Sequence
atgc intronic sequence ATGC exonic sequenceTAGGGAAGCAGCTATTGCAAGGATGCCTTCCATGATTGAGAAACAAGCTACAGCAGCTGTCGACGAATCAGCTGTTATTATTTTCGTTGTCGATGGCCAGgttctgtgcttatcttctatctccttaacttttctgtctttgcctttcttcctgttaggcttttcgattcctgccataaaaacaaagtccaacaacaaaa...
Basic information
species | Arabidopsis thaliana |
transcript | AT3G12080.2 |
intron # | 4 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G12080.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G302233_T01 (Zea mays), 5'ss of exon 4
TAGGGAAGCAGCTATTGCAAGGATGCCTTCCATGATTGAGAAACAAGCTACAGCAGCTGTCGACGAATCAGCTGTTATTATTTTCGTTGTCGATGGCCAGg-----ttctgtgcttatcttctatctc----cttaacttttctgtctttgcctttcttcctgttaggcttttcgattcctgccataaaaacaaagtccaacaacaaaa-----------------------------------------------------------------------------
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TAGAGAAGCTGCTATTGCAAGGATGCCATCAATGATTGAAAAACAAGCAGTTGCAGCTGTTGATGAAGCATCCGTCATACTATTCGTTGTGGATGGTCAGgcaggtttaggaaattatctttcttttctgctcatggaagtgctggtttaatatttgaattcacaacaaccttaaatatatgtacttctaatgctttccttgaacatttttgaccagaaattgttgttctataatttctcatttaagttccttttttactagtataatggtgtcaacatatttcag
upper sequence: AT3G12080.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv06s0004g02070.t01 (Vitis vinifera), 5'ss of exon 5
TAGGGAAGCAGCTATTGCAAGGATGCCTTCCATGATTGAGAAACAAGCTACAGCAGCTGTCGACGAATCAGCTGTTATTATTTTCGTTGTCGATGGCCAGgttctgtgcttatcttctatctccttaacttttctgtctttgcctttcttcctgttaggcttttcgattcctgccataaaaacaaagtccaac--aacaaaa-
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----------------------------------------AAACAAGCTACTGCAGCTATAGAAGAATCATCTGTTATTATATTTCTTGTCGATGGCCAGgta--gagttcattctat-tattctttacttgagtactgaataatttctttctaatgaacctttttgtttcatttattttcttccttctcttcttaatattat
upper sequence: AT3G12080.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv06s0004g02070.t01 (Vitis vinifera), 5'ss of exon 4
TAGG-GAAGCAGCTATTGCAAGGATGCCTTCCATGATTGAGAAACAAGCTACAGCAGCTGTCGACGAATCAGCTGTTATTATTTTCGTTGTCGATGGCCAGgttctgtgcttatcttctatctccttaacttttctgtctttgcctttcttcctgttaggcttttcgattcctgccataaaaacaaagtc--caacaacaaaa
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TACTCGTGATCGCCTCTATGGTAGAGCCTTTTG-GGGAGATTATGAATTCATGGTGATAGATACTGGAGGTGTCCTCACAATTTCAAAATCACAAGATAATgttatggaagaattagctattacaaaaaccattg---gtatggatgggattccacttgcctccagggaagcagctgttgcaaggatgcctacaatgattgagMapped 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|124715544|gb|EH806946.1|EH806946EST: TCGTTGTCGATGGCCAG GCAGGGCCATCAGGTGCTGATGTGGAAATTGCAGACTGGTTGCGGAAGTAC
genomic: TCGTTGTCGATGGCCAGgttctgtgct ... cgatatgcagGCAGGGCCATCAGGTGCTGATGTGGAAATTGCAGACTGGTTGCGGAAGTAC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TAGGGAAGCAGCTATTGCAAGGATGCCTTCCATGATTGAGAAACAAGCTACAGCAGCTGTCGACGAATCAGCTGTTATTATTTTCGTTGTCGATGGCCAGgttctgtgcttatcttctatctccttaacttttctgtctttgcctttcttcctgttaggcttttcgattcctgccataaaaacaaagtccaacaacaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctatctcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttcttcct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcgattcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caacaaca