RetrogeneDB ID: retro_cpor_63

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_4:28332592..28333675(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCPOG00000003132
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: PCMTD1
• Ensembl ID: ENSCPOG00000006593
• Aliases: None
• Description: None

Sequence

>retro_cpor_63
ATGGGCGGTGCTGTGAGTGCTGGTGAGGACAATGACGAACTGATCGATAATTTGAAGGAAGCACAGTATATACGGACAGA
ATTGGTGGAACAGGCCTTCAGAGCTATTGATCGAGCAGATTACTACCTGGAGGAGTTTAAAGAAAATGCCTACAAAGACT
TGGCGTGGAAGCATGGAAACATTCACCTCTCAGCCCCGTGCATCTACTCAGAAGTGATGGAGGCCCTGGATTTGCAGCCA
GGGCTTTCGTTTCTGAACTTGGGCAGTGGTACTGGATACCTCAGCTCCATGGTTGGCCTCATTTTAGGTCCTTTTGGTGT
GAACCATGGAGTGGAGCTTCATTCTGATGTGATAGAGTACGCAAAACAGAAACTGGACTTCTTCATCAGAACAAGTGACA
GCTTTGACAAGTTTGACTTCTGTGAACCCTCTTTTGTTACTGGCAATTGCCTGGAGATTTCTCCAGATTGTTCTCAGTAT
GATCGAGTGTACTGTGGGGCTGGTGTGCAGAAGGAACATGAGGAATACATGAAAAATCTTCTTAAAGTTGGAGGAATCCT
TGTCATGCCTCTGGAAGAGAAGTTGACCAAGATAACGCGCACAGGCCCTTCTGCTTGGGAAACGAAAAAGATTTTGGCTG
TTTCCTTTGCCCCTCTGGTCCAGCCCTGTCACTCAGAGTCAGGAAAGTCCAGACTTGTCCAGCTTCCACCACTTGCTGTA
CGCAGCCTCCAGGACTTGGCCCGCATTGCCATCCGGGGTACCATTAAAAAGATCATTCATCAGGAAGCTTTGAGCAAAAG
TGGAAATGGACTGAAGAACACTCCCAGATTTAAACGAAGGAGGGTCCGCCGCCGTCAAATGGAAACAATAGTCTTTTTGG
ACAAAGAAGTCTTTGCCAGTCGTATTTCCAACCCCTCTGACGACAACAGCTGTGAAGACTTGGAAGAGGAACGGAGGGAA
GAAGATAAAACTTCACTAGAAGCCAAGCCAGATCCTCCCGTGAACTTCCTGCGTCAGAAGGTCCTGAGCCTCCCTCTGCC
AGACCCCCTGAAATACTACTTGCTTTATTACAGAGAAAAATAA

Alignment

ORF - retro_cpor_63 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.39 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGGAVSAGEDNDDLIDNLKEAQYIRTERVEQAFRAIDRGDYYLEGYRDNAYKDLAWKHGNIHLSAPCIYS
          MGGAVSAGEDND.LIDNLKEAQYIRTE.VEQAFRAIDR.DYYLE....NAYKDLAWKHGNIHLSAPCIYS
Retrocopy MGGAVSAGEDNDELIDNLKEAQYIRTELVEQAFRAIDRADYYLEEFKENAYKDLAWKHGNIHLSAPCIYS

Parental  EVMEALKLQPGLSFLNLGSGTGYLSTMVGLILGPFGINHGIELHSDVVEYAKEKLESFIKNSDSFDKFEF
          EVMEAL.LQPGLSFLNLGSGTGYLS.MVGLILGPFG.NHG.ELHSDV.EYAK.KL..FI..SDSFDKF.F
Retrocopy EVMEALDLQPGLSFLNLGSGTGYLSSMVGLILGPFGVNHGVELHSDVIEYAKQKLDFFIRTSDSFDKFDF

Parental  CEPAFVVGNCLQIASDSHQYDRIYCGAGVQKDHENYMKILLKVGGILVMPIEDQLTQIMRTGQNTWESKN
          CEP.FV.GNCL.I..D..QYDR.YCGAGVQK.HE.YMK.LLKVGGILVMP.E..LT.I.RTG...WE.K.
Retrocopy CEPSFVTGNCLEISPDCSQYDRVYCGAGVQKEHEEYMKNLLKVGGILVMPLEEKLTKITRTGPSAWETKK

Parental  ILAVSFAPLVQPSKNDNGKPDSVGLPPCAVRNLQDLARIYIRRTLRNFINDEMQAK-GIPQRAPPKRKRK
          ILAVSFAPLVQP.....GK...V.LPP.AVR.LQDLARI.IR.T....I..E...K.G......P..KR.
Retrocopy ILAVSFAPLVQPCHSESGKSRLVQLPPLAVRSLQDLARIAIRGTIKKIIHQEALSKSGNGLKNTPRFKRR

Parental  RVKQR-INTYVFVGNQLIPQPLDSEEDEKMEEDNKEE-EEKDHSEAMKPEEPPQNLLREKIMKLPLPESL
          RV..R...T.VF..............D....ED..EE..E.D.........PP.N.LR.K...LPLP..L
Retrocopy RVRRRQMETIVFLDKEVFASRISNPSDDNSCEDLEEERREEDKTSLEAKPDPPVNFLRQKVLSLPLPDPL

Parental  KAYLTYFRDK
          K.YL.Y.R.K
Retrocopy KYYLLYYREK

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	5.35 RPM	28.18 RPM
SRP017611_kidney	4.71 RPM	103.85 RPM
SRP017611_liver	2.70 RPM	103.25 RPM
SRP040447_lung	2.75 RPM	55.28 RPM
SRP040447_skeletal_muscle	4.10 RPM	30.34 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_63 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_63 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000006593	1 retrocopy	retro_cpor_63 ,
Monodelphis domestica	ENSMODG00000009645	1 retrocopy	retro_mdom_640,
Oryctolagus cuniculus	ENSOCUG00000016958	2 retrocopies	retro_ocun_1571, retro_ocun_1682,