Sequence
atgc intronic sequence ATGC exonic sequencegcaagtgaatatgtttgatgttagagtggtcttagacatttgatttggtaggctttaattaattttttgtaattgtcaatctccagGGTTTCTCAACATGGAGCAGAAGAGATTTTAATACTTTCCTCAGGGCTTGTGAGAAGTATGGCCGCAACGACATAAAAAGCATTGCCTCTGAGATGGAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G06400.3 |
intron # | 20 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G06400.3 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GLYMA07G38050.1 (Glycine max), 3'ss of exon 20
gcaagtgaatatgtttgatgtt-----agagtggtcttagacatttg---atttggtaggctttaattaattttttgtaattgtcaatctccagGGTTTCTCAACATGGAGCAGAAGAGATTTTAATACTTTCCTCAGGGCTTGTGAGAAGTATGGCCGCAACGACATAAAAAGCATTGCCTCTGAGATGGAAG
| || | | | ||| || | | ||| || || | | |||| || ||||| || || | ||| ||| || | |||| || ||| |||||||| | | ||||||||| ||||| | ||||| ||||| ||||||||||| || || |||||| | ||||| |||||||||||||
gtgagcaattttttttataatttataaacaagggttatacacttctatttatttattattttttaa--aaattctggtatttggtaaacat-agGGATTTTCATCATGGAGCCGGAAGGATTTTAATGCTTTCATTAGGGCCTGTGAAAAGTATGGCCGAAATGATATAAAAGGTATTGCTTCTGAGATGGAAG
upper sequence: AT3G06400.3 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GLYMA17G02640.1 (Glycine max), 3'ss of exon 20
gcaagtgaatatgtttgatgtt---agagtggtcttagacatttg-atttggtaggctttaattaattttttgtaattgtcaatctccagGGTTTCTCAACATGGAGCAGAAGAGATTTTAATACTTTCCTCAGGGCTTGTGAGAAGTATGGCCGCAACGACATAAAAAGCATTGCCTCTGAGATGGAAG
| || ||| | ||| || | | | ||| ||| || |||| | || |||| || | | | ||| || | |||| || ||| |||||||| | | ||||||||| ||||| | ||||| ||||| ||||||||||| || || |||||| | ||||| |||||||||||||
gtgagcaaatttctttataatttataaacaagggttatacacttctatttatttattattttttaaattctggaatttggtaaacat-agGGATTTTCATCATGGAGCCGGAAGGATTTTAATGCTTTCATTAGGGCCTGTGAAAAGTATGGCCGAAATGATATAAAAGGTATTGCTTCTGAGATGGAAG
upper sequence: AT3G06400.3 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GLYMA15G10370.1 (Glycine max), 3'ss of exon 20
gcaagtgaatatgtttgatgttagagtg-gtcttagacatttgatttggtaggctttaattaattttttgtaattg-tcaatctccagGGTTTCTCAACATGGAGCAGAAGAGATTTTAATACTTTCCTCAGGGCTTGTGAGAAGTATGGCCGCAACGACATAAAAAGCATTGCCTCTGAGATGGAAG
|| || || ||| || || ||| | || | | | | || |||||| || ||| | ||| | |||| || || |||||||| | || ||||||||||||||| | ||||| || || || |||||||| || || ||| |||| ||||| |||||||||||||
----gtaaacatttttcccctttttttgcaaactaggctttcac----atggacccttttttatttttattatttggttaatat--agGGATTTTCTTCATGGAGCCGGAGGGATTTTAATACTTTCATTAGGGCCTGCGAAAAATATGGCCGAAATGATATACAAAGTATTGCTTCTGAGATGGAAG
upper sequence: AT3G06400.3 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GLYMA13G28720.1 (Glycine max), 3'ss of exon 20
gcaagtgaatatgtttgatgttagagtggtcttagacatttgatttggtaggctttaattaattttttgtaattg-tcaatctccagGGTTTCTCAACATGGAGCAGAAGAGATTTTAATACTTTCCTCAGGGCTTGTGAGAAGTATGGCCGCAACGACATAAAAAGCATTGCCTCTGAGATGGAAG
||||| | || || | || || | ||| | ||| | |||| ||||||||| || ||| | ||| | |||| || || |||||| | | || ||||||||||||||| | ||||| || || || |||||||| || || |||||| | ||||| |||||||||||||
----gtgaacaatttccccctttttgcaaact-aggc-tttcacatgg-accctttttttaatttttattatttggttaatat--agGGATTTTCTTCATGGACCCGGAGGGATTTTAATACTTTCATTAGGGCCTGCGAAAAATATGGCCGAAATGATATAAAAGGTATTGCTTCTGAGATGGAAG
upper sequence: AT3G06400.3 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 20
gcaagtgaatatgtttgatgttagagtggtcttagacatttgatttggtaggctttaattaattttttgtaattgtcaatctccagGGTTTCTCAACATGGAGCAGAAGAGATTTTAATACTTTCCTCAGGGCTTGTGAGAAGTATGGCCGCAACGACATAAAAAGCATTGCCTCTGAGATGGAAG
|||| || | | || | ||| || || |||||| ||| |||| ||| ||| | | |||| || ||| ||||||| ||||||||||| ||||||||| | ||||||||||||||||||||||| || || ||||||| ||||| ||||| |||||||
----gtgagtagaccatctactgtaggg----tagg-atctgttttggtttctttt--ctaatctttgacttttggtgaattgtagGGATTTTCATCATGGAGTAGAAGAGATTTCAATACTTTCATTAGGGCTTGTGAGAAGTATGGCCGGAATGATGTAAAAAGTATTGCTTCTGAAATGGAAGMapped 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|116473629|gb|EG516221.1|EG516221EST: ATCCCTTAACTACTGAAGAAGTAGAAGAAAAGGAGGGATTATTGGAGGAG GGTTTCTCAACATGGAGCAG
genomic: ATCCCTTAACTACTGAAGAAGTAGAAGAAAAGGAGGGATTATTGGAGGAGgcaagtgaat ... caatctccagGGTTTCTCAACATGGAGCAG
EST:
gi|116473628|gb|EG516220.1|EG516220EST: TCCCTTAACTACTGAAGAAGTAGAAGAAAAGGAGGGATTATTGGGAGGAG GGTTTCTCAACATGGAGCA
genomic: TCCCTTAACTACTGAAGAAGTAGAAGAAAAGGAGGGATTATTGG-AGGAGgcaagtgaat ... caatctccagGGTTTCTCAACATGGAGCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttagacatttgatttggtaggctttaattaattttttgtaattgtcaatctccagGGTTTCTCAACATGGAGCAGAAGAGATTTTAATACTTTCCTCAGGGCTTGTGAGAAGTATGGCCGCAACGACATAAAAAGCATTGCCTCTGAGATGGAAG
aattaat putative branch site (score: 3)
tctcc putative PPT
tttaattaattttttg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcaagtgaatatgtttgatgttagagtggtcttagacatttgatttggtaggctttaattaattttttgtaattgtcaatctccagGGTTTCTCAACATGGAGCAGAAGAGATTTTAATACTTTCCTCAGGGCTTGTGAGAAGTATGGCCGCAACGACATAAAAAGCATTGCCTCTGAGATGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG