RetrogeneDB ID: retro_cfam_70

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 27:45855224..45856181(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000016270
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000029695
• Aliases: None
• Description: None

Sequence

>retro_cfam_70
ATGAACCGGTTTGGTACCCGGTTGGTGGGAGCTACGGCCACGCCGCCGCCGCCGCCGCCGAAAGCCCGCAGCAATGAAAA
CCTGGACAAAATCGATATGTCTCTGGATGATATCATCAAATTGAATAGAAAGGAAGGAAAGAAGCAGAATTTTCCGAGAC
TAAATAGAAAACTCCAGCAAAGCAGTGCCCGGCAATTCAGGATGAGAGTGCGATGGGGAATCCAACAGAATTCTGGTTTT
GGCAAGAATAGTCTGAGCCGTAGAGGAAGGGTAATGCCTGGAAAGAGACGTCCTTATGGAGTTATCACTGGCCTTGCAGC
TAGGAAAGCAACTGGAATTCGAAAAGGAATTAGTCCTATGAATCGACCACCTCTTAGTGATAAGAATATAGAACGATATT
TTCCAGCATTAAAAAGGAAGGCCAACCTTCTGAGACAAAACGAAGTACAGAGAAAAGCAGTCGCAGTTCTCAAGAGACCT
AACCAGTTAAATAGAAAAAATAACATTCCAGCCAATTTTACCAGGAGTGGAAATAAATTAAGTCATCAGAAAGATACTCG
TCAGGCAACTTTTCTTTTCAGAAGAGGCCTAAAGGTTCAGGCCCAGTTGAACACAGAACAACTGCTAGATGATGTAGTAG
CAAAGAGAACTCGTCAATGGCGAACTTCCACCACAAATGGAGGAATTTTGACTGTCTCTATTGACAATCCTGGAGCAGTG
CAGTGCCCAGTAACTCAGAAACCACGGTTAACTCGTACTGCTGTACCCTCATTCTTGACAAAACGGGAGCAATCTGATGT
AAAGAAAGTTCCTAAAGGTGTCCCCCTACAATTTGACATAAATAGTGTTGGAAAACAGACAGGGATGACTTTGAATGAGC
GATTTGGGATCCTGAAGGAACAAAGAGCCACTCTCACGTTCAACAAAGGAGGAAGCCGTTTTGTAACCGTGGGATAG

Alignment

ORF - retro_cfam_70 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100.0 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DDIIKLNRKEGKKQNFPRLNRKLQQSSARQFRMRVRWGIQQNSGFGKNSLSRRGRVMPGKRRPYGVITGL
          DDIIKLNRKEGKKQNFPRLNRKLQQSSARQFRMRVRWGIQQNSGFGKNSLSRRGRVMPGKRRPYGVITGL
Retrocopy DDIIKLNRKEGKKQNFPRLNRKLQQSSARQFRMRVRWGIQQNSGFGKNSLSRRGRVMPGKRRPYGVITGL

Parental  AARKATGIRKGISPMNRPPLSDKNIERYFPALKRKANLLRQNEVQRKAVAVLKRPNQLNRKNNIPANFTR
          AARKATGIRKGISPMNRPPLSDKNIERYFPALKRKANLLRQNEVQRKAVAVLKRPNQLNRKNNIPANFTR
Retrocopy AARKATGIRKGISPMNRPPLSDKNIERYFPALKRKANLLRQNEVQRKAVAVLKRPNQLNRKNNIPANFTR

Parental  SGNKLSHQKDTRQATFLFRRGLKVQAQLNTEQLLDDVVAKRTRQWRTSTTNGGILTVSIDNPGAVQCPVT
          SGNKLSHQKDTRQATFLFRRGLKVQAQLNTEQLLDDVVAKRTRQWRTSTTNGGILTVSIDNPGAVQCPVT
Retrocopy SGNKLSHQKDTRQATFLFRRGLKVQAQLNTEQLLDDVVAKRTRQWRTSTTNGGILTVSIDNPGAVQCPVT

Parental  QKPRLTRTAVPSFLTKREQSDVKKVPKGVPLQFDINSVGKQTGMTLNERFGILKEQRATLTFNKGGSRFV
          QKPRLTRTAVPSFLTKREQSDVKKVPKGVPLQFDINSVGKQTGMTLNERFGILKEQRATLTFNKGGSRFV
Retrocopy QKPRLTRTAVPSFLTKREQSDVKKVPKGVPLQFDINSVGKQTGMTLNERFGILKEQRATLTFNKGGSRFV

Parental  TVG
          TVG
Retrocopy TVG

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	9.32 RPM	5.54 RPM
SRP017611_brain	3.65 RPM	4.37 RPM
SRP017611_kidney	4.89 RPM	7.26 RPM
SRP017611_liver	1.89 RPM	2.47 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_70 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_70 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_70 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 31 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014874	1 retrocopy	retro_btau_1572,
Canis familiaris	ENSCAFG00000029695	1 retrocopy	retro_cfam_70 ,
Choloepus hoffmanni	ENSCHOG00000002881	2 retrocopies	retro_chof_1068, retro_chof_114,
Callithrix jacchus	ENSCJAG00000016488	2 retrocopies	retro_cjac_1639, retro_cjac_623,
Cavia porcellus	ENSCPOG00000011463	2 retrocopies	retro_cpor_1039, retro_cpor_586,
Dasypus novemcinctus	ENSDNOG00000007807	6 retrocopies	retro_dnov_1010, retro_dnov_1224, retro_dnov_1311, retro_dnov_2013, retro_dnov_442, retro_dnov_570,
Erinaceus europaeus	ENSEEUG00000001433	1 retrocopy	retro_eeur_13,
Echinops telfairi	ENSETEG00000000700	1 retrocopy	retro_etel_765,
Homo sapiens	ENSG00000122068	2 retrocopies	retro_hsap_4291, retro_hsap_476,
Gorilla gorilla	ENSGGOG00000011665	1 retrocopy	retro_ggor_450,
Macaca mulatta	ENSMMUG00000006626	1 retrocopy	retro_mmul_577,
Nomascus leucogenys	ENSNLEG00000015547	2 retrocopies	retro_nleu_1047, retro_nleu_889,
Pongo abelii	ENSPPYG00000014456	2 retrocopies	retro_pabe_258, retro_pabe_3497,
Pan troglodytes	ENSPTRG00000015796	1 retrocopy	retro_ptro_357,
Sorex araneus	ENSSARG00000009996	1 retrocopy	retro_sara_148,
Sarcophilus harrisii	ENSSHAG00000005704	1 retrocopy	retro_shar_242,
Tupaia belangeri	ENSTBEG00000005595	4 retrocopies	retro_tbel_2469, retro_tbel_2943, retro_tbel_4257, retro_tbel_791,