RetrogeneDB ID: retro_cpor_434

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_15:22361201..22361643(-)
• Located in intron of: ENSCPOG00000008020

Retrocopy information

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

Parental gene information

• Parental gene symbol: YWHAZ
• Ensembl ID: ENSCPOG00000020285
• Aliases: None
• Description: None

Sequence

>retro_cpor_434
ACTCTTCTGGAAAAGTTCTTGGTCCCCAGTGCTTCACAAGCAGAGAGCAAAGTCTTCTATTTGAAAATGAAGAGAGACTA
CTACTCTTGCTTGGCCAAGGTTGCTGCTGGTGATGACAAGAAAGGGATGGTGAATCAATCACAACAAGCATACCAAGAAG
CTTTTGAAATCAGCAAAAAGGAAATTCAACCACTGCGTCCTATCAGATTGGGTCTGGCTCTTAGCTTCTCTGTGCTCTAT
TATGAGATTCTGAACTCTCCAGAGAAAGCCTGTTCTCTGACAAAGACAGATAGATGATGAAGCCATTGCTGAACTTGATA
CATTAAGTGAAGAGGCATAACAGGACAGCATGCTAATAGTGCAATTACTGAGAGACAACTTGACATTGTAGACATCAGAA
AGCTAAGGAGATGAAGCTGAAACAGGAAAAGGAGGGGAAAAT

Alignment

ORF - retro_cpor_434 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.41 %
• Parental protein coverage: 60.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SLLEKFLIPNASQAESKVFYLKMKGDYYRYLAEVAAGDDKKGIVDQSQQAYQEAFEISKKEMQPTHPIRL
          .LLEKFL.P.ASQAESKVFYLKMK.DYY..LA.VAAGDDKKG.V.QSQQAYQEAFEISKKE.QP..PIRL
Retrocopy TLLEKFLVPSASQAESKVFYLKMKRDYYSCLAKVAAGDDKKGMVNQSQQAYQEAFEISKKEIQPLRPIRL

Parental  GLALNFSVFYYEILNSPEKACSLAKT-AFDEAIAELDTLSEESYKDSTLIMQLLRDNLTLWTSDTQGDEA
          GLAL.FSV.YYEILNSPEKACSL.KT...DEAIAELDTLSEE...DS.LI.QLLRDNLTL.TS...GDEA
Retrocopy GLALSFSVLYYEILNSPEKACSLTKT>IDDEAIAELDTLSEEA*QDSMLIVQLLRDNLTL*TSES*GDEA

Parental  EAGEGGEN
          E.G.GGEN
Retrocopy ETGKGGEN

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
SRP017611_brain	0.00 RPM	310.76 RPM
SRP017611_kidney	0.10 RPM	57.89 RPM
SRP017611_liver	0.00 RPM	21.33 RPM
SRP040447_lung	0.00 RPM	92.13 RPM
SRP040447_skeletal_muscle	0.00 RPM	17.82 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_434 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_434 was not experimentally validated.

Homology

Retrocopy orthology:

Cavia porcellus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 26 parental genes, and 99 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000008694	2 retrocopies	retro_acar_25, retro_acar_44,
Bos taurus	ENSBTAG00000000236	4 retrocopies	retro_btau_1482, retro_btau_635, retro_btau_68, retro_btau_910,
Canis familiaris	ENSCAFG00000000580	6 retrocopies	retro_cfam_1302, retro_cfam_1521, retro_cfam_158, retro_cfam_1840, retro_cfam_233, retro_cfam_465,
Choloepus hoffmanni	ENSCHOG00000002798	9 retrocopies	retro_chof_1572, retro_chof_1703, retro_chof_1890, retro_chof_2321, retro_chof_2346, retro_chof_2669, retro_chof_292, retro_chof_315, retro_chof_933,
Callithrix jacchus	ENSCJAG00000015844	5 retrocopies	retro_cjac_1769, retro_cjac_2164, retro_cjac_3000, retro_cjac_31, retro_cjac_881,
Cavia porcellus	ENSCPOG00000008007	1 retrocopy	retro_cpor_307,
Cavia porcellus	ENSCPOG00000011321	4 retrocopies	retro_cpor_135, retro_cpor_1463, retro_cpor_616, retro_cpor_668,
Cavia porcellus	ENSCPOG00000020285	5 retrocopies	retro_cpor_220, retro_cpor_323, retro_cpor_434 , retro_cpor_592, retro_cpor_644,
Dasypus novemcinctus	ENSDNOG00000001672	10 retrocopies	retro_dnov_1007, retro_dnov_117, retro_dnov_1354, retro_dnov_1579, retro_dnov_1769, retro_dnov_1907, retro_dnov_1993, retro_dnov_2588, retro_dnov_892, retro_dnov_99,
Ficedula albicollis	ENSFALG00000005860	1 retrocopy	retro_falb_13,
Felis catus	ENSFCAG00000032017	4 retrocopies	retro_fcat_1563, retro_fcat_1631, retro_fcat_1697, retro_fcat_60,
Gallus gallus	ENSGALG00000010725	1 retrocopy	retro_ggal_3,
Gorilla gorilla	ENSGGOG00000022133	9 retrocopies	retro_ggor_1092, retro_ggor_1754, retro_ggor_211, retro_ggor_2379, retro_ggor_2997, retro_ggor_2998, retro_ggor_3020, retro_ggor_499, retro_ggor_544,
Loxodonta africana	ENSLAFG00000004944	2 retrocopies	retro_lafr_1089, retro_lafr_112,
Myotis lucifugus	ENSMLUG00000017323	3 retrocopies	retro_mluc_1617, retro_mluc_1686, retro_mluc_296,
Macaca mulatta	ENSMMUG00000006489	7 retrocopies	retro_mmul_1859, retro_mmul_1883, retro_mmul_2136, retro_mmul_2247, retro_mmul_2422, retro_mmul_2503, retro_mmul_451,
Mus musculus	ENSMUSG00000022285	3 retrocopies	retro_mmus_163, retro_mmus_2187, retro_mmus_744,
Oryctolagus cuniculus	ENSOCUG00000000734	2 retrocopies	retro_ocun_1091, retro_ocun_248,
Pongo abelii	ENSPPYG00000018791	7 retrocopies	retro_pabe_103, retro_pabe_1242, retro_pabe_2047, retro_pabe_3417, retro_pabe_3740, retro_pabe_556, retro_pabe_89,
Pelodiscus sinensis	ENSPSIG00000003703	1 retrocopy	retro_psin_13,
Sarcophilus harrisii	ENSSHAG00000012671	2 retrocopies	retro_shar_126, retro_shar_409,
Sus scrofa	ENSSSCG00000006062	2 retrocopies	retro_sscr_222, retro_sscr_35,
Ictidomys tridecemlineatus	ENSSTOG00000023864	3 retrocopies	retro_itri_162, retro_itri_483, retro_itri_887,
Taeniopygia guttata	ENSTGUG00000012078	1 retrocopy	retro_tgut_4,
Tursiops truncatus	ENSTTRG00000015906	4 retrocopies	retro_ttru_15, retro_ttru_1540, retro_ttru_207, retro_ttru_455,
Vicugna pacos	ENSVPAG00000005865	1 retrocopy	retro_vpac_350,