RetrogeneDB ID: retro_cpor_275

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_112:4235129..4235727(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPID
• Ensembl ID: ENSCPOG00000001046
• Aliases: None
• Description: None

Sequence

>retro_cpor_275
GAAAAACCTGCCAAACTGTACATTATTGCACAATGTGAAGACCAGAAAGAAGGTGATGGCTGGGGAACATTTCTAAAAGA
TAGCTCTGGTGACAGCCATCCAGATTTCCCTGAAGGTACAGATGTAAATTTAAAAGCTGTAGTTAAAATTGTATTACTAA
CAGAAGACTTAAACACTGAAAATACTTTTTTTAAATACCAGAACTGGGGACACGGCCATTACAAAATACACAGAGGTTTT
ATGATATGTGGATAGTTTAAAGGCAGTTACCTAGGAAGCAGACAGATGCAGGATGCAGTCTACAACCTTGAGCTGTGTGT
TAAATACTGGTGCTGATGGACTGGAGGCATCAGATTGGCAGGGAGCCAAATCTACAGTGATTTTTGAGGCTCCTACAACA
GACCATCAAACACCAAAGCACTGTGTCCTGGAGGATGAAAAGGACTGAAAGAATCTGACCTAGCACTGGCTGATCTTAAA
AAAGCACAAAAGATAGCACCAGAAGCTCAAGCCATCCAGGCAGAACTGCTCAAAGTCCAAGAAGAGATAACAGCACAAAA
AAGATAAAGAGGAGGCAGTATATGCCAAAATGTTTGCT

Alignment

ORF - retro_cpor_275 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.9 %
• Parental protein coverage: 54.32 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EKPAKLCVIAECGELKEGDDWGIFPKDGSGDCHPDFPEDSDVDFKDVDKILLITEDLKNLGNTFFKSQNW
          EKPAKL..IA.C...KEGD.WG.F.KD.SGD.HPDFPE..DV..K.V.KI.L.TEDL.N..NTFFK.QNW
Retrocopy EKPAKLYIIAQCEDQKEGDGWGTFLKDSSGDSHPDFPEGTDVNLKAVVKIVLLTEDL-NTENTFFKYQNW

Parental  -EMAIKKYRKVLRYVDSSKAILPEAAAPRLQPVALSCVLNIGACKLKLSDWQGAVDSCL-EALEMD-PSN
          ...AI.KY..VL.YVDS.KA...EA...R.Q...LSCVLN.GA..L..SDWQGA......EA...D.PSN
Retrocopy >DTAITKYTEVL*YVDSLKAVT*EADRCRMQSTTLSCVLNTGADGLEASDWQGAKSTVIFEAPTTD<PSN

Parental  TKALYRKAQGWQGLKEYDQALADLKKAQEIAPEDKAIQAELLKVKQKIKAQ-KDKEKAVYAKMFA
          TKAL.....G..GLKE.D.ALADLKKAQ.IAPE..AIQAELLKV...I.AQ.KDKE.AVYAKMFA
Retrocopy TKALC--PGG*KGLKESDLALADLKKAQKIAPEAQAIQAELLKVQEEITAQ>KDKEEAVYAKMFA

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	34.86 RPM
SRP017611_kidney	0.00 RPM	31.30 RPM
SRP017611_liver	0.00 RPM	42.53 RPM
SRP040447_lung	0.00 RPM	21.01 RPM
SRP040447_skeletal_muscle	0.00 RPM	41.92 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_275 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_275 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 5 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000001046	2 retrocopies	retro_cpor_275 , retro_cpor_436,
Echinops telfairi	ENSETEG00000012655	2 retrocopies	retro_etel_10, retro_etel_633,
Felis catus	ENSFCAG00000028926	2 retrocopies	retro_fcat_494, retro_fcat_559,
Macaca mulatta	ENSMMUG00000017768	2 retrocopies	retro_mmul_281, retro_mmul_348,
Rattus norvegicus	ENSRNOG00000027408	1 retrocopy	retro_rnor_188,