Sequence
atgc intronic sequence ATGC exonic sequenceAGCAAACAGAGTTGCGACAGTGGTTGCAAATGAATGGAAAGATGGTAATGATAAAGTGATGCCTGTGAAGCAATGGCTTGAAGAAAGAAGGTTTCTACAGgtttactttgatatgattgcccttttcctaaatttgtggaatccagattctttgaagtgacaaaggcacacaaccttacattctcactctttaactctcttcttgcag
Basic information
species | Arabidopsis thaliana |
transcript | AT1G68060.1 |
intron # | 7 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G68060.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: LOC_Os12g44340.1 (Oryza sativa), 5'ss of exon 7
AGCAAACAGAGTTGCGACAGTGGTTGCAAATGAATGGAAAGATGGTAATGATAAAGTGATGCCTGTGAAGCAATGGCTTGAAGAAAGAAGGTTTCTACAGgtt-----tactttgatatgat--tgcccttttcctaaatt--tgtgga---atccag----attctttgaagtgacaaaggcacacaaccttacattctc-----------actctttaactc-tcttcttgcag------------------------------------------
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GGCAAATAGAGTTGCAGTAGTGGTGGCAAATGAATGGAAAGATGGCAATGATAAAGTAATGCCTGTTAAACAATGGTTAGAAGAACGGAGGATTTTACAAgtaagtaatgctatcatttaattatgtgctattgctgacttgttctggatggatacagtgaagccttttaatgcaacaattgttttcacttttccccactcctaaacggagtatactatggttcatctttttggggtctaatttgttgggaattttcttttctttctttcttttgcag
upper sequence: AT1G68060.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: LOC_Os02g50320.2 (Oryza sativa), 5'ss of exon 7
AGCAAACAGAGTTGCGACAGTGGTTGCAAATGAATGGAAAGATGGTAATGATAAAGTGATGCCTGTGAAGCAATGGCTTGAAGAAAGAAGGTTTCTACAGgtttactttg-atatgattgccc-ttttcctaaatttgtggaatccagattctttgaagtgacaaag-gcacacaaccttacattctcactctttaactc-tcttcttgcag
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AGCAAACAGAGTTGCTGTTGTAGTTGCAAATGAGTGGAAAGATGCTAATGACAAAGTAATGCCTGTCAAACAGTGGCTTGAAGAGCGCAGGTTTCTGCAGgtaaagatgatatacttctgtttgttttttgaagctcatctacggttgtccatgcaaagtcacacttcacatcatatattcaatttttatggcatgacaaatgtttcttcag
upper sequence: AT1G68060.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GRMZM2G017525_T01 (Zea mays), 5'ss of exon 3
AGCAAACAGAGTTGCGACAGTGGTTGCAAATGAATGGAAAGATGGTAATGATAAAGTGATGCCTGTGAAGCAATGGCTTGAAGAAAGAAGGTTTCTACAGgtttactttgatatgattgccctttt---cctaaatt--tgtggaatccagattctttgaagtgacaaaggcacacaaccttacattctc---actctttaa-----ctctcttcttgcag
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AGCAAATAGGGTTGCAGTAGTGGTGGCAAATGAGTGGAAAGATGGCGATGATAAAGTAATGCCTGTTAAACGATGGCTCGAGGAGCGAAGGATTCTGCAAgta-agtgaaatatatcttttcttctagttttaagctgctaccgagttgctcgtggtagatttgtacaagttcttcagcggtgaattttattgatttgttgaatattgtctttttttgcag
upper sequence: AT1G68060.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GRMZM2G008556_T01 (Zea mays), 5'ss of exon 7
AGCAAACAGAGTTGCGACAGTGGTTGCAAATGAATGGAAAGATGGTAATGATAAAGTGATGCCTGTGAAGCAATGGCTTGAAGAAAGAAGGTTTCTACAGgttta----------------ctttgatatgattgcccttttcct-------aaatttgtggaa---tccagattctttgaagtgacaaaggcacacaaccttacattctcactctttaactctcttcttgcag-----------------------
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AGCAAACAGAGTTGCTTCTGTTGTTGCTAATGAGTGGAAAGATTCTAATGACAAGGTGATGCCAGTTAAACAGTGGCTTGAAGAGCGTAGGTTCTTCCAGgttggatggttaaactagcattttctttaccaatgtacttttttttgtattcaactctgcacaaatatgcatattctttggtgaaacaaaa-tgtaccacctgctggacatggttcttttcttgagtatcatatgtgatactttcttgtttctacag
upper sequence: AT1G68060.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA05G34560.1 (Glycine max), 5'ss of exon 7
AGCAAACAGAGTTGCGACAGTGGTTGCAAATGAATGGAAAGATGGTAATGATAAAGTGATGCCTGTGAAGCAATGGCTTGAAGAAAGAAGGTTTCTACAGgtttactttgata-tgattgcccttttcctaaatttgtggaatccagattctttgaagtgacaaaggcacacaaccttacattctcactc--tttaactctcttcttgcag----------------------
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AGCAAACAGAGTAGCTGTAGTGGTTGCAAATGAATGGAAAGATGCTAATGACAAAGTGATGCCTGTGAAACAATGGCTTGAAGAACGACGATTTTTGCAGgtgaatattatttctgattcctttggatttaaactttcgtggtt----ttttttaaagt-atatatcttcctgcatttggcttccccttcaatgtggttttcattttgtttttaccaaactacactcttatag
upper sequence: AT1G68060.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA08G05100.1 (Glycine max), 5'ss of exon 7
AGCAAACAGAGTTGCGACAGTGGTTGCAAATGAATGGAAAGATGGTAATGATAAAGTGATGCCTGTGAAGCAATGGCTTGAAGAAAGAAGGTTTCTACAGgtttactttgatatgattgcccttttcctaaatttgtggaatccagattctttgaagtgacaaaggcacacaaccttacattc--tcactctttaactctcttcttgcag-------------------------
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AGCAAACAGAGTAGCTGTAGTGGTTGCAAATGAATGGAAAGATGCTAATGACAAAGTGATGCCTGTGAAACAATGGCTTGAAGAACGACGATTCTTGCAGgtggatatcatttctgattcctttggatttaatcttttgtgccttt-ttttttataaaaaaaagtatatatcttcttgcatttggtttcccttcaatacggtttccatttttttaccaaactacacttttattag
upper sequence: AT1G68060.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA02G09390.1 (Glycine max), 5'ss of exon 7
AGCAAACAGAGTTGCGACAGTGGTTGCAAATGAATGGAAAGATGGTAATGATAAAGTGATGCCTGTGAAGCAATGGCTTGAAGAAAGAAGGTTTCTACAGgt----ttactttgatatgattgccc--ttttcctaaatttgtggaatccagattctttgaagtgacaaaggcacacaaccttacattctcactctttaactctcttcttgcag------------------------------------------
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AGCAAACAGAGTAGCTGTTGTGGTTGCAAATGAATGGAAAGATGCCAATGATAAAGTGATGCCTGTCAAACAATGGCTTGAAGAACGCCGATTCTTGCAGgtaatatttttttgttttactctgccaattcatctgaatttagtggtt---gagtttttgaattccattactctttctgc-ttatatttcttttttatagtaat-ttcccgcatctggcttcgctttccacttattattaaattgaattcttatag
upper sequence: AT1G68060.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA07G26540.1 (Glycine max), 5'ss of exon 7
AGCAAACAGAGTTGCGACAGTGGTTGCAAATGAATGGAAAGATGGTAATGATAAAGTGATGCCTGTGAAGCAATGGCTTGAAGAAAGAAGGTTTCTACAGgt----ttactttgatatgattgcccttttcctaaatttgtggaatccagattctttgaagtgacaaaggcacacaaccttacattctcactctttaactctcttcttgcag------------------------------------------
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AGCAAACAGAGTAGCTGTTGTGGTTGCAAATGAATGGAAAGATGCTAATGATAAAGTGATGCCTGTCAAACAGTGGCTTGAAGAACGTCGATTCTTGCAGgtaatatttttttgctttactctgccaattcatctgaatttagtggttgagttctt--gacttccatgactctttttgcttatatttcttcttttatattaatttcccacatttggcttcgctttccgcttattattaaattgcattcttatag
upper sequence: AT1G68060.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: Vv01s0011g05790.t01 (Vitis vinifera), 5'ss of exon 7
AGCAAACAGAGTTGCGACAGTGGTTGCAAATGAATGGAAAGATGGTAATGATAAAGTGATGCCTGTGAAGCAATGGCTTGAAGAAAGAAGGTTTCTACAGgtt--tactttgatatgattgcccttttc---ctaaatttgtggaatccagattctttga----agtgacaaaggcacacaacctt----acattctcactctttaact-----------ctcttcttgcag
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TGCAAACAGGGTGGCAGTAGTTGTAGCAAATGAATGGAAAGATGCTAATGACAAGGTGATGCCCGTAAAACAATGGCTAGAGGAACGGCGATTCTTGCAAgtaaatactctgaagttcttattgtttcaaaacttgagctattatttactgtttctttttctttgatcatgactgtgtttggcttttgtagtttccacagtttgtaattgttaccaaaacctcttgttacagMapped 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|47831253|gb|CK120937.1|CK120937EST: ATAAAGTGATGCCTGTGAAGCAATGGCTTGAAGAAAGAAGGTTTCTACAG GGAGAAATGCAGCAACTCCGCGATAAGCTTGCCATATCAGATCGAGCTGCG
genomic: ATAAAGTGATGCCTGTGAAGCAATGGCTTGAAGAAAGAAGGTTTCTACAGgtttactttg ... cttcttgcagGGAGAAATGCAGCAACTCCGCGATAAGCTTGCCATATCAGATCGAGCTGCG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
AGCAAACAGAGTTGCGACAGTGGTTGCAAATGAATGGAAAGATGGTAATGATAAAGTGATGCCTGTGAAGCAATGGCTTGAAGAAAGAAGGTTTCTACAGgtttactttgatatgattgcccttttcctaaatttgtggaatccagattctttgaagtgacaaaggcacacaaccttacattctcactctttaactctcttcttgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG