Sequence
atgc intronic sequence ATGC exonic sequencegtactatatgcgatttgaaataactattatcgagttttcttagactatcctctttcgctaatgaacattttcctgtaaatatatgcacagAAAGAAGGGAGACAGCGTGGAACATGGAGTGGGAAGAAAACTGACTCTGATTTCTACAAAAAAATT
Basic information
species | Arabidopsis thaliana |
transcript | AT2G18876.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G18876.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA17G07040.2 (Glycine max), 3'ss of exon 8
gtactatatgcgatttgaaataactattatcgagttttcttagac--tatcctctttcgctaatgaacattttcctgtaaatatatgcacagAAAGAAGGGAGACAGCGTGGAACATGGAGTGGGAAGAAAACTGACTCTGATTTCTACAAAAAAATT
| | | | | | || | | || ||| ||| || ||| | |||| | | | | | | | |||||| |||||||| || ||||||||||||| |||||||||| ||||| |||||| || ||||| |||
-------gtaccagct-atccatttagtttggactttgcttggaagatattcaatttcatgagaatttggtatttatgatgtgtgtaaacagAAGGAAGGGAGGCAACGTGGAACATGGAATGGGAAGAAAGCTGACAATGATTTTTATAAAAAGATT
upper sequence: AT2G18876.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA13G00980.1 (Glycine max), 3'ss of exon 8
gtactatatgcgatttgaaataactattatcgagttttcttagactatcctct-ttcgctaatgaacattttcctgtaa-atatatgcacagAAAGAAGGGAGACAGCGTGGAACATGGAGTGGGAAGAAAACTGACTCTGATTTCTACAAAAAAATT
| | | | | | || | | || ||| ||| || || | | || | || | | | | | | | | |||||| |||||||| || ||||||||||||| |||||||||| ||||| |||||| || ||||| |||
-------gtaccagct-atccatgtagtttggactttgcttggaagatattttatttcatgataatttggtatttatgatgtgtgtaaacagAAGGAAGGGAGGCAACGTGGAACATGGAATGGGAAGAAAGCTGACAATGATTTTTATAAAAAGATT
upper sequence: AT2G18876.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv11s0052g00890.t01 (Vitis vinifera), 3'ss of exon 8
gtacta-tatgcgatttgaaataact---attatcgagttttcttagactatcctctttcgctaatgaacattttcctgtaaatatatgcacagAAAGAAGGGAGACAGCGTGGAACATGGAGTGGGAAGAAAACTGACTCTGATTTCTACAAAAAAATT
|| | | ||| | ||| || ||| || |||| || | | |||| | || | || | || | | ||||||||||||| |||| ||||| ||||||| ||| ||||| |||||| ||||||||| |||||||||
gtgtcagtctgccaattgcttgttctgagatttctgaatttttttggttgaaagcatttcataattggcctttgtgct----tggtgtaaacagAAAGAAGGGCGACAACGTGGGACATGGAATGGAAAGAAGACTGACAATGATTTCTATAAAAAAATT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttcttagactatcctctttcgctaatgaacattttcctgtaaatatatgcacagAAAGAAGGGAGACAGCGTGGAACATGGAGTGGGAAGAAAACTGACTCTGATTTCTACAAAAAAATT
cgctaat putative branch site (score: 3)
tgtaaatatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtactatatgcgatttgaaataactattatcgagttttcttagactatcctctttcgctaatgaacattttcctgtaaatatatgcacagAAAGAAGGGAGACAGCGTGGAACATGGAGTGGGAAGAAAACTGACTCTGATTTCTACAAAAAAATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA