RetrogeneDB ID: retro_cpor_723

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_25:20347444..20347825(+)
• Located in intron of: ENSCPOG00000005924

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHRAC1
• Ensembl ID: ENSCPOG00000010427
• Aliases: None
• Description: None

Sequence

>retro_cpor_723
ATGGCACCTGTGCCCTTAGGCAATGGCAAGTGTAGGGAGCTGAGTCTCTGGTTGTTTCTCTGTCTTTTATCCTGCTCATC
ATAAAGAGTTTCCCTGAACTGTCAGGCTTCAACCAAGAGGTTCTGGTGATCCCGAAAAAGCCACAGATCTCTTTGTTCTG
TATGGCACCACCGCTTCCTGCAGACATGGCCTTGGAAAAGAAAAGAAAGCACTGACTAGCAGTGATTTAGCAAATATTCG
AGGGGACCAGAAACTTTTCCATTTCTTGCAAATGTTACCGAGGAAGGTTTTAGATAGTAGTACCTGAAAATGCTTAAAGA
GGAGAGGGCAAAAGACCAAGTAAGCCCTGGTGATATAAGTGATGATGACGAAGCTGAGTCC

Alignment

ORF - retro_cpor_723 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.55 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MADVAVGKDKCGEQRL-VSLPLSRIRVIMKSSPEVSSINQEALVLTAK-ATELFVQYLATYSYRHGSGKE
          MA.V..G..KC.E..L.....LS.I..I.KS.PE.S..NQE.LV...K.AT.LFV.Y..T.S.RHG.GKE
Retrocopy MAPVPLGNGKCRELSL<LVVSLSFILLIIKSFPELSGFNQEVLVIPKK<ATDLFVLYGTTASCRHGLGKE

Parental  RKALTYSDLANTAEESETFQFLADILPKKILASK-YLKMLKEKREDDEANDGEESDDDEAES
          .KALT.SDLAN.......F.FL...LP.K.L.S..YLKMLKE.R..D....G..SDDDEAES
Retrocopy KKALTSSDLANIRGDQKLFHFL-QMLPRKVLDSS<YLKMLKEERAKDQVSPGDISDDDEAES

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	4.03 RPM
SRP017611_kidney	0.00 RPM	4.29 RPM
SRP017611_liver	0.00 RPM	1.22 RPM
SRP040447_lung	0.00 RPM	7.16 RPM
SRP040447_skeletal_muscle	0.00 RPM	6.74 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_723 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_723 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 7 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005017	1 retrocopy	retro_amel_1736,
Cavia porcellus	ENSCPOG00000010427	5 retrocopies	retro_cpor_1545, retro_cpor_721, retro_cpor_722, retro_cpor_723 , retro_cpor_724,
Loxodonta africana	ENSLAFG00000001188	1 retrocopy	retro_lafr_932,
Monodelphis domestica	ENSMODG00000000756	2 retrocopies	retro_mdom_1379, retro_mdom_355,
Ochotona princeps	ENSOPRG00000008780	2 retrocopies	retro_opri_636, retro_opri_726,
Pan troglodytes	ENSPTRG00000020621	1 retrocopy	retro_ptro_2764,
Ictidomys tridecemlineatus	ENSSTOG00000008105	1 retrocopy	retro_itri_358,