RetrogeneDB ID: retro_cpor_1458

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_88:4459821..4461421(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCT7
• Ensembl ID: ENSCPOG00000019869
• Aliases: None
• Description: None

Sequence

>retro_cpor_1458
CCCACACCAGTTATATTGTTGAAAGAGGCAACTGACAGCTCCCAAGGTATTCTTCAGCTTGTGAGTAACATCAGTGCCTG
CCAGGTGATTGCCGAGGCTGTAAGAACCACCCTAGTCCCCACGGCATGGACAAGCTTATTGTGGATGGCTGAGGAAAAGC
AACAATTTCTAATGATGGGGCCACAATTTTGAAACTTCTTGATGTCGTCCATCCTGCAGCAAAGACTTTGGTGGACACTG
CCAAATCCCAAGATGCTGAGGTTCGTGATGGTACCACCTCAGTAACCCTGCTGGCTGCAGAGATTCTGAAGCAGGTGAAA
TCATAAGTGGAGGAAGGTTTGCCCCCCAGATCATCATCCAAGCTTTCTGCACAGCCACACAGTTGGCAATTAACAAGATC
AAAGAGATTGCTGTAACTGTGAAGAAGCAAGATAAAGTGGAGCAGAGGAAACTGCTGGAGAAGTGTGCCATGACAGCTCT
GAGCTCCCAGCAGAAAGCCTTCTTTGCTAAGATGGTGGTTGATGCTGTGATGATGCCTGAGGATTTGCTGCAGCTTAAAA
TGATTGGAATCAAGAAGGTACAGGGTGAAGCCCTAGAGGAGTCTCAGCTGGTGGGAGGTGTGGCGTTCAAGAAGACTTTC
TCTTATGCTGGGTTTGAAATGCAACCTAAAAAGTACAATAACCCCATGATCACCTTATTAAATGCTGAACTTGAGCTGAA
AGCTGAGAAAGACAATGCTGAAATCAGAGTCCGTACAGTGGAGGATTATCAGGCAATCGTTGATGCTGAGTGGAACATTC
TCTATGACAAGTTAGAGAAGATCTACAATTCTGGAGCCAAAGTTGTTTTATCCAAATTCCCTACTGGGGATGTAGCCACC
CAGTACTTTGCCAATAGAAACATGTTCTGTGCCGGCCGGGTGCCTGAGGGACATTTGAACAGGACAATGATGGCCTGCGG
AGGTTCGATCCAGACCAGTGTGAACGCTCTATCAGCAGATGTGCTGAGCCGCTGCCAGCTGTTTGAAGAAACCCAGATTG
GAGGTGAAAGGTACAGTTTCTTCACTGGTTGCCCCAAGGCCAAGACTTGCACCTTCATCCTCCATGGCGGTGCTGAGCAG
TTTATGGTGGACACAGAGCAGTCTCTGCATGATGCCATCATGATCGTCATACGGACCATCAAGAATGATTCAGTGGTGGC
TGGTGGTGGGGCCATCGAGATGGAGCTCTCTAAGTACTTATGGGATTACTCAAGGACTATCCCAGGAAAACAGCAGCTAC
TGATTAGAGCATATGCCAAGGCCTTGGAGGTTATCCCACGGCAGCTATGTGACAGTGCTGGCTTTGATGCCATAAACATC
TTGAACAAGTTGTGGACTAGGCATGCCCAGGGGGGCATGTGATATGGGGTGGACATCAACAATGAGGACATTACTGACAA
CTCTGAAGCCTTTGTGTGGGAGCCAGCTATGGTGCGGCTCAATGCCCTGACAGCAGCCTCTGAGGCTGCACGCCTTATCG
TGTCTGTGGATGAGATCATCAGGAACCCTCACTCCACTGTGTATGCTCCTCCAGCAGCTGCCCGGGGCAGGGGCCAGGGC

Alignment

ORF - retro_cpor_1458 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.26 %
• Parental protein coverage: 99.81 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PTPVILLKEGTDSSQGIPQLVSNISACQVIAEAVRTTL-GPRGMDKLIVDGRGKATISNDGATILKLLDV
          PTPVILLKE.TDSSQGI.QLVSNISACQVIAEAVRTTL..P.GMDKLIVDG.GKATISNDGATILKLLDV
Retrocopy PTPVILLKEATDSSQGILQLVSNISACQVIAEAVRTTL<SPHGMDKLIVDG*GKATISNDGATILKLLDV

Parental  VHPAAKTLVDIAKSQDAEVGDGTTSVTLLAAEFLKQVKPYVEEGLHP-QIIIRAFRTATQLAINKIKEIA
          VHPAAKTLVD.AKSQDAEV.DGTTSVTLLAAE.LKQVK..VEEGL.P.QIII.AF.TATQLAINKIKEIA
Retrocopy VHPAAKTLVDTAKSQDAEVRDGTTSVTLLAAEILKQVKS*VEEGLPP<QIIIQAFCTATQLAINKIKEIA

Parental  VTVKKQDKVEQRKLLEKCAMTALSSKLISQQKAFFAKMVVDAVMMLDDLLQLKMIGIKKVQGGALEESQL
          VTVKKQDKVEQRKLLEKCAMTALS....SQQKAFFAKMVVDAVMM..DLLQLKMIGIKKVQG.ALEESQL
Retrocopy VTVKKQDKVEQRKLLEKCAMTALS----SQQKAFFAKMVVDAVMMPEDLLQLKMIGIKKVQGEALEESQL

Parental  VAGVAFKKTFSYAGFEMQPKKYNNPMIALLNVELELKAEKDNAEIRVHTVEDYQAIVDAEWNILYDKLEK
          V.GVAFKKTFSYAGFEMQPKKYNNPMI.LLN.ELELKAEKDNAEIRV.TVEDYQAIVDAEWNILYDKLEK
Retrocopy VGGVAFKKTFSYAGFEMQPKKYNNPMITLLNAELELKAEKDNAEIRVRTVEDYQAIVDAEWNILYDKLEK

Parental  IYNSGAKVVLSKLPIGDVATQYFADRDMFCAGRVPEEDLKRTMMACGGSIQTSVNALSADVLGRCQLFEE
          IYNSGAKVVLSK.P.GDVATQYFA.R.MFCAGRVPE..L.RTMMACGGSIQTSVNALSADVL.RCQLFEE
Retrocopy IYNSGAKVVLSKFPTGDVATQYFANRNMFCAGRVPEGHLNRTMMACGGSIQTSVNALSADVLSRCQLFEE

Parental  TQIGGERYNFFTGCPKAKTCTFILRGGAEQFMEETERSLHDAIMIVRRAIKNDSVVAGGGAIEMELSKYL
          TQIGGERY.FFTGCPKAKTCTFIL.GGAEQFM..TE.SLHDAIMIV.R.IKNDSVVAGGGAIEMELSKYL
Retrocopy TQIGGERYSFFTGCPKAKTCTFILHGGAEQFMVDTEQSLHDAIMIVIRTIKNDSVVAGGGAIEMELSKYL

Parental  RDYSRTIPGKQQLLIGAYAKALEIIPRQLCDNAGFDATNILNKLRARHAQGGMWYGVDINNEDITDNFEA
          .DYSRTIPGKQQLLI.AYAKALE.IPRQLCD.AGFDA.NILNKL..RHAQGGM.YGVDINNEDITDN.EA
Retrocopy WDYSRTIPGKQQLLIRAYAKALEVIPRQLCDSAGFDAINILNKLWTRHAQGGM*YGVDINNEDITDNSEA

Parental  FVWEPAMVRINALTAASEAACLIVSVDETIKNPRSTVDAPPAAGRGRGRG
          FVWEPAMVR.NALTAASEAA.LIVSVDE.I.NP.STV.APPAA.RGRG.G
Retrocopy FVWEPAMVRLNALTAASEAARLIVSVDEIIRNPHSTVYAPPAAARGRGQG

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	0.29 RPM	124.29 RPM
SRP017611_kidney	0.10 RPM	163.52 RPM
SRP017611_liver	0.09 RPM	98.33 RPM
SRP040447_lung	0.08 RPM	151.73 RPM
SRP040447_skeletal_muscle	0.08 RPM	108.58 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1458 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1458 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 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000008879	1 retrocopy	retro_cfam_151,
Cavia porcellus	ENSCPOG00000019869	1 retrocopy	retro_cpor_1458 ,
Homo sapiens	ENSG00000135624	1 retrocopy	retro_hsap_3354,
Gorilla gorilla	ENSGGOG00000007766	1 retrocopy	retro_ggor_2274,
Macropus eugenii	ENSMEUG00000000416	1 retrocopy	retro_meug_1995,
Macaca mulatta	ENSMMUG00000012448	1 retrocopy	retro_mmul_2093,
Nomascus leucogenys	ENSNLEG00000010414	1 retrocopy	retro_nleu_1175,
Otolemur garnettii	ENSOGAG00000009162	2 retrocopies	retro_ogar_2001, retro_ogar_2698,
Pongo abelii	ENSPPYG00000012297	1 retrocopy	retro_pabe_2760,
Pan troglodytes	ENSPTRG00000012060	1 retrocopy	retro_ptro_2133,
Rattus norvegicus	ENSRNOG00000015630	2 retrocopies	retro_rnor_2179, retro_rnor_535,
Tupaia belangeri	ENSTBEG00000002066	2 retrocopies	retro_tbel_3708, retro_tbel_3751,