Sequence
atgc intronic sequence ATGC exonic sequencegtatattagtatttttttaattttggatttgtttgtaaacatgaattttgggtttctgctgtacttgaaatcttgttttagcaactgtgtgatcttttcgtaattttgttcccttggtttaaggaaaagCTGCCTCCAACAGATTCTAGGCTCCGACCAGATCAACGACACTTGGAGAACGGTGAATATGAGAAGGCAAATGAAGAGAAACAAAGATTAGAGAGAAGAC
Basic information
species | Arabidopsis thaliana |
transcript | AT4G12460.2 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G12460.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os08g05870.1 (Oryza sativa), 3'ss of exon 7
gtatattagtatttttttaattttggatttgtttgtaaacatgaattttgggtttctgctgtacttgaaatcttgttttagcaactgtgtgatcttttcgtaattttgttcccttggtttaaggaaaagCTGCCTCCAACAGATTCTAGGCTCCGACCAGATCAACGACACTTGGAGAACGGTGAATATGAGAAGGCAAATGAAGAGAAACAAAGATTAGAGAGAAGAC
| ||| |||| ||||||| | || | ||| |||| | | ||| ||||| | |||| | | || | ||||| || || ||||| || ||||| |||| | ||||| || || || | |||||||||||||||||||||||||| | ||||| | || || ||
--------------------------gtatgtgtgtagtcatgaatactccacaagctttgaa-ttgtttacttgatatcaagactcaatgatcctaattgaattgattggtcatgttcaaagGACAAACTCCCTCCTACTGATTCACGGCTAAGGCCAGACCAGCGGCATCTAGAGAACGGTGAATATGAGAAGGCAAACGCGGAGAAGCTGAGGTTGGAAC------
upper sequence: AT4G12460.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G409265_T03 (Zea mays), 3'ss of exon 3
gtatattagtatttttttaattttggatttgtttgtaaacatgaattttgggtttctgctgtacttgaaatcttgtt--ttagcaactgtgtgatcttttcgtaattttgttcccttggtttaaggaaaagCTGCCTCCAACAGATTCTAGGCTCCGACCAGATCAACGACACTTGGAGAACGGTGAATATGAGAAGGCAAATGAAGAGAAACAAAGATTAGAGAGAAGAC
||| ||||| | | | | | | ||| | | ||| || ||| | | || | | | ||| | ||||| ||||||| |||||||| ||||| ||||| ||||| ||||||||||||| ||| ||||||| || || || |||||||| |||| || |||| | | ||||
----------------------------------gtacacatggaacataaatataacccatcattggacttccgttagttcttaacc-tataatgctaaggcacatttctacccttttgttaagGAGAAGCTGCCACCAACGGATTCAAGGCTGAGACCAGATCAACGTCACCTGGAGAATGGGGAGTACGAGAAGGCCAATGCTGAAAAACTGCGTCTCGAGA------
upper sequence: AT4G12460.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G061099_T01 (Zea mays), 3'ss of exon 8
gtatattagtatttttttaattttggatttgtttgtaaacatgaattttgggtttctgctgtacttgaaatcttgtt--ttagcaactgtgtgatcttttcgtaattttgttcccttggtttaaggaaaagCTGCCTCCAACAGATTCTAGGCTCCGACCAGATCAACGACACTTGGAGAACGGTGAATATGAGAAGGCAAATGAAGAGAAACAAAGATTAGAGAGAAGAC
||| ||||| | | | | | | || | | | |||| | ||| || || || | | || ||||||| |||||||| || || ||||| ||||| ||||||||||||| ||| ||||||| || || || |||||||| |||| || |||| | | ||||
----------------------------------gtacacatggaacatacatatatcccataatctgagttctgttagctcttaacctaaaaggctacgacacatcttttacgctcttgttaagGAGAAGCTGCCACCGACGGATTCAAGGCTGAGACCAGATCAACGGCACCTGGAGAATGGGGAGTACGAGAAGGCCAATGCTGAAAAACTGCGCCTCGAGA------
upper sequence: AT4G12460.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv02s0154g00250.t01 (Vitis vinifera), 3'ss of exon 7
