RetrogeneDB ID: retro_cpor_1324

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_7:50451156..50452069(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PABPC3
• Ensembl ID: ENSCPOG00000012917
• Aliases: None
• Description: None

Sequence

>retro_cpor_1324
GAACGTACTTTGGACACTACAGGTTTTTTTGATGTTATAAAGGGCAAATCCAGCTGCGCCAAGTGGTCTTTATCACTTTG
TCAAAATGGAGCAGGTCACAAAACTCATTAGAAATTTGGGCAGATCCATTGATAATAAAGCACTGTATGACACATTTCCT
GCTTTTGTTAACATCCTTCATGCAAGGTGGAAAATGGTCCCAAGAGCTATGGATTTGTGCGTTTTCAGACACAGGAAGCA
GCTGAAAGAATGACTGAAAATAACAAATGCTTCTAAAATGATCACAAGGTATTTGTTGAACAATTCAAATCTCATAAACA
AGAAGCAGAATGTGGAGCTAGGATAAAGAGCTCAACAATATTTACATCAAGAATTTTGGAGAAGACAGGGATGATGAGCA
CATTAACGATCTCTTTGGCAAATCTGGACCTGCTTTAGGTGTGAAAAGAACAACCAGAGAAAGTGGGAAATCCAAAGAAT
TTGGACTGGGAAGCTTTGAAAGACATGAAGACATACAGAAAGCTGTGGATGAGATAAATGGCAAGGGGCTCAGTGGAAAA
ACAAACCTCTGTTGTTTGGGTTCAGACCAAAAAAAGTGGAACGCCAGACAGAACTTAAGTGCAAATTTGAACAGATGAAG
TAAGATAGGATCACTGGTTACCAGGGTGTGGACCTTTAGCTGAAAAATGGCAGTGGTGGTATTGATGAATGTCTCCAGAA
AGAGTTTGCTTGATCACCAGCAGATCACCAGCAGAAAGGCTGTAACAGAGGGTGATTGCAGTGGAGGGTTTGGTTTTGTA
TGTTTCTCTTCCCCCGTAGAAGCCATTAAAGTAGTTACAGAAATGAACAGTAGGATTGGGGCCACAAGCCACTAGTTTAG
CACAAAGAAAGGCAGACACTAGCTCACCTCACT

Alignment

ORF - retro_cpor_1324 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.23 %
• Parental protein coverage: 54.9 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  ERALDTMNF-DVIKGKPVRIMWSQRDPSLRKSGVGNI-FIKNLDKSIDNKALYDTFSAFGNIL-SCKVVC
          ER.LDT..F.DVIKGK.....WS....SL...G.G....I.NL..SIDNKALYDTF.AF.NIL.SCKV..
Retrocopy ERTLDTTGFFDVIKGKSSCAKWSL---SLCQNGAGHK>LIRNLGRSIDNKALYDTFPAFVNIL<SCKV--

Parental  DENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAK-EFTNVYIKNFGED
          .ENG.K.YGFV.F.TQEAAER..E..N....ND.KVFV..FKS.K..EAE.GAR.K.E..N.YIKNFGED
Retrocopy -ENGPKSYGFVRFQTQEAAERMTEN-NKCF*NDHKVFVEQFKSHKQ-EAECGARIK<ELNNIYIKNFGED

Parental  MDDERLKDLFGKFGPALSVKVMTDESGKSKGFGFVSFERHEDAQKAVDEMNGKELNGKQ--IYVGRAQK-
          .DDE...DLFGK.GPAL.VK..T.ESGKSK.FG..SFERHED.QKAVDE.NGK.L.GK......G..QK.
Retrocopy RDDEHINDLFGKSGPALGVKRTTRESGKSKEFGLGSFERHEDIQKAVDEINGKGLSGKTNLCCLGSDQK<

Parental  KVERQTELKRKFEQMKQDRITRYQGVNLYVKNLDDGIDDERLRKEFS-PFGTITSAKVMMEGGRSKGFGF
          KVERQTELK.KFEQMK.DRIT.YQGV.L..KN...GI.DE.L.KEF......ITS.K...EG..S.GFGF
Retrocopy KVERQTELKCKFEQMK*DRITGYQGVDL*LKNGSGGI-DECLQKEFA>DHQQITSRKAVTEGDCSGGFGF

Parental  VCFSSPEEATKAVTEMNGRIVAT-KPLYVALAQRKEERQAHLT
          VCFSSP.EA.K.VTEMN.RI.AT.KPL............AHLT
Retrocopy VCFSSPVEAIKVVTEMNSRIGAT<KPL---V*HKERQTLAHLT

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	0.06 RPM	138.61 RPM
SRP017611_kidney	1.15 RPM	281.61 RPM
SRP017611_liver	0.04 RPM	180.38 RPM
SRP040447_lung	0.00 RPM	660.94 RPM
SRP040447_skeletal_muscle	0.00 RPM	97.26 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1324 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1324 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 19 parental genes, and 35 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000348	1 retrocopy	retro_amel_1650,
Choloepus hoffmanni	ENSCHOG00000008178	1 retrocopy	retro_chof_2531,
Callithrix jacchus	ENSCJAG00000015833	5 retrocopies	retro_cjac_1586, retro_cjac_2571, retro_cjac_3218, retro_cjac_4039, retro_cjac_41,
Cavia porcellus	ENSCPOG00000002044	1 retrocopy	retro_cpor_1379,
Cavia porcellus	ENSCPOG00000009552	2 retrocopies	retro_cpor_1330, retro_cpor_77,
Cavia porcellus	ENSCPOG00000012917	1 retrocopy	retro_cpor_1324 ,
Dasypus novemcinctus	ENSDNOG00000008718	2 retrocopies	retro_dnov_1530, retro_dnov_2259,
Felis catus	ENSFCAG00000001874	1 retrocopy	retro_fcat_1927,
Homo sapiens	ENSG00000070756	1 retrocopy	retro_hsap_88,
Gorilla gorilla	ENSGGOG00000006785	1 retrocopy	retro_ggor_1986,
Myotis lucifugus	ENSMLUG00000012245	1 retrocopy	retro_mluc_579,
Macaca mulatta	ENSMMUG00000017786	2 retrocopies	retro_mmul_1462, retro_mmul_895,
Monodelphis domestica	ENSMODG00000006222	4 retrocopies	retro_mdom_123, retro_mdom_1867, retro_mdom_216, retro_mdom_43,
Mus musculus	ENSMUSG00000022283	2 retrocopies	retro_mmus_102, retro_mmus_2164,
Oryctolagus cuniculus	ENSOCUG00000004354	1 retrocopy	retro_ocun_13,
Pongo abelii	ENSPPYG00000018790	3 retrocopies	retro_pabe_2373, retro_pabe_68, retro_pabe_854,
Rattus norvegicus	ENSRNOG00000008639	3 retrocopies	retro_rnor_1228, retro_rnor_2321, retro_rnor_265,
Sarcophilus harrisii	ENSSHAG00000011267	1 retrocopy	retro_shar_24,
Tarsius syrichta	ENSTSYG00000004229	2 retrocopies	retro_tsyr_1743, retro_tsyr_273,