Sequence
atgc intronic sequence ATGC exonic sequencegtaagcatttcttatgcttcattttccataattttttgctagtaaattgggtgacatgtcatctttatgctcttttgttaaattcttcgcagCACCTGGTCATCTGGAAAAAGTATTGAAAGAACAAATCGCCGAGGGACAACCCAGGACGCATAGACCGTGGAAGAAAATTATTGTTGTTGTTGAGGGTAT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G48780.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G48780.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA16G26210.1 (Glycine max), 3'ss of exon 6
gtaagcatttctta---tg-cttcattttccataattttttgctagtaaattgggtgaca-tgtcatctttatgctcttttgttaaattctt---cgcagCACCTGGTCATCTGGAAAAAGTATTGAAAGAACAAATCGCCGAGGGACAACCCAGGACGCATAGACCGTGGAAGAAAATTATTGTTGTTGTTGAGGGTAT
||| ||| | | || || |||| |||| | || | | | ||| || | | || | | || | || || | || ||| || |||||| ||| |||| |||| ||||||||| || ||||||||||| ||||| ||||| || |||||||| || || ||| |||| ||||| ||
gtatttttttttcaatttgtctctatttgtgttaatatgatgttgctcacagaggttgcagtattatttattctctttcttcttggttatttacctacagAGCCATCTCATCTAGAAGAAGTGTTGAGAGAACAAATTGCTGAGGGACAACCTAGGACACATAGGCCTTGGAAGAAGATAATGGTTATTGTGGAGGGGAT
upper sequence: AT3G48780.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA02G07250.1 (Glycine max), 3'ss of exon 6
--gtaagcatttct-tatgcttc-attttccataattttttgctagtaaattgggtgaca-tgtcatctttatgctcttttgttaaattctt---cgcagCACCTGGTCATCTGGAAAAAGTATTGAAAGAACAAATCGCCGAGGGACAACCCAGGACGCATAGACCGTGGAAGAAAATTATTGTTGTTGTTGAGGGTAT
| | |||| | || ||| |||| |||| | || | | | ||| || | | || | | || | || || | || ||| || |||||| ||| |||| || | ||||||||| || ||||||||||| ||||| ||||| || |||||||| || || |||||||| ||||| ||
ttgcatttttttcaatttgtttctatttgtgttaatatgatgttgctcacagaggttgcagtattatttattcactttcttcttggctatttacctacagAGCCATCTCATCTAGAAGAAGTGTTAAGAGAACAAATTGCTGAGGGACAACCTAGGACACATAGGCCTTGGAAGAAGATAATGGTTGTTGTGGAGGGGAT
upper sequence: AT3G48780.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv17s0000g00500.t01 (Vitis vinifera), 3'ss of exon 6
----gtaagcatttcttatgcttcattttccataattttttgctagtaaa-------ttgggtgacatgtcatctttatgctcttttgttaaattcttcgcagCACCTGGTCATCTGGAAAAAGTATTGAAAGAACAAATCGCCGAGGGACAACCCAGGACGCATAGACCGTGGAAGAAAATTATTGTTGTTGTTGAGGGTAT
|| ||| | | || || ||| ||| ||| ||| ||| ||| ||| | | || |||| | | ||| | || | || ||| ||| |||| ||||| |||| ||||||||| || |||||||||||| |||| |||||||| |||||||| || ||||||||||| || || ||
gtatgttgatattgcatttgtttt-tttggagtaaatttaccctatgaaacatacatttgagtgt--tcttatggatatggttctatgtcatctttcttatagTACCATCTCACTTGGAGAAAGTTTTGAGAGAACAAATTGCTGAGGGACAACCCCGGACACATAGACCATGGAAGAAGATAATTGTTGTTGTGGAAGGAAT
upper sequence: AT3G48780.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv14s0068g01300.t01 (Vitis vinifera), 3'ss of exon 6
gtaagcatt--tcttatgcttcattttccataat--------tttttgctagtaaattgggtgacatgtcat-ctttatgctctt-ttgttaaattcttcgcagCACCTGGTCATCTGGAAAAAGTATTGAAAGAACAAATCGCCGAGGGACAACCCAGGACGCATAGACCGTGGAAGAAAATTATTGTTGTTGTTGAGGGTAT
||||| | || ||||| |||||| ||| | |||| | | ||||| | | ||| |||| | || ||| | || | ||||||| |||| |||| |||| |||| ||||||||| || || ||||| ||||||||||||||||| |||||||| || || |||||||| ||||| ||
----gcattaattttctgcttggttttcctgaatgcacatactctttggaatttaattgaaatattttccatgctttgtttctttattgccattttgcttccagCACCCTCTCATTTGGAGGAAGTTTTGAGAGAACAAATTGCTGAAGGACAGCCCAGGACGCATAGACCTTGGAAGAAGATCATAGTTGTTGTGGAGGGAAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gctagtaaattgggtgacatgtcatctttatgctcttttgttaaattcttcgcagCACCTGGTCATCTGGAAAAAGTATTGAAAGAACAAATCGCCGAGGGACAACCCAGGACGCATAGACCGTGGAAGAAAATTATTGTTGTTGTTGAGGGTAT
ttcttcgc CT-rich tract
ttttgttaaattctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagcatttcttatgcttcattttccataattttttgctagtaaattgggtgacatgtcatctttatgctcttttgttaaattcttcgcagCACCTGGTCATCTGGAAAAAGTATTGAAAGAACAAATCGCCGAGGGACAACCCAGGACGCATAGACCGTGGAAGAAAATTATTGTTGTTGTTGAGGGTAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA