RetrogeneDB ID: retro_cfam_1995

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 9:10550782..10551652(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000013284
• Aliases: None
• Description: None

Sequence

>retro_cfam_1995
AGTTATGATGGCGATATGCAAGGCCAAGAAGTTAACAGTCTTTTGAACAAAGTAGAAGAAAGAATGAAAGACTGAGTCAG
GACAGTACTGAGCGGGTGAAGCAGTTACCACCCATACTTCGAGGAGGGGCCATTGACAGATACTGGCCCACTGCTCATGG
TCGCCTGGTTGAGTATGACATAGATGAAGTAGTGTATGATGAAGATTCACCTTATCAGAACACTAAAATTTTACACTCGA
AGCAGTTTGGATATATTCTCATCCTTAGTGGGGATGTTAATCTGGCGGAGAGTGATTTGGCGTTTACCCAGGACATCAAG
GGCAGTGGAAAAGAAGACTACAGTGGCAAAGATGTACTGATTCTGGGGGGTGGAGATGGGGCATATTATGTGAAATAGTC
AAACTGAAACCAAAGATGGTCACTATGGTAGAGATTGACCAAATGGTGATTGATGAATATAAGAAATACATGCGGAAAAC
ATGTGGTGACGTCTTAAACAATCTTAAAGGAGACTCCTATCAGGTTCTAATAGAAGACTGTATTCCAGTACTGAAGAGGT
ACGCCAAAGAAGGGGAGAGAGTTTGATTATGTGATTAATGATTTGACAGCTGTTCCAATCTCCACATCTCCAGAAGAAGA
TCCACATGGGAGTTTCTCAGACTGATTCTTGACCTCTAATGAAAGTACTGAAACAAGATGGGAAATATTTTACACAGGGT
AACTGTGTGAATTTGACAGAAGCCTTGTTGCTCTATGAAGAACAGCTTGGGCACTTGTATTGTCCTGTGGAATTCTCAAA
GGAGATCATCTGTGTTCCCTCATACTTGGAATTGTGGGTATTTTACACTGTTTGGAAGAAAGCTAAACCT

Alignment

ORF - retro_cfam_1995 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.27 %
• Parental protein coverage: 79.4 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  SYDGDSQGQEVDSLLNKVEERMKE-LSQDSTGRVKRLPPIVRGGAIDRYWPTADGRLVEYDIDEVVYDED
          SYDGD.QGQEV.SLLNKVEERMK..LSQDST.RVK.LPPI.RGGAIDRYWPTA.GRLVEYDIDEVVYDED
Retrocopy SYDGDMQGQEVNSLLNKVEERMKD<LSQDSTERVKQLPPILRGGAIDRYWPTAHGRLVEYDIDEVVYDED

Parental  SPYQNIKILHSKQFGNILILSGDVNLAESDLAYTQAIMGSGKEDYSGKDVLILGGGDG-GILCEIVKLKP
          SPYQN.KILHSKQFG.ILILSGDVNLAESDLA.TQ.I.GSGKEDYSGKDVLILGGGDG.GILCEIVKLKP
Retrocopy SPYQNTKILHSKQFGYILILSGDVNLAESDLAFTQDIKGSGKEDYSGKDVLILGGGDG<GILCEIVKLKP

Parental  KMVTMTCLNIDQMVIDGCKKYMRKTCGDVLDNLKGDCYQVLIEDCIPVLKRYAKE-GREFDYVINDLTAV
          KMVTM....IDQMVID..KKYMRKTCGDVL.NLKGD.YQVLIEDCIPVLKRYAKE.GREFDYVINDLTAV
Retrocopy KMVTM--VEIDQMVIDEYKKYMRKTCGDVLNNLKGDSYQVLIEDCIPVLKRYAKE>GREFDYVINDLTAV

Parental  PISTSPEED-STWEFLRLILDL-SMKVLKQDGKYFTQGNCVNLTEALSLYEEQLGRLYCPVEFSKEIVCV
          PISTSPEED.STWEFLRLILDL..MKVLKQDGKYFTQGNCVNLTEAL.LYEEQLG.LYCPVEFSKEI.CV
Retrocopy PISTSPEED<STWEFLRLILDL<LMKVLKQDGKYFTQGNCVNLTEALLLYEEQLGHLYCPVEFSKEIICV

Parental  PSYLELWVFYTVWKKAKP
          PSYLELWVFYTVWKKAKP
Retrocopy PSYLELWVFYTVWKKAKP

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	0.25 RPM	51.78 RPM
SRP017611_brain	0.95 RPM	41.28 RPM
SRP017611_kidney	2.77 RPM	196.20 RPM
SRP017611_liver	0.29 RPM	19.00 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1995 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1995 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1995 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 49 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000018382	1 retrocopy	retro_btau_1412,
Canis familiaris	ENSCAFG00000013284	3 retrocopies	retro_cfam_1076, retro_cfam_1995 , retro_cfam_613,
Callithrix jacchus	ENSCJAG00000033933	1 retrocopy	retro_cjac_518,
Cavia porcellus	ENSCPOG00000006176	2 retrocopies	retro_cpor_729, retro_cpor_889,
Echinops telfairi	ENSETEG00000010098	2 retrocopies	retro_etel_1066, retro_etel_1540,
Homo sapiens	ENSG00000102172	5 retrocopies	retro_hsap_243, retro_hsap_3168, retro_hsap_3193, retro_hsap_3611, retro_hsap_4826,
Gorilla gorilla	ENSGGOG00000003123	3 retrocopies	retro_ggor_1335, retro_ggor_2437, retro_ggor_3009,
Microcebus murinus	ENSMICG00000000192	3 retrocopies	retro_mmur_1421, retro_mmur_1484, retro_mmur_699,
Myotis lucifugus	ENSMLUG00000013185	3 retrocopies	retro_mluc_471, retro_mluc_530, retro_mluc_92,
Macaca mulatta	ENSMMUG00000020392	2 retrocopies	retro_mmul_2003, retro_mmul_2574,
Monodelphis domestica	ENSMODG00000007897	1 retrocopy	retro_mdom_412,
Mus musculus	ENSMUSG00000071708	6 retrocopies	retro_mmus_2162, retro_mmus_2170, retro_mmus_2837, retro_mmus_3502, retro_mmus_3628, retro_mmus_994,
Nomascus leucogenys	ENSNLEG00000009955	4 retrocopies	retro_nleu_1664, retro_nleu_2200, retro_nleu_2208, retro_nleu_2755,
Oryctolagus cuniculus	ENSOCUG00000006016	2 retrocopies	retro_ocun_1458, retro_ocun_1918,
Pongo abelii	ENSPPYG00000020182	4 retrocopies	retro_pabe_2649, retro_pabe_2810, retro_pabe_3752, retro_pabe_38,
Pteropus vampyrus	ENSPVAG00000016785	1 retrocopy	retro_pvam_524,
Rattus norvegicus	ENSRNOG00000007688	2 retrocopies	retro_rnor_1934, retro_rnor_938,
Tupaia belangeri	ENSTBEG00000012109	3 retrocopies	retro_tbel_1630, retro_tbel_1893, retro_tbel_3570,
Vicugna pacos	ENSVPAG00000007543	1 retrocopy	retro_vpac_50,