RetrogeneDB ID: retro_cpor_257

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_11:20078359..20078860(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PCBP3
• Ensembl ID: ENSCPOG00000003648
• Aliases: None
• Description: None

Sequence

>retro_cpor_257
TGCCAGAAGAGAATTATCACTTTGACTAGACCCATTAATGTCATCTTCGAAGCCTTTGCTATGATTATTGATAAACTGGA
AGAGGACATCAGCAGCTCTCTGACCAGAAGCACAACTGCTTATAGGCCTCTGGTCCCTCTGATACTGATGGTCCCTGCTA
GTCCATGTGGCTCTCTCATTGGAAAAGGCGGTTGCAAGATCAAGGAAATACGAGAAAGTTCAAGGCCTCAGGTCCAAGTT
TGGGGGATAGGCTTTCCAATCCTGCTACTGCTGTCACCCTGCAAGTCACCACTGAGTGTGTCAGACAGATCTGGGTGATC
ATGCTGGAGACTTTCCCAGTCCCCACTGAAGGTCGTGACTGTCCCATGCAGGCCCAAGCCATCAAGTTTTCTAGTCATCT
TTGTAGGTAGTCAGGCTTAAAGCATTTAAGGACAATACCCCATTCCACAGTCAAATCTGACCAAGCTTCACCAGTTGGCC
AGACAGTAGTCCCATTTCCCC

Alignment

ORF - retro_cpor_257 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.86 %
• Parental protein coverage: 50.15 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  CPERIVTITGPTDAIFKAFAMIAYKFEEDIINSMSNSPATSKPPVTLRLVVPASQCGSLIGKGGSKIKEI
          C..RI.T.T.P...IF.AFAMI..K.EEDI..S...S.....P.V.L.L.VPAS.CGSLIGKGG.KIKEI
Retrocopy CQKRIITLTRPINVIFEAFAMIIDKLEEDISSSLTRSTTAYRPLVPLILMVPASPCGSLIGKGGCKIKEI

Parental  RESTGAQVQV-AGDMLPNSTERAVTISGTPDAIIQCVKQICVVMLES---PPKGATIPY-RPKPASTPVI
          RES...QVQV..GD.L.N....AVT...T......CV.QI.V.MLE....P..G...P..RPKP.S..VI
Retrocopy RESSRPQVQV<LGDRLSNPA-TAVTLQVTTE----CVRQIWVIMLETFPVPTEGRDCPM>RPKPSSFLVI

Parental  FAGGQAYTIQGQYAIPHPDQLTKLHQLAMQQTPFP
          F.G.QA..I.GQY.IP....LTKLHQLA.Q...FP
Retrocopy FVGSQA*SI*GQYPIPQ-SNLTKLHQLARQ*SHFP

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	3.74 RPM
SRP017611_kidney	0.00 RPM	0.10 RPM
SRP017611_liver	0.00 RPM	0.00 RPM
SRP040447_lung	0.00 RPM	0.18 RPM
SRP040447_skeletal_muscle	0.00 RPM	0.00 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_257 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_257 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 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000000967	2 retrocopies	retro_cpor_193, retro_cpor_97,
Cavia porcellus	ENSCPOG00000003648	1 retrocopy	retro_cpor_257 ,
Dipodomys ordii	ENSDORG00000003640	2 retrocopies	retro_dord_742, retro_dord_748,
Myotis lucifugus	ENSMLUG00000003074	1 retrocopy	retro_mluc_574,
Nomascus leucogenys	ENSNLEG00000002639	1 retrocopy	retro_nleu_2044,
Oryctolagus cuniculus	ENSOCUG00000002696	1 retrocopy	retro_ocun_1257,
Rattus norvegicus	ENSRNOG00000001245	1 retrocopy	retro_rnor_2656,
Sorex araneus	ENSSARG00000007629	1 retrocopy	retro_sara_414,
Tursiops truncatus	ENSTTRG00000015075	1 retrocopy	retro_ttru_1095,