RetrogeneDB ID: retro_sscr_296

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 12:47820465..47820702(+)
• Located in intron of: ENSSSCG00000017791

Retrocopy information

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

Parental gene information

• Parental gene symbol: COX7A2
• Ensembl ID: ENSSSCG00000004480
• Aliases: None
• Description: Sus scrofa COX7A2 protein (COX7A2), mRNA. [Source:RefSeq mRNA;Acc:NM_001097484]

Sequence

>retro_sscr_296
TTACTGCGGACCCTGCTGGTTCTGTGTCAGATTGCCCAGAAGACAGTAAGTCCTCCTTCACACAGCCAGTTTGAAAATAA
AGTTCCATAGAAACAAAAGCTATTTCTAGAGTCTAATAGAATTCCACTGCATCTAAAGGGTGGAGTAGCAGGTGCCCTCC
TGTATAGTGCCACCATGATTCTTAGAGTTGGTTGCCGTCTATATCAGCTGGCTGTGGCTTCATTTCCCAGGAAGCAG

Alignment

ORF - retro_sscr_296 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.2 %
• Parental protein coverage: 98.8 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLRNLLALRQIAQRTISTASRRQLENKVAEKQKLFQEDNGIPVHLKGGIGDAFLYRATMILTVGGTAYTI
          .LR.LL.L.QIAQ.T.S..S..Q.ENKV..KQKLF.E.N.IP.HLKGG...A.LY.ATMIL.VG......
Retrocopy LLRTLLVLCQIAQKTVSPPSHSQFENKVP*KQKLFLESNRIPLHLKGGVAGALLYSATMILRVG---CRL

Parental  YQLAVASLPKKQ
          YQLAVAS.P.KQ
Retrocopy YQLAVASFPRKQ

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	0.13 RPM	56.41 RPM
SRP014902_testis	0.00 RPM	56.72 RPM
SRP018288_heart	0.03 RPM	77.04 RPM
SRP018288_kidney	0.00 RPM	177.31 RPM
SRP018288_liver	0.00 RPM	57.41 RPM
SRP018288_lung	0.10 RPM	14.97 RPM
SRP018856_adipose	0.00 RPM	91.69 RPM
SRP035408_brain	0.03 RPM	35.16 RPM
SRP035408_liver	0.00 RPM	23.57 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_296 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_296 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_296 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 46 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014453	1 retrocopy	retro_amel_723,
Bos taurus	ENSBTAG00000005096	6 retrocopies	retro_btau_1071, retro_btau_1230, retro_btau_1436, retro_btau_1469, retro_btau_1703, retro_btau_507,
Callithrix jacchus	ENSCJAG00000010305	2 retrocopies	retro_cjac_1523, retro_cjac_4129,
Cavia porcellus	ENSCPOG00000007404	2 retrocopies	retro_cpor_1300, retro_cpor_527,
Dipodomys ordii	ENSDORG00000015425	2 retrocopies	retro_dord_701, retro_dord_790,
Homo sapiens	ENSG00000112695	2 retrocopies	retro_hsap_1434, retro_hsap_2961,
Gorilla gorilla	ENSGGOG00000005865	2 retrocopies	retro_ggor_1104, retro_ggor_2051,
Loxodonta africana	ENSLAFG00000002313	1 retrocopy	retro_lafr_811,
Microcebus murinus	ENSMICG00000015747	3 retrocopies	retro_mmur_381, retro_mmur_548, retro_mmur_799,
Nomascus leucogenys	ENSNLEG00000004949	2 retrocopies	retro_nleu_1412, retro_nleu_735,
Pongo abelii	ENSPPYG00000016781	2 retrocopies	retro_pabe_1187, retro_pabe_2456,
Pteropus vampyrus	ENSPVAG00000010401	6 retrocopies	retro_pvam_1144, retro_pvam_1408, retro_pvam_443, retro_pvam_57, retro_pvam_656, retro_pvam_741,
Rattus norvegicus	ENSRNOG00000042903	1 retrocopy	retro_rnor_52,
Sus scrofa	ENSSSCG00000004480	1 retrocopy	retro_sscr_296 ,
Ictidomys tridecemlineatus	ENSSTOG00000002536	5 retrocopies	retro_itri_435, retro_itri_464, retro_itri_608, retro_itri_890, retro_itri_892,
Tupaia belangeri	ENSTBEG00000007294	7 retrocopies	retro_tbel_1177, retro_tbel_178, retro_tbel_3617, retro_tbel_4102, retro_tbel_4330, retro_tbel_738, retro_tbel_781,
Tursiops truncatus	ENSTTRG00000007874	1 retrocopy	retro_ttru_669,