RetrogeneDB ID: retro_sscr_131

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 1:196815171..196815539(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VBP1
• Ensembl ID: ENSSSCG00000012811
• Aliases: None
• Description: von Hippel-Lindau binding protein 1 [Source:HGNC Symbol;Acc:12662]

Sequence

>retro_sscr_131
TTGGGAGAAGTGGCCACAGGGAATGGGTGGCAGCTCCACCTAGGGATTCCTGAGGTTTGTTTTGGTGGAAGATGTAGATT
TCTTCATGAAACAGCCTGGTAATGAGAATCCAATTACAGCACTAAAGAAGCTGGATGAACAGTACCAGAAGAAGTATAAA
TTTATGAAATTCAAACCTGCTCAAAAGCAAAGGAGGATAAAAGGTCATATTCCTGAAATAAAGCAGACTTTAGAACTTCT
AAAATAGATGCAGAGATAAAAAAAGAGAGTCCATCAATTCACTGGAGACCAGATTCTTACTGGCAGATGAACTGTATTGC
AAAGCTTCAGTTCCTCCTATCAATAAAGTGTGTCTGTGGTTGGTGGCA

Alignment

ORF - retro_sscr_131 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.81 %
• Parental protein coverage: 60.91 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LGEVAAGNGRRLHLGIPEAVF-VEDVDSFMKQPGNETADTVLKKLDEQYQK-YKFMELNLAQKKRRLKGQ
          LGEVA.GNG..LHLGIPE..F.VEDVD.FMKQPGNE...T.LKKLDEQYQK.YKFM....AQK.RR.KG.
Retrocopy LGEVATGNGWQLHLGIPEVCF>VEDVDFFMKQPGNENPITALKKLDEQYQKKYKFMKFKPAQKQRRIKGH

Parental  IPEIKQTLEILKYMQK-KK-ESTSSLETRFLLADNLYCKASVPPTDKVCLWLGA
          IPEIKQTLE.LK.MQ..KK.ES..SLETRFLLAD.LYCKASVPP..KVCLWL.A
Retrocopy IPEIKQTLELLK*MQR>KKRESINSLETRFLLADELYCKASVPPINKVCLWLVA

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	4.38 RPM
SRP014902_testis	0.00 RPM	13.44 RPM
SRP018288_heart	0.00 RPM	48.43 RPM
SRP018288_kidney	0.00 RPM	37.53 RPM
SRP018288_liver	0.00 RPM	27.50 RPM
SRP018288_lung	0.00 RPM	16.50 RPM
SRP018856_adipose	0.00 RPM	15.09 RPM
SRP035408_brain	0.00 RPM	30.55 RPM
SRP035408_liver	0.00 RPM	32.20 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_131 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_131 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_131 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009058	2 retrocopies	retro_amel_1232, retro_amel_1346,
Canis familiaris	ENSCAFG00000019639	2 retrocopies	retro_cfam_1030, retro_cfam_573,
Cavia porcellus	ENSCPOG00000013652	1 retrocopy	retro_cpor_466,
Dasypus novemcinctus	ENSDNOG00000019432	1 retrocopy	retro_dnov_694,
Dipodomys ordii	ENSDORG00000004628	2 retrocopies	retro_dord_213, retro_dord_587,
Latimeria chalumnae	ENSLACG00000016144	1 retrocopy	retro_lcha_18,
Macaca mulatta	ENSMMUG00000015095	1 retrocopy	retro_mmul_124,
Mus musculus	ENSMUSG00000031197	1 retrocopy	retro_mmus_2220,
Nomascus leucogenys	ENSNLEG00000014475	1 retrocopy	retro_nleu_537,
Oryctolagus cuniculus	ENSOCUG00000017448	2 retrocopies	retro_ocun_233, retro_ocun_747,
Otolemur garnettii	ENSOGAG00000016566	1 retrocopy	retro_ogar_3121,
Sarcophilus harrisii	ENSSHAG00000002823	1 retrocopy	retro_shar_7,
Sus scrofa	ENSSSCG00000012811	1 retrocopy	retro_sscr_131 ,
Ictidomys tridecemlineatus	ENSSTOG00000006684	1 retrocopy	retro_itri_1492,
Tupaia belangeri	ENSTBEG00000007833	5 retrocopies	retro_tbel_3084, retro_tbel_3369, retro_tbel_3652, retro_tbel_553, retro_tbel_632,
Tarsius syrichta	ENSTSYG00000002205	1 retrocopy	retro_tsyr_2032,
Tursiops truncatus	ENSTTRG00000016258	1 retrocopy	retro_ttru_988,