Sequence
atgc intronic sequence ATGC exonic sequence...tttgtttcaacatttaatttcaagtgatcattgattatcatgccgtaaataacaaacacctacttgacatctcatggatgaccttggttattactttcagGGGATTAGACAGGAGGTTATTGTTGATTTGGTGGAGCAGTGTCGAACTTACAAGCAGAGAGTGGTTCACCTTGTCAACTCAACTTC
Basic information
species | Glycine max |
transcript | GLYMA17G26440.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G26440.2 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os06g22650.1 (Oryza sativa), 3'ss of exon 6
----tttgtttcaacatttaatttcaagtgatcattgattatcatgccgtaaataacaaacacctacttgacatctcatggatgaccttggttat---------tacttt--------------------------------cagGGGATTAGACAGGAGGTTATTGTTGATTTGGTGGAGCAGTGTCGAACTTACAAGCAGAGAGTGGTTCACCTTGTCAACTCAACTTC
||| | ||||| | |||| | || || | | | | | | | || ||| | | | | | ||| || | || ||| | || || ||| ||||| | ||||||||||||||||| || | ||||| || ||||| ||||||||||||| ||||| || |||||||||||||| |
gtaattttcctgtacattgcagttcatataat-gttcagaaaggtactgcagagaaaaaagatccattccatttctagtgtaggatctttttgataaaattggatatttttgctgccaagatgctaaaatgtaatgaatacacagGGTCTAAGACAGGAGGTTATTGTGGACCTTGTGGATCAATGTCGTTCTTACAAGCAGAGGGTGGTACAGCTTGTCAACTCAACCAC
upper sequence: GLYMA17G26440.2 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os01g12880.1 (Oryza sativa), 3'ss of exon 6
tttgtttcaacatttaatttcaagtgatcattgattatcatgccgtaaataacaaacacctacttgacatctcatggatgaccttggtt-attacttt-----cagGGGATTAGACAGGAGGTTATTGTTGATTTGGTGGAGCAGTGTCGAACTTACAAGCAGAGAGTGGTTCACCTTGTCAACTCAACTTC
| ||||| || | | | || || | ||| | | | || ||| | | | | | | || | ||| | | |||| | ||||| | || |||||||| ||||| || | || || |||||||| |||||||||||||||||||| | || || || | || |
--aggttcaa-atctgtacttatatgttccatacttagt-tac--ttaacaacctccttttgtgttaggtttactgattttgtttgtctgactactctgtacacagGGACTAAGGCAGGAGGTAATTGTGGAGCTTGTTGATCAGTGTCGCACTTACAAGCAGAGAGTGGTACTACTAGTTAATGCTACCGC
upper sequence: GLYMA17G26440.2 (Glycine max), 3'ss of exon 6
lower sequence: AT4G32760.1 (Arabidopsis thaliana), 3'ss of exon 6
tttgtttcaacatttaatttca-agtgatca------ttgattatca-tgccgtaaataaca-aacacctacttgacatc--tcatggatgaccttggttattactttcagGGGATTAGACAGGAGGTTATTGTTGATTTGGTGGAGCAGTGTCGAACTTACAAGCAGAGAGTGGTTCACCTTGTCAACTCAACTTC
|| || ||||| || || |||| | || ||| | || | ||| | || | |||| | | |||| | | || | | |||||| | | ||| |||||||| || ||| |||||||||||||||| || ||||| || |||||||| ||||| |||||||| |||||
---gtaacacgatttagttgcagagtgtttgagctacctgtttacaagtgtaggctatagcccaaaatatactaaataatgatcattcttctcgtttttggatttattcagGATCTCAAACAAGAGGTTATGGTCGATCTGGTGGAGCAGTGTCGTACATACAAACAAAGAGTGGTGCACCTCGTCAACTCGACTTC
upper sequence: GLYMA17G26440.2 (Glycine max), 3'ss of exon 6
lower sequence: Vv04s0008g03720.t01 (Vitis vinifera), 3'ss of exon 6
------tttgtttcaacatttaatttcaagtgatcattgattatcatgccgtaaataacaaacacctacttgacatctcatggatgaccttggttattactttcagGGGATTAGACAGGAGGTTATTGTTGATTTGGTGGAGCAGTGTCGAACTTACAAGCAGAGAGTGGTTCACCTTGTCAACTCAACTTC
||||| ||| | || | || | || |||| | | || | || | | || | | ||| | | || || | | | |||||| | || ||||||||||| | || ||||| || |||||||| || |||||||| |||||||| |||||||||||||||||| |
tatgcatttgtgtcatccttgaggtttttttttgcacatattagatttctttagtt--cagtctctgtgttcatgt----tgggttatttttgtcctaattaacagGGGCTCAGGCAGGAGGTTATCATGGACTTGGTAGATCAGTGTCGGACATACAAGCAAAGAGTGGTCCACCTTGTCAACTCAACTGCMapped 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|16105990|gb|BI893730.1|BI893730EST: TGGATGTTCTTGCAGAAATGCTCAATGCCTTAGACCCTAGTAACAAAGAA GGGATTAGACAGGAGGTTATTGCTGATTTGGTGGAGCAGTGTCGAACTTAC
genomic: TGGATGTTCTTGCAGAAATGCTCAATGCCTTAGACCCTAGTAACAAAGAAgtaagttact ... ttactttcagGGGATTAGACAGGAGGTTATTGTTGATTTGGTGGAGCAGTGTCGAACTTAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taaataacaaacacctacttgacatctcatggatgaccttggttattactttcagGGGATTAGACAGGAGGTTATTGTTGATTTGGTGGAGCAGTGTCGAACTTACAAGCAGAGAGTGGTTCACCTTGTCAACTCAACTTC
ttactttc CT-rich tract
ttattacttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttgtttcaacatttaatttcaagtgatcattgattatcatgccgtaaataacaaacacctacttgacatctcatggatgaccttggttattactttcagGGGATTAGACAGGAGGTTATTGTTGATTTGGTGGAGCAGTGTCGAACTTACAAGCAGAGAGTGGTTCACCTTGTCAACTCAACTTC
- - - - - - - - - - caagtga
- - - - - - - - - - - - - - - - - - -tcatgcc
- - - - - - - - - - - - - - - - - - - - - - - - - -acaaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catggat