RetrogeneDB ID: retro_cpor_700

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_24:20576864..20577353(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DSTN
• Ensembl ID: ENSCPOG00000005573
• Aliases: None
• Description: None

Sequence

>retro_cpor_700
GCCTCAAGAGTGTGAGTTGCTGAGGAAGTGTGTTGCACTTTGTATGACATGAAAGTTCAAATGCTCCACACCAGAGGAAA
TCAAAAAAAGAAATAAGGCTGTCATTTTTTTTTTGTCTCAATGCAGACAAAAAAATGCATCATCATTGAAGAAGGCAAAG
AGATCTTGGTTAGAGATGTGGATGTGACCATCACCAATCCCCTGAAACCTGTTGTGGGGATGCTTCCTAGGAAGGACTGT
CGCTATGCCTTGCACTAGGCGAGCTTCTAGACTAAGGAGTCCAGGAAAGAAAAGCTGATGTTCTTTGTGTGGGCCTCGGA
ACTGGCCCACAAAAGAGTAAGATGATCTACACCAGCTCAGGGATACCACCAAACTGACTTTCCAAACCATGAAACAGGAG
TGTTAAGCAAAGGGCCAGAAGACCTCAACCTGGCTTGCATTGCCTTAAATCTGAGCAAGCCCATGCTTGCAGCCTTCAAA
GAGTGTCCA

Alignment

ORF - retro_cpor_700 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.48 %
• Parental protein coverage: 98.79 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ASGVQVADEVCRIFYDMKVRKCSTPEEIKKRKKAVIFCLSAD-KKCIIVEEGKEILVGDVGVTITDPFKH
          AS.V.VA.EVC...YDMKV....T....KK.........S...KKCII.EEGKEILV.DV.VTIT.P.K.
Retrocopy ASRV*VAEEVCCTLYDMKVQMLHTRGNQKKK*GCXXXXVSMQTKKCIIIEEGKEILVRDVDVTITNPLKP

Parental  FVGMLPEKDCRYALYDASFETKESRKEELMFFLWAPELA-PLKSKMIYASS-KDAIKKKFQGIKHECQA-
          .VGMLP.KDCRYAL..ASF.TKESRKE.LMFF.WA.ELA.P.KSKMIY.SS..D..K..FQ..K.EC.A.
Retrocopy VVGMLPRKDCRYALH*ASF*TKESRKEKLMFFVWASELA<PQKSKMIYTSS<RDTTKLTFQTMKQEC*A<

Parental  NGPEDLNRACIAEKLGGSLIVAFEGCP
          .GPEDLN.ACIA..L......AF..CP
Retrocopy KGPEDLNLACIALNLSKPMLAAFKECP

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	83.11 RPM
SRP017611_kidney	0.00 RPM	128.03 RPM
SRP017611_liver	0.00 RPM	125.05 RPM
SRP040447_lung	0.00 RPM	169.38 RPM
SRP040447_skeletal_muscle	0.00 RPM	44.46 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_700 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_700 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.

---

Parental genes homology:

Parental genes homology involve 21 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000015434	1 retrocopy	retro_btau_880,
Choloepus hoffmanni	ENSCHOG00000003110	5 retrocopies	retro_chof_1308, retro_chof_1656, retro_chof_1758, retro_chof_2297, retro_chof_72,
Cavia porcellus	ENSCPOG00000005573	2 retrocopies	retro_cpor_700 , retro_cpor_812,
Cavia porcellus	ENSCPOG00000008996	1 retrocopy	retro_cpor_1003,
Dasypus novemcinctus	ENSDNOG00000000934	1 retrocopy	retro_dnov_24,
Erinaceus europaeus	ENSEEUG00000011893	1 retrocopy	retro_eeur_529,
Homo sapiens	ENSG00000125868	1 retrocopy	retro_hsap_952,
Gorilla gorilla	ENSGGOG00000009007	1 retrocopy	retro_ggor_768,
Microcebus murinus	ENSMICG00000013687	1 retrocopy	retro_mmur_765,
Macaca mulatta	ENSMMUG00000013786	1 retrocopy	retro_mmul_782,
Mus musculus	ENSMUSG00000015932	1 retrocopy	retro_mmus_3314,
Nomascus leucogenys	ENSNLEG00000009679	1 retrocopy	retro_nleu_2458,
Oryctolagus cuniculus	ENSOCUG00000027456	1 retrocopy	retro_ocun_1891,
Ochotona princeps	ENSOPRG00000000976	2 retrocopies	retro_opri_1078, retro_opri_696,
Pongo abelii	ENSPPYG00000010727	1 retrocopy	retro_pabe_812,
Pan troglodytes	ENSPTRG00000013275	1 retrocopy	retro_ptro_659,
Pteropus vampyrus	ENSPVAG00000000420	1 retrocopy	retro_pvam_1275,
Rattus norvegicus	ENSRNOG00000005924	1 retrocopy	retro_rnor_1710,
Sus scrofa	ENSSSCG00000007085	1 retrocopy	retro_sscr_954,
Tupaia belangeri	ENSTBEG00000017634	8 retrocopies	retro_tbel_1206, retro_tbel_1977, retro_tbel_2425, retro_tbel_2880, retro_tbel_2881, retro_tbel_4020, retro_tbel_679, retro_tbel_851,
Tursiops truncatus	ENSTTRG00000007291	1 retrocopy	retro_ttru_1503,