RetrogeneDB ID: retro_cfam_1336

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 3:27748599..27749100(+)
• Located in intron of: ENSCAFG00000009138

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS8
• Ensembl ID: ENSCAFG00000004745
• Aliases: None
• Description: ribosomal protein S8 [Source:HGNC Symbol;Acc:10441]

Sequence

>retro_cfam_1336
CGCCGCATACACACAGTACGAGTCCGGAGAGGCAATAAGAGGTACTGAGCCTTGAGGCTAGACATGGGGAACTTCTCCTG
GGGCTCGGAGTGTTGTACGCACAAAACCAGGATTATGGATGTCTATAGTGCATCCAACAATGAACTGGTCTGCACCAAGA
CCCTGATGAAGAACTGTATCGTGCTCACTGGCAGCACACCGAACCGACAGTGGTACGAGTCCCACTATGCACTGCCCCTG
GGACGCAGAAGGAGGCCAAGCTGACGCCTGGGGAGGAAGAGATTTTAAATAAAAAAACGATCAAAGAAAATTCAGAAGAA
GTATGATGAAAGGAAAAAGAATGCCAAAATCAGTAGTCTTCTGGAGGAGCAGTTCCAACAGGGCAAGCTTCTTGCATGCA
CCGCTTCGAGACCAGGCCAGTGTGGCCGGGCAGGTGGCTATGTGCTAGAAGGCAAGGAGCTGGAGTTCTATCTGAGGAAA
ATCAAAGCCTGGAAAGGCAAA

Alignment

ORF - retro_cfam_1336 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.65 %
• Parental protein coverage: 80.77 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RRIHTVRVRGGNKKYRALRLDVGNFSWGSECCTRKTRIIDVVYNASNNELVRTKTLVKNCIVLIDSTPYR
          RRIHTVRVR.GNK.Y.ALRLD.GNFSWGSECCT.KTRI.DV.Y.ASNNELV.TKTL.KNCIVL..STP.R
Retrocopy RRIHTVRVRRGNKRY*ALRLDMGNFSWGSECCTHKTRIMDV-YSASNNELVCTKTLMKNCIVLTGSTPNR

Parental  QWYESHYALPLGRK-KGAKLTPEEEEILN-KKRSKKIQKKYDERKKNAKISSLLEEQFQQGKLLACIASR
          QWYESHYALPLGR..K.AKLTP.EEEILN.KKRSKKIQKKYDERKKNAKISSLLEEQFQQGKLLAC.ASR
Retrocopy QWYESHYALPLGRR<KEAKLTPGEEEILN>KKRSKKIQKKYDERKKNAKISSLLEEQFQQGKLLACTASR

Parental  PGQCGRADGYVLEGKELEFYLRKIKARKGK
          PGQCGRA.GYVLEGKELEFYLRKIKA.KGK
Retrocopy PGQCGRAGGYVLEGKELEFYLRKIKAWKGK

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	0.17 RPM	459.42 RPM
SRP017611_brain	0.16 RPM	158.55 RPM
SRP017611_kidney	0.92 RPM	1224.13 RPM
SRP017611_liver	0.73 RPM	281.50 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1336 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1336 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1336 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 26 parental genes, and 144 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000015697	1 retrocopy	retro_acar_124,
Ailuropoda melanoleuca	ENSAMEG00000014147	3 retrocopies	retro_amel_1883, retro_amel_373, retro_amel_972,
Bos taurus	ENSBTAG00000015285	2 retrocopies	retro_btau_1388, retro_btau_1593,
Canis familiaris	ENSCAFG00000004745	8 retrocopies	retro_cfam_1336 , retro_cfam_1662, retro_cfam_1730, retro_cfam_2139, retro_cfam_2177, retro_cfam_261, retro_cfam_589, retro_cfam_791,
Callithrix jacchus	ENSCJAG00000004197	5 retrocopies	retro_cjac_1068, retro_cjac_181, retro_cjac_3138, retro_cjac_6, retro_cjac_951,
Cavia porcellus	ENSCPOG00000000723	3 retrocopies	retro_cpor_1099, retro_cpor_335, retro_cpor_621,
Dasypus novemcinctus	ENSDNOG00000025236	3 retrocopies	retro_dnov_1717, retro_dnov_802, retro_dnov_908,
Dipodomys ordii	ENSDORG00000009287	1 retrocopy	retro_dord_429,
Felis catus	ENSFCAG00000022996	4 retrocopies	retro_fcat_1222, retro_fcat_200, retro_fcat_456, retro_fcat_962,
Gorilla gorilla	ENSGGOG00000005645	5 retrocopies	retro_ggor_1127, retro_ggor_1170, retro_ggor_1357, retro_ggor_1465, retro_ggor_556,
Macropus eugenii	ENSMEUG00000001388	1 retrocopy	retro_meug_119,
Microcebus murinus	ENSMICG00000008024	4 retrocopies	retro_mmur_1180, retro_mmur_1434, retro_mmur_1501, retro_mmur_380,
Myotis lucifugus	ENSMLUG00000001559	30 retrocopies	retro_mluc_1114, retro_mluc_1132, retro_mluc_1165, retro_mluc_1277, retro_mluc_1288, retro_mluc_1418, retro_mluc_1467, retro_mluc_1476, retro_mluc_1486, retro_mluc_1634, retro_mluc_1656, retro_mluc_1689, retro_mluc_1808, retro_mluc_1911, retro_mluc_1938, retro_mluc_2043, retro_mluc_2055, retro_mluc_2085, retro_mluc_2111, retro_mluc_2153, retro_mluc_2182, retro_mluc_2209, retro_mluc_2414, retro_mluc_460, retro_mluc_662, retro_mluc_730, retro_mluc_773, retro_mluc_820, retro_mluc_821, retro_mluc_906,
Macaca mulatta	ENSMMUG00000015270	2 retrocopies	retro_mmul_275, retro_mmul_70,
Monodelphis domestica	ENSMODG00000028389	1 retrocopy	retro_mdom_998,
Mustela putorius furo	ENSMPUG00000013485	6 retrocopies	retro_mputfur_334, retro_mputfur_337, retro_mputfur_493, retro_mputfur_780, retro_mputfur_908, retro_mputfur_986,
Nomascus leucogenys	ENSNLEG00000014147	1 retrocopy	retro_nleu_34,
Oryctolagus cuniculus	ENSOCUG00000012476	1 retrocopy	retro_ocun_168,
Otolemur garnettii	ENSOGAG00000006922	16 retrocopies	retro_ogar_1156, retro_ogar_1746, retro_ogar_1895, retro_ogar_2501, retro_ogar_2529, retro_ogar_2556, retro_ogar_2699, retro_ogar_2723, retro_ogar_2947, retro_ogar_308, retro_ogar_3291, retro_ogar_3436, retro_ogar_394, retro_ogar_521, retro_ogar_730, retro_ogar_805,
Pan troglodytes	ENSPTRG00000000659	1 retrocopy	retro_ptro_30,
Pteropus vampyrus	ENSPVAG00000009859	10 retrocopies	retro_pvam_1285, retro_pvam_1315, retro_pvam_1345, retro_pvam_403, retro_pvam_419, retro_pvam_463, retro_pvam_514, retro_pvam_578, retro_pvam_685, retro_pvam_991,
Rattus norvegicus	ENSRNOG00000018768	2 retrocopies	retro_rnor_222, retro_rnor_235,
Sarcophilus harrisii	ENSSHAG00000000111	5 retrocopies	retro_shar_408, retro_shar_472, retro_shar_480, retro_shar_636, retro_shar_667,
Sus scrofa	ENSSSCG00000003930	4 retrocopies	retro_sscr_353, retro_sscr_550, retro_sscr_607, retro_sscr_919,
Tupaia belangeri	ENSTBEG00000000418	20 retrocopies	retro_tbel_1066, retro_tbel_1537, retro_tbel_1538, retro_tbel_163, retro_tbel_1699, retro_tbel_2356, retro_tbel_244, retro_tbel_2580, retro_tbel_3058, retro_tbel_3230, retro_tbel_3478, retro_tbel_3905, retro_tbel_3950, retro_tbel_4241, retro_tbel_4250, retro_tbel_4530, retro_tbel_552, retro_tbel_803, retro_tbel_827, retro_tbel_934,
Tarsius syrichta	ENSTSYG00000005525	5 retrocopies	retro_tsyr_1412, retro_tsyr_1507, retro_tsyr_2176, retro_tsyr_552, retro_tsyr_734,