RetrogeneDB ID: | retro_eeur_131 | ||
Retrocopy location | Organism: | Hedgehog (Erinaceus europaeus) | |
| Coordinates: | GeneScaffold_8155:69359..69996(+) | ||
| Located in intron of: | ENSEEUG00000011085 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | THAP1 | ||
| Ensembl ID: | ENSEEUG00000003332 | ||
| Aliases: | None | ||
| Description: | THAP domain containing, apoptosis associated protein 1 [Source:HGNC Symbol;Acc:20856] |
Retrocopy-Parental alignment summary:
>retro_eeur_131
ATGGTGCAGTCCTGTACCGCCTACGGCTGCAAGAACCCATACGATAAGGATAAGCCCATTTCTTTTCACAAGTTTCCTCT
TACACGACCTAATCTTTGTAAAGAATGTGAAGCAGCTGATAGAAGAAAAAACTTTAAGTCAACAAAGTACAGCAGTATTT
GTTCAGAACACTTTACTCCAGACTGCTTTAAGAGGGAATGCAACAACAAGTTATTGAAGGAGAATGCTGTGCCCACAATA
TTTCTCTGTACTGAACCGCATGACAAGAAGGAAGAGCTACTGGAACCACAGCGACAGCTTCACCCGCCTCCTTTAGCACC
TCTCATTTCCCAAGTTGATGCTGCAATTGGATTACTCATGCCTCCTCTTCAGACCCATGATAACCTCTCAGATTCCTGTG
ACCTCAACTATACCGTGGAGGATACCATGCACCAGAGAAAAAGAATTCATCAGCTAGAACAACAAGTTGAAAAACTGAGA
AAGAAGTTCAAGACTGCACAGCAGCGATGCAGAAGACAGGAACGACAGCTTAAGAAGTTAAAGGAGGTTTTACACTTCCA
AAGAGAAAGAAGACACACCAGAGAGAGGTTATGTGATTCTACCAAATGACTACTTTGAAATAGTTGAAGTACCGGCA
ORF - retro_eeur_131 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 86.92 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MVQSCSAYGCKNRYDKDKPVSFHKFPLTRPNLCKEWEAAVRRKNFKPTKYSSICSEHFTPDCFKRECNNK |
| MVQSC.AYGCKN.YDKDKP.SFHKFPLTRPNLCKE.EAA.RRKNFK.TKYSSICSEHFTPDCFKRECNNK | |
| Retrocopy | MVQSCTAYGCKNPYDKDKPISFHKFPLTRPNLCKECEAADRRKNFKSTKYSSICSEHFTPDCFKRECNNK |
| Parental | LLKENAVPTIFLCTEPHDKKEELLEPQGQLHPPPLAPPISQVDAAIGLLMPPLQTPDNLSVFCDHNYTVE |
| LLKENAVPTIFLCTEPHDKKEELLEPQ.QLHPPPLAP.ISQVDAAIGLLMPPLQT.DNLS..CD.NYTVE | |
| Retrocopy | LLKENAVPTIFLCTEPHDKKEELLEPQRQLHPPPLAPLISQVDAAIGLLMPPLQTHDNLSDSCDLNYTVE |
| Parental | DTMHQRKRIHQLEQQVEKLRKKLKTAQQRCRRQERQLEKLKEVV-HFQKEKEDTPERGYVILPNDYFEIV |
| DTMHQRKRIHQLEQQVEKLRKK.KTAQQRC.R......K....V....KEKEDTPERGYVILPNDYFEIV | |
| Retrocopy | DTMHQRKRIHQLEQQVEKLRKKFKTAQQRC-RRQERQLKKLKEV>YTSKEKEDTPERGYVILPNDYFEIV |
| Parental | EVPA |
| EVPA | |
| Retrocopy | EVPA |
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 |
|---|---|---|
| SRP017611_brain | 0 .81 RPM | 2 .58 RPM |
| SRP017611_kidney | 0 .94 RPM | 4 .88 RPM |
| SRP017611_liver | 0 .00 RPM | 2 .25 RPM |
Erinaceus europaeus was not studied using ChIP-Seq data.
Erinaceus europaeus was not studied using EST data.
Erinaceus europaeus was not studied using FANTOM5 data.
retro_eeur_131 was not experimentally validated.
Retrocopy orthology:
Erinaceus europaeus 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 3 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Erinaceus europaeus | ENSEEUG00000003332 | 2 retrocopies |
retro_eeur_131 , retro_eeur_172,
|
| Myotis lucifugus | ENSMLUG00000003837 | 1 retrocopy | |
| Oryctolagus cuniculus | ENSOCUG00000001391 | 1 retrocopy |