Sequence
atgc intronic sequence ATGC exonic sequencegtgagattatctgtgctatactgtttgtatatgtgttatttgacttgggccccaaagattttcagaggcgtttagctagatgtgatgttggtgtccaggaatatgttctgtttgttctgttcatgcattaaaattgatgttgacatgcatttactttctgatgcagGAATCACTTGAAAAGATTGCTCCTACATGGATGAATGTCTCGCTGACAATGAAAAACGATCCAGAAACTGATAAGGCATTTGGATGGGTGCTGGAAAT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G13500.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G13500.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os01g16600.1 (Oryza sativa), 3'ss of exon 3
gtgagattatctgtgctatactgtttgtatatgtgttatttga---cttgggccccaaagat-tttcagaggcgtttagctagatgtgatgttggtgtccaggaatatgttctgtttgttctg--ttcatgcattaaaattgatgttgacatgcatttactttctga-------tgcagGAATCACTTGAAAAGATTGCTCCTACATGGATGAATGTCTCGCTGACAATGAAAAACGATCCAGAAACTGATAAGGCATTTGGATGGGTGCTGGAAAT
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-----gtaacacatattgcagaattgacgtg-gtataccttgaagtctcatgcatgaggagtatttccttggattttatttttacattacttacatg-ccagttgctagttattaatgttttgaattgatgagcttcaatttttaactctatcc-cttatcatctgaggaaacttttagATACAACTTGAGAAGATTGCCCCTACATGGATGAATGTATCGATTCAAATGAAAGAAGATCAGGAGACAGATAAAGCTTTTGGATGGGTCTTGGAAAT
upper sequence: AT5G13500.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA13G26610.1 (Glycine max), 3'ss of exon 4
gtgagattatctgtgctatactgtttgtatatgtgttatttgacttgggccccaaagattttcagaggcgtttagctagatgtgatgttggtgtccaggaatatgttctgtttgttctgttcatgcattaaaattgatgttgacatgcatttactttctgatgcagGAATCACTTGAAAAGATTGCTCCTACATGGATGAATGTCTCGCTGACAATGAAAAACGATCCAGAAACTGATAAGGCATTTGGATGGGTGCTGGAAAT
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--------------------------------------------------------gcctgcccaactaacctaactaacta--attcccttactaacagacac---ctaactaa-caactaatgggtgtctactgatg--gacttc--tctatttttttcttcagGATTTGATTGCAAAGATTGCCCCCACATGGATGAATATTTCTTTGAAGATGAAAGAGGATCCAGAGACTGATAAAGCTTTTGGATGGGTGCTAGAAAT
upper sequence: AT5G13500.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA15G37490.2 (Glycine max), 3'ss of exon 4
gtgagattatctgtgctatactgtttgtatatgtgttatttgacttgggccccaaagattttcagaggcgtttagctagatgtgatgttggtgtccaggaatatgttctgtttgttc-tgttcatgcattaaaattgatgttgacatgcatttactttctgatgcagGAATCACTTGAAAAGATTGCTCCTACATGGATGAATGTCTCGCTGACAATGAAAAACGATCCAGAAACTGATAAGGCATTTGGATGGGTGCTGGAAAT
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--------------------------------------------------------aactatcctaa----ctaactagctcccttactaacggaca-----acttactaactactaatgggtatctactaa--tggacttctctctcatttttttctttctttcagGATTTGATCGCAAAGATTGCCCCCACATGGATGAATATTTCTTTGAAGATGAAAGAGGACCCAGAGACTGATAAAGCTTTTGGATGGGTGCTAGAAAT
upper sequence: AT5G13500.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv13s0084g00830.t01 (Vitis vinifera), 3'ss of exon 3
gtgagattatctgtgctatactgtttgtatatgtgttatttgacttgggccccaaagattttcagaggcgtttagctagatgtgatgttggtgtccaggaatatgttctgtttgttctgttcatgcattaaaattg-atgttgacatgcatttactttctgatgcagGAATCACTTGAAAAGATTGCTCCTACATGGATGAATGTCTCGCTGACAATGAAAAACGATCCAGAAACTGATAAGGCATTTGGATGGGTGCTGGAAAT
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------------------------------------------------------------------atccaaaagccgcactttctttctttatttttttgctccctcatttttttttctgtaaaaatgtgaattacattttggtttac-ttaattgtcccgtgcagGAGTTGTTGGAGAAGATTGCGCCTACATGGATGAATGTTTCTTTGAGAATGAAAGATGACCCAGAAACTGATAAAGTATTTGGATGGGTGCTAGAAATMapped 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|86075298|gb|DR371055.1|DR371055EST: CAGTAACAAATATCGACCCCATTGGCAACTCTCCTGTTATCATAAGCAAG GAATCACTTGAAAAGATTGCTCCTACATGGATGAATGTCTCGCTGACAATG
genomic: CAGTAACAAATATCGACCCCATTGGCAACTCTCCTGTTATCATAAGCAAGgtgagattat ... tctgatgcagGAATCACTTGAAAAGATTGCTCCTACATGGATGAATGTCTCGCTGACAATG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgttctgttcatgcattaaaattgatgttgacatgcatttactttctgatgcagGAATCACTTGAAAAGATTGCTCCTACATGGATGAATGTCTCGCTGACAATGAAAAACGATCCAGAAACTGATAAGGCATTTGGATGGGTGCTGGAAAT
ttctgat putative branch site (score: 3)
tttactttct CT-rich tract
attaaaattgatgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagattatctgtgctatactgtttgtatatgtgttatttgacttgggccccaaagattttcagaggcgtttagctagatgtgatgttggtgtccaggaatatgttctgtttgttctgttcatgcattaaaattgatgttgacatgcatttactttctgatgcagGAATCACTTGAAAAGATTGCTCCTACATGGATGAATGTCTCGCTGACAATGAAAAACGATCCAGAAACTGATAAGGCATTTGGATGGGTGCTGGAAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA