Sequence
atgc intronic sequence ATGC exonic sequencegtaagcattcatgaaaatgatcaaacttggtatctatctatctttagaaactttattttatatggtttactgattgtagaagttgtttcttatagGTTGTGAAAGATGGGTATCAATGGAGGAAATATGGACAGAAAGTGACTAGAGACAATCCATCTCCAAGAGCTTACTTCAAATGTGCTTGTGCTCCAAGCT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G80840.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G80840.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os02g08440.4 (Oryza sativa), 3'ss of exon 2
---------------------------gtaagcat-tcatgaaaatgatcaaacttggtatctatctatctttaga---aactttattttatatggtttactgattgtagaagttgtttcttatagGTTGTGAAAGATGGGTATCAATGGAGGAAATATGGACAGAAAGTGACTAGAGACAATCCATCTCCAAGAGCTTACTTCAAATGTGCTTGTGCTCCAAGCT
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gtacgaatccccaaccccaattaacatccgatcatctcatttcatgtgcctaacttaacttctttttgttctgaattctagccttgattaattaattaatcctgttcttgcaatgaatccatgcagGTGGTGAAAGATGGGTACCAATGGAGGAAGTATGGTCAGAAGGTCACCAAGGACAACCCCTGCCCAAGAGCCTACTTCAGATGCTCATTTGCTCCCGCCT
upper sequence: AT1G80840.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA15G00570.1 (Glycine max), 3'ss of exon 3
gtaagcattcatgaaaatgatcaaacttggtatctatctatctttagaa-actttattttatatggtttactgattgtagaagttgtttcttatagGTTGTGAAAGATGGGTATCAATGGAGGAAATATGGACAGAAAGTGACTAGAGACAATCCATCTCCAAGAGCTTACTTCAAATGTGCTTGTGCTCCAAGCT
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gtaag-attcttaacagcaactgagcacaaaaagtcataaccattgttgtgcattagtttgacaggttt-ttcattttttttctacttgtttccagATTGTGAAAGATGGATATCAATGGAGGAAATATGGACAAAAGGTGACCAGAGATAACCCTTCTCCAAGAGCATATTTCAAGTGCTCTTTTGCTCCAAGCT
upper sequence: AT1G80840.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA13G44730.1 (Glycine max), 3'ss of exon 3
gtaagcattcatgaaaatgatcaaacttggtatctatctatctttag-aaactttattttatatggtttactgattgtagaagttgtttcttatagGTTGTGAAAGATGGGTATCAATGGAGGAAATATGGACAGAAAGTGACTAGAGACAATCCATCTCCAAGAGCTTACTTCAAATGTGCTTGTGCTCCAAGCT
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gtaag-attcttaacagcaactgagcataaaaagtcattaccattgttgtgcattagtttgacaggcttttcattttt-----ttcgtgtatccagATTGTGAAAGATGGATATCAATGGAGGAAATATGGACAAAAGGTGACCAGGGATAACCCTTCTCCAAGAGCATATTTCAAGTGCTCTTTTGCTCCAAGCT
upper sequence: AT1G80840.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA08G23380.3 (Glycine max), 3'ss of exon 3
gtaagcattcatgaaaatgatcaaacttggtatct--atctatctttagaaactttatt---ttatatggtttactgattgtagaagttgtttc-ttatagGTTGTGAAAGATGGGTATCAATGGAGGAAATATGGACAGAAAGTGACTAGAGACAATCCATCTCCAAGAGCTTACTTCAAATGTGCTTGTGCTCCAAGCT
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gtgagtctctttactagtactctcctttggttctttgacatagcatagactatttaaatagggtaagtgtttgacagatttttcattgtatgtggttttagATTGTGAAAGATGGATACCAATGGAGGAAATATGGACAAAAGGTGACCAGAGATAACCCTTACCCTAGAGCATATTTCAAGTGCTCTTTTGCTCCAAGCT
upper sequence: AT1G80840.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv09s0018g00240.t01 (Vitis vinifera), 3'ss of exon 3
gtaagc-----attcatgaa-aatgatcaaacttggt--atctatctatctttagaaactttattttatatggtttactgattgtagaagttgtttcttatagGTTGTGAAAGATGGGTATCAATGGAGGAAATATGGACAGAAAGTGACTAGAGACAATCCATCTCCAAGAGCTTACTTCAAATGTGCTTGTGCTCCAAGCT
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gtaagtccaaaacccacaaataattggcgactttggtggattattctgtgaacaccatccggatagtgaatgatcgatcgagcaatttctttatgttttacagGTGGTGAAGGATGGATACCAGTGGAGGAAATATGGCCAAAAGGTCACCAGAGACAACCCCTCTCCGAGAGCCTACTTCAAATGCTCTTTTGCTCCTAGCTMapped 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|301501211|gb|HO206751.1|HO206751EST: AGAAAGTCTCAAGGGTCTATTACAAGACCGAAGCTTCTGACACTACCCTC GTTGTGAAAGATGGGTATCAATGGAGGAAATATGGACAGAAAGTGACTAGA
genomic: AGAAAGTCTCAAGGGTCTATTACAAGACCGAAGCTTCTGACACTACCCTCgtaagcattc ... tttcttatagGTTGTGAAAGATGGGTATCAATGGAGGAAATATGGACAGAAAGTGACTAGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctttagaaactttattttatatggtttactgattgtagaagttgtttcttatagGTTGTGAAAGATGGGTATCAATGGAGGAAATATGGACAGAAAGTGACTAGAGACAATCCATCTCCAAGAGCTTACTTCAAATGTGCTTGTGCTCCAAGCT
tactgat putative branch site (score: 2)
ttgtttctt putative PPT
aaactttattttatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagcattcatgaaaatgatcaaacttggtatctatctatctttagaaactttattttatatggtttactgattgtagaagttgtttcttatagGTTGTGAAAGATGGGTATCAATGGAGGAAATATGGACAGAAAGTGACTAGAGACAATCCATCTCCAAGAGCTTACTTCAAATGTGCTTGTGCTCCAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT