RetrogeneDB ID: retro_sscr_954

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 7:117345551..117345815(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DSTN
• Ensembl ID: ENSSSCG00000007085
• Aliases: None
• Description: Sus scrofa destrin (actin depolymerizing factor) (DSTN), mRNA. [Source:RefSeq mRNA;Acc:NM_001004031]

Sequence

>retro_sscr_954
AAAAATTGTCGCTATGCTTTGTAGGATGCAAGCTTTGAAATCAAGGAATCGAGAAAAGTGGAGTTGATGGTTTTTTATGG
GCACCAGAAACTAGCACCTCTGAAAAGTAAAAAGATCTATGTGAGCTCCAAGGACACGACCAATGAGAAATTTCAAGCCA
TAAAACACGAATGTCAAGCAAATGATCCAGAAGACCTCAATTGGGCTTGAATTGCTGAAAAACTAGGTGGATCCATGATT
GTAGCTTTTGAAGGATGCCCTGTG

Alignment

ORF - retro_sscr_954 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.0 %
• Parental protein coverage: 53.66 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KDCRYALYDASFETKESRKEELMFF-LWAPE-LAPLKSKMIYASSKDAIKKKFQGIKHECQANGPEDLNR
          K.CRYAL.DASFE.KESRK.ELM.F.LWAPE.LAPLKSK.IY.SSKD....KFQ.IKHECQAN.PEDLN.
Retrocopy KNCRYAL*DASFEIKESRKVELMVF<LWAPE>LAPLKSKKIYVSSKDTTNEKFQAIKHECQANDPEDLNW

Parental  ACIAEKLGGSLIVAFEGCPV
          A.IAEKLGGS.IVAFEGCPV
Retrocopy A*IAEKLGGSMIVAFEGCPV

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
SRP014902_placenta	0.00 RPM	261.35 RPM
SRP014902_testis	0.00 RPM	103.11 RPM
SRP018288_heart	0.00 RPM	221.07 RPM
SRP018288_kidney	0.00 RPM	514.49 RPM
SRP018288_liver	0.00 RPM	88.27 RPM
SRP018288_lung	0.00 RPM	265.36 RPM
SRP018856_adipose	0.00 RPM	171.14 RPM
SRP035408_brain	0.00 RPM	313.70 RPM
SRP035408_liver	0.00 RPM	127.64 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_954 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_954 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_954 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
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,
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	ENSSSCG00000001959	2 retrocopies	retro_sscr_1198, retro_sscr_327,
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,