Sequence
atgc intronic sequence ATGC exonic sequenceAATTCAATGCCAGCCGCTGCAGGAGCTGTTGCCGCAGCAGCGGTAGCTGATCAAATGCTTGGACCGAAAGAAGATAGACATCTAGCAATTGTCCTGgtatttgtagccacatagatgttggtcatagtttctgcaggtcttttagcttatgtttcctagtttgattgtaaggagctggacgttgttgtggctggctattttatttaacttataaacgtaaatggaaaaaaaaaaaaaaagactggatgttctgattcacaccattcccgtcaaaattgtattag
Basic information
species | Arabidopsis thaliana |
transcript | AT1G07110.1 |
intron # | 6 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G07110.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: LOC_Os03g18310.1 (Oryza sativa), 5'ss of exon 5
AATTCAATGCCAGCCGCTGCAGGAGCTGTTGCCGCAGCAGCGGTAGCTGATCAAATGCTTGGACCGAAAGAAGATAGACATCTAGCAATTGTCCTGgtatttgtagccacatagatgttggtcatagtttctgcaggtcttttagcttatgtttcctagtttgattgtaaggagctggacgttgttgtggctggctattttatttaacttataaacgtaaatggaaaaaaaaaaaaaaagactggatgttctgattcacaccattcccgtcaaaattgtattag
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---GACATGCCAGCAGCTGAAGGAGCTGTTGCAGCAGCAGCTGTAGCTGATCAAATGTATGGCCCAAAGGAGGATCGCAAGTTGGCAATTGTGCTGgtacttttcatattattagaatgaatcattccttt-----atcttccacctt-tatttgtta--tggattgttggctattgatcacttccttagatgatt--tataccag------------------------------------------------------------------------------
upper sequence: AT1G07110.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA18G06770.1 (Glycine max), 5'ss of exon 8
AATTCAATGCCAGCCGCTGCAGGAGCTGTTGCCGCAGCAGCGGTAGCTGATCAAATGCTTGGACCGAAAGAAGATAGACATCTAGCAATTGTCCTGgtatttg------tagccacatagatgttggtcatagtttctgcaggtcttttagcttatgtttcctagtttgattgtaaggagctggacgttgttgtggctggctattttatttaacttataaacgtaaatggaaaaaaaaaaaaaaagactggatgttctgattcacaccattcccgtcaaaattgtattag
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AATTCAATGCCAGCTGCTGCTGGAGCTGTTGCTGCTGCAGCTGTTGCTGATCAGATGCTGGGTCCCAAGGAAGATAGACATTTGGCAATTATCCTGgtatttggcatgattagtagttagttactgatgcaaaacttgataattagtttcgattttgtttcctattttgttatgagataattagtttctatcttgt----------------------------------------------------------------------------------------------
upper sequence: AT1G07110.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA11G27870.1 (Glycine max), 5'ss of exon 7
AATTCAATGCCAGCCGCTGCAGGAGCTGTTGCCGCAGCAGCGGTAGCTGATCAAATGCTTGGACCGAAAGAAGATAGACATCTAGCAATTGTCCTGgtatttgtagccacatagatgttggtcata-gtttctgcaggtcttttagcttatgtttcctagtttgattgtaagg-agctggacgttgttgtggctggctattttatttaacttataaacgtaaatggaaaaaaaaaaaaaaagactggatgttctgattcacaccattcccgtcaaaattgtattag
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AATTCAATGCCAGCTGCTGCTGGAGCCGTCGCTGCTGCAGCTGTTGCTGATCAGATGCTGGGTCCCAAGGAAGATAGACATTTGGGAATTATCCTGgtatttttc-tggcatgatgagtagttagatactgatgcaaaacttgataatta-gcttc--gattttattatgagataattagtttccatcttgtttagtttc--------------------------------------------------------------------------------------
upper sequence: AT1G07110.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA02G39390.1 (Glycine max), 5'ss of exon 6
