RetrogeneDB ID: retro_cfam_1179

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 25:12498985..12499299(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MAX
• Ensembl ID: ENSCAFG00000016212
• Aliases: None
• Description: MYC associated factor X [Source:HGNC Symbol;Acc:6913]

Sequence

>retro_cfam_1179
ATGAACGATGAGGGTGACAGGACACCCAGGGGGAGAGCAGTGGAACCGAGCTTTCAACCCACAGGTGACGAACGGGCTCA
CCATAATGCACCAGAATGAAAGCCTAGGGACCGCAAAGGCAGCCTTCACAGTGTGCAGGCCTCGGTCCCAGCACCCCAAG
CAAAGGAGGCATCCCGGCCCAAATCCTAGACAAGGCCACCGAGCGCATCCAGTGTATACGAAGGAAAAACCACACACACC
AGCAAGACATTGATGACCTCAAGCAGCAGACGGCACCTCTGGAGCAGCAAGCCCCGGCCCTGGAGAAGGTGAGG

Alignment

ORF - retro_cfam_1179 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.75 %
• Parental protein coverage: 66.25 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSDNDDIEVESDEEQPRFQSAADKRAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASR-AQILDKATE
          M.D..D.........P.FQ...D.RAHHNA.E.K.RD..K.S.HS...SVP..Q...ASR.AQILDKATE
Retrocopy MNDEGDRTPRGRAVEPSFQPTGDERAHHNAPE*KPRDR-KGSLHSVQASVPAPQAKEASR<AQILDKATE

Parental  YIQYMRRKNHTHQQDIDDLKRQNALLEQQVRALEKAR
          .IQ..RRKNHTHQQDIDDLK.Q.A.LEQQ..ALEK.R
Retrocopy RIQCIRRKNHTHQQDIDDLKQQTAPLEQQAPALEKVR

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	37.00 RPM
SRP017611_brain	0.00 RPM	13.73 RPM
SRP017611_kidney	0.00 RPM	7.99 RPM
SRP017611_liver	0.00 RPM	5.66 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1179 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1179 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1179 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 16 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003472	2 retrocopies	retro_amel_1261, retro_amel_1606,
Canis familiaris	ENSCAFG00000016212	2 retrocopies	retro_cfam_1179 , retro_cfam_1325,
Callithrix jacchus	ENSCJAG00000019702	2 retrocopies	retro_cjac_2057, retro_cjac_2556,
Cavia porcellus	ENSCPOG00000010172	1 retrocopy	retro_cpor_710,
Erinaceus europaeus	ENSEEUG00000003973	3 retrocopies	retro_eeur_216, retro_eeur_344, retro_eeur_37,
Echinops telfairi	ENSETEG00000002967	1 retrocopy	retro_etel_1294,
Felis catus	ENSFCAG00000010347	1 retrocopy	retro_fcat_278,
Macaca mulatta	ENSMMUG00000004341	1 retrocopy	retro_mmul_1648,
Mustela putorius furo	ENSMPUG00000006859	3 retrocopies	retro_mputfur_1218, retro_mputfur_1615, retro_mputfur_192,
Mus musculus	ENSMUSG00000059436	8 retrocopies	retro_mmus_2891, retro_mmus_2892, retro_mmus_2893, retro_mmus_2894, retro_mmus_2991, retro_mmus_2992, retro_mmus_2993, retro_mmus_2994,
Nomascus leucogenys	ENSNLEG00000014373	1 retrocopy	retro_nleu_1122,
Ochotona princeps	ENSOPRG00000016245	1 retrocopy	retro_opri_945,
Pongo abelii	ENSPPYG00000005911	1 retrocopy	retro_pabe_3097,
Rattus norvegicus	ENSRNOG00000008049	3 retrocopies	retro_rnor_1653, retro_rnor_1877, retro_rnor_2369,
Ictidomys tridecemlineatus	ENSSTOG00000028142	1 retrocopy	retro_itri_42,
Tupaia belangeri	ENSTBEG00000012645	1 retrocopy	retro_tbel_3407,