Sequence
atgc intronic sequence ATGC exonic sequencegtaatcatctcataattaattaaattgtttacaaatgttgtttgcttttgcacttttgccgttatgcttatattatattttggctcttcttgtccctttagTTGAAATATCATGACACTGGAAGAGAGAAAGAATACTTGCCACAAGTTGGTCAGTGGAATATGATGAACAAG
Basic information
species | Glycine max |
transcript | GLYMA06G23920.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G23920.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os06g39640.1 (Oryza sativa), 3'ss of exon 9
gtaatcatctcataattaattaaattgtttacaaatgttgtttgcttttgcacttttgccgttatgcttatattatattttggctct----tcttgtc-cctttagTTGAAATATCATGACACTGGAAGAGAGAAAGAATACTTGCCACAAGTTGGTCAGTGGAATATGATGAACAAG
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---------------------gtatgatttgc---ctttgttaatctcagtagttggctaactgctctcagctaataatttgggtatgaaattttgtggctttcagCTGAAATATCATGATACTGGGAAGGAAAAGGAGTGCTTGCCACAAGTTGGTCAGTGGAACATGGTGAACAAG
upper sequence: GLYMA06G23920.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G079080_T01 (Zea mays), 3'ss of exon 9
---gtaatcatctcataattaattaaattgtttacaaatgttgtttgcttttgcacttttgccgtta--tgcttatattatat---tttggctcttcttgtccctttagTTGAAATATCATGACACTGGAAGAGAGAAAGAATACTTGCCACAAGTTGGTCAGTGGAATATGATGAACAAG
||| || | || | | | || || || | || | | | || |||| |||| || | || | | || || | || ||||||| |||||||||||||||| ||||||||| | ||| ||||| |||||||||||||| ||| | ||||||
gtaagaataattttatg--tcacttttttcctttcaggagcaccttacactattatccatgaggttagttgctcattgttgatgcatcgaacaatttttttgaattcagTTGAAGTATCATGACACTGGAAAAGAGAAAGAGTGCTTACCACAGGTTGGTCAGTGGAACATGGTAAACAAG
upper sequence: GLYMA06G23920.1 (Glycine max), 3'ss of exon 9
lower sequence: AC189879.3_FGT003 (Zea mays), 3'ss of exon 8
------gtaatc--atctca---taattaattaaattgtttacaaatgttgtttgcttttgcacttttgccgttat--gcttata--ttatattttggctc-ttcttgtccctttagTTGAAATATCATGACACTGGAAGAGAGAAAGAATACTTGCCACAAGTTGGTCAGTGGAATATGATGAACAAG
||||| || ||| | ||| ||| || || | || | | | || || || || ||| || | || | || | | |||| || || |||| |||||||||||||||| ||||||||| | ||| ||||| |||||||||||||| ||| | ||||||
gtgaggataatcttatgtcactgttattcattttttttcttttgggagcaccttacactattatttatgacgctagtagctcattgttgatgtgctgaataacttttgtgaattcagCTGAAGTATCATGACACTGGAAAAGAGAAAGAGTGCTTACCACAGGTTGGTCAGTGGAACATGGTAAACAAG
upper sequence: GLYMA06G23920.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv11s0016g04620.t01 (Vitis vinifera), 3'ss of exon 9
gtaatcatctcataattaattaaattgtttacaaatgttgtttgctt-ttgcac-ttttgccgttatgcttatattatattt-tggctct-tcttgtccctt--tagTTGAAATATCATGACACTGGAAGAGAGAAAGAATACTTGCCACAAGTTGGTCAGTGGAATATGATGAACAAG
||| || ||| | || ||| ||| | |||| | | | || || | | |||| | |||| | |||| |||| ||| | |||||||| || || |||| ||| |||||||| ||||| ||||||||||| |||||||||| ||||||
--------------------gtaatgtttaacatccccttttctcttattggatattttaacatggt-ctgatctaaaatttgttcctctattttgttccttgatagCTTAAATATCACGATACCGGAAAAGAAAAAGAATATTTGCCGCAAGTTGGTCAATGGAATATGACAAACAAG
upper sequence: GLYMA06G23920.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ15357 (Selaginella moellendorffii), 3'ss of exon 10
gtaatcatctcataattaattaaattgtttacaaatgttgtttgcttttgcacttttgccgtt-atgcttatattatattttggctcttcttgtccctttagTTGAAATATCATGACACTGGAAGAGAGAAAGAATACTTGCCACAAGTTGGTCAGTGGAATATGATGAACAAG
| | | | ||| || ||| | | | | | || || | ||||||| |||||||| |||||| | |||||||| | | | || |||||||| |||||||||||||||||||||
-------------------------------------------------gtatgtcttccgaagatcgttaattcaagctctaacgttttctgac-----agTTGAAGTATCATGATACTGGACGGGAGAAAGACTGCCTTCCTCAAGTTGGGCAGTGGAATATGATGAACAAG
upper sequence: GLYMA06G23920.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ24991 (Selaginella moellendorffii), 3'ss of exon 10
gtaatcatctcataattaattaaattgtttacaaatgttgtttgcttttgcacttttgccgttatgc-ttatattatattttggctcttcttgtccctttagTTGAAATATCATGACACTGGAAGAGAGAAAGAATACTTGCCACAAGTTGGTCAGTGGAATATGATGAACAAG
| | | | ||| | ||| | | | | || || | ||||||| |||||||| |||||| | |||||||| | | | || |||||||| |||||||||||||||||||||
-------------------------------------------------gtatgtcttccgaagaccgttaattcaagctcaaacgttttctgac-----agTTGAAGTATCATGATACTGGACGGGAGAAAGACTGCCTTCCTCAAGTTGGGCAGTGGAATATGATGAACAAGMapped 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|192297193|gb|FG988289.1|FG988289EST: TAGACAGCAAGCTTGCATCAGTTGAGGCTCGGGTTCTTCCGGCTCCATGG TTGAAATATCATGACACTGGAAGAGAGAAAGAATACTTGCCACAAGTTGGT
genomic: TAGACAGCAAGCTTGCATCAGTTGAGGCTCGGGTTCTTCCGGCTCCATGGgtaatcatct ... gtccctttagTTGAAATATCATGACACTGGAAGAGAGAAAGAATACTTGCCACAAGTTGGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgcacttttgccgttatgcttatattatattttggctcttcttgtccctttagTTGAAATATCATGACACTGGAAGAGAGAAAGAATACTTGCCACAAGTTGGTCAGTGGAATATGATGAACAAG
ttttggctcttcttgt CT-rich tract
ttatgcttatattata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatcatctcataattaattaaattgtttacaaatgttgtttgcttttgcacttttgccgttatgcttatattatattttggctcttcttgtccctttagTTGAAATATCATGACACTGGAAGAGAGAAAGAATACTTGCCACAAGTTGGTCAGTGGAATATGATGAACAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA