RetrogeneDB ID: retro_cpor_118

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_30:13628681..13630910(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCPOG00000027609
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000009391
• Aliases: None
• Description: None

Sequence

>retro_cpor_118
ATGGCGGCCCGGCTTATGCAAGCTGCAAGATGTCCTACAGATGAATTATCTTTAACCAACTGTGCAGTTGTAAACGAAAC
AGATTTTCAGTCCAACCAGCATGTGGTTGTGAGAACCTCTTCTAATCACAAGTTCACTTTTACTCTGAGGACCCATCCGT
CAGTGGTTCCAGGGAGCACTGCATTCAGCTTACCCCAGCGAAAATGGGCTGGACTTTCTATTGGACAAGAAATAGAAGTC
TCTTTATATACATTTGACAAAGCCAAACAGTGTATTGGCACAATGACCATCGAGATTGATTTCCTGCAGAAAAAAAGCAT
TGACTCCAATCCTTATGATACTGACAAGATGGCAGCAGAGTTTATTCAGCAGTTCAACAACCAGGCCTTCTCAGTGGGAC
AGCAGCTTGTGTTTAGCTTCAATGAAAAGCTTTTTGGCTTATTGGTGAAGGATATTGAAGCCATGGATCCTAGCATCTTG
AAAGGAGAGGCTGTGACAGGTAAAAGACAGAAGATTGAAGTAGGACTGGTTGTTGGAAACAGTCAAGTTGCATTTGAAAA
AGCAGAAAAATCATCACTCAATCTTATTGGCAAAGCTAAAACCAAGGAAAATCGCCAGTCTATTATCAATCCTGATTGGA
ACTTTGAAAAAATGGGAATAGGAGGTCTGGACAAAGAATTTTCAGATATTTTTCGACGAGCATTTGCTTCCCGAGTATTT
CCTCCAGAGATTGTGGAACAGATGGGTTGTAAACATGTTAAAGGCATCCTGTTATATGGGCCCCCAGGATGTGGTAAGAC
TCTCTTGGCTCTACAGATTGGCAAGATGTTGAATGCAAGAGAGCCCAAAGTGGTCAATGGACCAGAAAATCTTAACAAAT
ATGTGGGTGAATCAGAGGCTAACATTCACAAACTTTTTGCTGATGCTGAAGAGGAGCAAAGGAGGCTTGGTGCTAACACT
GGTTTGCACATCATCATCTTTGATGAAATTGATGCCATCTGCAAACAGAGAGGGAGCATGGCTGGTAGCACTGGGATTCA
CAACACTGTTGTCAATCAGTTGTTGTCCAAAATTGATGGGGTAGAGCAGCTGAACAACATCCTTGTCATTGGAATGACCA
ATAGACCAGATCTGATTGATGAGGCTCTCCTTCAACCTGGAAGACTGGAAGTCAAAATGGAGATAGGCTTGCCAGATGAG
AAAGGTCGACTACAGATCCTTCACATCCACACAGCAAGGATGAGAGACCATCAATTGCTCTCTACTGATGTAGATATTAA
AGAACTGGCTGTGGAGACCAAGAATTTCAGTGGTGCTGAACTGGAGGGTCTGGTGCGAGCAGCACAGTCCACTGCTATGA
ACAGACATATAAAGGCCAGTACAAAAGTGGAAGTGGACATAGAGAAAGCAGAGAGCCTGAAGGTAACAAGAGGAGACTTC
CTTGCTTCATTGGAGAATGGTATCAAACCAGCATTTGGCACAAACCAAGAGGATTATGCAAGTTACATTATGAATGGAAT
TATCAAGTGGGGTGATCCAGTTACTCGAGTTCTGGATGATGGGGAGCTTTTGGTCCAGCAGACTAAAAACAGTGATCGTA
CACCATTGGTCAGCGTCCTTTTGGAAGGCCCTCCTCACAGTGGGAAGACTGCTTTAGCTGCAAAGAGTGCAGAGGAATCC
AACTTGCGCTTCATCAAGATCTGTTCTCCTAATAAGATGATTGGCTTTTATGAGACTTGTAAGTGTCAGGCCATGAAAAA
GATCTTTGATGATGCATACAAATCTCAGCTCAGCTGTGTGGTTGTGGATGACATTGAGAGATTACTTGATTATGTCGCCA
TTGGCCCCCGGTTTTCTAATTTGGTATTACAGGCTCTTCTTGTGGTACTGAAAAAAGCACCACCTCAGGGCTGCAAGCTT
CTTATCATTGGGACCACTAGCCGCATAGATGTCCTTCAGGAAATGGAAATGCTTAATGCTTTTAGCACCACCATCCATGT
GCCTAATATTGCCACAGGAGAGCAGCTGTTGGAAGCTTTAGAGCTTTTGGGCAACTTCAACGATAAGGAACATACCACAA
TTTCACAAGTCAAAGGGAAGAAAGTCTGGGCAGGAATCAAGAAGTTGCTAATGCTGATCGAGATGTCCCTGCAGATGGAC
CCTGACTATCGTGTGAAAAAATTCTTGGCCCTCTTAAGAGAAGAAGGAGCTAGCCCCCTTGACTTTGAA

Alignment

ORF - retro_cpor_118 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.22 %
• Parental protein coverage: 99.87 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MQAARCPTDELSLTNCAVVNETDFQSNQHVVVRTSSNHKFTFTLRTHPSVVPGSIAFSLPQRKWAGLSIG
          MQAARCPTDELSLTNCAVVNETDFQSNQHVVVRTSSNHKFTFTLRTHPSVVPGS.AFSLPQRKWAGLSIG
Retrocopy MQAARCPTDELSLTNCAVVNETDFQSNQHVVVRTSSNHKFTFTLRTHPSVVPGSTAFSLPQRKWAGLSIG

Parental  QEIEVSLYTFDKAKQCIGTMTIEIDFLQKKSIDSNPYDTDKMAAEFIQQFNNQAFSVGQQLVFSFNEKLF
          QEIEVSLYTFDKAKQCIGTMTIEIDFLQKKSIDSNPYDTDKMAAEFIQQFNNQAFSVGQQLVFSFNEKLF
Retrocopy QEIEVSLYTFDKAKQCIGTMTIEIDFLQKKSIDSNPYDTDKMAAEFIQQFNNQAFSVGQQLVFSFNEKLF

Parental  GLLVKDIEAMDPSILKGEAATGKRQKIEVGLVVGNSQVAFEKAEKSSLNLIGKAKTKENRQSIINPDWNF
          GLLVKDIEAMDPSILKGEA.TGKRQKIEVGLVVGNSQVAFEKAEKSSLNLIGKAKTKENRQSIINPDWNF
Retrocopy GLLVKDIEAMDPSILKGEAVTGKRQKIEVGLVVGNSQVAFEKAEKSSLNLIGKAKTKENRQSIINPDWNF

Parental  EKMGIGGLDKEFSDIFRRAFASRVFPPEIVEQMAGCKHVKGILLYGPPGCGKTLLARQIGKMLNAREPKV
          EKMGIGGLDKEFSDIFRRAFASRVFPPEIVEQM.GCKHVKGILLYGPPGCGKTLLA.QIGKMLNAREPKV
Retrocopy EKMGIGGLDKEFSDIFRRAFASRVFPPEIVEQM-GCKHVKGILLYGPPGCGKTLLALQIGKMLNAREPKV

Parental  VNGPEILNKYVGESEANIRKLFADAEEEQRRLGANSGLHIIIFDEIDAICKQRGSMAGSTGVHDTVVNQL
          VNGPE.LNKYVGESEANI.KLFADAEEEQRRLGAN.GLHIIIFDEIDAICKQRGSMAGSTG.H.TVVNQL
Retrocopy VNGPENLNKYVGESEANIHKLFADAEEEQRRLGANTGLHIIIFDEIDAICKQRGSMAGSTGIHNTVVNQL

Parental  LSKIDGVEQLNNILVIGMTNRPDLIDEALLRPGRLEVKMEIGLPDEKGRLQILHIHTARMRDHQLLSTDV
          LSKIDGVEQLNNILVIGMTNRPDLIDEALL.PGRLEVKMEIGLPDEKGRLQILHIHTARMRDHQLLSTDV
Retrocopy LSKIDGVEQLNNILVIGMTNRPDLIDEALLQPGRLEVKMEIGLPDEKGRLQILHIHTARMRDHQLLSTDV

Parental  DIKELAVETKNFSGAELEGLVRAAQSTAMNRHIKASTKVEVDMEKAESLKVTRGDFLASLENDIKPAFGT
          DIKELAVETKNFSGAELEGLVRAAQSTAMNRHIKASTKVEVD.EKAESLKVTRGDFLASLEN.IKPAFGT
Retrocopy DIKELAVETKNFSGAELEGLVRAAQSTAMNRHIKASTKVEVDIEKAESLKVTRGDFLASLENGIKPAFGT

Parental  NQEDYASYIMNGIIKWGDPVTRVLDDGELLVQQTKNSDRTPLVSVLLEGPPHSGKTALAAKIAEESNFPF
          NQEDYASYIMNGIIKWGDPVTRVLDDGELLVQQTKNSDRTPLVSVLLEGPPHSGKTALAAK.AEESN..F
Retrocopy NQEDYASYIMNGIIKWGDPVTRVLDDGELLVQQTKNSDRTPLVSVLLEGPPHSGKTALAAKSAEESNLRF

Parental  IKICSPDKMIGFSETAKCQAMKKIFDDAYKSQLSCVVVDDIERLLDYVPIGPRFSNLVLQALLVLLKKAP
          IKICSP.KMIGF.ET.KCQAMKKIFDDAYKSQLSCVVVDDIERLLDYV.IGPRFSNLVLQALLV.LKKAP
Retrocopy IKICSPNKMIGFYETCKCQAMKKIFDDAYKSQLSCVVVDDIERLLDYVAIGPRFSNLVLQALLVVLKKAP

Parental  PQGRKLLIIGTTSRKDVLQEMEMLHAFSTTIHVPNIATGEQLLEALELLGNFKDKERTTISQQVKGKKVW
          PQG.KLLIIGTTSR.DVLQEMEML.AFSTTIHVPNIATGEQLLEALELLGNF.DKE.TTIS.QVKGKKVW
Retrocopy PQGCKLLIIGTTSRIDVLQEMEMLNAFSTTIHVPNIATGEQLLEALELLGNFNDKEHTTIS-QVKGKKVW

Parental  IGIKKLLMLIEMSLQMDPEYRVKKFLALLREEGASPLDFE
          .GIKKLLMLIEMSLQMDP.YRVKKFLALLREEGASPLDFE
Retrocopy AGIKKLLMLIEMSLQMDPDYRVKKFLALLREEGASPLDFE

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	18.75 RPM	338.94 RPM
SRP017611_kidney	1.15 RPM	30.46 RPM
SRP017611_liver	0.48 RPM	11.62 RPM
SRP040447_lung	0.68 RPM	30.82 RPM
SRP040447_skeletal_muscle	0.18 RPM	8.80 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_118 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_118 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.

---

Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000009391	1 retrocopy	retro_cpor_118 ,