Sequence
atgc intronic sequence ATGC exonic sequencegtatgtaattcacacgtatttaattctctttacatatccagtaaaaattggcattttggttctgtcctcaatggtcttggttatggtatatgtgttgactgtttttacattcctgctccagATTTAATAAATTTGACTTCCCACCAATATTCCATCGTGATGGGGATACTAATCCAGATGAGATACGG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G48500.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G48500.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G091419_T01 (Zea mays), 3'ss of exon 6
gtatgtaattcacacgtatttaattctctttacatatccagtaaaaattggcattttggttctgtcctcaatggtcttggttatggtatatgtgttgac-tgtttttacattcctgctccagATTTAATAAATTTGACTTCCCACCAATATTCCATCGTGATGGGGATACTAATCCAGATGAGATACGG
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----gtgagtaccactgttatcattgtgtcctcagttctgataatat---gaatattaatgccagttgccata---tcggtgcttgagtttattccaatgtgtatttcccttctgactgcagATTTAATAGATTCGACTTCCCACCAATATTTCACCGTAAGGAGGATACTAACCTAGAGCAGTTGTGG
upper sequence: AT3G48500.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA06G18080.1 (Glycine max), 3'ss of exon 6
---------------------------------------------------gtatgtaattcacacgtatttaattctctttacat--atccagtaaa-----------aattggcattt------tggttctgtcctcaatggtcttggttatggtatatgtgttgactg-------tttttacattcctgctccagATTTAATAAATTTGACTTCCCACCAATATTCCATCGTGATGGGGATACTAATCCAGATGAGATACGG
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gtatgattatttatgtgtttttgacattcaactttctgtaattcattcttagtacatagtttaatctttattaatt-tgatcacattgaagcagtgaacttatgtttttaattcactcttagtacatagtttaatctttattagt-ttgatcacattgaagcagtaaacttaatatttttttcattttcatgcttcagCTTTAACAAATTTGACTTCCCACCAATATTTCATCGTGATGAAGATACTAATGAAGATGAAATACGG
upper sequence: AT3G48500.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA04G36900.1 (Glycine max), 3'ss of exon 7
gtatgtaattcacacgtatttaattctctttacatatccagtaaaaattggcattttggttctgtcctcaatggtcttggttatggtatatgtgttgactgtttttacattcctgctccagATTTAATAAATTTGACTTCCCACCAATATTCCATCGTGATGGGGATACTAATCCAGATGAGATACGG
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---------------atttttaattcattct---tagttagtacatagtttaatctttattaa---tttgatcacattgaagccgtaagtttaatattttattttcattttcatgcttcagCTTTAACAAATTTGACTTCGCACCAATATTTCATCGTGATGAAGATACTAATGAAGATGAAATACGG
upper sequence: AT3G48500.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv17s0000g01850.t01 (Vitis vinifera), 3'ss of exon 6
--------gtatgtaattcaca--cgtatttaattctctttacatatcc-agtaaaaattggcattttggttctgtcctcaatggtc-ttggttatggtatatgtgttgactgtttttacattcct-------gctccagATTTAATAAATTTGACTTCCCACCAATATTCCATCGTGATGGGGATACTAATCCAGATGAGATACGG
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gtacgcaaatttattcttgacaactgttctccattcttcgtgtctgttttagtataatattgaagctgatgtctgataggagttgtgatcagctattttaaaactattggtatttcatgcacttgtctccatggttgcagCTTTAACAGATTTGATTTTCCACCAATATTTCATCATGATGAGGATACTAATCCAGATGAATTACGGMapped 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|164030818|gb|ES160289.1|ES160289EST: CGGTTTCCCTTGGAGTTGCGCTTCGTCCATCCTAACATAGATCACATGAT ATTTAATAAATTTGACTTCCCACCAATATTCCATCGTGATGGGGATACTAA
genomic: CGGTTTCCCTTGGAGTTGCGCTTCGTCCATCCTAACATAGATCACATGATgtatgtaatt ... cctgctccagATTTAATAAATTTGACTTCCCACCAATATTCCATCGTGATGGGGATACTAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctcaatggtcttggttatggtatatgtgttgactgtttttacattcctgctccagATTTAATAAATTTGACTTCCCACCAATATTCCATCGTGATGGGGATACTAATCCAGATGAGATACGG
tgttgac putative branch site (score: 3)
ttcctgctcc putative PPT
tttttacatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtaattcacacgtatttaattctctttacatatccagtaaaaattggcattttggttctgtcctcaatggtcttggttatggtatatgtgttgactgtttttacattcctgctccagATTTAATAAATTTGACTTCCCACCAATATTCCATCGTGATGGGGATACTAATCCAGATGAGATACGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG