RetrogeneDB ID: retro_cpor_1385

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_79:7507911..7508357(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TRIM44
• Ensembl ID: ENSCPOG00000011263
• Aliases: None
• Description: None

Sequence

>retro_cpor_1385
CAGCTCATCTGCGTGCTGTGTGCAGTCATTTTGGTGCACCAAGGCCAAAAGCTATCTATTCTACATGAAACCTTCTAACA
ACTAACAAGCAAAGACTAGGTGGACTAAAGCCTACTATGATAGAGCTGCTGGAAAGGCTAAAGCTCAAGAGCTCAGATCT
TAAAGTAACTTGGAACCAGATAAAGGTATTTATACAGAAAAATTTTAAAATGATCAGAAAGTTATTACTGATGAGGAGTA
AAAGTCCCTTCACCTAGTGGACACCCATGAAGCAATAGCCATGGCTAATGTGATGAAGATATTTGGGACATGCAATGGCA
CACAGAATGGTTGATGACTCAGATGGCCCAGGCCTAGGAACAACTTGATACCTCTAATGAATAGCTGAGCCAAAGACAGA
AAGCAATGAAGAAAGACCCAGTGTTGCCAGTGAAGAACAGGCAACA

Alignment

ORF - retro_cpor_1385 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.64 %
• Parental protein coverage: 57.92 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  QLICVLCPVIGAHQGHQLSTLDEAFEELRSKD-SGGLKAAMIELVERLKFKSSDPKVTRDQMKVFIQQEF
          QLICVLC.VI..HQG..LS.L.E.F..L.SKD..GGLK..MIEL.ERLK.KSSD.KVT..Q.KVFIQ..F
Retrocopy QLICVLCAVILVHQGQKLSILHETF*QLTSKD<LGGLKPTMIELLERLKLKSSDLKVTWNQIKVFIQKNF

Parental  KKV-QKVIADEEQKALHLVDIQEAMATAHVTEILA-DIQSHMDRLMTQMAQAKEQLDTSNE-SAEPKAEV
          K...QKVI.DEE.K.LHLVD..EA.A.A.V..I...D.Q.H...LMTQMAQA.EQLDTSNE..AEPK.E.
Retrocopy KMI<QKVITDEE*KSLHLVDTHEAIAMANVMKIFG<DMQWHTEWLMTQMAQA*EQLDTSNE<IAEPKTES

Parental  NENTHSGTSEEEDT
          NE...S..SEE..T
Retrocopy NEERPSVASEEQAT

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	20.71 RPM
SRP017611_kidney	0.00 RPM	10.05 RPM
SRP017611_liver	0.00 RPM	2.44 RPM
SRP040447_lung	0.00 RPM	10.95 RPM
SRP040447_skeletal_muscle	0.00 RPM	4.69 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1385 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1385 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000011263	1 retrocopy	retro_cpor_1385 ,
Ictidomys tridecemlineatus	ENSSTOG00000023760	1 retrocopy	retro_itri_1209,