RetrogeneDB ID: retro_sscr_998

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 8:71362324..71362618(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AP1S2
• Ensembl ID: ENSSSCG00000012142
• Aliases: None
• Description: adaptor-related protein complex 1, sigma 2 subunit [Source:HGNC Symbol;Acc:560]

Sequence

>retro_sscr_998
AGATATGCCAGTCTGTATTTTTGCTGTGCTATTGAGGATCAGGACAATGAACTAATTACCCTGGAAATAATTCATCATTA
CGTGGAATTACTTGACAAGTATTTTGACGGTGTGTGTGAACTTGATATCATCTTTAATTTTGAGAAGGATTATTTTATTT
TGGATGAGTTTCTTTTGGGAGAAGAAGTTCAGGAAACATCCAAGAAAAATGTCCTTAAAGCAACTGAGCAGGCCGATCTA
CTGCAGGAGGAAGTTGAAACCCCACGTAGTGTTCTTGAAGAAATTGGACTGACA

Alignment

ORF - retro_sscr_998 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.86 %
• Parental protein coverage: 62.42 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RYASLYFCCAIEDQDNELITLEIIHRYVELLDKYFGSVCELDIIFNFEKAYFILDEFLLGGEVQETSKKN
          RYASLYFCCAIEDQDNELITLEIIH.YVELLDKYF..VCELDIIFNFEK.YFILDEFLLG.EVQETSKKN
Retrocopy RYASLYFCCAIEDQDNELITLEIIHHYVELLDKYFDGVCELDIIFNFEKDYFILDEFLLGEEVQETSKKN

Parental  VLKAIEQADLLQEEAETPRSVLEEIGLT
          VLKA.EQADLLQEE.ETPRSVLEEIGLT
Retrocopy VLKATEQADLLQEEVETPRSVLEEIGLT

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	20.18 RPM
SRP014902_testis	0.42 RPM	25.32 RPM
SRP018288_heart	0.03 RPM	79.45 RPM
SRP018288_kidney	0.00 RPM	8.96 RPM
SRP018288_liver	0.16 RPM	3.84 RPM
SRP018288_lung	0.00 RPM	17.21 RPM
SRP018856_adipose	0.03 RPM	5.62 RPM
SRP035408_brain	0.00 RPM	33.06 RPM
SRP035408_liver	0.00 RPM	6.69 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_998 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_998 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_998 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020420	1 retrocopy	retro_btau_1308,
Callithrix jacchus	ENSCJAG00000004393	1 retrocopy	retro_cjac_2312,
Dasypus novemcinctus	ENSDNOG00000013888	1 retrocopy	retro_dnov_1786,
Monodelphis domestica	ENSMODG00000017197	7 retrocopies	retro_mdom_1189, retro_mdom_1329, retro_mdom_1441, retro_mdom_1470, retro_mdom_1616, retro_mdom_1987, retro_mdom_903,
Otolemur garnettii	ENSOGAG00000011342	3 retrocopies	retro_ogar_2038, retro_ogar_265, retro_ogar_3453,
Procavia capensis	ENSPCAG00000000733	1 retrocopy	retro_pcap_386,
Pteropus vampyrus	ENSPVAG00000010218	1 retrocopy	retro_pvam_783,
Sorex araneus	ENSSARG00000000117	1 retrocopy	retro_sara_575,
Sarcophilus harrisii	ENSSHAG00000013119	2 retrocopies	retro_shar_651, retro_shar_690,
Sus scrofa	ENSSSCG00000012142	1 retrocopy	retro_sscr_998 ,
Ictidomys tridecemlineatus	ENSSTOG00000008517	1 retrocopy	retro_itri_131,
Tupaia belangeri	ENSTBEG00000008834	2 retrocopies	retro_tbel_2173, retro_tbel_4575,
Tarsius syrichta	ENSTSYG00000005290	2 retrocopies	retro_tsyr_1953, retro_tsyr_854,
Vicugna pacos	ENSVPAG00000007642	1 retrocopy	retro_vpac_596,