RetrogeneDB ID: retro_cfam_586

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 13:63188447..63189736(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000031249
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000008357
• Aliases: None
• Description: None

Sequence

>retro_cfam_586
ATGGCCCTGTTGCACTCCGGTCGCGTCCTGTCTGGGGTCGCCGCCGCCTTCCACCCAGGCCTCGCTGGTGCGGCTTCTGC
GAGAGCCAGTTCCTGGTGGACCCATGTGGAAATGGGGCCTCCAGACCCCATCCTGGGAGTCACAGAAGCCTTTAAGAGAG
ACACTAACAGCAAAAAGATGAATCTGGGAGTTGGCGCCTATCGGGATGATAATGGAAAGCCTTATGTGCTCCCTAGTGTC
CGGAAGGCAGAGGCCCAGATTGCTGCAAAAAATTTGGACAAAGAATACCTGCCCATTGCTGGACTTGCTGAATTTTGTAA
GGCATCTGCAGAACTAGCCCTGGGTGAGAACAATGAAGTGTTGAAAAGTAGCCGGTATGTCACCGTGCAGACCATTTCTG
GAACAGGGGCATTGAGGATTGGAGCCAGTTTTCTGCAAAGATTTTTTAAGTTCAGCCAAGATGTCTTTCTGCCCAAACCA
TCCTGGGGAAACCATACACCAATCTTCAGGGACGCTGGCATGCAGCTACATGGTTATCGATACTATGACCCCAAGACGTG
CGGCTTTGATTTCACAGGCGCTATAGAGGACATTTCGAAAATGCCACAGCAAAGTGTTCTTCTCCTGCATGCCTGTGCCC
ACAATCCCACGGGAGTAGACCCCCGCCCTGAGCAATGGAAGGAAATAGCAACAGTGGTGAAGAAAAATAATCTCTTTGCA
TTCTTTGACATGGCCTACCAAGGCTTTGCCAGTGGTGATGGTAACAAGGATGCCTGGGCTGTACGCCACTTCATCGAACA
AGGCATTAATGTTTGTCTCTGCCAATCCTATGCCAAGAACATGGGCTTATACGGTGAGCGTGTAGGAGCCTTCACTGTGG
TCTGCAAGGATGCTGATGAAGCTAAAAGGGTGGAGTCACAGTTGAAGATCTTGATCCGTCCCATGTATTCCAACCCTCCA
ATCAATGGGGCCCGAATTGCCTCAACCATCCTGACCAGCCCTGACCTGCGAAAACAATGGTTGCAGGAAGTAAAAGGCAT
GGCCGACCGCATCATTAGCATGCGTACTCAGCTGGTCTCCAACCTCAAGAAGGAGGGCTCCTCCCACAATTGGCAGCACA
TCACTGACCAGATTGGCATGTTTTGTTTCACAGGACTAAAGCCTGAACAGGTGAGAGGCTGACCAAGGAGTTCTCCATCT
ACATGACAAAGGATGGCCGCATCTCTGTGGCAGGGGTCACATCTGGCAATGTGGGCTACCTTGCCCATGCCATTCACCAG
GTTACCAAG

Alignment

ORF - retro_cfam_586 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.77 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MALLHSGRVLSGVAAAFHPGLAGAASARASSWWTHVEMGPPDPILGVTEAFKRDTNSKKMNLGVGAYRDD
          MALLHSGRVLSGVAAAFHPGLAGAASARASSWWTHVEMGPPDPILGVTEAFKRDTNSKKMNLGVGAYRDD
Retrocopy MALLHSGRVLSGVAAAFHPGLAGAASARASSWWTHVEMGPPDPILGVTEAFKRDTNSKKMNLGVGAYRDD

Parental  NGKPYVLPSVRKAEAQIAAKNLDKEYLPIAGLAEFCKASAELALGENNEVLKSSRYVTVQTISGTGALRI
          NGKPYVLPSVRKAEAQIAAKNLDKEYLPIAGLAEFCKASAELALGENNEVLKSSRYVTVQTISGTGALRI
Retrocopy NGKPYVLPSVRKAEAQIAAKNLDKEYLPIAGLAEFCKASAELALGENNEVLKSSRYVTVQTISGTGALRI

Parental  GASFLQRFFKFSQDVFLPKPSWGNHTPIFRDAGMQLHGYRYYDPKTCGFDFTGAIEDISKMPQQSVLLLH
          GASFLQRFFKFSQDVFLPKPSWGNHTPIFRDAGMQLHGYRYYDPKTCGFDFTGAIEDISKMPQQSVLLLH
Retrocopy GASFLQRFFKFSQDVFLPKPSWGNHTPIFRDAGMQLHGYRYYDPKTCGFDFTGAIEDISKMPQQSVLLLH

Parental  ACAHNPTGVDPRPEQWKEIATVVKKNNLFAFFDMAYQGFASGDGNKDAWAVRHFIEQGINVCLCQSYAKN
          ACAHNPTGVDPRPEQWKEIATVVKKNNLFAFFDMAYQGFASGDGNKDAWAVRHFIEQGINVCLCQSYAKN
Retrocopy ACAHNPTGVDPRPEQWKEIATVVKKNNLFAFFDMAYQGFASGDGNKDAWAVRHFIEQGINVCLCQSYAKN

Parental  MGLYGERVGAFTVVCKDADEAKRVESQLKILIRPMYSNPPINGARIASTILTSPDLRKQWLQEVKGMADR
          MGLYGERVGAFTVVCKDADEAKRVESQLKILIRPMYSNPPINGARIASTILTSPDLRKQWLQEVKGMADR
Retrocopy MGLYGERVGAFTVVCKDADEAKRVESQLKILIRPMYSNPPINGARIASTILTSPDLRKQWLQEVKGMADR

Parental  IISMRTQLVSNLKKEGSSHNWQHITDQIGMFCFTGLKPEQV-ERLTKEFSIYMTKDGRISVAGVTSGNVG
          IISMRTQLVSNLKKEGSSHNWQHITDQIGMFCFTGLKPEQV.ERLTKEFSIYMTKDGRISVAGVTSGNVG
Retrocopy IISMRTQLVSNLKKEGSSHNWQHITDQIGMFCFTGLKPEQV<ERLTKEFSIYMTKDGRISVAGVTSGNVG

Parental  YLAHAIHQVTK
          YLAHAIHQVTK
Retrocopy YLAHAIHQVTK

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	1.13 RPM	42.25 RPM
SRP017611_brain	4.76 RPM	45.81 RPM
SRP017611_kidney	6.21 RPM	69.87 RPM
SRP017611_liver	2.83 RPM	54.68 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_586 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_586 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_586 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 18 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017346	3 retrocopies	retro_amel_1805, retro_amel_815, retro_amel_846,
Canis familiaris	ENSCAFG00000008357	2 retrocopies	retro_cfam_586 , retro_cfam_816,
Callithrix jacchus	ENSCJAG00000011234	1 retrocopy	retro_cjac_2916,
Equus caballus	ENSECAG00000016504	1 retrocopy	retro_ecab_694,
Felis catus	ENSFCAG00000025552	3 retrocopies	retro_fcat_1068, retro_fcat_1888, retro_fcat_381,
Homo sapiens	ENSG00000125166	4 retrocopies	retro_hsap_4687, retro_hsap_473, retro_hsap_960, retro_hsap_971,
Gorilla gorilla	ENSGGOG00000005767	3 retrocopies	retro_ggor_2912, retro_ggor_449, retro_ggor_774,
Macropus eugenii	ENSMEUG00000012574	1 retrocopy	retro_meug_2109,
Microcebus murinus	ENSMICG00000008954	1 retrocopy	retro_mmur_480,
Macaca mulatta	ENSMMUG00000006000	1 retrocopy	retro_mmul_1337,
Mustela putorius furo	ENSMPUG00000004862	1 retrocopy	retro_mputfur_567,
Mus musculus	ENSMUSG00000031672	1 retrocopy	retro_mmus_2701,
Oryctolagus cuniculus	ENSOCUG00000003871	1 retrocopy	retro_ocun_1516,
Otolemur garnettii	ENSOGAG00000000551	2 retrocopies	retro_ogar_2182, retro_ogar_827,
Pongo abelii	ENSPPYG00000007413	3 retrocopies	retro_pabe_3640, retro_pabe_823, retro_pabe_901,
Pan troglodytes	ENSPTRG00000008185	4 retrocopies	retro_ptro_3115, retro_ptro_354, retro_ptro_665, retro_ptro_670,
Rattus norvegicus	ENSRNOG00000011782	1 retrocopy	retro_rnor_2695,
Tupaia belangeri	ENSTBEG00000001808	1 retrocopy	retro_tbel_3799,