RetrogeneDB ID: retro_cfam_11

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 10:757064..757601(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000000132
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000008456
• Aliases: None
• Description: None

Sequence

>retro_cfam_11
ATGCCGGCTTACCACTCTTCTCTCATGGACCCTGACACCAAACTCATTGGAAACATGGCATTGTTGCCTATCAGAAGTCA
ATTCAAAGGACCCGCCCCTAGAGAGACAAAAGATACAGATATTGTGGATGAAGCCATTTATTACTTCAAGGCCAATGTCT
TCTTCAAAAACTATGAGATTAAGAATGAAGCCGATAGAACCTTGATATATATAACACTCTACATTTCTGAGTGTCTAAAG
AAACTCCAAAAGTGTAATTCCAAAAGCCAAGGTGAAAAAGAAATGTATACACCGGGAATCACTAATTTCCCCATTCCTGG
AGAGCCTGGTTTTCCACTTAATGCAATTTATGCCAAACCTGCAAACAAACAGGAAGATGAGGTGATGAGGGCCTACTTAC
AGCAGCTGAGACAAGAGACTGGACTGAGACTTTGTGAGAAAGTTTTTGACCCTCAGAATGATAAGCCAAGCAAGTGGTGG
ACTTGCTTTGTGAAGAGACAGTTCATGAACAAGAGTCTTTCAGGACCTGGACAGTAA

Alignment

ORF - retro_cfam_11 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.31 %
• Parental protein coverage: 87.68 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LQAYHSSLMDPDTKLIGNMALLPIRSQFKGPAPRETKDTDIVDEAIYYFKANVFFKNYEIKNEADRTLIY
          ..AYHSSLMDPDTKLIGNMALLPIRSQFKGPAPRETKDTDIVDEAIYYFKANVFFKNYEIKNEADRTLIY
Retrocopy MPAYHSSLMDPDTKLIGNMALLPIRSQFKGPAPRETKDTDIVDEAIYYFKANVFFKNYEIKNEADRTLIY

Parental  ITLYISECLKKLQKCNSKSQGEKEMYTLGITNFPIPGEPGFPLNAIYAKPANKQEDEVMRAYLQQLRQET
          ITLYISECLKKLQKCNSKSQGEKEMYT.GITNFPIPGEPGFPLNAIYAKPANKQEDEVMRAYLQQLRQET
Retrocopy ITLYISECLKKLQKCNSKSQGEKEMYTPGITNFPIPGEPGFPLNAIYAKPANKQEDEVMRAYLQQLRQET

Parental  GLRLCEKVFDPQNDKPSKWWTCFVKRQFMNKSLSGPGQ
          GLRLCEKVFDPQNDKPSKWWTCFVKRQFMNKSLSGPGQ
Retrocopy GLRLCEKVFDPQNDKPSKWWTCFVKRQFMNKSLSGPGQ

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	7.14 RPM	43.85 RPM
SRP017611_brain	4.68 RPM	43.27 RPM
SRP017611_kidney	5.75 RPM	55.67 RPM
SRP017611_liver	1.02 RPM	14.94 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_11 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_11 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_11 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 25 parental genes, and 55 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000008456	1 retrocopy	retro_cfam_11 ,
Callithrix jacchus	ENSCJAG00000009360	1 retrocopy	retro_cjac_242,
Dasypus novemcinctus	ENSDNOG00000004987	2 retrocopies	retro_dnov_2619, retro_dnov_685,
Erinaceus europaeus	ENSEEUG00000011531	2 retrocopies	retro_eeur_122, retro_eeur_99,
Echinops telfairi	ENSETEG00000006992	2 retrocopies	retro_etel_116, retro_etel_1323,
Felis catus	ENSFCAG00000004132	2 retrocopies	retro_fcat_1048, retro_fcat_73,
Homo sapiens	ENSG00000111229	5 retrocopies	retro_hsap_2431, retro_hsap_303, retro_hsap_3425, retro_hsap_892, retro_hsap_918,
Loxodonta africana	ENSLAFG00000006166	3 retrocopies	retro_lafr_1119, retro_lafr_763, retro_lafr_840,
Microcebus murinus	ENSMICG00000005485	2 retrocopies	retro_mmur_1009, retro_mmur_1507,
Macaca mulatta	ENSMMUG00000006492	3 retrocopies	retro_mmul_1105, retro_mmul_1174, retro_mmul_543,
Monodelphis domestica	ENSMODG00000011628	1 retrocopy	retro_mdom_71,
Mustela putorius furo	ENSMPUG00000002151	2 retrocopies	retro_mputfur_1346, retro_mputfur_1540,
Nomascus leucogenys	ENSNLEG00000002802	4 retrocopies	retro_nleu_239, retro_nleu_283, retro_nleu_3078, retro_nleu_389,
Oryctolagus cuniculus	ENSOCUG00000011908	1 retrocopy	retro_ocun_1252,
Otolemur garnettii	ENSOGAG00000013424	1 retrocopy	retro_ogar_2855,
Oreochromis niloticus	ENSONIG00000003785	1 retrocopy	retro_onil_18,
Procavia capensis	ENSPCAG00000011858	2 retrocopies	retro_pcap_421, retro_pcap_441,
Pongo abelii	ENSPPYG00000004947	6 retrocopies	retro_pabe_1735, retro_pabe_1790, retro_pabe_2838, retro_pabe_376, retro_pabe_769, retro_pabe_792,
Sorex araneus	ENSSARG00000000546	2 retrocopies	retro_sara_529, retro_sara_601,
Sarcophilus harrisii	ENSSHAG00000014805	3 retrocopies	retro_shar_144, retro_shar_439, retro_shar_576,
Sus scrofa	ENSSSCG00000009821	1 retrocopy	retro_sscr_177,
Ictidomys tridecemlineatus	ENSSTOG00000011979	1 retrocopy	retro_itri_1350,
Tarsius syrichta	ENSTSYG00000002953	4 retrocopies	retro_tsyr_1150, retro_tsyr_1341, retro_tsyr_2103, retro_tsyr_794,
Tursiops truncatus	ENSTTRG00000015083	2 retrocopies	retro_ttru_713, retro_ttru_880,
Vicugna pacos	ENSVPAG00000008404	1 retrocopy	retro_vpac_225,