RetrogeneDB ID: | retro_acar_79 | ||
Retrocopy location | Organism: | Anole lizard (Anolis carolinensis) | |
| Coordinates: | 2:37540517..37542202(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSACAG00000016475 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | TRIM2 | ||
| Ensembl ID: | ENSACAG00000015934 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_acar_79
ATGGATGTCCTGCAGCGAACTCCAGAAAATAGCATTGAGGAGTCTTCCATCCTGGAGACTGTCACAGCTGTTGCTGCAGG
GAAACCACTTTCCTGCCCCAATCATGAAGGAAATTTGATGGAATTTTACTGTCAGTCTTGTGAGACAGCCATGTGCCGGG
AATGTACAGAAGGAGAGCATGCGGAGCATCCCACAGTGCCTCTCAAGGATGTTGTTGAACAACACAAGGGTTCTCTTCAA
GCACAATAGATGCTGTCAATAAAAGACTTCCAGAGATAGATACTGCACTTCATTTCATATCTGAAATTATACATCAGCTG
ACCAACCAAAAGACCAACATCGTTGATGAAATTCATTCCACTTTTGATGAACTCCAGAAAACTTTAAATGTTCGCAAGAG
TGTACTACTTATGGAACTGGAAGTCAATTATGGCCTTAAACATAAAGTTTTGCAGAATCAACTTGATACCCTCTTGGAAG
GACAGGAAAACATTAAGAGTTGTAGCAATTTTACAGCCCAAGCACTCAATCATGGAACAGAAACAGAAGTCTTGCTTGTC
AAGAAGCAAATGAGTGACAAGCTGAACGATCTGGCTGACAGAGATTTCCCACTGCAGCCCCGCGAAAATGATCAGCTGGA
CTTCATAGTGGAAACAGATGGGCTGAAGAAGTCCATTCATAACCTTGGCACTATTTTAACCACAAATGCTGTTGCTTCTG
AAACAGTGGCCACAGGCGAAGGGCTGAAGCAGACGGTGATAGGACAGCCTATGTCAGTCACCATCACTACTAAGGACAAG
GATGGTGAGCTCTGCAAATCTGGGAACGCTTACCTGACTGCTGAGCTGAGTACCCCTGATGGGAGTGTAGCCGATGGAGA
AATACTTGACAACAAAAATGGCACTTACGAATGTCTGTATACTGTCCAGAAAGAAGGGGATTTTACTCTTTCACTGAGAC
TCTATGATCAGCATATTAGGGGCAGCCCATTCAAACTCAAGTTAATCAGATCAGCGGATGTGTCCCCGACCACTGAAGGA
GTTAAAAGGCGTGTGAAGTCTCCTGGTAGTGGCCATGTAAAGCAGAAGGCGGTAAAAAGACCGGCTAGTTTGTACAGCAC
TGGCAAAAGGGAAGAGAACCCCATTGAAGATGATTTGATCTTCAGAGTAGGTACCAAAGGGAGAAACAAAGGAGAGTTTA
CAAATCTTCAGGGAGTAGCTGCATCTACAAATGGAAAAATATTAATAGCAGATAGCAATAATCAGTGTGTACAGGTGTTT
TCCACTGATGGCCAGTTCAAGAGCCGTTTTGGTATTCGGGGAAGGTCTCCCGGTCAGTTGCAGCGGCCTACAGGAGTGGC
TGTGCATCCTTGTGGGGACATCATTATTGCCGACTATGATAATAAATGGGTTAGCATATTCTCCTCTGATGGAAAATTTA
AGACAAAAATTGGGTCTGGAAAACTTATGGGACCAAAAGGTGTTTCTGTGGATCGAAATGGGCACATCATTGTTGTGGAC
AACAAAGCATGTTGTGTGTTCATCTTCCAGCCTAATGGAAAAATAGTAACCAGGTTTGGAAGCCGAGGCAACGGAGACAA
ACAGTTTGCAGGTCCCCATTTTGCAGCTGTCAACCACAATAATGAAATTATTATTACTGATTTCCACAATCATTCTGTCA
AGGTA
ORF - retro_acar_79 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 99.11 % |
| Parental protein coverage: | 85.41 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MDVLQRTPENSIEESSILETVTAVAAGKPLSCPNHEGNLMEFYCQSCETAMCRECTEGEHAEHPTVPLKD |
| MDVLQRTPENSIEESSILETVTAVAAGKPLSCPNHEGNLMEFYCQSCETAMCRECTEGEHAEHPTVPLKD | |
| Retrocopy | MDVLQRTPENSIEESSILETVTAVAAGKPLSCPNHEGNLMEFYCQSCETAMCRECTEGEHAEHPTVPLKD |
| Parental | VVEQHKGSLQAQ-LDAVNKRLPEIDTALHFISEIIHQLTNQKTNIVDEIHSTFDELQKTLNVRKSVLLME |
| VVEQHKGSLQAQ..DAVNKRLPEIDTALHFISEIIHQLTNQKTNIVDEIHSTFDELQKTLNVRKSVLLME | |
| Retrocopy | VVEQHKGSLQAQ<IDAVNKRLPEIDTALHFISEIIHQLTNQKTNIVDEIHSTFDELQKTLNVRKSVLLME |
| Parental | LEVNYGLKHKVLQNQLDTLLEGQENIKSCSNFTAQALNHGTETEVLLVKKQMSDKLNDLADRDFPLQPRE |
| LEVNYGLKHKVLQNQLDTLLEGQENIKSCSNFTAQALNHGTETEVLLVKKQMSDKLNDLADRDFPLQPRE | |
| Retrocopy | LEVNYGLKHKVLQNQLDTLLEGQENIKSCSNFTAQALNHGTETEVLLVKKQMSDKLNDLADRDFPLQPRE |
| Parental | NDQLDFIVETDGLKKSIHNLGTILTTNAVASETVATGEGLKQTVIGQPMSVTITTKDKDGELCKSGNAYL |
| NDQLDFIVETDGLKKSIHNLGTILTTNAVASETVATGEGLKQTVIGQPMSVTITTKDKDGELCKSGNAYL | |
| Retrocopy | NDQLDFIVETDGLKKSIHNLGTILTTNAVASETVATGEGLKQTVIGQPMSVTITTKDKDGELCKSGNAYL |
| Parental | TAELSTPDGSVADGEILDNKNGTYEFLYTVQKEGDFTLSLRLYDQHIRGSPFKLKLIRSADVSPTTEGVK |
| TAELSTPDGSVADGEILDNKNGTYE.LYTVQKEGDFTLSLRLYDQHIRGSPFKLKLIRSADVSPTTEGVK | |
| Retrocopy | TAELSTPDGSVADGEILDNKNGTYECLYTVQKEGDFTLSLRLYDQHIRGSPFKLKLIRSADVSPTTEGVK |
| Parental | RRVKSPGSGHVKQKAVKRPASMYSTGKRKENPIEDDLIFRVGTKGRNKGEFTNLQGVAASTNGKILIADS |
| RRVKSPGSGHVKQKAVKRPAS.YSTGKR.ENPIEDDLIFRVGTKGRNKGEFTNLQGVAASTNGKILIADS | |
| Retrocopy | RRVKSPGSGHVKQKAVKRPASLYSTGKREENPIEDDLIFRVGTKGRNKGEFTNLQGVAASTNGKILIADS |
| Parental | NNQCVQVFSTDGQFKSRFGIRGRSPGQLQRPTGVAVHPCGDIIIADYDNKWVSIFSSDGKFKTKIGSGKL |
| NNQCVQVFSTDGQFKSRFGIRGRSPGQLQRPTGVAVHPCGDIIIADYDNKWVSIFSSDGKFKTKIGSGKL | |
| Retrocopy | NNQCVQVFSTDGQFKSRFGIRGRSPGQLQRPTGVAVHPCGDIIIADYDNKWVSIFSSDGKFKTKIGSGKL |
| Parental | MGPKGVSVDRNGHIIVVDNKACCVFIFQPNGKIVTRFGSRGNGDKQFAGPHFAAVNHNNEIIITDFHNHS |
| MGPKGVSVDRNGHIIVVDNKACCVFIFQPNGKIVTRFGSRGNGDKQFAGPHFAAVNHNNEIIITDFHNHS | |
| Retrocopy | MGPKGVSVDRNGHIIVVDNKACCVFIFQPNGKIVTRFGSRGNGDKQFAGPHFAAVNHNNEIIITDFHNHS |
| Parental | VKV |
| VKV | |
| Retrocopy | VKV |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)
Expression validation based on RNA-Seq data:
| Library | Retrocopy expression | Parental gene expression |
|---|---|---|
| SRP009831_adrenal | 0 .07 RPM | 0 .79 RPM |
| SRP009831_brain | 0 .19 RPM | 99 .37 RPM |
| SRP009831_dewlap | 0 .72 RPM | 131 .79 RPM |
| SRP009831_embryo | 0 .12 RPM | 25 .84 RPM |
| SRP009831_heart | 0 .10 RPM | 15 .77 RPM |
| SRP009831_liver | 0 .00 RPM | 3 .97 RPM |
| SRP009831_lung | 0 .10 RPM | 18 .08 RPM |
| SRP009831_ovary | 0 .58 RPM | 136 .56 RPM |
| SRP009831_skeletal_muscle | 0 .04 RPM | 7 .98 RPM |
Anolis carolinensis was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_acar_79 retrocopy.
Anolis carolinensis was not studied using FANTOM5 data.
retro_acar_79 was not experimentally validated.
Retrocopy orthology:
Anolis carolinensis does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Anolis carolinensis | ENSACAG00000015934 | 1 retrocopy |
retro_acar_79 ,
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