAAATGCAAATTTGTGGCGCAGTGCTTTGTA
|| || || | | | |||||| | | | | | || || ||||| | ||| | || |||| | || ||| ||| | |||||||||||||| |||||||| || || ||||||||||| || ||||||||||| || || ||| | | || | || ||||||||| |
gtactctggactagcgtcacccttagatgtatgctattgatatttttcatcattcaacgtctggtagtctagatcagtgtacccagttgagtatgttctactcttctaatgttcgaagatcaatccaact-ttgaatatttcaggagctttcatgagttgtacgttctttccttggttattgcagAAAGAAGAATATCTTCAAGTTGGCTCAGGGAGAGTACATTGCGCCCGAGAAGATTGAGAACGTCTACCTGCGAAGTCGGTTCATTGCACAGTGCTTTATTMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|10843907|gb|BF067252.1|BF067252EST: GGAGATATTGGGACGTGGTTACCTGGTGGTCGTCTCAAAATTATTGATAG GAAGAAGAATATCTTTAAGTTGGCACAAGGCGAGTACATTGCTCCTGAGAA
genomic: GGAGATATTGGGACGTGGTTACCTGGTGGTCGTCTCAAAATTATTGATAGgtaagatagc ... ttttgtttagGAAGAAGAATATCTTTAAGTTGGCACAAGGCGAGTACATTGCTCCTGAGAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaaacattgactgaatttgtcaagcatattaatgaaagattaccattttgtttagGAAGAAGAATATCTTTAAGTTGGCACAAGGCGAGTACATTGCTCCTGAGAAGATTGAAAATGTATACGCCAAATGCAAATTTGTGGCGCAGTGCTTTGTA
tattaat putative branch site (score: 2)
ttttgttt putative PPT
atattaatgaaagatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
caatgacacccctagtatcctgtctactttctcagcccactttttaaaacattgactgaatttgtcaagcatattaatgaaagattaccattttgtttagGAAGAAGAATATCTTTAAGTTGGCACAAGGCGAGTACATTGCTCCTGAGAAGATTGAAAATGTATACGCCAAATGCAAATTTGTGGCGCAGTGCTTTGTA
- - gacaccc
- - - - - - - - - cctgtct
- - - - - - - - - - - - - - - - -agcccac
- - - - - - - - - - - - - - - - - - - - - - - - - -ttgactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caagcat