RetrogeneDB ID: retro_sscr_874

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 6:76870710..76871094(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KIAA1143
• Ensembl ID: ENSSSCG00000011308
• Aliases: None
• Description: KIAA1143 [Source:HGNC Symbol;Acc:29198]

Sequence

>retro_sscr_874
ATAAGCAAGCAGAACCAGGTGATCTACATGGGGCTAGTCAAGTCGGCTTTCCTGGCCTGTTTCAAGGAATGGGTTGGCTG
CAGGGAAGGGACCCCTGAAGAAACCAAGGAATCCTGCCTCAGCTCCCAGATGAAGATGGTGATCACAGTGACAAAGAAAA
TAACACTTCTAAGTGGTGGTTTTGAAAAAGCGAGCCCTGTCAGCTGAAGAAGTCAGGAAGATTAAAGCAGAAATTAAGGC
TGCCAGAGCAGATGAAGAACCAGCTTCAGCTGATGGAAGAATGTTGTATTGAAAACCAGTGAAGTGTTGCTCAGATGAAA
AGTATTTGGGTTTAACAGCAAGCTCAAAAAAAGACGATGAAATAAATAAGACTTAGTTAAAAAG

Alignment

ORF - retro_sscr_874 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.91 %
• Parental protein coverage: 82.58 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSKRNQVSYVRPAEPAFLARFKERVGYREGPTIETKR-IQPQLPDEDADHSDKEDEQPQ-VVVLKKGDLS
          .SK.NQV.Y......AFLA.FKE.VG.REG...ETK..I.PQLPDED.DHSDKE......VVVLKK..LS
Retrocopy ISKQNQVIYMGLVKSAFLACFKEWVGCREGTPEETKE<ILPQLPDEDGDHSDKENNTSK<VVVLKKRALS

Parental  -EEVMKIKAEIKAAKADEEPASADGRIMYRKPVKRSSDEKYSGLTASS-KKKKTNEEDVINK
          .EEV.KIKAEIKAA.ADEEPASADGR..Y.KPVK..SDEKY.GLTASS.KK...N..D...K
Retrocopy AEEVRKIKAEIKAARADEEPASADGRMLY*KPVKCCSDEKYLGLTASS<KKRR*NK*DLVKK

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	1.59 RPM
SRP014902_testis	0.00 RPM	4.38 RPM
SRP018288_heart	0.00 RPM	6.94 RPM
SRP018288_kidney	0.00 RPM	5.12 RPM
SRP018288_liver	0.00 RPM	2.88 RPM
SRP018288_lung	0.00 RPM	2.95 RPM
SRP018856_adipose	0.00 RPM	4.34 RPM
SRP035408_brain	0.00 RPM	16.83 RPM
SRP035408_liver	0.00 RPM	5.96 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_874 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_874 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_874 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014132	1 retrocopy	retro_cfam_2208,
Homo sapiens	ENSG00000163807	2 retrocopies	retro_hsap_1399, retro_hsap_2762,
Nomascus leucogenys	ENSNLEG00000005987	1 retrocopy	retro_nleu_666,
Oryctolagus cuniculus	ENSOCUG00000000929	2 retrocopies	retro_ocun_1601, retro_ocun_432,
Pongo abelii	ENSPPYG00000013954	1 retrocopy	retro_pabe_2250,
Pan troglodytes	ENSPTRG00000014824	1 retrocopy	retro_ptro_1869,
Pteropus vampyrus	ENSPVAG00000012438	2 retrocopies	retro_pvam_367, retro_pvam_458,
Sus scrofa	ENSSSCG00000011308	2 retrocopies	retro_sscr_844, retro_sscr_874 ,
Ictidomys tridecemlineatus	ENSSTOG00000010817	1 retrocopy	retro_itri_307,