RetrogeneDB ID: retro_cpor_1111

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_47:9954373..9954677(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000005452
• Aliases: None
• Description: None

Sequence

>retro_cpor_1111
GTTAGGATCTCTGTTCCTGCTTCCAATAATATGCAGTCTGGGGTGAACAACACGAAGAAATGGAAAATGGAGTTTGATAT
CAGGGAGCGATGGGAAAACCCTTTGATGGATTGGACATCAACAGCTTATTCCTTGTCCAACATGGTTCTAACCTCTGGTA
CCAAAGAAGATGCAGTTGCCTTTTCAGAAAAAAAGAAAAATGGATGGAACTATGACATTGACGAAAGGAAAGTTCCCAAA
GCTAAGTCTGAATCTTAACGGTGCAAACTCTTCTTGGGACAAAAGAGCAAGAGTATCCACAAAA

Alignment

ORF - retro_cpor_1111 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.49 %
• Parental protein coverage: 80.49 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VRIFVPARNNMQSGVNNTKKWKMEFDTRERWENPLMGWASTADPLSNMVLTFSTKEDAVAFA--EKNGWS
          VRI.VPA.NNMQSGVNNTKKWKMEFD.RERWENPLM.W.STA..LSNMVLT..TKEDAVAF......GW.
Retrocopy VRISVPASNNMQSGVNNTKKWKMEFDIRERWENPLMDWTSTAYSLSNMVLTSGTKEDAVAFSXXXXXGWN

Parental  YDVEERKVPKPKSKS-YGANFSWNKRTRVSTK
          YD..ERKVPK.KS.S..GAN.SW.KR.RVSTK
Retrocopy YDIDERKVPKAKSES>NGANSSWDKRARVSTK

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	15.76 RPM
SRP017611_kidney	0.10 RPM	35.59 RPM
SRP017611_liver	0.00 RPM	25.59 RPM
SRP040447_lung	0.00 RPM	15.69 RPM
SRP040447_skeletal_muscle	0.00 RPM	58.79 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1111 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1111 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 11 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000005452	1 retrocopy	retro_cpor_1111 ,
Erinaceus europaeus	ENSEEUG00000015851	3 retrocopies	retro_eeur_133, retro_eeur_30, retro_eeur_347,
Macropus eugenii	ENSMEUG00000001362	1 retrocopy	retro_meug_651,
Microcebus murinus	ENSMICG00000015138	1 retrocopy	retro_mmur_355,
Monodelphis domestica	ENSMODG00000019465	1 retrocopy	retro_mdom_1227,
Mus musculus	ENSMUSG00000021764	1 retrocopy	retro_mmus_3372,
Ochotona princeps	ENSOPRG00000013784	1 retrocopy	retro_opri_508,
Procavia capensis	ENSPCAG00000013496	1 retrocopy	retro_pcap_268,
Pongo abelii	ENSPPYG00000015455	1 retrocopy	retro_pabe_193,
Sus scrofa	ENSSSCG00000016893	1 retrocopy	retro_sscr_999,
Tupaia belangeri	ENSTBEG00000004605	1 retrocopy	retro_tbel_2068,