gtatattagtatttttttaattttggatttgtttgtaaacatgaattttgggtttctgctgtacttgaaatcttgttttagcaactgtgtgatcttttcgtaattttgttcccttggtttaaggaaaagCTGCCTCCAACAGATTCTAGGCTCCGACCAGATCAACGACACTTGGAGAACGGTGAATATGAGAAGGCAAATGAAGAGAAACAAAGATTAGAGAGAAGAC
|| || | | || | | ||| | ||| | || ||||| || ||| || | | | || |||| |||| ||||| || |||| || | || ||||||| ||||| || || || ||||| || || |||||||||||||||| | ||||| || |||||||| |||||||||| ||| |||| | | |||||||
--gtagagataatgtattgaatcaatttttttatgtgcatattcattttcctcttatgc-atatctaattgtcttttatagct-ctgtctgatcc---cgggtatttgatcac--ggattaagGAGAAGCTCCCACCCACGGATTCAAGACTTAGACCAGATCAACGACATCTAGAGAATGGAGAATATGAAAAGGCAAATGCAGAAAAACTACGGTTAGAGA------
upper sequence: AT4G12460.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: EFJ15167 (Selaginella moellendorffii), 3'ss of exon 8
gtatattagtatttttttaattttggatttgtttgtaaacatgaattttgggtttctgctgtacttgaaatcttgttttagcaactgtgtgatcttttcgtaattttgttcccttggttta-aggaaaagCTGCCTCCAACAGATTCTAGGCTCCGACCAGATCAACGACACTTGGAGAACGGTGAATATGAGAAGGCAAATGAAGAGAAACAAAGATTAGAGAGAAGAC
|| || || | | || || | | | | | |||| |||||||| ||||||||||| | || |||| ||||||||||| ||||| ||||||||||| ||| |||| ||| || || | | || ||
--------------------------------------------------------------------------gtctttcaaagcattt-attcgctcaagttctcatggtaaaagcgtgcagGAGAAGCTGCCACCAACAGATTCCCGACTGAGACCTGATCAACGACATTTGGAAAACGGTGAATACGAGCAGGCTAATTCCGAAAAGCTGCGGTTGGAAG------
upper sequence: AT4G12460.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: EFJ08416 (Selaginella moellendorffii), 3'ss of exon 9
gtatattagtatttttttaattttggatttgtttgtaaacatgaattttgggtttctgctgtacttgaaatcttgttttagcaactgtgtgatcttttc-gtaattttgttcccttggtttaaggaaaagCTGCCTCCAACAGATTCTAGGCTCCGACCAGATCAACGACACTTGGAGAACGGTGAATATGAGAAGGCAAATGAAGAGAAACAAAGATTAGAGAGAAGAC
|| || || | | || | || | || | | | |||| |||||||| ||||||||||| | || |||| ||||||||||| ||||| ||||||||||| ||| |||| ||| || || | | |||||
--------------------------------------------------------------------------gtctttcaaagcatttattcgctcaagttctcatggtaaaacgcgtgcagGAGAAGCTGCCACCAACAGATTCCCGACTGAGACCTGATCAACGACATTTGGAAAACGGTGAATACGAGCAGGCTAATTCCGAAAAGCTGCGGTTAGAAG------ atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttttagcaactgtgtgatcttttcgtaattttgttcccttggtttaaggaaaagCTGCCTCCAACAGATTCTAGGCTCCGACCAGATCAACGACACTTGGAGAACGGTGAATATGAGAAGGCAAATGAAGAGAAACAAAGATTAGAGAGAAGAC
taattttgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatattagtatttttttaattttggatttgtttgtaaacatgaattttgggtttctgctgtacttgaaatcttgttttagcaactgtgtgatcttttcgtaattttgttcccttggtttaaggaaaagCTGCCTCCAACAGATTCTAGGCTCCGACCAGATCAACGACACTTGGAGAACGGTGAATATGAGAAGGCAAATGAAGAGAAACAAAGATTAGAGAGAAGAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA