Sequence
atgc intronic sequence ATGC exonic sequencegtaatcatcaatagagtagaacatcctttcggtttatgctgtcattctaattgccttttgtggtctccgtagATGTCTTATACTGAGAGGAAATGGGGAGCTTTCACTTCTTGATTTGGTTGATGGACGAGAGAGGGAACTTACAGACTCAGTTGAACTATTTTGGGTGACA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G28350.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G28350.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA09G39270.1 (Glycine max), 3'ss of exon 9
---------------------gtaatcatcaatagag--tagaacatcctttcggtttatgctgtcattctaattgccttttg----tggtct-ccgtagATGTCTTATACTGAGAGGAAATGGGGAGCTTTCACTTCTTGATTTGGTTGATGGACGAGAGAGGGAACTTACAGACTCAGTTGAACTATTTTGGGTGACA
| || ||| | | | | | || |||| || |||| | || ||| || || | | |||||||| | ||| |||||| |||||||||||||||||||||||| |||| ||||||||| ||||| | ||||| || |||||||||||||||||||| ||
atgtaactagaatactaggatggaagcattcacggggggttgggggggggggggggttatactttcatatgactttcctcatgaaagtgatttgttgtagATGTTTGATATTGAGAGCAAATGGGGAGCTTTCACTTCTTGACTTGGATGATGGACGGGAGAGAAACCTTACTGATTCAGTTGAACTATTTTGGGTCACC
upper sequence: AT5G28350.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA18G47050.1 (Glycine max), 3'ss of exon 9
-------------------------gtaatcatcaatagagtagaacatcctttcggtttatgctgtcattctaattgccttttg----tggtct-ccgtagATGTCTTATACTGAGAGGAAATGGGGAGCTTTCACTTCTTGATTTGGTTGATGGACGAGAGAGGGAACTTACAGACTCAGTTGAACTATTTTGGGTGACA
| | |||| | | | | || |||| || |||| | || ||| || || | | |||||||| | ||| |||||| |||||||||||||||||||||||| |||| ||||||||| ||||| | || || || |||||||||||||||||||| ||
gtgtaactagaatatgaggatggaagcattcatgcgtggggaggggggggggg--gggttatactttcatatgactttcctcatgaaagtgatttgttgtagATGTTTGATATTGAGAGCAAATGGGGAGCTTTCACTTCTTGACTTGGATGATGGACGGGAGAGAAATCTCACTGATTCAGTTGAACTATTTTGGGTCACC
upper sequence: AT5G28350.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv15s0046g01890.t01 (Vitis vinifera), 3'ss of exon 9
-------gtaatcatcaatagagtagaacatcctttcggtttatgctgtcattctaattgccttttgtggtctccgtagATGTCTTATACTGAGAGGAAATGGGGAGCTTTCACTTCTTGATTTGGTTGATGGACGAGAGAGGGAACTTACAGACTCAGTTGAACTATTTTGGGTGACA
| ||| | | | || || | || | | |||| | | ||| | || |||||| | ||| |||||| ||||||||||||||||| ||||| ||| ||||||||| || || || || || || || |||||| |||||||||| ||
gtatgttcttatccttcaaaatgttaaatagaactttctcacacaacatacttctgactacctgca--tgccttgccagATGTTTGATATTGAGAGTGAATGGGGAGCTTTCACTACTTGACCTGGATGATGGACGTGAAAGAGAGCTCACGGATTCTGTTGAATTATTTTGGGTTACC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agaacatcctttcggtttatgctgtcattctaattgccttttgtggtctccgtagATGTCTTATACTGAGAGGAAATGGGGAGCTTTCACTTCTTGATTTGGTTGATGGACGAGAGAGGGAACTTACAGACTCAGTTGAACTATTTTGGGTGACA
ttctaat putative branch site (score: 2)
tctccgt putative PPT
attctaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatcatcaatagagtagaacatcctttcggtttatgctgtcattctaattgccttttgtggtctccgtagATGTCTTATACTGAGAGGAAATGGGGAGCTTTCACTTCTTGATTTGGTTGATGGACGAGAGAGGGAACTTACAGACTCAGTTGAACTATTTTGGGTGACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG