RetrogeneDB ID: retro_cfam_1014

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 21:26708893..26709292(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AKIRIN2
• Ensembl ID: ENSCAFG00000003082
• Aliases: None
• Description: akirin 2 [Source:HGNC Symbol;Acc:21407]

Sequence

>retro_cfam_1014
GACAGCGATACCAACTCTGAATCAGAACAACTTCTGTACAACATAAAACAAGAGTATAAACGCATGCAGAAGAGAAGACA
TTTAGAAACTAGTTTCCAACAGACAGATCCATGTTGTACTTCTGAGGCACAACCACATGCATTTCTCCTCAGTGGACCAG
CTTCACCAGGGACTTCATCTGCAACATCCTCACCATTAAAAAAAGAACAACCCTTATTTACTCTACGACAGGTTGGGATG
ATCTGTGAACGTTTGTTGAAAGAACGTGAAGAGAAAGTTCGAGAAGAGTATGAAGAAATATTGAACACAAAACTTGCAGA
ACAATATGATGCATTTGTGAAGTTTATGCATGATCAAATAATGCAACGATACAGAGAACAGCCTGCTAGTTATGTTTCA

Alignment

ORF - retro_cfam_1014 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.73 %
• Parental protein coverage: 65.52 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DVSSRLTTEQILYNIKQEYKRMQKRRHLETSFQQTDPCCTSEAQPHAFLLSGPASPGTSSATSSPLKKEQ
          D.......EQ.LYNIKQEYKRMQKRRHLETSFQQTDPCCTSEAQPHAFLLSGPASPGTSSATSSPLKKEQ
Retrocopy DSDTNSESEQLLYNIKQEYKRMQKRRHLETSFQQTDPCCTSEAQPHAFLLSGPASPGTSSATSSPLKKEQ

Parental  PLFTLRQVGMICERLLKEREEKVREEYEEILNTKLAEQYDAFVKFTHDQIMRRYGEQPASYVS
          PLFTLRQVGMICERLLKEREEKVREEYEEILNTKLAEQYDAFVKF.HDQIM.RY.EQPASYVS
Retrocopy PLFTLRQVGMICERLLKEREEKVREEYEEILNTKLAEQYDAFVKFMHDQIMQRYREQPASYVS

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP012049_cerebellum	0.00 RPM	23.35 RPM
SRP017611_brain	0.00 RPM	18.10 RPM
SRP017611_kidney	0.00 RPM	7.59 RPM
SRP017611_liver	0.00 RPM	4.13 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1014 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1014 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1014 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003082	1 retrocopy	retro_cfam_1014 ,
Canis familiaris	ENSCAFG00000003186	4 retrocopies	retro_cfam_1099, retro_cfam_1915, retro_cfam_2086, retro_cfam_810,
Choloepus hoffmanni	ENSCHOG00000012160	1 retrocopy	retro_chof_413,
Callithrix jacchus	ENSCJAG00000000769	1 retrocopy	retro_cjac_2231,
Dasypus novemcinctus	ENSDNOG00000000549	1 retrocopy	retro_dnov_1788,
Homo sapiens	ENSG00000135334	1 retrocopy	retro_hsap_2991,
Gorilla gorilla	ENSGGOG00000002448	1 retrocopy	retro_ggor_2071,
Macaca mulatta	ENSMMUG00000002824	1 retrocopy	retro_mmul_1914,
Pongo abelii	ENSPPYG00000016831	1 retrocopy	retro_pabe_2477,
Pan troglodytes	ENSPTRG00000018409	1 retrocopy	retro_ptro_2023,
Rattus norvegicus	ENSRNOG00000008288	1 retrocopy	retro_rnor_1499,
Sorex araneus	ENSSARG00000006084	1 retrocopy	retro_sara_701,
Sarcophilus harrisii	ENSSHAG00000011555	2 retrocopies	retro_shar_363, retro_shar_579,
Sus scrofa	ENSSSCG00000004307	1 retrocopy	retro_sscr_897,