Sequence
atgc intronic sequence ATGC exonic sequenceACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAGCTTTGATGCCATGGGTCTTCAAGAGAACCTTCTCAGGGgtatttatgcttatggtatgtgtgtaggaacttgaaaaagctatcttttgtgatttatgtcttagattagaacattatctcatgcgtgcttctgttttttcttag
Basic information
species | Arabidopsis thaliana |
transcript | AT3G13920.4 |
intron # | 3 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G13920.4 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA04G05580.1 (Glycine max), 5'ss of exon 3
ACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAGCTTTGATGCCATGGGTCTTCAAGAGAACCTTCTCAGGGgtatttatgcttatggtatgtgtgtaggaacttgaaaaagctatcttttgtgatttatgtcttagattagaacattatctcatgcgtgcttctgttttttcttag-----------
||| || |||||| || || || || ||||| || ||| ||| ||||||||||| ||||| | || ||||||||||| |||||||||||||| |||||||||| | | || || | | ||| || | ||| | ||| | || | | | | | || ||
-ACTGATGGGCAAGAT---TTTTTTACTTCTTATGACGAAGTTTGTGAAAGCTTTGATGCTATGGGATTGCAGGAGAACCTTCTGAGGGGTATTTATGCATATGgtatgttcattaatattttaatttacaacaattttaaatct-tgtttgagaaatttaatttctattggttaggtctgcatcaaacctgagattaatttaca
upper sequence: AT3G13920.4 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA15G03020.1 (Glycine max), 5'ss of exon 3
ACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAGCTTTGATGCCATGGGTCTTCAAGAGAACCTTCTCAGGGgtatttatgcttatggtatgtgtgtaggaacttgaaaaagctatcttttgtgatttatgtc-ttagattagaacattatct-catgcgtgcttctgttttttcttag----------
||| |||||||| || ||||| || |||||||| || |||| || |||||||| ||||| |||||||| || |||||||| || || ||||||||||||||| || || | | |||| || |||| | ||| ||| | || |||| || ||||
-GCTGATGGACAAGA---ATTTTTCACTTCATATGATGAAGTCTATGATAGTTTTGATGCAATGGGCCTTCAAGAAAATCTTCTCAGAGGCATATATGCTTATGgtatg-acaagtgatgtttcctttgtt-tcttcagttgcttatttaattattgaggaatactaggaatatgctcttttaaacacactcttgacaacgggttc
upper sequence: AT3G13920.4 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA13G16570.1 (Glycine max), 5'ss of exon 3
ACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAGCTTTGATGCCATGGGTCTTCAAGAGAACCTTCTCAGGGgtatttatgcttatggtatgtgtgtaggaacttgaaaaagctatcttttgtgatttatg--tcttagattagaacattatctcatgcgtgcttctgttttttcttag--------
||| ||||| || ||||||||||||||||| || ||| |||| || ||||| || |||||| | || || || ||||||||||| ||||| || |||||||| | | | | | || ||| || || | || || | | | | | | || || || || ||
-TCTGATGGACAGGAC---TTCTTCACATCCTATGACGAGGTTTATGATAGTTTTGACGCTATGGGTTTGCAGGAAAATCTTCTCAGGGGAATTTACGCATATGgtattttaaatattcttcctatggattgccattggtgtttcattgttttttaatgaataaaccaccaattttgtcctcaaattattgaacagtctctaac
upper sequence: AT3G13920.4 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA06G05580.1 (Glycine max), 5'ss of exon 3
ACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAGCTTTGATGCCATGGGTCTTCAAGAGAACCTTCTCAGGGgtatttatgcttatggtatgtgtgt--aggaacttgaaaaagctatcttttgtgatttatgtcttagattagaacattatctcatgcgtgcttctgttttttcttag---------
||| || |||||| || || || || ||||| || ||| ||| ||||||||||| ||||| | || ||||||||||| |||||||||||||| || ||||||| | | | ||||| | || ||| | || ||| | ||| | || | | | | | ||| ||
-ACTGATGGGCAAGAT---TTTTTTACTTCTTATGACGAAGTTTGTGAAAGCTTTGATGCTATGGGATTGCAGGAGAACCTTCTGAGGGGTATTTATGCATACGgtatgttcattaatatatttgaatgtacgataattt-tagttcttgtttgagaactttagtttctattgtttagctctgcatcaaatctgagattaattta
upper sequence: AT3G13920.4 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA17G06110.1 (Glycine max), 5'ss of exon 3
ACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAGCTTTGATGCCATGGGTCTTCAAGAGAACCTTCTCAGGGgtatttatgcttatggtatgtgtg-taggaacttgaaaaagctatcttttgtgatttat--gtcttagattagaacattatctcatgcgtgcttctgttttttcttag-------
||| ||||| || ||||||||||||||||| || ||| |||| || ||||| || |||||| | || ||||| ||||||||||| ||||| || || ||||| | | || | | | | || ||| ||||| | || || | | | | | | || || | || ||
-TCTGATGGACAGGAC---TTCTTCACATCCTATGACGAGGTTTATGATAGTTTTGACGCTATGGGTTTGCAGGAGAATCTTCTCAGGGGAATTTACGCATACGgtatttttaatattctttcttgggatttgccattggtgttttattgttttttaatgaataaaccaccaattttgtcctcaaactattgagtatctatcag
upper sequence: AT3G13920.4 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA09G07530.3 (Glycine max), 5'ss of exon 3
ACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAGCTTTGATGCCATGGGTCTTCAAGAGAACCTTCTCAGGGgtatttatgcttatggtatgtgtgtaggaacttgaaaaagctatcttttgtgattt-atgtcttagattagaacattatctcatgcgtgcttctgttttttcttag----------
|| || || ||| |||||||||||||| ||||| ||| |||| || |||||||| ||||| | |||||||| || || || || |||||||| ||||||| | | || || ||||| | |||| || | | | | | |||| | | | | || | ||
-TCCGATGGTCAGGAT---TTCTTCACATCCTACGATGAGGTTTATGACAGTTTTGATGCTATGGGCTTGCAAGAGAATCTCCTGAGAGGCATTTATGCATATGgtagatttaactttctttatgtcctcttacttttttaattttattttccaaaccaaga-gttattttgtattttatcgtgatgacaattgtaatttttttt
upper sequence: AT3G13920.4 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA08G20300.2 (Glycine max), 5'ss of exon 3
ACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAGCTTTGATGCCATGGGTCTTCAAGAGAACCTTCTCAGGGgtatttatgcttatggtatgtgtgtaggaacttgaaaaagctatcttttg-----tgatttatgtcttagattagaacattatctcatgcgtgcttctgttttttcttag------
||| || ||||| |||||||| || |||||||| || |||| ||||||||||| ||||| | |||||||| ||||| | || || |||||||||||||||| | | | ||| | | | |||| | ||| || ||| | | | ||| ||| || |||
-ACTGATGGGCAAGA---ATTCTTCACCTCTTATGATGAAGTGTATGACAGCTTTGATGCAATGGGATTGCAAGAGAATCTTCTGCGAGGCATATATGCTTATGgtatgtac-tggcatattgtgatccccttattttaaatgtttattcatatctgttacagtgccgattgctctgagagactttaaaattcagttaaaaatat
upper sequence: AT3G13920.4 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA07G00950.1 (Glycine max), 5'ss of exon 3
ACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAGCTTTGATGCCATGGGTCTTCAAGAGAACCTTCTCAGGGgtatttatgcttatggtatgtgtgtaggaacttgaaaaagctatcttttgtgatt-tatgtcttagattagaacattatctcatgcgtg---cttctgttttttcttag--------
||| || ||||| |||||||| || ||||| || || |||| ||||||||||||||||| | |||||||| ||||| | || || |||||||||||||||| | | | |||| ||| || || || || | | | || | | | | | | | ||| || |||
-ACTGATGGGCAAGA---ATTCTTCACCTCATATGACGAAGTCTATGACAGCTTTGATGCCATGGGATTGCAAGAGAATCTTCTGCGAGGCATATATGCTTATGgtatgtac-tggcatattgatccccatattttaaatgcttatacatatctg-ttgcagtgtcaattgctctgcgagactttaaaattcagttaaaagtataa
upper sequence: AT3G13920.4 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA13G42360.1 (Glycine max), 5'ss of exon 3
ACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAGCTTTGATGCCATGGGTCTTCAAGAGAACCTTCTCAGGGgtatttatgcttatggtatg--------tgtgtaggaacttgaaaaagctatcttttgtgatttatgtcttagattagaa---cattatctcatgcgtgcttctgttttttcttag
|| |||||||| || ||||| || ||||| || || |||| || |||||||| ||||| |||||||| || ||||| || || || ||||||||||||||| | | | ||| | | | || | ||| ||| | | ||| | | ||| | | | || || | | |
-GCCGATGGACAAGA---ATTTTTCACTTCATATGACGAAGTCTATGATAGTTTTGATGCAATGGGCCTTCAAGAAAATCTTCTGAGAGGCATATATGCTTATGgtatggcaaattatttttcctttctttcttcaattgcttatt-taattcttgtggaatactaggaatatactattttaaacacactcttgacaatgggttg
upper sequence: AT3G13920.4 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv11s0016g01920.t01 (Vitis vinifera), 5'ss of exon 2
ACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAGCTTTGATGCCATGGGTCTTCAAGAGAACCTTCTCAGGGgtatttatgcttatggtatgtgtgtaggaacttgaaaaagctatcttttgtgatttatgtcttagattagaacattatctcatg---cgtgcttctgttttttcttag-------
||| ||||| ||| ||||||||||| |||||||| ||| |||| || |||||| | |||||| | |||||||| |||||||| || |||||||| ||||||| | | | | | ||||| | ||| | | ||| | | ||| | | | |||||| | | | |
-ACTGATGGACAGGAT---TTCTTCACATCTTATGATGAGGTTTATGATAGTTTTGATTCTATGGGTTTGCAAGAGAATCTTCTCAGAGGCATTTATGCATATGgtagaccaatcatgtttcaatattattttctttctaggtttttttattatgatgtatgattgcttgaaatctcttgcttccatgatcaatcaatggtttaMapped 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|116436248|gb|EG478840.1|EG478840EST: TGTTCATGAGAGCTTTGATGCCATGGGTCTTCAAGAGAACCTTCTCAGGGGTATTTATGCTTATG
genomic: TGTTCATGAGAGCTTTGATGCCATGGGTCTTCAAGAGAACCTTCTCA---G-------G-----Ggtatttatgc
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAGCTTTGATGCCATGGGTCTTCAAGAGAACCTTCTCAGGGgtatttatgcttatggtatgtgtgtaggaacttgaaaaagctatcttttgtgatttatgtcttagattagaacattatctcatgcgtgcttctgttttttcttag
- - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA