RetrogeneDB ID: retro_sscr_1207

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: X:83543705..83544032(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000030980
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ZFAND6
• Ensembl ID: ENSSSCG00000001779
• Aliases: None
• Description: zinc finger, AN1-type domain 6 [Source:HGNC Symbol;Acc:30164]

Sequence

>retro_sscr_1207
CAGCCAAGCCCTATATCAAATCAGTCACTTTTATCACAATCTGTAGCATCTTCCCAAGTCAACAGTACATCTGTGGACAA
AGCAATACCTGAAACAGAAGACCTGCAACCTTCAGTATCGGATACCGCACAGCAGCCATCTGAAGAGCAAAGCAAATCTC
TTGAAAAACCAAAACAAAAAAATAATTGCTGTTTCATGTGCAGGAAGAAAGTGGGAATTACTGGGTTTTAATGCTGGTGT
GGAAATGTTTACTATGGTGTACACCGTTACTCAGATGAACACAATTGCTCTTACAATTACAAAGCTGACACTGCTGAGAA
AATCCAG

Alignment

ORF - retro_sscr_1207 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.82 %
• Parental protein coverage: 52.15 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QSTPVPNQSLLSESVASSQVDSTSVDKAIPETEDLQASVSDTAQQPSEEQSKSLEKPKQKKNRCFMCRKK
          Q..P..NQSLLS.SVASSQV.STSVDKAIPETEDLQ.SVSDTAQQPSEEQSKSL.......N.CFMCRKK
Retrocopy QPSPISNQSLLSQSVASSQVNSTSVDKAIPETEDLQPSVSDTAQQPSEEQSKSLXXXXXXXNCCFMCRKK

Parental  VGLTGFECRCGNVYCGVHRYSDVHNCSYNYKADAAEKIR
          VG.TGF.C.CGNVY.GVHRYSD.HNCSYNYKAD.AEKI.
Retrocopy VGITGF*CWCGNVYYGVHRYSDEHNCSYNYKADTAEKIQ

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	32.25 RPM
SRP014902_testis	0.00 RPM	47.81 RPM
SRP018288_heart	0.00 RPM	48.38 RPM
SRP018288_kidney	0.00 RPM	128.75 RPM
SRP018288_liver	0.00 RPM	88.91 RPM
SRP018288_lung	0.00 RPM	31.26 RPM
SRP018856_adipose	0.00 RPM	36.15 RPM
SRP035408_brain	0.00 RPM	35.83 RPM
SRP035408_liver	0.00 RPM	58.95 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_1207 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_1207 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_1207 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012321	1 retrocopy	retro_btau_593,
Choloepus hoffmanni	ENSCHOG00000009491	2 retrocopies	retro_chof_1516, retro_chof_2072,
Felis catus	ENSFCAG00000012931	2 retrocopies	retro_fcat_1024, retro_fcat_1998,
Homo sapiens	ENSG00000086666	1 retrocopy	retro_hsap_4153,
Gorilla gorilla	ENSGGOG00000015621	1 retrocopy	retro_ggor_2790,
Loxodonta africana	ENSLAFG00000006722	1 retrocopy	retro_lafr_587,
Monodelphis domestica	ENSMODG00000019428	1 retrocopy	retro_mdom_685,
Nomascus leucogenys	ENSNLEG00000008870	1 retrocopy	retro_nleu_1387,
Pan troglodytes	ENSPTRG00000007361	2 retrocopies	retro_ptro_1375, retro_ptro_2824,
Rattus norvegicus	ENSRNOG00000013506	1 retrocopy	retro_rnor_2019,
Sus scrofa	ENSSSCG00000001779	2 retrocopies	retro_sscr_1206, retro_sscr_1207 ,