Sequence
atgc intronic sequence ATGC exonic sequencegtaaatttctttcatgagcttgtctagtgaagttttaggctaatgcatttgccatcaagtggagttatgttttgaagctcattcatgctgttttgttcttcgtgtattgtttagCACAGTGAACAGTGATGGATTTAAACCAAATTTGGAGACCCAACTTGTTCCGCTACTGGCAACAAAATCAGATGAATCCTCAGCAGAGTCCAAGGACAAA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G04710.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G04710.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA20G32790.1 (Glycine max), 3'ss of exon 2
gtaaatttctttcatgagcttgtctagtgaagttttaggctaatgcatttgccatcaagtggagttatgttttgaagctcattcatgctgttttgttcttcgtgt-attgtttagCACAGTGAACAGTGATGGATTTAAACCAAATTTGGAGACCCAACTTGTTCCGCTACTGGCAACAAAATCAGATGAATCCTCAGCAGAGTCCAAGGACAAA
||||| ||| | ||| | | || || | || | ||||| || | | | | | | || | | || || || | ||||||||||||||||||| ||||| |||||||||||| | ||||| || ||| ||| |||| ||| || | || || | || || ||||| |||
------ttcttccatta-cttcttt------gtcatataccggtgt-tctgcca-cagaaacatgcaagctaccagcagattctatctccctctcttatttgttttattgtttagCACAGTGAACCAGGATGGGTTTAAACCAAATCTAGAGACTCATCTTCATCCTTTACTCTCAATGAAGCCTGAGGACACTTCTTTGGAATCCAACTCCAAG
upper sequence: AT5G04710.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA10G34800.1 (Glycine max), 3'ss of exon 2
gtaaatttctttcatgagcttgtctagtgaagttttaggctaatgcatttgccatcaagtggagtta--tgttttgaagctcattcatgctgttttgttct-tcgtgtattgtttagCACAGTGAACAGTGATGGATTTAAACCAAATTTGGAGACCCAACTTGTTCCGCTACTGGCAACAAAATCAGATGAATCCTCAGCAGAGTCCAAGGACAAA
| ||| | || | | || || || | || | ||||| | | | | | || ||| || | || || | || |||||||||||||||||||| ||||| |||||||||||| | ||||| || ||| |||| |||| ||| ||| | || || | || || ||||| |||
----------tccattactttcttt------gtcatatgccagtgt-tctgccacagaaacatgcaagctaccagcagattctatcaccctctcttatttggtggtttattgtttagCACAGTGAACCTGGATGGTTTTAAACCAAATCTAGAGACTCATCTTCTTCCTTTACTCTCAATGAAACCTGAGGACACTTCTTTGGAATCCAACTCCAAG
upper sequence: AT5G04710.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv13s0106g00700.t01 (Vitis vinifera), 3'ss of exon 4
--gtaaatttctttcatgagcttgtctagtgaagttttaggctaatgcatttgccatcaagtggagttatgttttgaagctcattcatgctgttttgttcttcgtgtattgtttagCACAGTGAACAGTGATGGATTTAAACCAAATTTGGAGACCCAACTTGTTCCGCTACTGGCAACAAAATCAGATGAATCCTCAGCAGAGTCCAAGGACAAA
|||| | | | || | || || | |||| | || | ||| | | ||| ||||| | | ||| | |||| | | ||||||||||||||||||| |||||||||||||||||| | ||||| || || |||| |||| ||||||||| || ||| | || |||||||||| || |||
atttaaaactggcttttacatatggtttgtaaattgttagtttc---tgttggttgccaaat----ctgtgt------gctcacttgt---ttttcggccttcttttgttgtttagCACAGTGAACAAGGATGGATTTAAACCAAATCTTGAGACTCACCTAATTCCATTACTCGCAACAAAACTTGAGGAAGCATCTTCAGAGTCCAAAGAGAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggagttatgttttgaagctcattcatgctgttttgttcttcgtgtattgtttagCACAGTGAACAGTGATGGATTTAAACCAAATTTGGAGACCCAACTTGTTCCGCTACTGGCAACAAAATCAGATGAATCCTCAGCAGAGTCCAAGGACAAA
ttatgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaatttctttcatgagcttgtctagtgaagttttaggctaatgcatttgccatcaagtggagttatgttttgaagctcattcatgctgttttgttcttcgtgtattgtttagCACAGTGAACAGTGATGGATTTAAACCAAATTTGGAGACCCAACTTGTTCCGCTACTGGCAACAAAATCAGATGAATCCTCAGCAGAGTCCAAGGACAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG