RetrogeneDB ID: retro_cpor_66

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_22:9896130..9896679(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCPOG00000023915
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: CBX3
• Ensembl ID: ENSCPOG00000015168
• Aliases: None
• Description: chromobox homolog 3 [Source:HGNC Symbol;Acc:1553]

Sequence

>retro_cpor_66
ATGGCGTCCAATAAAACTACATTGCAAAAAATGGGAAAGAAACAAAATGGAAAAAGTAAAAAAGTTGAGGAAGCAGAGCC
TGAAGAATTTGTGGTAGAAAAAGTACTGGACCGCCGTGTAGTGAATGGGAAGGTGGAATATTTTCTGAAGTGGAAGGGAT
TTACAGATGCTGACAATACATGGGAACCTGAAGAAAATTTAGATTGTCCAGAGTTAATTGAAGCATTTCTTAATTCTCAA
AAAGCTGGTAAAGAAAAAGATGGTACAAAACGAAAATCTTTATCTGACAGTGAATCTGATGATAGCAAATCAAAGAAAAA
AAGAGATGCTGCTGACAAACCTAGAGGCTTTGCTAGAGGTCTTGATCCTGAACGAATAATTGGTGCCACAGACAGTAGTG
GGGAATTGATGTTTCTCATGAAATGGAAAGATTCAGATGAGGCTGACTTGGTGCTGGCAAAAGAGGCAAATATGAAATGT
CCTCAAATTGTAATCGCTTTTTATGAAGAGAGACTAACCTGGCATTCTTGTCCAGAAGATGAAGCTCAA

Alignment

ORF - retro_cpor_66 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.05 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MASNKTTLLHNMEDTENECSLKVEEAEPEEFVVEKVLDRRVVNGKVEYFLKWKGFTDEHSADNTWEPEEN
          MASNKTTL...M....N..S.KVEEAEPEEFVVEKVLDRRVVNGKVEYFLKWKGFTD...ADNTWEPEEN
Retrocopy MASNKTTL-QKMGKKQNGKSKKVEEAEPEEFVVEKVLDRRVVNGKVEYFLKWKGFTD---ADNTWEPEEN

Parental  LDCPELIEAFLNSQKAGKEKDGTKRKSLSDSESDDSKSKKKRDAADKPRGFARGLDPERIIGATDSSGEL
          LDCPELIEAFLNSQKAGKEKDGTKRKSLSDSESDDSKSKKKRDAADKPRGFARGLDPERIIGATDSSGEL
Retrocopy LDCPELIEAFLNSQKAGKEKDGTKRKSLSDSESDDSKSKKKRDAADKPRGFARGLDPERIIGATDSSGEL

Parental  MFLMKWKDSDEADLVLAKEANMKCPQIVIAFYEERLTWHSCPEDEAQ
          MFLMKWKDSDEADLVLAKEANMKCPQIVIAFYEERLTWHSCPEDEAQ
Retrocopy MFLMKWKDSDEADLVLAKEANMKCPQIVIAFYEERLTWHSCPEDEAQ

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	21.80 RPM	13.57 RPM
SRP017611_kidney	21.46 RPM	8.90 RPM
SRP017611_liver	7.09 RPM	3.96 RPM
SRP040447_lung	12.33 RPM	14.68 RPM
SRP040447_skeletal_muscle	7.26 RPM	6.79 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_66 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_66 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 63 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013843	22 retrocopies	retro_chof_1128, retro_chof_1147, retro_chof_1156, retro_chof_1178, retro_chof_1210, retro_chof_1223, retro_chof_132, retro_chof_1569, retro_chof_1672, retro_chof_1779, retro_chof_1863, retro_chof_1962, retro_chof_222, retro_chof_2269, retro_chof_2347, retro_chof_2379, retro_chof_2435, retro_chof_2695, retro_chof_411, retro_chof_676, retro_chof_87, retro_chof_936,
Cavia porcellus	ENSCPOG00000015168	1 retrocopy	retro_cpor_66 ,
Felis catus	ENSFCAG00000015224	6 retrocopies	retro_fcat_1005, retro_fcat_1103, retro_fcat_1485, retro_fcat_1519, retro_fcat_336, retro_fcat_473,
Homo sapiens	ENSG00000122565	9 retrocopies	retro_hsap_1071, retro_hsap_1145, retro_hsap_1902, retro_hsap_2332, retro_hsap_2771, retro_hsap_3368, retro_hsap_3650, retro_hsap_766, retro_hsap_910,
Nomascus leucogenys	ENSNLEG00000014931	9 retrocopies	retro_nleu_141, retro_nleu_1685, retro_nleu_2462, retro_nleu_373, retro_nleu_397, retro_nleu_511, retro_nleu_676, retro_nleu_944, retro_nleu_964,
Ochotona princeps	ENSOPRG00000011713	9 retrocopies	retro_opri_103, retro_opri_159, retro_opri_209, retro_opri_300, retro_opri_429, retro_opri_569, retro_opri_598, retro_opri_728, retro_opri_733,
Sorex araneus	ENSSARG00000008011	2 retrocopies	retro_sara_496, retro_sara_709,
Sarcophilus harrisii	ENSSHAG00000017913	1 retrocopy	retro_shar_153,
Sus scrofa	ENSSSCG00000016711	4 retrocopies	retro_sscr_1031, retro_sscr_204, retro_sscr_420, retro_sscr_755,