RetrogeneDB ID: retro_cpor_1537

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_95:4577090..4578539(+)
• Located in intron of: ENSCPOG00000008720

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCDC41
• Ensembl ID: ENSCPOG00000008997
• Aliases: None
• Description: None

Sequence

>retro_cpor_1537
AGACTGGAGAAAGATAAAGAAGAGCTACATAACCGGCTGCTCGCTGTTGATCCCACAAGACACATGAAGCGAGTGGAGCA
GCTTCTTCAAGAGAAAGCCCATTTGGGTCAGAAATTAAAAGGGTTAGAGACCGAGGTAGCAGAACTAAGGGCTGAAAAAG
AGAATTCTGGTGCTCAGGTAGAAAACGTCCAAAGAATACAGGTGTGGCAGTTGGCTGAGATGCAGGCTATAGTCAGGTCC
CTGGAGACTGAAAAACAATCGGTCAAGTTGCAGGCTGAACGCCTGGAAAAAGAGCTGCAATCAAGCAATGAACAAAATAT
GTCTTTGATCAGTAAATTGCATAAAGCTGACTAAGAAATAAGCACACTGACCAGTACAATAAAGGAGCTGAAACACTCAA
AGAAGCTAGAAATAACAGACATCAAACTGGAGGCAGCAAGAGCTAAGAGTGAGCTAGAAAGAGAAAGAAATAAGATTCAA
AGTGAACTGGATAGCCTACAGTCAGACAATGAAATTCTCAAATCAGCTGTTGAACACCACAAAACGCTCTTAGTACAAAA
AGATCGTGAGTTAGTATGTAAAGTACAAGCTGCCAAGGAAGAAGGTTATCAGAAGCTTGTGGTATTACAAGATGAAAAGC
TGGAGCTTGAGAACAGATTAGCAGATTTAGAGAAAATGAAAGTGGAGCACGATATTTGGAGGCAATCTGAGAAGGATCAG
CACGAGGAGAAACTGCGGGCGGGCTTCACAGATGGCAGAGGAGTCGGCCCGAAGGGAACTTCAGAGTATTAGGTTAAAAC
TTCAGCAACAGATTGTGAATATTGAAAATGCTGAGAAAGAAAAAAATAAAAATTCTGATCTGAAACAGCAAATCAGTACC
TTGCAGATCCAAGTAACCTCACTGACTCAGTCTGAGAATGAACTGCTGAATTCAAACCAAATGCTGAAGGAAATGGTGGA
GAGGTTAAAGCAAGAATGCCGTCACTTAAGAAGCCAAGCGGAAAAACTACAGCTAGAAGTTGAAAAGACATTGGAAGAGA
AACAGATTCAGTGGTTGGAAGAAAAGCACAAGCTTCAAGAACATATCACAGACCGAGAAGAAAAGTATAATCAGGCGAAA
GAGAAACTACAGAGAGCTGCAACTGCCCAGAAAAAGAGAAAGTCTCTTCATGAAAACAAACTGAAGCGCCTGCAAGAAAA
GGTGGATGTGTTGGAGGCCAAGAGAGAAGAGTTAGAAGCCGAGAATCAGGTGCTGACCAGACAAAATGTTCCATTTGAAG
AATATACAAGGCTTCAGAAAAGACTAAAGGATGTACAGAGAAGACATAATGAATTTCGAAGTCTGATTTTGGTCCCTAAC
ATTCCTCCACCAACATCCATCAATCCCGTTAGCTGTCAGGCGTCAGCCATGGCCCCGGGCGTGGAGCTCTGCTTCCCCCT
CTCGTGCAG

Alignment

ORF - retro_cpor_1537 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.2 %
• Parental protein coverage: 68.86 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RLEKDKEELHSRLLAVDPTRHMKRVEQLLQEKAHLGQKLKGLETEVAELRAEKENSGAQVESVQRIQVRQ
          RLEKDKEELH.RLLAVDPTRHMKRVEQLLQEKAHLGQKLKGLETEVAELRAEKENSGAQVE.VQRIQV.Q
Retrocopy RLEKDKEELHNRLLAVDPTRHMKRVEQLLQEKAHLGQKLKGLETEVAELRAEKENSGAQVENVQRIQVWQ

Parental  LAEMQATVRSLEAEKQSVKLQAERLEKELQSTSEQNMSLISKLHKADQEISTLTSTIKELKHSKKLEITD
          LAEMQA.VRSLE.EKQSVKLQAERLEKELQS..EQNMSLISKLHKAD.EISTLTSTIKELKHSKKLEITD
Retrocopy LAEMQAIVRSLETEKQSVKLQAERLEKELQSSNEQNMSLISKLHKAD*EISTLTSTIKELKHSKKLEITD

Parental  IKLEAARAKSELERERNKIQSELDGLQSDNEILKSAVEHHKTLLVEKDRELVRKVQAAKEEGYQKLVVLQ
          IKLEAARAKSELERERNKIQSELD.LQSDNEILKSAVEHHKTLLV.KDRELV.KVQAAKEEGYQKLVVLQ
Retrocopy IKLEAARAKSELERERNKIQSELDSLQSDNEILKSAVEHHKTLLVQKDRELVCKVQAAKEEGYQKLVVLQ

Parental  DEKLELENRLADLEKMKVEHDIWRQSEKDQHEEKLRA-SQMAEEAARR-ELQSIRLKLQQQIVNIENAEK
          DEKLELENRLADLEKMKVEHDIWRQSEKDQHEEKLRA......E...R.ELQSIRLKLQQQIVNIENAEK
Retrocopy DEKLELENRLADLEKMKVEHDIWRQSEKDQHEEKLRA>ASQMAEESARRELQSIRLKLQQQIVNIENAEK

Parental  EKNENSDLKQQISSLQIQVTSLTQSENELLNSNQMLKEMVERLKQECRHLKSQAEKLQLEVEKTLEEKQI
          .....SDLKQQIS.LQIQVTSLTQSENELLNSNQMLKEMVERLKQECRHL.SQAEKLQLEVEKTLEEKQI
Retrocopy XXXXXSDLKQQISTLQIQVTSLTQSENELLNSNQMLKEMVERLKQECRHLRSQAEKLQLEVEKTLEEKQI

Parental  QWLEEKHKLQERITDREEKYNQAKEKLQRAATAQKKRKSLHENKLKRLQEKVDVLEAKREELEAENQVLT
          QWLEEKHKLQE.ITDREEKYNQAKEKLQRAATAQKKRKSLHENKLKRLQEKVDVLEAKREELEAENQVLT
Retrocopy QWLEEKHKLQEHITDREEKYNQAKEKLQRAATAQKKRKSLHENKLKRLQEKVDVLEAKREELEAENQVLT

Parental  RQNVPFEEYTRLQKRLKDIQRRHNEFRSLILVPNIPPPASINPVSFQASAMAPGVELCF-PPLVQ
          RQNVPFEEYTRLQKRLKD.QRRHNEFRSLILVPNIPPP.SINPVS.QASAMAPGVELCF.PPLVQ
Retrocopy RQNVPFEEYTRLQKRLKDVQRRHNEFRSLILVPNIPPPTSINPVSCQASAMAPGVELCF<PPLVQ

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	0.12 RPM	11.91 RPM
SRP017611_kidney	0.00 RPM	6.49 RPM
SRP017611_liver	0.13 RPM	6.96 RPM
SRP040447_lung	0.03 RPM	12.26 RPM
SRP040447_skeletal_muscle	0.05 RPM	15.22 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1537 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1537 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009750	1 retrocopy	retro_amel_1376,
Callithrix jacchus	ENSCJAG00000002860	1 retrocopy	retro_cjac_1662,
Cavia porcellus	ENSCPOG00000008997	1 retrocopy	retro_cpor_1537 ,
Rattus norvegicus	ENSRNOG00000007859	1 retrocopy	retro_rnor_384,