Sequence
atgc intronic sequence ATGC exonic sequence...ttatgtataaattacttagcatttaacaacaatagggggtactacttatttttatgtgctaaaaactaatccaagttccaatgaattgtctgtttgaataGCCATTTAAGGACATGATTGAAGGGATGAGGCTGGATCTGAGAAAGTCAAGATACAATAACTTTGATGAACTCTACCTTTACTGCTACTATGTAGCTGGG
Basic information
species | Glycine max |
transcript | GLYMA18G13700.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G13700.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os12g43130.1 (Oryza sativa), 3'ss of exon 3
------------------------------ttatgtataaattactt--agcatttaacaacaatagggggtactacttatttttatgtgctaaaaactaatccaagttccaatgaattgtctgtttgaataGCCATTTAAGGACATGATTGAAGGGATGAGGCTGGATCTGAGAAAGTCAAGATACAATAACTTTGATGAACTCTACCTTTACTGCTACTATGTAGCTGGG-
||| || | ||| | | ||| | | | | | | | | || || | | | || || | || | | | | ||||||| || |||||||||||||| |||||||| || ||| | || ||||| || | | ||||||||| |||||||| ||||||||||| || |||||
gtacagccaacaaaaaagctactgtaaaagcaggatatgaagtgcttttaaaagttattagta-cacagtaaattggtgacacgcatttgtctgatgtttctgcaccgtcg---ggatctcttttatttacagCCATTCAAAGACATGATTGAAGGAATGAGGCTTGACCTGTGGAAATCAAGGTATAGGAGCTTTGATGAGCTCTACCTCTACTGCTACTACGTTGCTGGCA
upper sequence: GLYMA18G13700.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv12s0028g00960.t01 (Vitis vinifera), 3'ss of exon 3
---------------------------------------------------------------------------------ttatgtataaattacttagcatttaacaacaatagggggtactacttatttttatgtgctaaaaactaatcca-agttcca-atg-----aattgtctgtttgaataGCCATTTAAGGACATGATTGAAGGGATGAGGCTGGATCTGAGAAAGTCAAGATACAATAACTTTGATGAACTCTACCTTTACTGCTACTATGTAGCTGGG-
|| | | || ||| | | ||| || || || ||| ||| | || || | | ||||| ||| |||| ||| ||| |||| || || |||||||| ||||| ||||| |||| |||||||| ||||||||||| | ||||||||| ||||| || |||||||| ||||| |||||
gtacatttatatgggctcaaaactgattcacccatcttgcattttagctgctaatcaacctatgaacacgcacacatatgaacatttgatgagtaggtagtacattgtgacag-agcacatattatgggcctttctgtatcatgaatatataaacacttccacatgttaataattttctttttatgcagCCCTTCAAAGACATGATAGAAGGAATGAGATTGGACCTGAGAAAATCAAGATACAACAGCTTTGATGAGCTCTATCTGTACTGCTATTATGTTGCTGGAAMapped 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|151394940|gb|EV264811.1|EV264811EST: TATGATGCTGCCCTCTCAGATACAGTTTCAAAGTACCCAGTTGATATACA GCCATTTAAGGACATGATTGAAAGGGATGAGGCTGGATCTGAGAAAGTCAA
genomic: TATGATGCTGCCCTCTCAGATACAGTTTCAAAGTACCCAGTTGATATACAggtagaccaa ... tgtttgaataGCCATTTAAGGACATGATTGAA-GGGATGAGGCTGGATCTGAGAAAGTCAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttatttttatgtgctaaaaactaatccaagttccaatgaattgtctgtttgaataGCCATTTAAGGACATGATTGAAGGGATGAGGCTGGATCTGAGAAAGTCAAGATACAATAACTTTGATGAACTCTACCTTTACTGCTACTATGTAGCTGGG
aactaat putative branch site (score: 2)
tctgttt putative PPT
taaaaactaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttatgtataaattacttagcatttaacaacaatagggggtactacttatttttatgtgctaaaaactaatccaagttccaatgaattgtctgtttgaataGCCATTTAAGGACATGATTGAAGGGATGAGGCTGGATCTGAGAAAGTCAAGATACAATAACTTTGATGAACTCTACCTTTACTGCTACTATGTAGCTGGG
- - - - - - - - - - - - aacaaca
- - - - - - - - - - - - - - - - - gggggta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -taaaaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccaatga