RetrogeneDB ID: retro_cfam_1312

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 29:28578870..28579897(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: YBX1
• Ensembl ID: ENSCAFG00000002541
• Aliases: None
• Description: Y box binding protein 1 [Source:HGNC Symbol;Acc:8014]

Sequence

>retro_cfam_1312
GGAGTGGAGAGCAGACCCCAGAGAGCCCTGAGCAGCTGCACCCCTGGCCCCAGTCATGATCACCCAAACCCTGAACAGCA
AGGCAGAGACCAGCAGCCACCCTCGCCCTCACTGCTGCCCACACCAGGCCTGGCACCACGGGCAGCAGGGCAGGGAGGGG
TGGCCGGTGGCCCGTGGGGCCTCACATGGGCGGCACCTGCCTGACAGAGACCAGAAGGTCATCACAACAAATGTTTTCAG
AACATTTGTAAACTGTTTCAACATAAGAAAAGGATTTGGTTTCCCCAACAGGAATGACACCAAGGAAGATATATCTGTCC
ACCAGGTTGCCATGAAGAATAACCCCAGAAAGTACCTTCGCAGCATAGAGATGGAGAGACTGTGGAGTGTGATGTTGTTG
AAGGAAAAATGGGTGTGGACACAGCAAATGTACCCGGCCTTGGTGGGGTTCCAGTCAAAGCAGTAAATACACAGTAGACC
GAAACCATTATAGACGCCATCCACTTGGCAGGGCCCCCCACTCAGTTACCCGCAGAATTACCAGGATCATGAGAGTGGGG
AAAAGAACAAGGGATCGGAAAGTACTCCCTAAGGCCAGGCCCAACAGTGCCCACTCCACTGCAGGCTACGTACGGTTCCC
ACCTTACTAATGTGGAGACCCTATGGGCGTCAACCACAGTTTTCCAACCCTCCTGTGCAGGGAGAAGGGATGGCAGGTGC
TGACAACCAGGTGCACAAGAACAAGGTAGACCAGTGAGACAGAGTATGAATCGAGGTTATAGACCACGATCCCATACAGG
TCCTCCTCACCAAAGACAATCTAGAGAGGATGGCAACAAGGATGATAAGGAAAATCAAGCAGATGACCCCAAGATCAGCA
GCCACCTCAACGTCAGTACCACCGCAACTTCAACTACCTACACAGATGCCCAGAAAACCCTAAACCACAAGATGGCAAAG
AGACCAAAGCAGTCGATCCACCAGCTAACACTTCGTCCCACTCTGAGCTGAGCAGGGCAGGGCTGAG

Alignment

ORF - retro_cfam_1312 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.36 %
• Parental protein coverage: 95.54 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  GLPSTPGQGVAASPSEPPGQASEAETQQPPAAPPAAPALSAADTKPGTTGSGAGSGGPGGLTSAAPA-GG
          G..S.P..........P.......E.Q.....PP....L......P...G.G...GGP.GLT.AAPA...
Retrocopy GVESRPQRALSSCTPGPSHDHPNPEQQGRDQQPPSPSLLPTPGLAPRAAGQGGVAGGPWGLTWAAPA>DR

Parental  DKKVIATKVLGT-VKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVG-DGETVEFDVVEGEK
          D.KVI.T.V..T.V..FN.R.G.GF.NRNDTKED..VHQ.A.K.NNPRKYLRS...DGETVE.DVVEG..
Retrocopy DQKVITTNVFRTFVNCFNIRKGFGFPNRNDTKEDISVHQVAMK-NNPRKYLRSIE<DGETVECDVVEGKM

Parental  GAEAANVTGPGGVPV-QGSKYAADRNHYRRYPRRR-GPPRNYQQNYQNSESGEKNEGSESAPEGQAQQRR
          G...ANV.G.GGVPV.Q.SKY..DRNHYRR.P..R.GPP..Y.QNYQ..ESGEKN.GSES.P.GQAQQ..
Retrocopy GVDTANVPGLGGVPV<QSSKYTVDRNHYRRHPLGR<GPPLSYPQNYQDHESGEKNKGSESTP*GQAQQCP

Parental  PY-RRRRFPPYYMRRPYGRRPQYSNPPVQGEVMEGADNQ-GAGEQGRPVRQNMYRGYRPRFRRGPPRQRQ
          ...R.R..P...M.RPYGR.PQ.SNPPVQGE.M.GADNQ.GA.EQGRPVRQ.M.RGYRPR...GPP.QRQ
Retrocopy LHCRLRTVPTLLMWRPYGRQPQFSNPPVQGEGMAGADNQ<GAQEQGRPVRQSMNRGYRPRSHTGPPHQRQ

