Sequence
atgc intronic sequence ATGC exonic sequencegtaaatgaaaaatcgaataatttagttaagccattttccgacagtctcttctaatttgtgtgtgtaaatcgtttttatgatattttaacttaaattcgtcatattttaattcagtggtaatgttaacactgtttatcttcttctttgcacatagttttaatgtatcacatgccactagGTAGCAGCACTTGCTATGGAGGACATGATAGCTTGGATGCAAGAAGGTGGTCAA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G07110.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G07110.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os05g07130.2 (Oryza sativa), 3'ss of exon 9
gtaaatgaaaaatcgaataatttagttaagccattttccgacagtctcttctaatttgtgtgtgtaaatcgtttttatgatattttaacttaaattcgtcatattttaattcagtggtaatgttaacactgtttatcttct-tctttgcacatagttttaatgtatcacatgccactagGTAGCAGCACTTGCTATGGAGGACATGATAGCTTGGATGCAAGAAGGTGGTCAA
||| || || ||| || |||||| || ||| ||| |||| | | ||| || |||| | | ||| || | | | | |||| || || | ||||||||||||||||||| ||||||||| | || || ||
------------------------------------------------------------------------tttgattggatgagaaccaaa---cgtcatg----aagcaagtattaacattaaatttatatatatttagtcttactagcaaatttcaacatttacgttttttccagGTGGCTGCTTTAGCTATGGAGGACATGATAGATTGGATGCATGGGGGAGGACAG
upper sequence: AT1G07110.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA11G27870.1 (Glycine max), 3'ss of exon 10
gtaaatgaaaaatcgaataatttagttaagccattttccgacagtctcttctaatttgtgtgtgtaaatcgtttttatgatattttaacttaaattcgtcatattttaattcagtggtaatgttaacactgtttatcttcttctttgcacatagttttaatgtatcacatgccactagGTAGCAGCACTTGCTATGGAGGACATGATAGCTTGGATGCAAGAAGGTGGTCAA
| | | | || ||| | ||| | | | || | ||| | ||| ||| || |||||||||||||||||||| ||||| |||||||||||||| || | || || |||||| |||||||||||||||| || ||
------------------------------------------------------------------------------tacttctaatatttgatttattatagatggttctcataaaggtgacaccacattgaccctttctctgtgtacatagttttaatgtatcacgtgccattagGTAGCAGCACTGGCATTTGAAGATATGATATCTTGGATGCAAGAAGGAGGCCAG
upper sequence: AT1G07110.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA18G06770.1 (Glycine max), 3'ss of exon 11
gtaaatgaaaaatcgaataatttagttaagccattttccgacagtctcttctaatttgtgtgtgtaaatcgtttttatgatattttaacttaaattcgtcatattttaattcagtggtaatgttaacactgtttatcttcttctttgcacatagttttaatgtatcacatgccactagGTAGCAGCACTTGCTATGGAGGACATGATAGCTTGGATGCAAGAAGGTGGTCAA
| | | | || ||| | ||| | || || || | ||| | ||| ||| || |||||||||||||||||||| ||||| |||||||||||||| || | || || ||||| ||||||||||||||||||| ||
------------------------------------------------------------------------------tacttctaatttttgatttataatagatggttttcgtaaagttgacaccacgttgaccctttctctgtgtacatagttttaatgtatcacgtgccattagGTAGCAGCACTGGCATTTGAAGATATGATCTCTTGGATGCAAGAAGGTGGCCAG
upper sequence: AT1G07110.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA11G27410.1 (Glycine max), 3'ss of exon 15
gtaaatgaaaaatcgaataatttagttaagccattttccgacagtctcttctaatttgtgtgtgtaaatcgtttttatgatattttaacttaaattcgtcatattttaattcagtggtaatgttaacactgtttatcttcttctttgcacatagttttaatgtatcacatgccactagGTAGCAGCACTTGCTATGGAGGACATGATAGCTTGGATGCAAGAAGGTGGTCAA
| | | | || ||| | ||| | | | || | ||| | ||| ||| || || ||||||||||||||||| ||||| |||||||||||||| || | || || ||||| ||||||||||||||||||| ||
------------------------------------------------------------------------------tacttctaatatttgatttataatagatggttctcataaagttgacaccacattgaccctttctctgtgtacgtagttttaatgtatcacgtgccattagGTAGCAGCACTGGCATTTGAAGATATGATCTCTTGGATGCAAGAAGGTGGCCAG
upper sequence: AT1G07110.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 9
gtaaatgaaaaatcgaataatttagttaagccattttccgacagtctcttctaatttgtgtgtgtaaatcgtttttatgatattttaacttaaattcgtcatattttaattcagtggtaatgttaacactgtttatcttcttctttgcacatagttttaatgtatcacatgccactagGTAGCAGCACTTGCTATGGAGGACATGATAGCTTGGATGCAAGAAGGTGGTCAA
| | |||| | || | | || | || |||||| | | || | | | |||||||||||||||||||||||||||||||||||||||||||||| || || ||||| || |||||| ||||||||||||| || || ||
--------------------------------------------------------------------------ccactaaatttgatttttcttggatgatg----gacaaggttttaatgtgacttttattgacccttttctttgcacatagttttaatgtatcacatgccactagGTAGCAGCCCTGGCAATGGATGATATGATATCTTGGATGCAAGAGGGCGGCCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taacactgtttatcttcttctttgcacatagttttaatgtatcacatgccactagGTAGCAGCACTTGCTATGGAGGACATGATAGCTTGGATGCAAGAAGGTGGTCAA
atagttttaatgtat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaatgaaaaatcgaataatttagttaagccattttccgacagtctcttctaatttgtgtgtgtaaatcgtttttatgatattttaacttaaattcgtcatattttaattcagtggtaatgttaacactgtttatcttcttctttgcacatagttttaatgtatcacatgccactagGTAGCAGCACTTGCTATGGAGGACATGATAGCTTGGATGCAAGAAGGTGGTCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG