RetrogeneDB ID: retro_cfam_1559

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 34:36947995..36948380(-)
• Located in intron of: ENSCAFG00000015455

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000009702
• Aliases: None
• Description: None

Sequence

>retro_cfam_1559
ATGCTGGGAAATTCACCATTACCACTGCCAGAAAGAGCGATTTATGGCTTTGTTCTTTTCTTAAGCTCCCAATTTGGCTT
CATACTGTATCTTGTGGGGGCTTTTATTCCTAAATCTTGACTAAACTCCTTAGGCTTAATCTACTGGTCTCAAAAATATT
AGGCAGTTGTACTACCTGTGTACCTTCTCATTACTATAGTAATCAGTTATGAATAAATCTGATTGAGTACCTCTCCACTC
AACTCCATTCATACATTCACAGACAACTATGCTAAAAATCAACAGCAGAAGAAATACCAAGACACCAGCCCAACCTTAAG
AGATAGTTCCTGTTGGTGAAGTCAACTAAATATTCTTTCTTGGAGCCAAAGAACTTTATGTCAAA

Alignment

ORF - retro_cfam_1559 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.4 %
• Parental protein coverage: 99.25 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MVENSPSPLPERAIYGFVLFLSSQFGFILYLVWAFIPESWLNSLGLTYWPQKYWAVALPVYLLIIILIGY
          M..NSP.PLPERAIYGFVLFLSSQFGFILYLV.AFIP.S.LNSLGL.YW.QKY.AV.LPVY.....LI..
Retrocopy MLGNSPLPLPERAIYGFVLFLSSQFGFILYLVGAFIPKS*LNSLGLIYWSQKY*AVVLPVY----LLITI

Parental  VLLFGINMMSTSPLNSIHTITDNYAKNQQQKKYQEEAIPALRD-IPISEVNQMFFLATKEHYAK
          V........STSPLNSIHT.TDNYAKNQQQKKYQ....P.LRD..P..EVN..FFL..KE.Y.K
Retrocopy VISYE*I*LSTSPLNSIHTFTDNYAKNQQQKKYQDTS-PTLRD>VPVGEVN*IFFLGAKELYVK

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	9.91 RPM
SRP017611_brain	0.00 RPM	11.11 RPM
SRP017611_kidney	0.00 RPM	17.30 RPM
SRP017611_liver	0.07 RPM	4.93 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1559 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1559 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1559 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 25 parental genes, and 71 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000009702	4 retrocopies	retro_cfam_1022, retro_cfam_1559 , retro_cfam_1976, retro_cfam_238,
Callithrix jacchus	ENSCJAG00000002683	2 retrocopies	retro_cjac_1276, retro_cjac_2587,
Cavia porcellus	ENSCPOG00000007156	2 retrocopies	retro_cpor_426, retro_cpor_680,
Equus caballus	ENSECAG00000019349	1 retrocopy	retro_ecab_348,
Felis catus	ENSFCAG00000028400	8 retrocopies	retro_fcat_1269, retro_fcat_1286, retro_fcat_1408, retro_fcat_1495, retro_fcat_1671, retro_fcat_181, retro_fcat_1859, retro_fcat_729,
Homo sapiens	ENSG00000185808	4 retrocopies	retro_hsap_163, retro_hsap_1909, retro_hsap_2110, retro_hsap_2423,
Gorilla gorilla	ENSGGOG00000010275	3 retrocopies	retro_ggor_1397, retro_ggor_1508, retro_ggor_1639,
Myotis lucifugus	ENSMLUG00000005475	3 retrocopies	retro_mluc_1419, retro_mluc_1444, retro_mluc_2084,
Macaca mulatta	ENSMMUG00000016211	2 retrocopies	retro_mmul_377, retro_mmul_624,
Monodelphis domestica	ENSMODG00000020988	1 retrocopy	retro_mdom_1807,
Mustela putorius furo	ENSMPUG00000008312	5 retrocopies	retro_mputfur_1069, retro_mputfur_1388, retro_mputfur_421, retro_mputfur_642, retro_mputfur_826,
Mus musculus	ENSMUSG00000022940	1 retrocopy	retro_mmus_2841,
Nomascus leucogenys	ENSNLEG00000004523	4 retrocopies	retro_nleu_1235, retro_nleu_1276, retro_nleu_1558, retro_nleu_2444,
Oryctolagus cuniculus	ENSOCUG00000022451	3 retrocopies	retro_ocun_586, retro_ocun_664, retro_ocun_881,
Otolemur garnettii	ENSOGAG00000011097	1 retrocopy	retro_ogar_2382,
Pongo abelii	ENSPPYG00000011409	3 retrocopies	retro_pabe_1787, retro_pabe_1993, retro_pabe_464,
Pan troglodytes	ENSPTRG00000013897	3 retrocopies	retro_ptro_1397, retro_ptro_1547, retro_ptro_156,
Pteropus vampyrus	ENSPVAG00000000857	3 retrocopies	retro_pvam_1100, retro_pvam_1182, retro_pvam_682,
Sarcophilus harrisii	ENSSHAG00000014284	1 retrocopy	retro_shar_548,
Sus scrofa	ENSSSCG00000012061	1 retrocopy	retro_sscr_1085,
Ictidomys tridecemlineatus	ENSSTOG00000010943	5 retrocopies	retro_itri_1237, retro_itri_1258, retro_itri_1869, retro_itri_616, retro_itri_897,
Tupaia belangeri	ENSTBEG00000001803	4 retrocopies	retro_tbel_1750, retro_tbel_2361, retro_tbel_3162, retro_tbel_655,
Tarsius syrichta	ENSTSYG00000009899	1 retrocopy	retro_tsyr_47,
Tursiops truncatus	ENSTTRG00000007711	3 retrocopies	retro_ttru_1043, retro_ttru_677, retro_ttru_883,
Vicugna pacos	ENSVPAG00000009781	3 retrocopies	retro_vpac_166, retro_vpac_387, retro_vpac_639,