Sequence
atgc intronic sequence ATGC exonic sequenceGGAGAGATGGGAGAGAGAGATTGACTGGATGGCATTGCAAGGAATTAACCTGCCTCTAGCATTCACTGGACAAGAAGCTATTTGGCAAAAGGTTTTCAAGgtaaaaagtcagattgcattagtaattgtttgctgtgacatgattagatattgcaacttttttatttaatataagttgatatataccgctaaccaagttctatatcaattttgtttag
Basic information
species | Arabidopsis thaliana |
transcript | AT5G13690.1 |
intron # | 4 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G13690.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: LOC_Os04g55730.1 (Oryza sativa), 5'ss of exon 4
GGAGAGATGGGAGAGAGAGATTGACTGGATGGCATTGCAAGGAATTAACCTGCCTCTAGCATTCACTGGACAAGAAGCTATTTGGCAAAAGGTTTTCAAGgtaaaaagtcagattgcattagtaattgtttgctgtgacatgattagatattgcaacttttttatttaatataagttgatatataccgctaaccaagttctatatcaattttgtttag
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GGAGCGCTGGGAGAAGGAAATTGACTGGATGGCTCTTCAAGGTATCAATTTGCCTCTTGCTTTCACTGGTCAAGAAGCTATATGGCAGAAAGTTTTTCAGgtgcgtgtgtgttctgctcttttattaaaaaagcttgctgttcactgatactg-aatattttgatctatgcaatgtccgtgtgttct-tagatcaaaaaatg----------------
upper sequence: AT5G13690.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G033592_T01 (Zea mays), 5'ss of exon 4
GGAGAGATGGGAGAGAGAGATTGACTGGATGGCATTGCAAGGAATTAACCTGCCTCTAGCATTCACTGGACAAGAAGCTATTTGGCAAAAGGTTTTCAAGgtaaaaagtcagattgcattagtaattgtttgctgtgacatgattagatattgcaacttttttatttaatataagttgatatataccgctaaccaagttctatatcaattttgtttag
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GAAAAGATGGGAGAAAGAAATTGACTGGATGGCGCTTCAAGGAATTAACTTGCCTTTAGCATTTACTGGACAGGAATCTATCTGGCAGAAGGTTTTTAAGgtagtgtgacagac-acatctacatctctgaaatgttctatca--aagtttcac----cttatattttata-aaatatacttccattagtttttacagtttatagcac----------
upper sequence: AT5G13690.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv13s0064g00370.t01 (Vitis vinifera), 5'ss of exon 4
GGAGAGATGGGAGAGAGAGATTGACTGGATGGCATTGCAAGGAATTAACCTGCCTCTAGCATTCACTGGACAAGAAGCTATTTGGCAAAAGGTTTTCAAGgtaaaaagtcagat--tgcattagtaattgtttgctgtgacatgattagatattgcaacttttttatttaatataagttgatatataccgctaaccaagttctatatcaattttgtttag
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GGAAAGATGGGAGAAAGAGATAGACTGGATGGCTCTACAAGGAGTTAACTTGCCTTTGGCATTTAATGGGCAAGAAGCCATTTGGCAAAAAGTTTTCATGgtgaacaatttattgctacatttatatgttgatacatctaccaggttatgggctgatatttatctatc--atccagtatgtttcagcctatagatggagttc------------------
upper sequence: AT5G13690.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: PP1S329_23V6.1 (Physcomitrella patens), 5'ss of exon 4
GGAGAGATGGGAGAGAGAGATTGACTGGATGGCATTGCAAGGAATTAACCTGCCTCTAGCATTCACTGGACAAGAAGCTATTTGGCAAAAGGTTTTCAAGgtaaaaagtcagattgcattagtaattgtttgctgtgacatgattagatattgcaacttt--tttatttaatataagttgatatataccgctaaccaagttctatatcaattttgtttag
|||| ||||||| | ||| || || ||||||||||||||||| || || ||||||| |||||||| || ||||| ||| ||||||| ||||| ||| |||| || ||| || | || ||||| | || | | | || || || |||| | || | | | ||| | || | |
GGAGCGATGGGAAAAAGAAATAGATTGGATGGCATTGCAAGGTATCAATTTGCCTCTTGCATTCACAGGGCAAGAGGCTGTTTGGCAGAAGGTCTTCCAGgt---gggttgaatt---tttggaagtgtttccgactgaattacttg-cggtgtaaattgagtttaccggagggaaact--cttgctttgttaatgagtttgcagacat-----------
upper sequence: AT5G13690.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: EFJ23779 (Selaginella moellendorffii), 5'ss of exon 4
GGAGAGATGGGAGAGAGAGATTGACTGGATGGCATTGCAAGGAATTAACCTGCCTCTAGCATTCACTGGACAAGAAGCTATTTGGCAAAAGGTTTTCAAGgtaaaaagtcagattgcattagtaattgtttgctgtgacatgattagatattgcaacttttttatttaatataagttgatatataccgctaaccaagttctatatcaattttgtttag
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GAAAAGGTGGAGGAAAGAGATAGACTGGATGGCCTTGCAGGGAATCAACTTACCTCTTGCATTCACCGGCCAGGAAACTATATGGCAAAAAGTTTTCGAGgt---ttggcagtgtatgggagtt-ctgtgtgtgcttatatt-ttcgttgctgacag-------------------------------------------------------------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|116415708|gb|EG458300.1|EG458300EST: TGCCTCTAGCATTCACTGGACAAGAAGCTATTTGGCAAAAGGTTTTCAAG AGGTTCAATATCAGCAAAGAAGATCTGGATGATTATTTTGGTGGACCAGCG
genomic: TGCCTCTAGCATTCACTGGACAAGAAGCTATTTGGCAAAAGGTTTTCAAGgtaaaaagtc ... ttttgtttagAGGTTCAATATCAGCAAAGAAGATCTGGATGATTATTTTGGTGGACCAGCG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GGAGAGATGGGAGAGAGAGATTGACTGGATGGCATTGCAAGGAATTAACCTGCCTCTAGCATTCACTGGACAAGAAGCTATTTGGCAAAAGGTTTTCAAGgtaaaaagtcagattgcattagtaattgtttgctgtgacatgattagatattgcaacttttttatttaatataagttgatatataccgctaaccaagttctatatcaattttgtttag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC