Sequence
atgc intronic sequence ATGC exonic sequencegtaatgtgtgaaaagtcttcagcatgttcaaactcacatttgctttattcttgattgtactgcctctagttaagatcatatttatttttgcacggtttatttgacattctttagGAGGAAAGAAAGACTCTAGACAGGGAGTTGGCTCGTGCCAAGGTAACAGCAAACAGAGTAGCTGTTGTGGTTGCAAATGAATGGAAAGATGCTAATGATA
Basic information
species | Glycine max |
transcript | GLYMA07G26540.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G26540.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os02g50320.2 (Oryza sativa), 3'ss of exon 6
gtaatgtgtgaaaagtcttcagcatgttcaaactcacatttgctttattcttgattgtactgcctctagttaagatcatatttatttttgcacggtttatttgacattctttagGAGGAAAGAAAGACTCTAGACAGGGAGTTGGCTCGTGCCAAGGTAACAGCAAACAGAGTAGCTGTTGTGGTTGCAAATGAATGGAAAGATGCTAATGATA
| ||| | | ||| || |||| | ||| ||| | ||| | | | | | || || ||| ||||||||||||| | ||| ||| | ||| | || || || || || |||||||||||||| |||||||| ||||||||||| ||||||||||||||||| |
------------------gtaacatcctttactgttgctttcggataatcttcactgttctgtacgcaaaaaagttgacccatgctaatctctaacca---tggcacactt-agGAGGAAAGAAAAATTCTTGACCGTGAGCTTGCGCGGGCAAAAGTTACAGCAAACAGAGTTGCTGTTGTAGTTGCAAATGAGTGGAAAGATGCTAATGACA
upper sequence: GLYMA07G26540.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os06g14080.1 (Oryza sativa), 3'ss of exon 6
---gtaatgtgtgaaaagtcttcagcatgttcaaactcacatttgctttattcttgattgtactgcctctagttaagatcatatttatttttgcacggtttatttgacattctttagGAGGAAAGAAAGACTCTAGACAGGGAGTTGGCTCGTGCCAAGGTAACAGCAAACAGAGTAGCTGTTGTGGTTGCAAATGAATGGAAAGATGCTAATGATA
|| | | | || |||| | | ||| | | | | | | | | || ||| | | | | || || | | ||| | |||| ||| |||||| || || | || | |||||||| || || ||||||||||| || |||||||||||||| || || ||||||||| ||||||| |
gtaacaacctattctttgactattgcatatgtca--tcatgtcttcatgagctct--tccccccttctataggaacagtt-cactcatgcttatttaacatttatgatcattaccagGACCAAAAAAAGACACTTGAATGTGAACTTGCTCGTGCAAAAGTTACAGCAAACAGGGTTGCTGTTGTGGTTGCCAACGAGTGGAAAGATTCTAATGACA
upper sequence: GLYMA07G26540.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os12g44340.1 (Oryza sativa), 3'ss of exon 6
gtaatgtgtgaaaagtcttcagcatgttcaaactcacatttgctttattcttgattgtactgcctctagttaagatcatatttatttttgcacggtttatttgacattctttagGAGGAAAGAAAGACTCTAGACAGGGAGTTGGCTCGTGCCAAGGTAACAGCAAACAGAGTAGCTGTTGTGGTTGCAAATGAATGGAAAGATGCTAATGATA
|||||| ||| || |||| || | ||| | || | | || | | | || || | || ||||| || | ||| | |||| ||||| || ||||| || | || | |||||||| ||||| | ||||| ||||| || || ||||| ||||||||||||||||||| |||||||
gtaatgcatgatgccctgagcacacgttc---ctgatgtttattcta--cctaatagaatgg----taattgatgcca-atttacacttatgc--------tgatgtc----agGAAGAAAGGAAAACTCTTGATCGTGAACTAGCTCGTGCGAAGGTTTCGGCAAATAGAGTTGCAGTAGTGGTGGCAAATGAATGGAAAGATGGCAATGATA
upper sequence: GLYMA07G26540.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM5G832989_T01 (Zea mays), 3'ss of exon 6
gtaatgtgtgaaaagtcttcagcatgttcaaactcacatttgctttattcttgattgtactgcctctagttaagatcatatttatttttgcacggtttatttgacattct-ttagGAGGAAAGAAAGACTCTAGACAGGGAGTTGGCTCGTGCCAAGGTAACAGCAAACAGAGTAGCTGTTGTGGTTGCAAATGAATGGAAAGATGCTAATGATA
| | || || | ||||| | | ||| ||| | | || || ||| | ||||||| | | | | | || | | |||||| |||| || | || ||| | || | ||||| || || || || ||||| || || ||||||||||| ||||| || ||||||||||||||||| |
----------tagatcaatcttcacttgcaaacaggc-----cattactctgcaatttattgattctttacacaatcatatgacctgtgctattttcttttcatgacacaattagGAAGAAAAGAAAATTCGTGACCGTGAACTTGCTCGAGCTAAAGTTACTGCAAATAGGGTTGCTGTTGTGGTCGCAAACGAGTGGAAAGATGCTAATGACA
upper sequence: GLYMA07G26540.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G008556_T01 (Zea mays), 3'ss of exon 6
gtaatgtgtgaaaagtct-tcagcatgttcaaactcacatttgctttattcttgattgtactgcctctagttaagatcatatttatttttgcacggtttatttgacattctttagGAGGAAAGAAAGACTCTAGACAGGGAGTTGGCTCGTGCCAAGGTAACAGCAAACAGAGTAGCTGTTGTGGTTGCAAATGAATGGAAAGATGCTAATGATA
|||| | | | | | || ||| ||| | | ||| || | ||| || | || | ||| || || | | |||| | |||||| |||| | || || ||| | || | || ||||| || || |||||||||||||| ||| ||| ||||| ||||| ||||||||| ||||||| |
gtaacaaactatcatttgattacttcatttgccttcaaattcgtgtcattttt---tacact-tttcacatgaacacttgattcatgcttatgcttatgatttta------ttagGAAGAAAAGAGAACACTTGACCGTGAACTTGCACGTGCAAAAGTTACAGCAAACAGAGTTGCTTCTGTTGTTGCTAATGAGTGGAAAGATTCTAATGACA
upper sequence: GLYMA07G26540.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G68060.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaatgtgtgaaaagtcttcagcatgttcaaactcacatttgctttattcttgattgtactgcctctagttaagatcatatttatttttgcacggtttatttgacattctttagGAGGAAAGAAAGACTCTAGACAGGGAGTTGGCTCGTGCCAAGGTAACAGCAAACAGAGTAGCTGTTGTGGTTGCAAATGAATGGAAAGATGCTAATGATA
| | ||| | |||||| | | | | || || || | || | | | || | | | || | | | |||| ||| |||| ||||| ||| |||| | || ||||| ||||| |||||||||||||| || ||||||||||||||||||||||||| ||||||||
---------------------gtaagttaa----tacattt-ccgaaaaaagaagtatagaatctttactcaactgatgaaggaatatttcttgctctact------tttgcagGAAGAACGAAAAACTCTTGACCGGGAACTTGCGCGTGCAAAGGTTACAGCAAACAGAGTTGCGACAGTGGTTGCAAATGAATGGAAAGATGGTAATGATA
upper sequence: GLYMA07G26540.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G24764.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaatgtgtgaaaagtcttcagcatgttcaaactcacatttgctttattcttgattgtactgcctctagttaagatcatatttatttttgcacggtttat-ttgacattctttagGAGGAAAGAAAGACTCTAGACAGGGAGTTGGCTCGTGCCAAGGTAACAGCAAACAGAGTAGCTGTTGTGGTTGCAAATGAATGGAAAGATGCTAATGATA
| |||| ||| || | | ||| | | | || | | | || | || | || | | | || | || | || |||| || | || ||||| ||| ||||| | || ||||| ||||| |||||||||||||| || |||||| |||||||| |||||||||| ||||||||
-----------------------gtaactaaac--acacttcataaagtctctaatttcttgtcacaa--caattgcctactgatgtaggaataattcttgtttttgtctttcagGAAGAGCGGAAAACTCTTGACCGGGAGCTTGCACGTGCAAAGGTTACAGCAAACAGAGTTGCCACTGTGGTAGCAAATGAGTGGAAAGATGGTAATGATA
upper sequence: GLYMA07G26540.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv01s0011g05790.t01 (Vitis vinifera), 3'ss of exon 6
gtaatgtgtgaaaagtcttcagca--tgttcaaactcacatttgctttattcttgattgtactgcctctagtta--agatcatatttatttttgcacggtttatttgacattcttt---------------agGAGGAAAGAAAGACTCTAGACAGGGAGTTGGCTCGTGCCAAGGTAACAGCAAACAGAGTAGCTGTTGTGGTTGCAAATGAATGGAAAGATGCTAATGATA
|||||||| | | || | | || || | || | ||| | || | ||| ||||||| | || || | || | || ||| | ||| | ||| || ||||||||||||| || || ||||||||| |||| ||||| |||||||| |||||||| || || || || || |||||||||||||||||||||||||| |
gtaatgtgccatttttaaacaataaatattgaacattgcaagtcatttcaggcttatatttttgcatctagttggcatatgccatgtgttctatcattgttgagttgtctttccttttcttttggaccttcagGAGGAAAGAAAAACCCTCGACAGGGAGCTGGCCCGTGCAAAGGTAACTGCAAACAGGGTGGCAGTAGTTGTAGCAAATGAATGGAAAGATGCTAATGACA
upper sequence: GLYMA07G26540.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ18059 (Selaginella moellendorffii), 3'ss of exon 6
gtaatgtgtgaaaagtcttcagcatgttcaaactcacatttgctttattcttgattgtactgcctctagttaagatcatatttatttttgcacggtttatttgacattctttagGAGGAAAGAAAGACTCTAGACAGGGAGTTGGCTCGTGCCAAGGTAACAGCAAACAGAGTAGCTGTTGTGGTTGCAAATGAATGGAAAGATGCTAATGATA
||| |||| | || | | | | | | || | | | |||||| || | | ||| || || |||| |||| |||||||||||||||||||||||||| || || || |||||||| |||||||| ||||| || || |
--------------------------------------------------------gtagtgccgccagccacctttgggtcgcactcaccccacattgtctttttaccattagGAAGAGAAACGGACGCTTGAGCGGGAACTGGCGCGTGCCAAGGTAACAGCAAACAGAGTGGCAGTCGTCGTTGCAAACGAATGGAAGGATGCAAACGACA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgcctctagttaagatcatatttatttttgcacggtttatttgacattctttagGAGGAAAGAAAGACTCTAGACAGGGAGTTGGCTCGTGCCAAGGTAACAGCAAACAGAGTAGCTGTTGTGGTTGCAAATGAATGGAAAGATGCTAATGATA
atttgac putative branch site (score: 4)
cattcttt CT-rich tract
tagttaagatcatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatgtgtgaaaagtcttcagcatgttcaaactcacatttgctttattcttgattgtactgcctctagttaagatcatatttatttttgcacggtttatttgacattctttagGAGGAAAGAAAGACTCTAGACAGGGAGTTGGCTCGTGCCAAGGTAACAGCAAACAGAGTAGCTGTTGTGGTTGCAAATGAATGGAAAGATGCTAATGATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG