RetrogeneDB ID: retro_cpor_1448

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_851:28311..28690(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHIC2
• Ensembl ID: ENSCPOG00000024493
• Aliases: None
• Description: None

Sequence

>retro_cpor_1448
CACGTCACCATATTTGGTTTAAGCAACAAATTCAAATCTGAATTTCCTTCTTCACTAACTGGAAAAGTCACTCTTGAAGA
ATTTAAAGCCAGCATCCACAGAGTTAATAAGCTGTCTGAAGAAGAAGCTTCCTGTGTATAGACGTGGCTACTTCGGACGG
CCTTTGTTGTTGCTGCTCTTTAGGTTGCAGGATGTGGCCAGTTATTTAGCTCAGGAAAAGGGCACGAAGATGGACTGGGA
AGTTATTAGAGTGGAAAAACAACAGGTTTCACCACTAGGTGTGCTTACGCTGCAACCTGAGCAAAAGGATATGTGAACCG
GAAACTTGGTGGAATATGACATCCTCATAAAATGTTTACCAAAGACGCCGAGTTTTCAA

Alignment

ORF - retro_cpor_1448 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.47 %
• Parental protein coverage: 76.97 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  HVTVFGLSNKFESEFPSSLTGKVAPEEFKASINRVN-SCLKKSLPVNVR-WLLCGC-LCCCCTLGCSMWP
          HVT.FGLSNKF.SEFPSSLTGKV..EEFKASI.RVN.SCLKK.LPV..R.WLL....LCCCC.LGC.MWP
Retrocopy HVTIFGLSNKFKSEFPSSLTGKVTLEEFKASIHRVN>SCLKKKLPVYRR<WLLRTA<LCCCCSLGCRMWP

Parental  VICLSKRTRRSIEKLLEWENNRLYHKLCLHWRLSKRKCE-TNNMMEYVILIEFLPKTPIFR
          VI.L.KR.RR...KLLEW.NNR..H..CL...LSKR.CE.T.N..EY.ILI..LPKTP.F.
Retrocopy VI*LRKRARRWTGKLLEWKNNRFHH*VCLRCNLSKRICE<TGNLVEYDILIKCLPKTPSFQ

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	0.06 RPM	2.19 RPM
SRP017611_kidney	0.00 RPM	2.93 RPM
SRP017611_liver	0.00 RPM	1.78 RPM
SRP040447_lung	0.00 RPM	6.99 RPM
SRP040447_skeletal_muscle	0.00 RPM	2.61 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1448 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1448 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
Cavia porcellus	ENSCPOG00000024493	1 retrocopy	retro_cpor_1448 ,
Latimeria chalumnae	ENSLACG00000006603	1 retrocopy	retro_lcha_22,
Loxodonta africana	ENSLAFG00000012248	1 retrocopy	retro_lafr_953,
Macaca mulatta	ENSMMUG00000006382	1 retrocopy	retro_mmul_1372,