Parental  PREDGNEEDKENQGDE-TQGQQPPQRRYRRNFNYRRRRPENPKPQDGKETKAADPPAENSSAPE-AEQGG
          .REDGN..DKENQ.D...Q.QQPPQR.Y.RNFNY..R.PENPKPQDGKETKA.DPPA..SS..E.AEQG.
Retrocopy SREDGNKDDKENQADD<PQDQQPPQRQYHRNFNYLHRCPENPKPQDGKETKAVDPPANTSSHSE<AEQGR

Parental  AE
          AE
Retrocopy AE

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	132.42 RPM
SRP017611_brain	0.00 RPM	22.31 RPM
SRP017611_kidney	0.00 RPM	138.55 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_1312 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1312 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1312 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 125 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000494	9 retrocopies	retro_amel_1280, retro_amel_1358, retro_amel_141, retro_amel_1486, retro_amel_215, retro_amel_418, retro_amel_625, retro_amel_837, retro_amel_909,
Canis familiaris	ENSCAFG00000002541	4 retrocopies	retro_cfam_1312 , retro_cfam_2118, retro_cfam_758, retro_cfam_91,
Callithrix jacchus	ENSCJAG00000003155	6 retrocopies	retro_cjac_1261, retro_cjac_1701, retro_cjac_2718, retro_cjac_3156, retro_cjac_4172, retro_cjac_817,
Cavia porcellus	ENSCPOG00000010888	3 retrocopies	retro_cpor_654, retro_cpor_833, retro_cpor_905,
Felis catus	ENSFCAG00000022604	6 retrocopies	retro_fcat_145, retro_fcat_1554, retro_fcat_1956, retro_fcat_241, retro_fcat_503, retro_fcat_631,
Homo sapiens	ENSG00000065978	4 retrocopies	retro_hsap_1433, retro_hsap_3886, retro_hsap_4250, retro_hsap_4301,
Loxodonta africana	ENSLAFG00000007597	1 retrocopy	retro_lafr_804,
Microcebus murinus	ENSMICG00000014984	19 retrocopies	retro_mmur_1098, retro_mmur_1285, retro_mmur_1326, retro_mmur_1435, retro_mmur_1437, retro_mmur_1445, retro_mmur_1621, retro_mmur_199, retro_mmur_315, retro_mmur_413, retro_mmur_581, retro_mmur_640, retro_mmur_676, retro_mmur_679, retro_mmur_726, retro_mmur_837, retro_mmur_900, retro_mmur_919, retro_mmur_942,
Macaca mulatta	ENSMMUG00000013136	5 retrocopies	retro_mmul_1139, retro_mmul_1423, retro_mmul_2017, retro_mmul_423, retro_mmul_861,
Nomascus leucogenys	ENSNLEG00000012324	7 retrocopies	retro_nleu_1053, retro_nleu_1188, retro_nleu_1312, retro_nleu_1601, retro_nleu_1749, retro_nleu_1888, retro_nleu_270,
Oryctolagus cuniculus	ENSOCUG00000028047	2 retrocopies	retro_ocun_1519, retro_ocun_1953,
Otolemur garnettii	ENSOGAG00000006784	25 retrocopies	retro_ogar_1127, retro_ogar_1246, retro_ogar_1350, retro_ogar_1371, retro_ogar_1497, retro_ogar_2011, retro_ogar_2018, retro_ogar_2302, retro_ogar_2359, retro_ogar_2607, retro_ogar_2654, retro_ogar_3170, retro_ogar_3225, retro_ogar_324, retro_ogar_3303, retro_ogar_3316, retro_ogar_3317, retro_ogar_3366, retro_ogar_3416, retro_ogar_3474, retro_ogar_448, retro_ogar_572, retro_ogar_678, retro_ogar_690, retro_ogar_753,
Pongo abelii	ENSPPYG00000001466	7 retrocopies	retro_pabe_1216, retro_pabe_1320, retro_pabe_2054, retro_pabe_2292, retro_pabe_3167, retro_pabe_3388, retro_pabe_3502,
Pteropus vampyrus	ENSPVAG00000005504	7 retrocopies	retro_pvam_1255, retro_pvam_1348, retro_pvam_1391, retro_pvam_145, retro_pvam_405, retro_pvam_76, retro_pvam_971,
Sorex araneus	ENSSARG00000007896	1 retrocopy	retro_sara_559,
Tupaia belangeri	ENSTBEG00000015642	9 retrocopies	retro_tbel_1183, retro_tbel_1955, retro_tbel_2347, retro_tbel_2694, retro_tbel_2702, retro_tbel_2961, retro_tbel_3590, retro_tbel_4037, retro_tbel_4478,
Tarsius syrichta	ENSTSYG00000006915	6 retrocopies	retro_tsyr_1030, retro_tsyr_173, retro_tsyr_2037, retro_tsyr_610, retro_tsyr_840, retro_tsyr_996,
Tursiops truncatus	ENSTTRG00000001353	2 retrocopies	retro_ttru_461, retro_ttru_746,
Vicugna pacos	ENSVPAG00000000068	2 retrocopies	retro_vpac_235, retro_vpac_647,