RetrogeneDB ID: retro_cpor_61

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_4:28063391..28063778(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCPOG00000004136
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: PCBD1
• Ensembl ID: ENSCPOG00000012703
• Aliases: None
• Description: None

Sequence

>retro_cpor_61
ATGGCAGCGGCCCTCGGGGCGCGCAGGACGAGGGTGCGCTCGCTGGCTGCACTTCGGGGCGGGAGCCGGAGCCTGGCGAC
CCAGCCTTCAGATTCACAGCTGTTGATTGCAGAGGAGAGGAACCAGATTCTACTTGACCTTAAAAATGTAGGATGCTCAG
AATTAAGTGAGAGAAATGCCATCTACAAAGAATTTTCCTTCAAAAATTTTAATCAGGCCTTTGGCTTTATGTCCCGAGTT
GCCTTGCAAGCAGAGAAGATAAATCATCACCCCGAATGGTTCAATGTGTACAAGGTCCAGCTAACACTCACATCCCATGA
CTGTGGAGGACTGACCAAAAGAGATGTGCAGCTGGCCAAGTTTATTGAAAAAGCATCTATTTTTGTG

Alignment

ORF - retro_cpor_61 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.7 %
• Parental protein coverage: 91.26 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LSAEERDQLLPNLRAVGWNELEGRDAIFKQFHFKDFNRAFGFMTRVALQAEKLDHHPEWFNVYNKVHITL
          L.AEER.Q.L..L..VG..EL..R.AI.K.F.FK.FN.AFGFM.RVALQAEK..HHPEWFNVY.KV..TL
Retrocopy LIAEERNQILLDLKNVGCSELSERNAIYKEFSFKNFNQAFGFMSRVALQAEKINHHPEWFNVY-KVQLTL

Parental  STHECAGLSERDINLASFIEQVAV
          ..H.C.GL..RD..LA.FIE....
Retrocopy TSHDCGGLTKRDVQLAKFIEKASI

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	0.75 RPM	6.04 RPM
SRP017611_kidney	1.88 RPM	48.99 RPM
SRP017611_liver	0.61 RPM	168.41 RPM
SRP040447_lung	1.79 RPM	41.77 RPM
SRP040447_skeletal_muscle	0.24 RPM	6.41 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_61 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_61 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 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011866	1 retrocopy	retro_btau_1478,
Cavia porcellus	ENSCPOG00000012703	1 retrocopy	retro_cpor_61 ,
Felis catus	ENSFCAG00000001235	1 retrocopy	retro_fcat_1478,
Loxodonta africana	ENSLAFG00000001397	1 retrocopy	retro_lafr_1028,
Myotis lucifugus	ENSMLUG00000016074	3 retrocopies	retro_mluc_1534, retro_mluc_2459, retro_mluc_462,
Procavia capensis	ENSPCAG00000007201	1 retrocopy	retro_pcap_46,
Sus scrofa	ENSSSCG00000010275	1 retrocopy	retro_sscr_744,
Takifugu rubripes	ENSTRUG00000017869	1 retrocopy	retro_trub_26,
Tursiops truncatus	ENSTTRG00000005775	1 retrocopy	retro_ttru_1541,
Vicugna pacos	ENSVPAG00000004496	1 retrocopy	retro_vpac_69,