Sequence
atgc intronic sequence ATGC exonic sequenceTACACCTTTAAAAGATGTGCTCAAGCATTCAGGTTTGAAGATTGATGATATATCTGCAGTGGAACTAATAGGAGGAGCTACTAGAGTTCCCAAACTACAGgtaggttttcatgctctcaaagccaatcaatttggcattctcatccaaaactgggggactttcactttttttttcttttcaaatgaagctaagatataatttttgttttaattacag
Basic information
species | Arabidopsis thaliana |
transcript | AT4G16660.1 |
intron # | 4 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G16660.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: LOC_Os02g48110.1 (Oryza sativa), 5'ss of exon 3
TACACCTTTAAAAGATGTGCTCAAGCATTCAGGTTTGAAGATTGATGATATATCTGCAGTGGAACTAATAGGAGGAGCTACTAGAGTTCCCAAACTACAGgtaggttttcatgctctcaaagccaatcaatttggcattctcatccaaaactgggggactttcactttttttttcttttcaaatgaagctaagatataatttttgttttaattacag
|| || | ||||| ||||| ||||| || |||||||||||||||| | ||| || ||| ||||||||||||||||| |||| || ||| | ||||| | ||| || ||| | | | | | || ||| || | | || | || | | | | | |||| | | || | ||
AACTCCAGTTAAAGAAGTGCTTGCACATTCTGGAATGAAGATTGATGATATCTATGCTGTAGAATTAATAGGAGGAGCTACTCGAGTACCAAAATTGCAGgtga------------ttaaactgaactcgtttttatgtttgaccttgtattgtggggctctaatggcattcaggcacatgactg---ccatgtttttatttctctcttg-tcact-
upper sequence: AT4G16660.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G158093_T01 (Zea mays), 5'ss of exon 3
TACACCTTTAAAAGATGTGCTCAAGCATTCAGGTTTGAAGATTGATGATATATCTGCAGTGGAACTAATAGGAGGAGCTACTAGAGTTCCCAAACTACAGgtaggttttcatgctctcaaagccaatcaatttggcattctcatccaaaactgggggactttcactttttttttcttttcaaatgaagctaagatataatttttgttttaattacag
|| || | ||||| ||||| | ||||| || ||||||| |||||||| | ||| || |||||||||||||||||||| || ||||| ||||| ||||| | || | || || | || | | ||| | | || || | | || |||| | | | || || ||| | | |||
GACTCCAGTTAAAGAAGTGCTGACACATTCTGGCATGAAGATCGATGATATCTATGCTGTAGAACTAATAGGAGGAGCTACCAGGGTTCCAAAACTGCAGgttaataaatttggtt---------gtcttttagatttttttacttaaactttgtggtgcttttcaaaatcatttttttatatcta---ttagctagaatcatcttcttagg-----
upper sequence: AT4G16660.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv04s0008g04410.t01 (Vitis vinifera), 5'ss of exon 3
TACACCTTTAAAAGATGTGCTCAAGCATTCAGGTTTGAAGATTGATGATATATCTGCAGTGGAACTAATAGGAGGAGCTACTAGAGTTCCCAAACTACAGgtaggttttcatgctctcaaagccaatcaatttggcattctcatccaaaactgggggact---ttcactttttttttcttttcaaatgaagctaagatataatttttgttttaattacag
|| ||| || || ||||| ||| |||||||||||||| ||||||| |||| ||||||||| || |||||||| || ||| |||| || || | ||||| | | |||| | || | ||| | || | || | | | ||| || | ||| || || | | |||| | | | |
TATTCCTGCGAAGGAAGTGCTTAAGAATTCAGGTTTGAAGGTTGATGAGATATATGCAGTGGAGCTGATAGGAGGTGCCACTCGAGTGCCAAAGTTGCAGgtttgcatcacctttctccagttttat-atattgccctttctgtgcatagaagcagcactgactttagtttaattaactctcccaatgcactagatagttg-------------------
upper sequence: AT4G16660.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv04s0043g00710.t01 (Vitis vinifera), 5'ss of exon 4
TACACCTTTAAAAGATGTGCTCAAGCATTCAGGTTTGAAGATTGATGATATATCTGCAGTGGAACTAATAGGAGGAGCTACTAGAGTTCCCAAACTACAGgtaggttttcatgctctcaaagccaatcaatttggcattctc-atccaaaactgggggactttcactttttttttcttttcaaatgaagctaagatataatttttgttttaattacag
|| | | | || || ||||| ||| |||||||||||||| ||||||| |||| ||||||||| || |||||||| || ||| |||| || || | ||||| | || ||| | | || ||| |||| || | || | | | ||| | | ||| | | || || | ||| |
TATTCTTGTGAAGGAAGTGCTTAAGAATTCAGGTTTGAAGGTTGATGAGATATATGCAGTGGAGCTGATAGGAGGTGCCACTCGAGTGCCAAAGTTGCAGgtttgcatttccttcctccagtttta-catattgccattttctgtgcatagaagcagcactgactttagtttaaattaactatcccaatgtactaaatagt-----------------
upper sequence: AT4G16660.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv09s0096g00090.t01 (Vitis vinifera), 5'ss of exon 5
TACACCTTTAAAAGATGTGCTCAAGCATTCAGGTTTGAAGATTGATGATATATCTGCAGTGGAACTAATAGGAGGAGCTACTAGAGTTCCCAAACTACAGgtaggttttcatgctctcaaagccaatcaatttggcattctc---atccaaaactgggg--gactttcactttttttttcttttcaaatgaagctaagatataatttttgttttaattacag
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TATTCCTGTGAAGGAAGTGCTTAAGAATTCAGGTTTGAAGGTTGATGAGATATATGCAGTGGAGCTGATAGGAGGTGCCACTCGAGTGCCAAAGTTGCAGgtttgcatttccttcctccagtttta-catattgccattttctgtgcttagaagcagcactgactttagtttaaattaactatcccaatgta-ctaaatagt--------------------Mapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|86060228|gb|DR355985.1|DR355985EST: TATCTGCAGTGGAACTAATAGGAGGAGCTACTAGAGTTCCCAAACTACAG AGCACAATCCAGGAATTTATTGGGAAACAACAGTTAGACAAACATCTAGAC
genomic: TATCTGCAGTGGAACTAATAGGAGGAGCTACTAGAGTTCCCAAACTACAGgtaggttttc ... ttaattacagAGCACAATCCAGGAATTTATTGGGAAACAACAGTTAGACAAACATCTAGAC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TACACCTTTAAAAGATGTGCTCAAGCATTCAGGTTTGAAGATTGATGATATATCTGCAGTGGAACTAATAGGAGGAGCTACTAGAGTTCCCAAACTACAGgtaggttttcatgctctcaaagccaatcaatttggcattctcatccaaaactgggggactttcactttttttttcttttcaaatgaagctaagatataatttttgttttaattacag
- - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT