RetrogeneDB ID: retro_cfam_1829

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 6:57072430..57073190(-)
• Located in intron of: ENSCAFG00000020179

Retrocopy information

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

Parental gene information

• Parental gene symbol: EI24
• Ensembl ID: ENSCAFG00000010898
• Aliases: None
• Description: etoposide induced 2.4 [Source:HGNC Symbol;Acc:13276]

Sequence

>retro_cfam_1829
AGTCTCCTCTTGTTTTATCAAGTGTTTATTCCTGCACTATAGTCAGTAACAGCCCAAACTATTGGTGATCCATCACAACA
TGGAGATGTTTGGTCATCGGTGAAATTCTTCTTTATCTCATTTTTCAGGGCTCTTTGGGTGCTCCCTCCATTTGTGCTTA
GCAAAGCTGTTAATGCCATTTCATCTCAAGACATAGCTGATCTGGCATTTGAGGTATCGGGGAGGAAGCCTCACCCATTC
CCCAGTGTCAGCAAAATAACTGCTGACATGCTCTTCAACCTTTGGCTGCAGGCTCCTTTCCACATCCAGGGGACGTCTGT
AGCCTCTTTCCCATCCATTATATTGGTCAGCTGGTTAGTCTTCTGCATACGTCCCTTCTCTACTCACCACACTGCTCTGA
ATATTGGTTCAATAAAGGAACTGAAGTGCACCAGCGGTTGTCAAGCACAGAGAAGAGGTGGCCTTACTACATTGGATTTG
GTTTGCCCTGGCTTTCCTCACAGCCATGCAGTCCTCATATACTATCAGTAGAGGCCCCTCTCCTCCTTTCCTCTGTTCAG
TATCAGCGTCAATGAAGCAAAGACCCCCAGCAAAGTATACCTTTCCTAGTTGTGCCTCTTCTCCTTGGTGGTTTTCTTAA
AGCAAAAGCCTTTTCCAGAAGATGATCTACCTGTAGTCTGCCCTGAGTAGCTCAACCTCTGCAGAGAAATTTCCATCCCC
ACATCCGTCTCCTGCCAGACTAAAAGCAGCTACAGGCAAC

Alignment

ORF - retro_cfam_1829 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.04 %
• Parental protein coverage: 75.29 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SLLLFYRVFIPVLQSVTAQIIGDPSLHGDVWSWLEFFLTSIFSALWVLPLFVLSKVVNAIWFQDIADLAF
          SLLLFY.VFIP.L.SVTAQ.IGDPS.HGDVWS...FF..S.F.ALWVLP.FVLSK.VNAI..QDIADLAF
Retrocopy SLLLFYQVFIPAL*SVTAQTIGDPSQHGDVWSSVKFFFISFFRALWVLPPFVLSKAVNAISSQDIADLAF

Parental  EVSGRKPHPFPSVSKIIADMLFNLLLQALFLIQGMFV-SLFPIHLVGQLVSLLHMSLLYSLYCFEYRWFN
          EVSGRKPHPFPSVSKI.ADMLFNL.LQA.F.IQG..V.SLFPIH..GQLVSLLH.SLLYS..C.EY.WFN
Retrocopy EVSGRKPHPFPSVSKITADMLFNLWLQAPFHIQGTSV<SLFPIHYIGQLVSLLHTSLLYSPHCSEY-WFN

Parental  KGIEMHQRLSNIERNWPYYFGFGLPLAFLTAMQSSYIISGCLFSIL-FPLFIISANEAKTPGKAYLFQLR
          KG.E.HQRLS..E..WPYY...G..L..L.....S..I.......L.FPLF.IS.NEAKTP.K.YL..L.
Retrocopy KGTEVHQRLSSTEKRWPYYI--GFGLPWLSSQPCSPHILSVEAPLL>FPLFSISVNEAKTPSKVYLS*LC

Parental  LFSLVVFL-SNRLFHKTVYLQSALSSSTSAEKFPSPHPSPAKLKAAAGH
          LFSLVVFL.S..LF.K..YL.SALSSSTSAEKFPSPHPSPA.LKAA.G.
Retrocopy LFSLVVFL>SKSLFQKMIYL*SALSSSTSAEKFPSPHPSPARLKAATGN

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	55.94 RPM
SRP017611_brain	0.00 RPM	45.73 RPM
SRP017611_kidney	0.00 RPM	170.18 RPM
SRP017611_liver	0.00 RPM	61.13 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1829 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1829 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1829 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 26 parental genes, and 69 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000990	2 retrocopies	retro_amel_1449, retro_amel_1681,
Bos taurus	ENSBTAG00000007202	2 retrocopies	retro_btau_1242, retro_btau_443,
Canis familiaris	ENSCAFG00000010898	1 retrocopy	retro_cfam_1829 ,
Choloepus hoffmanni	ENSCHOG00000012669	3 retrocopies	retro_chof_1433, retro_chof_1994, retro_chof_804,
Cavia porcellus	ENSCPOG00000007272	2 retrocopies	retro_cpor_132, retro_cpor_929,
Dasypus novemcinctus	ENSDNOG00000002362	4 retrocopies	retro_dnov_1083, retro_dnov_1421, retro_dnov_2143, retro_dnov_2345,
Equus caballus	ENSECAG00000015861	1 retrocopy	retro_ecab_1022,
Erinaceus europaeus	ENSEEUG00000003274	1 retrocopy	retro_eeur_435,
Felis catus	ENSFCAG00000015100	1 retrocopy	retro_fcat_1754,
Homo sapiens	ENSG00000149547	3 retrocopies	retro_hsap_236, retro_hsap_2782, retro_hsap_3804,
Loxodonta africana	ENSLAFG00000010888	15 retrocopies	retro_lafr_262, retro_lafr_263, retro_lafr_264, retro_lafr_265, retro_lafr_394, retro_lafr_395, retro_lafr_396, retro_lafr_397, retro_lafr_398, retro_lafr_399, retro_lafr_566, retro_lafr_589, retro_lafr_626, retro_lafr_627, retro_lafr_999,
Microcebus murinus	ENSMICG00000003023	3 retrocopies	retro_mmur_398, retro_mmur_498, retro_mmur_632,
Myotis lucifugus	ENSMLUG00000001583	1 retrocopy	retro_mluc_1249,
Macaca mulatta	ENSMMUG00000010009	3 retrocopies	retro_mmul_1443, retro_mmul_1653, retro_mmul_2244,
Nomascus leucogenys	ENSNLEG00000007451	3 retrocopies	retro_nleu_2149, retro_nleu_684, retro_nleu_853,
Oryctolagus cuniculus	ENSOCUG00000014670	1 retrocopy	retro_ocun_1578,
Otolemur garnettii	ENSOGAG00000001838	6 retrocopies	retro_ogar_1055, retro_ogar_1379, retro_ogar_2700, retro_ogar_2701, retro_ogar_659, retro_ogar_799,
Ochotona princeps	ENSOPRG00000013491	2 retrocopies	retro_opri_106, retro_opri_1130,
Procavia capensis	ENSPCAG00000012762	1 retrocopy	retro_pcap_452,
Pongo abelii	ENSPPYG00000004033	3 retrocopies	retro_pabe_2234, retro_pabe_3107, retro_pabe_416,
Pan troglodytes	ENSPTRG00000004444	4 retrocopies	retro_ptro_1202, retro_ptro_1883, retro_ptro_206, retro_ptro_2581,
Pteropus vampyrus	ENSPVAG00000004532	1 retrocopy	retro_pvam_1124,
Rattus norvegicus	ENSRNOG00000030391	1 retrocopy	retro_rnor_2605,
Sarcophilus harrisii	ENSSHAG00000017333	1 retrocopy	retro_shar_433,
Ictidomys tridecemlineatus	ENSSTOG00000004299	2 retrocopies	retro_itri_1343, retro_itri_1373,
Tarsius syrichta	ENSTSYG00000004747	2 retrocopies	retro_tsyr_1238, retro_tsyr_1423,