Sequence
atgc intronic sequence ATGC exonic sequencegtaaggctctacagtcttttgaataattatcttgtggaaaacaattgtgccagtgctagtctgaaatttttgaagatttagatttctcgataagttttctcagtcaattccatttaatatatgcttacaatttaatataaaaacatcaacatatacttttgcttgcccttcaacggttccaaatttctttttagGAGAAGTATGTATTCAAACATCCTCAACCAAAGAGACCTAAGTCGCTAAGGATTTATGAAGCACATGTTGGCATGAGTAGCACG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G03650.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G03650.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os04g33460.1 (Oryza sativa), 3'ss of exon 8
gtaaggctctacagtcttttgaataattatcttgtggaaaacaattgtgccagtgctagtctgaaatttttgaagatttagatt--tctcgataagttttctcagtcaattccatt-taatatatgcttacaatttaatataaaaacatcaacatatacttttgcttgcc--cttcaacggtt--ccaaatttctttttagGAGAAGTATGTATTCAAACATCCTCAACCAAAGAGACCTAAGTCGCTAAGGATTTATGAAGCACATGTTGGCATGAGTAGCACG
| || | | | |||| || ||| | || ||| | | ||| || || || | | || ||| | || || | | || || | || | | | | | || | | || ||| || || || | | ||| | | | |||| || ||||||||| ||||||||||||| || |||| || ||||| |||| |||||| ||||| |||| ||||||||| ||
----------gtatgtttctaccttacagtctttccacgaaatatttttcccttgcattttt----tttaaaaaaatctatgctcgtgtcactaaaaccttatag--aactgtgtaatactactttttttctttgttgatcaggatattccattttaacctttattttccatctcctaatgttgtttatacgcaactgcagGAAAAATATGTATTCCAACATCCTCAACCTAAACGACCAAATTCGCTGCGGATATATGAATCACATATTGGAATGAGTAGCCCG
upper sequence: AT5G03650.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os02g32660.2 (Oryza sativa), 3'ss of exon 8
gtaaggctctacagtcttttgaataattatcttgtggaaaacaattgtgccagtgctagtctgaaatttttgaagatttagatttctcgataagttttctcagtcaattccatttaatatatgcttacaatttaatataaaaacatcaacatatacttttg--cttgcccttcaacggttccaaatttctttttagGAGAAGTATGTATTCAAACATCCTCAACCAAAGAGACCTAAGTCGCTAAGGATTTATGAAGCACATGTTGGCATGAGTAGCACG
||| | | | | || | | | | | | | || || | | ||| | |||| | || | ||| || | | | | | | || ||| | | | | | | | | ||||| || | || || ||| | || || | |||||||||| ||||||| ||||||||||| || ||||| ||||| | |||| || ||| | |||||||| ||||||||||||
gtacctcccccccccccccccaacacgtg-cacacgccatttgaatatgttcttgttccttgaaaaaagtgcttcatttgtacttgtgaata--cttctgtaatgtccttggactcttggaaatttctctttttgt-tggcatctttagattgttctttttatctagttattaaaatgttttatatgactatgcagGAGAAGTACATATTCAAGCATCCTCAACCTAAAAGACCAAAGTCATTGCGGATATACGAAACTCATGTTGGAATGAGTAGCACG
upper sequence: AT5G03650.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G073054_T02 (Zea mays), 3'ss of exon 8
gtaaggctctacagtcttttgaataattatcttgtggaaaacaattgtgccagtgctagtctgaaatttttgaagatttagatttctcgataagttttctcagtcaattccatttaatatatgcttacaatttaatataaaaacatcaacatatacttttgcttgcccttcaacggttccaaatttctttttagGAGAAGTATGTATTCAAACATCCTCAACCAAAGAGACCTAAGTCGCTAAGGATTTATGAAGCACATGTTGGCATGAGTAGCACG
|||| | || || | || || | ||| | || | ||| | | | ||| || |||||| | || | | |||| ||||||| |||||||||||||| |||||||| ||| | || ||||| || |||| |||||| |||||||||| ||||||||| ||
-------------------------------------------------------------------------------agatga-tggactagctcattcctcaaaccaaacaccctat-tactctcttttttggttcacttcttcattttaaactttttatgacct-------atgcaaaatgc------agGAGAAATATGTATTCAAACACCCTCAACCTAAGCGGCCCAAGTCACTGCGGATATATGAATCACATGTTGGAATGAGTAGCCCG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaaacatcaacatatacttttgcttgcccttcaacggttccaaatttctttttagGAGAAGTATGTATTCAAACATCCTCAACCAAAGAGACCTAAGTCGCTAAGGATTTATGAAGCACATGTTGGCATGAGTAGCACG
tttcttttt CT-rich tract
aaatttcttttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaggctctacagtcttttgaataattatcttgtggaaaacaattgtgccagtgctagtctgaaatttttgaagatttagatttctcgataagttttctcagtcaattccatttaatatatgcttacaatttaatataaaaacatcaacatatacttttgcttgcccttcaacggttccaaatttctttttagGAGAAGTATGTATTCAAACATCCTCAACCAAAGAGACCTAAGTCGCTAAGGATTTATGAAGCACATGTTGGCATGAGTAGCACG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC