RetrogeneDB ID: retro_cpor_889

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_32:4718636..4719281(+)
• Located in intron of: ENSCPOG00000003305

Retrocopy information

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

Parental gene information

• Parental gene symbol: SMS
• Ensembl ID: ENSCPOG00000006176
• Aliases: None
• Description: None

Sequence

>retro_cpor_889
GCTGATGGTGGGACCATTCTAAAACGTCTACAGTCCATTTTCCAGGAACAGAGCATGGTGGAGTCAGTGCATACCTGGCA
GGACCATGGCCCCCTAGCAACCCAAATAATCAAAAATGGCAGTTTTGCCAATTTAAGAAATTATCTGCATGGATTGGTGT
TGCTGGATCTTCAGAGTTATGACCCCCAGGGTAAAGAAGAAATTGATAATTTTTTGAACAAAGTACAAGAGAGAATGAAA
GAACTGAATCAGGTCAGTATTGGGCTGGTGAAGTATTTGCCAACCATAGTTCAAGGTTGGGTTGTGGACAGATCCTGGCC
TATAGCTGGTGGGCCTCTGGTTGAGTACGACATAGATAAAGTAGTACACGATGAAGACGCACCTATCAGAATGTTAAGAT
TCTGCACTTGAAGCAATTTGGAAATATTCTCAGCCTTAGTGGGGATGTTAATTTGGCAGAGAGAGATTTGGCATATACCT
GGGGCCATCATGGGCAGTGGCAAAGAAGATTACACTGGCAAAGACCTACTGATTCTGGGAGGTGGAGATGGAGGAATATT
ATGAGAAATAGTCAAACTGAAACCAAAGATGGTCACTATGATAGAGGCTGACCAAGTGGTGATTGATGCATGTAAGAAAT
ACATG

Alignment

ORF - retro_cpor_889 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.37 %
• Parental protein coverage: 60.61 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ADGETILKGLQSIFQEQGMAESVHTWQDHGYLATYTNKNGSFANLRIYPHGLVLFDLQSYDSDSQGKEEI
          ADG.TILK.LQSIFQEQ.M.ESVHTWQDHG.LAT...KNGSFANLR.Y.HGLVL.DLQSYD...QGKEEI
Retrocopy ADGGTILKRLQSIFQEQSMVESVHTWQDHGPLATQIIKNGSFANLRNYLHGLVLLDLQSYDP--QGKEEI

Parental  DNLLNKVEERMKELSQASIGRVKRLPTIVRGGAIDRYWPTADGRLVEYDIDEVVYDEDSP-YQNIKILHS
          DN.LNKV.ERMKEL.Q.SIG.VK.LPTIV.G...DR.WP.A.G.LVEYDID.VV.DED.P.YQN.KILH.
Retrocopy DNFLNKVQERMKELNQVSIGLVKYLPTIVQGWVVDRSWPIAGGPLVEYDIDKVVHDEDAP<YQNVKILHL

Parental  KQFGNILILSGDVNLAESDLAYT-RAIMGSGKEDYTGKDVLILGGGDGGILCEIVKLKPKMVTMVEIDQM
          KQFGNIL.LSGDVNLAE.DLAYT..AIMGSGKEDYTGKD.LILGGGDGGIL.EIVKLKPKMVTM.E.DQ.
Retrocopy KQFGNILSLSGDVNLAERDLAYT>GAIMGSGKEDYTGKDLLILGGGDGGIL*EIVKLKPKMVTMIEADQV

Parental  VIDACKKYM
          VIDACKKYM
Retrocopy VIDACKKYM

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	18.35 RPM
SRP017611_kidney	0.00 RPM	23.66 RPM
SRP017611_liver	0.04 RPM	21.46 RPM
SRP040447_lung	0.00 RPM	26.99 RPM
SRP040447_skeletal_muscle	0.00 RPM	18.58 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_889 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_889 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 16 parental genes, and 46 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013284	3 retrocopies	retro_cfam_1076, retro_cfam_1995, retro_cfam_613,
Callithrix jacchus	ENSCJAG00000033933	1 retrocopy	retro_cjac_518,
Cavia porcellus	ENSCPOG00000006176	2 retrocopies	retro_cpor_729, retro_cpor_889 ,
Echinops telfairi	ENSETEG00000010098	2 retrocopies	retro_etel_1066, retro_etel_1540,
Homo sapiens	ENSG00000102172	5 retrocopies	retro_hsap_243, retro_hsap_3168, retro_hsap_3193, retro_hsap_3611, retro_hsap_4826,
Gorilla gorilla	ENSGGOG00000003123	3 retrocopies	retro_ggor_1335, retro_ggor_2437, retro_ggor_3009,
Microcebus murinus	ENSMICG00000000192	3 retrocopies	retro_mmur_1421, retro_mmur_1484, retro_mmur_699,
Myotis lucifugus	ENSMLUG00000013185	3 retrocopies	retro_mluc_471, retro_mluc_530, retro_mluc_92,
Macaca mulatta	ENSMMUG00000020392	2 retrocopies	retro_mmul_2003, retro_mmul_2574,
Monodelphis domestica	ENSMODG00000007897	1 retrocopy	retro_mdom_412,
Mus musculus	ENSMUSG00000071708	6 retrocopies	retro_mmus_2162, retro_mmus_2170, retro_mmus_2837, retro_mmus_3502, retro_mmus_3628, retro_mmus_994,
Nomascus leucogenys	ENSNLEG00000009955	4 retrocopies	retro_nleu_1664, retro_nleu_2200, retro_nleu_2208, retro_nleu_2755,
Oryctolagus cuniculus	ENSOCUG00000006016	2 retrocopies	retro_ocun_1458, retro_ocun_1918,
Pongo abelii	ENSPPYG00000020182	4 retrocopies	retro_pabe_2649, retro_pabe_2810, retro_pabe_3752, retro_pabe_38,
Rattus norvegicus	ENSRNOG00000007688	2 retrocopies	retro_rnor_1934, retro_rnor_938,
Tupaia belangeri	ENSTBEG00000012109	3 retrocopies	retro_tbel_1630, retro_tbel_1893, retro_tbel_3570,