RetrogeneDB ID: retro_ttru_1852

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_94560:22247..23029(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: PRKRA
• Ensembl ID: ENSTTRG00000009700
• Aliases: None
• Description: protein kinase, interferon-inducible double stranded RNA dependent activator [Source:HGNC Symbol;Acc:9438]

Sequence

>retro_ttru_1852
ATGTCTCAGAGCAGGCATCGTGCCGTGGCTCCGCCGCTGAAGTGTGAGGACAGTGGGACCTTCAGTTTGGGGAAGATGAT
CACAGCTAAGCCAGGGAAAACACCAATTCAGGTATTACATGTATACGGCATGAAGACCAAGAATATCCCAGTTTATGAAT
GTGAAAGATCCAATGTGCAAATACACTTGCCCACTTTCACCTTCAGAGTAACTGTTGGTGACATAACCTGCACAGGTGAA
GGTACAAGTAAGAAGCTGGCGAAACATAGAGCTTCTGAGGCTGCCATAAACATTTTGAAAGCCAGTGCAAGTATTTTCTT
TGCAGTTCCTGATCCCTTAATGCCTGACCCTTCCAAGCAACCGAAGAACCAGCTTAATCCTATTGGTTCATTACAGGAAT
TGGCTATTCATCATGGCTGGAGACTTCCTGATATACCCTTTCCCAGGAGGGAGGACCTGCTCCTAAGAGAGAATATACCA
CAATTTGCAGGCTAGAGTCATTCATGGAAACTGGAAAGGGGGCATCAAAGAAACAAGCCAAGAGAAATGCTGCTGAGAAA
TTTCTTGCCAAATTCAGTAATATCTCTCCAGAGAACCACATTTCTTTGACAAATGTGGTAGGACATTCTTTAGGTTGTAC
TTGGCATTCCTTGAGGATTTATCCTTGTGAAAAGATCAACTTACTGAAAAGAAGCCTCCTCAGTATTCCAAATACAGATT
ACATCCAGCTGCTTAGTGAAATTGCAAAGGAGCAAGGTTTTAATATAACACATTTGGATATA

Alignment

ORF - retro_ttru_1852 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.89 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSQSRHRAAAPPLEREDSGTFSLGKMITAKPGKTPIQVLHEYGMKTKNIPVYECERSDVQIHVPTFTFRV
          MSQSRHRA.APPL..EDSGTFSLGKMITAKPGKTPIQVLH.YGMKTKNIPVYECERS.VQIH.PTFTFRV
Retrocopy MSQSRHRAVAPPLKCEDSGTFSLGKMITAKPGKTPIQVLHVYGMKTKNIPVYECERSNVQIHLPTFTFRV

Parental  TVGDITCTGEGTSKKLAKHRAAEAAINILKANASICFAVPDPLMPDPSKQPKNQLNPIGSLQELAIHHGW
          TVGDITCTGEGTSKKLAKHRA.EAAINILKA.ASI.FAVPDPLMPDPSKQPKNQLNPIGSLQELAIHHGW
Retrocopy TVGDITCTGEGTSKKLAKHRASEAAINILKASASIFFAVPDPLMPDPSKQPKNQLNPIGSLQELAIHHGW

Parental  RLPE-YTLSQEGGPAHKREYTTICRLESFMETGKGASKKQAKRNAAEKFLAKFSNISPENHISLTNVVGH
          RLP..YTLSQEGGPA.KREYTTICRLESFMETGKGASKKQAKRNAAEKFLAKFSNISPENHISLTNVVGH
Retrocopy RLPD<YTLSQEGGPAPKREYTTICRLESFMETGKGASKKQAKRNAAEKFLAKFSNISPENHISLTNVVGH

Parental  SLGCTWHSLRNSPGEKINLLKRSLLSIPNTDYIQLLSEIAKEQGFNITYLDI
          SLGCTWHSLR..P.EKINLLKRSLLSIPNTDYIQLLSEIAKEQGFNIT.LDI
Retrocopy SLGCTWHSLRIYPCEKINLLKRSLLSIPNTDYIQLLSEIAKEQGFNITHLDI

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Tursiops truncatus was not studied using RNA-Seq expression data.

ChIP-Seq

Tursiops truncatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ttru_1852 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1852 was not experimentally validated.

Homology

Retrocopy orthology:

Tursiops truncatus 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 5 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
	ENSG00000180228	0 retrocopies
Macaca mulatta	ENSMMUG00000002185	1 retrocopy	retro_mmul_809,
Oryctolagus cuniculus	ENSOCUG00000005489	1 retrocopy	retro_ocun_1117,
Sorex araneus	ENSSARG00000003080	1 retrocopy	retro_sara_381,
Tursiops truncatus	ENSTTRG00000009700	1 retrocopy	retro_ttru_1852 ,