RetrogeneDB ID: retro_cpor_35

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_80:4568781..4569807(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCPOG00000024663
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: HOMER2
• Ensembl ID: ENSCPOG00000014688
• Aliases: None
• Description: None

Sequence

>retro_cpor_35
ATGGGAGAACCGCCCATCTTCACGACCCGAGCGCAAGTCTTTCAGATTGACCCCAGAACCAAGATGATCTGGGTGCCTCT
GAGCCGACAGGCAGTGGCCGTTTCCTATTTCTACGATGCCACAAGGAACAGCTATCGGATCATCAGTGTGGACGGAGACA
GGGTGATCATACACAGCACGATCACAACGAACATGTCCTTCACCAAAACGTCGCAGAGGTTTGGGCAGTGGGCGGACCGC
AAAGCCAACACAATGTTTGGGCTGGGGTTTTCTTCTGATCAGCAGCTGACGAAGTTTGCAGAGAAATTCCAAGAGGTCAA
AGAAGCTACCAAACTAGCCAGAGAAAAATCCCGGGAGCAACTGGGGACCTCGAATAATCATTCCCGAGCATCCAGGGCGG
ATGGGGCGGGCGAGGGAATGGCCCCTCCCGCAGATCCCGCCGACACCCGCCTCAAGGCGGAGGAGAAGCCGAAGGCTGCT
GTGACTCCGAGTGCCGCGCAGCTGGGGAAGTGGGAGCTGGAGCTGCAGACCCTGCGCGACAGCAACGCGCAGCTGAGCTC
GGCGCTGCAGGACTCGGCGGCCAGCGTGGAGCAGTGGAAGAAGCAGGTCTGCGCCTGCAGGGAGGAGAACGAGCGGCTGC
GCCAGCGGATCGAGGAGCTGGAAGAGCAGCGCCGCGAGACGGACGGGGAGCTGGAGGGCGCCACCCAGCTGAAGAGGACA
ATTGAGGCGCTGGAGTACAAACTCCGGGCGAAGGAGACAGAGGTGAAAGATCTCCGGGAACAAACCGAAGCCCTCCCTCA
GCTCAGATGGGAGTGTGACCGTGTCTCTGAGGAGCTGGGGGCAGCGGAGAGAGGCGATCACAACTTGGAAGGCGAAGTGC
GGTGCCTGAGGGTGGACCTTTCCAAGAGCAAGCGCAGGCGGCGTCCCCTGAGGTCTGACCTGAAGAGCTTCCTGAGCCGG
CTGGACAGAAAGATCGATGACCTCCGTGAAATCAGCCAAGGCCTCGCCGAGCTGGGCACCGACGAG

Alignment

ORF - retro_cpor_35 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.18 %
• Parental protein coverage: 99.13 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EQPIFTTRAHVFQIDPNTKKNWVPASKQAVTVSYFYDVTRNSYRIISVDGAKVIINSTITPNMTFTKTSQ
          E.PIFTTRA.VFQIDP.TK..WVP.S.QAV.VSYFYD.TRNSYRIISVDG..VII.STIT.NM.FTKTSQ
Retrocopy EPPIFTTRAQVFQIDPRTKMIWVPLSRQAVAVSYFYDATRNSYRIISVDGDRVIIHSTITTNMSFTKTSQ

Parental  KFGQWADSRANTVFGLGFSSEQQLTKFAEKFQEVKEAAKLAREKSQEKIETSSNHSQASSVNGTDDEKAS
          .FGQWAD..ANT.FGLGFSS.QQLTKFAEKFQEVKEA.KLAREKS.E...TS.NHS.AS...G.....A.
Retrocopy RFGQWADRKANTMFGLGFSSDQQLTKFAEKFQEVKEATKLAREKSREQLGTSNNHSRASRADGAGEGMAP

Parental  HAGPADTHLKSENDKLKIALTQSAANVKKWEIELQTLRESNARLTTALQESAASVEQWKKQFFICRDEND
          .A.PADT.LK.E..K.K.A.T.SAA...KWE.ELQTLR.SNA.L..ALQ.SAASVEQWKKQ...CR.EN.
Retrocopy PADPADTRLKAE-EKPKAAVTPSAAQLGKWELELQTLRDSNAQLSSALQDSAASVEQWKKQVCACREENE

Parental  QLRHKIDELEEQCNEINREKEKNSQLKRRIEELESELREKETELKDLRKQSEIIPQLMSECEYVSEKLEA
          .LR..I.ELEEQ..E...E.E...QLKR.IE.LE..LR.KETE.KDLR.Q.E..PQL..EC..VSE.L.A
Retrocopy RLRQRIEELEEQRRETDGELEGATQLKRTIEALEYKLRAKETEVKDLREQTEALPQLRWECDRVSEELGA

Parental  AERDNQNLEDKVRSLKTDIEESKYRQRHLKVELKSFLEVLDGKIDDLHDFRRGLSKLGTD
          AER...NLE..VR.L..D...SK.R.R.L...LKSFL..LD.KIDDL.....GL..LGTD
Retrocopy AERGDHNLEGEVRCLRVDLSKSKRRRRPLRSDLKSFLSRLDRKIDDLREISQGLAELGTD

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	6.44 RPM
SRP017611_kidney	0.00 RPM	0.10 RPM
SRP017611_liver	0.00 RPM	9.27 RPM
SRP040447_lung	0.00 RPM	7.54 RPM
SRP040447_skeletal_muscle	0.00 RPM	97.74 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_35 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_35 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 7 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015884	3 retrocopies	retro_cjac_3556, retro_cjac_3614, retro_cjac_3871,
Cavia porcellus	ENSCPOG00000014688	1 retrocopy	retro_cpor_35 ,
Equus caballus	ENSECAG00000023619	3 retrocopies	retro_ecab_1046, retro_ecab_661, retro_ecab_692,
Homo sapiens	ENSG00000103942	1 retrocopy	retro_hsap_1468,
Macaca mulatta	ENSMMUG00000008297	1 retrocopy	retro_mmul_2278,
Nomascus leucogenys	ENSNLEG00000010953	1 retrocopy	retro_nleu_3002,
Pongo abelii	ENSPPYG00000006735	5 retrocopies	retro_pabe_1209, retro_pabe_1210, retro_pabe_1217, retro_pabe_3566, retro_pabe_3568,