RetrogeneDB ID: retro_cfam_765

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 17:55985984..55987331(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CS
• Ensembl ID: ENSCAFG00000000115
• Aliases: None
• Description: Citrate synthase [Source:UniProtKB/TrEMBL;Acc:F1PV92]

Sequence

>retro_cfam_765
GCCAAGAATGCATCTTGTCTTGTTCTTGCCGCTTGGCATGCCAGTGCCTCCTCTACAAATTTGAAAGACATATTGGCGGA
CTTGATACCCAAGGCGCAGGCCAGAATAAAGACCTTCAGGCAGCAACATGGCAAGACAGTAGTGGACCAAATCACTGTGG
ACATGATGTACGGTGGCATGAGAGGCATGAAGGGATTAGTATATGAAACATCAGTTCTTGATCCTGATGAGGACATCCAT
TTCCGAGGCTACAGTATCCCTGAGTGCCAGAAACTGCTGCTTAAGGCTAAAGGCGGTGAAGAACCCCTGCCAGAGGGCTT
ATTTTGGTTGCTGGTAACTAGACAAATCCCAACAGAGGAACAGGTGTCTTGGCTCTCAAAAGAGTGGGCAAAGAGGGCAG
CTCTACCTTCCCATGTGGTCACCATGCTGGACAACTTTCCTACCAATCTACACCCTATGTCTCAGCTCAGTGCAGCCATT
ACAGCCCTCAACAGTGAAAGTAACTTTGCCAGAGCAGAGGGTATCAGCCGAACCAAGTACTGGGAGTTGATTTATGAAGA
TTGTATGGATCTGATCACAAAGATACCTTGTGTTGCAGCAAAGATTTACCAGAATCTCTACTGAGAGGGCAGCAGTATTG
GGGCCATTGACTCTAAGCTGGACTGGTCCCACAATTTTACCAACATTTTAGGCTATACTGATGCTCAGTTCACTGAGCTC
ATGCGCTTGTACCTCACCATCCACAGTGACCATGAGGGAGGCAATGTAAGTGCCCATACCAGCCACCTGGTGGGCAGTGC
CCTTTCAGACCCCTACCTGTCTTTTGCGGCAGCCGTGAATGGGCTAGCAGGGCCCCTGCATGGTTTGGAAAATCAGGAAG
TACTTGTTTGGCTGACACAACTACAGAAAGAAGTTGGCAAAGATGTGTCAGATGAGAAGTTACGAGACTAAATATGGAAC
ACACCGAACTCAGGACGGGTTGTCCCAGGCTATGGCCATGCAGTACTAAGGAAGACTGACCCACGATATACCTGTCAGCA
AGAGTTTGCTCTGAAACACCTGCCTCATGACTCCATGTTTAAGCTGGTTGCTCAGCTGTACAAGATTGTGCCCAATGTCC
TGTTAGAACAGGGCAAGGCCAAGAACCCTTGGCCCAGTGTAGATGCTCACAGTGGGGTGCTGCTCCAGTACTACAGCATG
ACAGAGAAGAATTACTACACAGTCCTGTTTGGGGTATCACGAGCACTGGGTGTACTCATACAGCTCATCTGGAGCTGAGC
CCTAGGCTTCCCACTAGAGAGGCCCAAGTCCATGAGCACAGATGGTCCAGTGAAGTTAGTGGACTCT

Alignment

ORF - retro_cfam_765 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.57 %
• Parental protein coverage: 96.37 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SKNASCLVLAARHASASSTNLKDILADLIPKEQARIKTFRQQHGKTVVGQITVDMMYGGMRGMKGLVYET
          .KNASCLVLAA.HASASSTNLKDILADLIPK.QARIKTFRQQHGKTVV.QITVDMMYGGMRGMKGLVYET
Retrocopy AKNASCLVLAAWHASASSTNLKDILADLIPKAQARIKTFRQQHGKTVVDQITVDMMYGGMRGMKGLVYET

Parental  SVLDPDEGIRFRGYSIPECQKLLPKAKGGEEPLPEGLFWLLVTGQIPTEEQVSWLSKEWAKRAALPSHVV
          SVLDPDE.I.FRGYSIPECQKLL.KAKGGEEPLPEGLFWLLVT.QIPTEEQVSWLSKEWAKRAALPSHVV
Retrocopy SVLDPDEDIHFRGYSIPECQKLLLKAKGGEEPLPEGLFWLLVTRQIPTEEQVSWLSKEWAKRAALPSHVV

Parental  TMLDNFPTNLHPMSQLSAAITALNSESNFARAYAEGINRTKYWELIYEDCMDLIAKLPCVAAKIYRNLYR
          TMLDNFPTNLHPMSQLSAAITALNSESNFARA..EGI.RTKYWELIYEDCMDLI.K.PCVAAKIY.NLY.
Retrocopy TMLDNFPTNLHPMSQLSAAITALNSESNFARA--EGISRTKYWELIYEDCMDLITKIPCVAAKIYQNLY*

Parental  EGSSIGAIDSKLDWSHNFTNMLGYTDAQFTELMRLYLTIHSDHEGGNVSAHTSHLVGSALSDPYLSFAAA
          EGSSIGAIDSKLDWSHNFTN.LGYTDAQFTELMRLYLTIHSDHEGGNVSAHTSHLVGSALSDPYLSFAAA
Retrocopy EGSSIGAIDSKLDWSHNFTNILGYTDAQFTELMRLYLTIHSDHEGGNVSAHTSHLVGSALSDPYLSFAAA

Parental  MNGLAGPLHGLANQEVLVWLTQLQKEVGKDVSDEKLRDYIWNTLNSGRVVPGYGHAVLRKTDPRYTCQRE
          .NGLAGPLHGL.NQEVLVWLTQLQKEVGKDVSDEKLRD.IWNT.NSGRVVPGYGHAVLRKTDPRYTCQ.E
Retrocopy VNGLAGPLHGLENQEVLVWLTQLQKEVGKDVSDEKLRD*IWNTPNSGRVVPGYGHAVLRKTDPRYTCQQE

Parental  FALKHLPHDSMFKLVAQLYKIVPNVLLEQGKAKNPWPNVDAHSGVLLQYYGMTEMNYYTVLFGVSRALGV
          FALKHLPHDSMFKLVAQLYKIVPNVLLEQGKAKNPWP.VDAHSGVLLQYY.MTE.NYYTVLFGVSRALGV
Retrocopy FALKHLPHDSMFKLVAQLYKIVPNVLLEQGKAKNPWPSVDAHSGVLLQYYSMTEKNYYTVLFGVSRALGV

Parental  LAQLIWSRALGFPLERPKSMSTDGLMKFVDS
          L.QLIWS.ALGFPLERPKSMSTDG..K.VDS
Retrocopy LIQLIWS*ALGFPLERPKSMSTDGPVKLVDS

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	0.04 RPM	91.05 RPM
SRP017611_brain	0.24 RPM	109.24 RPM
SRP017611_kidney	0.13 RPM	120.32 RPM
SRP017611_liver	0.00 RPM	26.76 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_765 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_765 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_765 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004371	1 retrocopy	retro_btau_386,
Canis familiaris	ENSCAFG00000000115	1 retrocopy	retro_cfam_765 ,
Choloepus hoffmanni	ENSCHOG00000000397	1 retrocopy	retro_chof_1803,
Callithrix jacchus	ENSCJAG00000011275	1 retrocopy	retro_cjac_2031,
Dasypus novemcinctus	ENSDNOG00000010907	2 retrocopies	retro_dnov_205, retro_dnov_468,
Echinops telfairi	ENSETEG00000012035	1 retrocopy	retro_etel_584,
Homo sapiens	ENSG00000062485	2 retrocopies	retro_hsap_1972, retro_hsap_3621,
Gorilla gorilla	ENSGGOG00000009096	2 retrocopies	retro_ggor_1432, retro_ggor_2445,
Macropus eugenii	ENSMEUG00000005657	2 retrocopies	retro_meug_1078, retro_meug_1304,
Microcebus murinus	ENSMICG00000017659	2 retrocopies	retro_mmur_1322, retro_mmur_394,
Macaca mulatta	ENSMMUG00000002483	2 retrocopies	retro_mmul_1502, retro_mmul_1840,
Mus musculus	ENSMUSG00000005683	1 retrocopy	retro_mmus_258,
Nomascus leucogenys	ENSNLEG00000017514	2 retrocopies	retro_nleu_1201, retro_nleu_809,
Oryctolagus cuniculus	ENSOCUG00000007216	1 retrocopy	retro_ocun_1183,
Pongo abelii	ENSPPYG00000004654	1 retrocopy	retro_pabe_2972,
Rattus norvegicus	ENSRNOG00000023520	1 retrocopy	retro_rnor_2518,
Sorex araneus	ENSSARG00000010093	2 retrocopies	retro_sara_360, retro_sara_628,
Sus scrofa	ENSSSCG00000021091	1 retrocopy	retro_sscr_321,
Sus scrofa	ENSSSCG00000022858	1 retrocopy	retro_sscr_322,
Tupaia belangeri	ENSTBEG00000006425	1 retrocopy	retro_tbel_4652,
Tarsius syrichta	ENSTSYG00000004483	1 retrocopy	retro_tsyr_1659,