RetrogeneDB ID: retro_cfam_116

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 8:59302498..59303365(+)
• Located in intron of: ENSCAFG00000017337

Retrocopy information

• Ensembl ID: ENSCAFG00000017339
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000019979
• Aliases: None
• Description: None

Sequence

>retro_cfam_116
ATGCCGGTCACCGGCAAGAGTTTCCGCCAGCGCCGGGCCGACTCAGAGTCGGAGGAAGATGAGCAGGACTCAGAGGAGGT
TCGATTAAAACTGGAAGAGACTCGCGAGGTGCAAAACTTGAGGAAGAGGCCCAACGGGGTGAGTGCTGTGGCCCTGCTGG
TAGGAGAGAAGGTACAAGAAGAGACCACCCTAGTGGATGATCCCTTTCAGATGAAGACAGGTGGTATGGTGGACATGAAG
AAACTGAAGGAAAGAGGCAAAGATAAGATCAGTGAAGAGGAAGACCTCCATCTGGGGACGTCATTTTCCGCAGAAACCAA
CAGAAGGGATGAGGATGCCGACATGATGAAGTACATTGAGACAGAGCTGAAAAAGAGGAAAGGGATTGTGGAACATGAAG
AACAGAAAGTCAAGCCGAAGAATGCAGAGGACTGTCTCTACAAACTTCCAGAAAACATCCGTGTTTCCTCAGCAAAGAAG
ACGGAAGAGATGCTCTCCAACCAGATGCTGAGCGGCATCCCCGAGGTGGACCTGGGCATCGATGCTAAAATAAAAAATAT
CATTTCCACGGAGGATGCCAAGGCCCGTCTGCTGGCAGAGCAGCAGAACAAGAAGAAAGACAGTGAGACATCTTTCGTGC
CCACCAACATAGCCATGAATTATGTGCAGCACAACCGATTTTATCATAAGGAGCTCAATGTCCCCGTACGGAGAAACAAA
GATGAGCCCAAAGCCCGACCCTTGAGAGTGGGTGACACGGAGAAGCCAGAGCCTGAGCGGTCCCCTCCTAACCGCAAGCA
TCCTGCTAATGAGAAGGCCACTGACGACTATCACTATGAGAAGTTCAAGAAGATGAACAGACGGTAC

Alignment

ORF - retro_cfam_116 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.57 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPVTGKSFRRRRADSESEEDEQDSEEVRLKLEETREVQNLRKRPNGVSAVALLVGEKVQEETTLVDDPFQ
          MPVTGKSFR.RRADSESEEDEQDSEEVRLKLEETREVQNLRKRPNGVSAVALLVGEKVQEETTLVDDPFQ
Retrocopy MPVTGKSFRQRRADSESEEDEQDSEEVRLKLEETREVQNLRKRPNGVSAVALLVGEKVQEETTLVDDPFQ

Parental  MKTGGMVDMKKLKERGKDKISEEEDLHLGTSFSAETNRRDEDADMMKYIETELKKRKGIVEHEEQKVKPK
          MKTGGMVDMKKLKERGKDKISEEEDLHLGTSFSAETNRRDEDADMMKYIETELKKRKGIVEHEEQKVKPK
Retrocopy MKTGGMVDMKKLKERGKDKISEEEDLHLGTSFSAETNRRDEDADMMKYIETELKKRKGIVEHEEQKVKPK

Parental  NAEDCLYELPENIRVSSAKKTEEMLSNQMLSGIPEVDLGIDAKIKNIISTEDAKARLLAEQQNKKKDSET
          NAEDCLY.LPENIRVSSAKKTEEMLSNQMLSGIPEVDLGIDAKIKNIISTEDAKARLLAEQQNKKKDSET
Retrocopy NAEDCLYKLPENIRVSSAKKTEEMLSNQMLSGIPEVDLGIDAKIKNIISTEDAKARLLAEQQNKKKDSET

Parental  SFVPTNMAVNYVQHNRFYHEELNAPVRRNKDEPKARPLRVGDTEKPEPERSPPNRKRPANEKATDDYHYE
          SFVPTN.A.NYVQHNRFYH.ELN.PVRRNKDEPKARPLRVGDTEKPEPERSPPNRK.PANEKATDDYHYE
Retrocopy SFVPTNIAMNYVQHNRFYHKELNVPVRRNKDEPKARPLRVGDTEKPEPERSPPNRKHPANEKATDDYHYE

Parental  KFKKMNRR
          KFKKMNRR
Retrocopy KFKKMNRR

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	41.62 RPM
SRP017611_brain	1.75 RPM	34.30 RPM
SRP017611_kidney	1.72 RPM	40.55 RPM
SRP017611_liver	0.22 RPM	15.37 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_116 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_116 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_116 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020307	1 retrocopy	retro_btau_1138,
Canis familiaris	ENSCAFG00000019979	1 retrocopy	retro_cfam_116 ,
Choloepus hoffmanni	ENSCHOG00000013895	3 retrocopies	retro_chof_1103, retro_chof_1747, retro_chof_978,
Callithrix jacchus	ENSCJAG00000020318	3 retrocopies	retro_cjac_1757, retro_cjac_2299, retro_cjac_2778,
Cavia porcellus	ENSCPOG00000009285	1 retrocopy	retro_cpor_712,
Dasypus novemcinctus	ENSDNOG00000019214	1 retrocopy	retro_dnov_1540,
Equus caballus	ENSECAG00000018958	1 retrocopy	retro_ecab_174,
Homo sapiens	ENSG00000136819	3 retrocopies	retro_hsap_2872, retro_hsap_2913, retro_hsap_320,
Gorilla gorilla	ENSGGOG00000013358	1 retrocopy	retro_ggor_1990,
Macropus eugenii	ENSMEUG00000010524	3 retrocopies	retro_meug_1046, retro_meug_1241, retro_meug_508,
Microcebus murinus	ENSMICG00000009596	1 retrocopy	retro_mmur_1466,
Macaca mulatta	ENSMMUG00000003795	2 retrocopies	retro_mmul_1460, retro_mmul_1870,
Monodelphis domestica	ENSMODG00000006832	1 retrocopy	retro_mdom_518,
Mus musculus	ENSMUSG00000026851	1 retrocopy	retro_mmus_2978,
Nomascus leucogenys	ENSNLEG00000017658	3 retrocopies	retro_nleu_1763, retro_nleu_614, retro_nleu_823,
Otolemur garnettii	ENSOGAG00000009770	1 retrocopy	retro_ogar_1015,
Pongo abelii	ENSPPYG00000019685	1 retrocopy	retro_pabe_2426,
Pan troglodytes	ENSPTRG00000021465	3 retrocopies	retro_ptro_1943, retro_ptro_1969, retro_ptro_258,
Sarcophilus harrisii	ENSSHAG00000012313	1 retrocopy	retro_shar_746,
Ictidomys tridecemlineatus	ENSSTOG00000020630	1 retrocopy	retro_itri_1783,
Tupaia belangeri	ENSTBEG00000013115	1 retrocopy	retro_tbel_514,