AATTCAATGCCAGCCGCTGCAGGAGCTGTTGCCGCAGCAGCGGTAGCTGATCAAATGCTTGGACCGAAAGAAGATAGACATCTAGCAATTGTCCTGgtatttgtagccacatagatgttg-gtcatagtttctgcaggtctttta---gcttatgtttcctagtttgattgtaaggagctggacgttgttgtggctggctattttatttaacttataaacgtaaatggaaaaaaaaaaaaaaagactggatgttctgattcacaccattcccgtcaaaattgtattag
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AATTCAATTCCAGCTGCTGCTGGAGCTGTTGCAGCTGCTGCGATTGCTGATCAGATGCTAGGTCCCAAAGAGCATAGACATTTGGCGATTGTCATGgtatta-----cacaaactttttaagcaacacttgttatcactttgttatgggctttgagttggagttttgagtgagattcaataagagacatcttgagaagtta---------------------------------------------------------------------------------------
upper sequence: AT1G07110.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA11G27410.1 (Glycine max), 5'ss of exon 11
AATTCAATGCCAGCCGCTGCAGGAGCTGTTGCCGCAGCAGCGGTAGCTGATCAAATGCTTGGACCGAAAGAAGATAGACATCTAGCAATTGTCCTGgtatttgtagccacatagatgttggtcata-gtttctgcaggtcttttagcttatgtttcctagtttgattgtaagg-agctggacgttgttgtggctggctat-tttatttaacttataaacgtaaatggaaaaaaaaaaaaaaagactggatgttctgattcacaccattcccgtcaaaattgtattag
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-------------------CTGGAGCTGTCGCTGCTGCAGCTGTTGCTGATCAGATGCTGGGTCCCAAGGAAGATAGACATTTGGCAATTATCCTGGTATTTTTC-TGGCATTATGAGTAgttagatactgatgcaaaacttgataatta-gtttc--gattttgttatgagataattagtttctatcttgtttagtttcatatttctatcttgtttag--------------------------------------------------------------------
upper sequence: AT1G07110.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: Vv06s0004g06920.t01 (Vitis vinifera), 5'ss of exon 6
AATTCAATGCCAGCCGCTGCAGGAGCTGTTGCCGCAGCAGCGGTAGCTGATCAAATGCTTGGACCGAAAGAAGATAGACATCTAGCAATTGTCCTGgtatttgtagccacatagatgttggtcatagtttctgcaggtcttttagcttatgtttcctagtttgattgtaaggagctggacgttgttgtggctggctattttatttaacttataaacgtaaatggaaaaaaaaaaaaaaagactggatgttctgattcacaccattcccgtcaaaattgtattag
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AATGCAATGCCAGCAGCTGCTGGAGCTGTTGCAGCTGCTGCTGTAGCTGATCAGATGCTTGGTCCGAAAGAGGATAGACATTTGGCAATTGTCCTGgtattttctgtca--------ttactgattgattttgactattcataattttaatgatgctactctattgacaa----ttcaatgtgattggaattcaa----acattaaaatcct------------------------------------------------------------------------Mapped 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|125212454|gb|EL227408.1|EL227408EST: TAGCAATTGTCCTG GTTGGCTTGCCTGCTCGAGGAAAGACTTTTACTGCAGCAAAGTTGACAAGA
genomic: TAGCAATTGTCCTGgtatttgtag ... attgtattagGTTGGCTTGCCTGCTCGAGGAAAGACTTTTACTGCAGCAAAGTTGACAAGA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
AATTCAATGCCAGCCGCTGCAGGAGCTGTTGCCGCAGCAGCGGTAGCTGATCAAATGCTTGGACCGAAAGAAGATAGACATCTAGCAATTGTCCTGgtatttgtagccacatagatgttggtcatagtttctgcaggtcttttagcttatgtttcctagtttgattgtaaggagctggacgttgttgtggctggctattttatttaacttataaacgtaaatggaaaaaaaaaaaaaaagactggatgttctgattcacaccattcccgtcaaaattgtattag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG