Sequence
atgc intronic sequence ATGC exonic sequencegtaaaaagtcagattgcattagtaattgtttgctgtgacatgattagatattgcaacttttttatttaatataagttgatatataccgctaaccaagttctatatcaattttgtttagAGGTTCAATATCAGCAAAGAAGATCTGGATGATTATTTTGGTGGACCAGCGTTTCTTGCTTGGGCTCGCATGGGAAATCTTCACGC
Basic information
species | Arabidopsis thaliana |
transcript | AT5G13690.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G13690.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G033592_T01 (Zea mays), 3'ss of exon 4
gtaaaaagtcagattgcattagtaattgt-ttgctgtgacatgattagatattgcaacttttttatttaatataagttgatatataccgctaaccaagttctatatcaattttgtttagAGGTTCAATATCAGCAAAGAAGATCTGGATGATTATTTTGGTGGACCAGCGTTTCTTGCTTGGGCTCGCATGGGAAATCTTCACGC
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----------------ttcttgtccccacgtcattttgaacttatgctgtgttttgagtttcttctcaacctcctgttgccatgggggccttattaa--tcaatg-cattttatttcagAGTTTTAATGTTACCGACAGAGATTTAGATGATTTTTTTGGTGGACCAGCTTTCCTTGCTTGGGCTAGAATGGGGAACTTGCATGG
upper sequence: AT5G13690.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA10G11720.1 (Glycine max), 3'ss of exon 4
gtaaaaagtcagattgcattagtaattgtttgctgtgacatgattagatattgcaacttttttatttaatataagttgatatataccgctaaccaagttctatatcaattttgtttagAGGTTCAATATCAGCAAAGAAGATCTGGATGATTATTTTGGTGGACCAGCGTTTCTTGCTTGGGCTCGCATGGGAAATCTTCACGC
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----------tgattcttgttgatataatttattttcataagaacaactacagctatttaatattttgttctctttcaatagctact--tgactaa------tatcttctaattgtagGATTTTAACATAAGTTCAAAAGACTTGAATAATTTCTTTGGTGGACCTGCTTTCCTTGCTTGGGCTCGCATGGGAAATTTACATGG
upper sequence: AT5G13690.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S329_23V6.1 (Physcomitrella patens), 3'ss of exon 4
gtaaaaagtcagattgcattagtaattgt-ttgctgtgacatgattagatat-tgcaacttttttatttaatataagttgatatataccgctaaccaagttctatatcaattttgtttagAGGTTCAATATCAGCAAAGAAGATCTGGATGATTATTTTGGTGGACCAGCGTTTCTTGCTTGGGCTCGCATGGGAAATCTTCACGC
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------gggaatagtaatttggtgagcctattgccatgaaggactttgatttgtttgattgatttgtt--atttatattatcatg-agtggtgggggagttgttgacagAG-----TGAAACGTTCAACTTAACCAAGGCTGAATTGGATGATTATTTTGGTGGACCAGGCTTTCTTGCCTGGGCTCGAATGGGCAACTTGAAGAGMapped 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
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttaatataagttgatatataccgctaaccaagttctatatcaattttgtttagAGGTTCAATATCAGCAAAGAAGATCTGGATGATTATTTTGGTGGACCAGCGTTTCTTGCTTGGGCTCGCATGGGAAATCTTCACGC
cgctaac putative branch site (score: 2)
ttttgttt putative PPT
atataagttgatatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaaagtcagattgcattagtaattgtttgctgtgacatgattagatattgcaacttttttatttaatataagttgatatataccgctaaccaagttctatatcaattttgtttagAGGTTCAATATCAGCAAAGAAGATCTGGATGATTATTTTGGTGGACCAGCGTTTCTTGCTTGGGCTCGCATGGGAAATCTTCACGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA