RetrogeneDB ID: retro_sscr_1177

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: X:130958420..130959248(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000012715
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000028454
• Aliases: None
• Description: None

Sequence

>retro_sscr_1177
ATGGAGGAGCAGCCGAAGGAGGGCGAGGCCGAGGTCGCGGAGCCCTGGTTCTCTAAGTGGGAGCGCCAGTGCCTGGCCGA
GGCCGAGCAGGAAGAGGAGCTGCCCCCCGATCTGCAGGAGGAGGCGGCCCCTGAGGCGGCGGGGCTCAGGAGCGAGCAGC
AGAAGCTGTGGCACCTCTTCCAGATCTCAGCCACCGCTGTGGCCCAGCTCTACAAGGATACGGGGTGCCAACAGCCAGGA
CTCTCCATGTGGGACCCCTTCCAGAATGCGGCCATGGCTGTGACCAGCCTCTACAAAGAGAGCGGGGATGCCCATCAACG
AAGTTTTGACCTGGGCATCCAGGTTGGCCACCAGCGTCGCATCCGAGATGTGCTGGAATGGGTGAAAAAGGGCCGGAGCA
CCATCCTCCGCGAAGATCTGATTAGCTTTCTGTGTGGCAAGGTGCCCCCCGCCACTCCGCCGCCCCGCACCCCGAGGACG
CCGCCGAAGCCACCCGCCGGGGCCGCCAGCCAGGCCGCGGCCACCGAGTCCAGCTCCTCGGTGGACGTCGACCTGCAGCC
GTTCCACGAGGCCATCGCCCTGCACGGCCTCAGCGGTGCCATGGCGAGCATCAGCGTGAGATCCGGCGCGCCGGGCTCGC
CGCCTCAGGCCAGCGGCGTCGCCGGCGGTGGCCGCCGAAGAAGTAGCTTCCTCGAGGACGACTCGAACCCCATCGACCCA
GAAGACCTGGCCCTGCGCCTGGACAGTGGGGGGACCCGCAAGCGCACCTCAGCCCAGTGCGGCGATGGCGACATAGACTC
CCCAAGCCACAAGCGCAACCGAATGGTC

Alignment

ORF - retro_sscr_1177 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.5 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEERKEEGEAEIQEHGPEHWFSKWERQCLAEAEQDEQLPPELQEEAAA-AAQPEHKQQKLWHLFQNSATA
          MEE...EGEAE......E.WFSKWERQCLAEAEQ.E.LPP.LQEEAA..AA.....QQKLWHLFQ.SATA
Retrocopy MEEQPKEGEAEVA----EPWFSKWERQCLAEAEQEEELPPDLQEEAAPEAAGLRSEQQKLWHLFQISATA

Parental  VAQLYKDRVCQQPGLSLWVPFQNAATAVTNLYKESVDTHQRSFDIGIQIGYQRRNKDVLAWVKKRRRTIR
          VAQLYKD..CQQPGLS.W.PFQNAA.AVT.LYKES.D.HQRSFD.GIQ.G.QRR..DVL.WVKK.R.TI.
Retrocopy VAQLYKDTGCQQPGLSMWDPFQNAAMAVTSLYKESGDAHQRSFDLGIQVGHQRRIRDVLEWVKKGRSTIL

Parental  REDLISFLCGKVPP----PRNSRAPPRLTVVSPNRATSTETSSSVETDLQPFREAIALHGLSGAMASISV
          REDLISFLCGKVPP....PR..R.PP.........A..TE.SSSV..DLQPF.EAIALHGLSGAMASISV
Retrocopy REDLISFLCGKVPPATPPPRTPRTPPKPPAGAASQAAATESSSSVDVDLQPFHEAIALHGLSGAMASISV

Parental  RSSTPGSPTHVSSGSNASRRRNGLHDVDLNTFISEEMALHLDNGGTRKRTSAQCGDVITDSPTHKRNRMI
          RS..PGSP...S......RRR......D.N....E..AL.LD.GGTRKRTSAQCGD...DSP.HKRNRM.
Retrocopy RSGAPGSPPQASGVAGGGRRRSSFLEDDSNPIDPEDLALRLDSGGTRKRTSAQCGDGDIDSPSHKRNRMV

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	20.04 RPM
SRP014902_testis	2.55 RPM	26.87 RPM
SRP018288_heart	0.03 RPM	20.69 RPM
SRP018288_kidney	0.39 RPM	26.99 RPM
SRP018288_liver	0.16 RPM	17.75 RPM
SRP018288_lung	0.10 RPM	16.09 RPM
SRP018856_adipose	1.55 RPM	8.29 RPM
SRP035408_brain	5.59 RPM	9.81 RPM
SRP035408_liver	0.26 RPM	9.66 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_1177 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_1177 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_1177 has 8 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4765
Pan troglodytes	retro_ptro_3172
Gorilla gorilla	retro_ggor_2968
Pongo abelii	retro_pabe_163
Mus musculus	retro_mmus_3460
Rattus norvegicus	retro_rnor_156
Canis familiaris	retro_cfam_147
Equus caballus	retro_ecab_1091

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010719	2 retrocopies	retro_amel_1715, retro_amel_88,
Canis familiaris	ENSCAFG00000018981	1 retrocopy	retro_cfam_147,
Cavia porcellus	ENSCPOG00000010925	1 retrocopy	retro_cpor_101,
Dasypus novemcinctus	ENSDNOG00000015893	3 retrocopies	retro_dnov_1575, retro_dnov_2266, retro_dnov_827,
Equus caballus	ENSECAG00000009430	1 retrocopy	retro_ecab_1091,
Homo sapiens	ENSG00000182831	1 retrocopy	retro_hsap_4765,
Gorilla gorilla	ENSGGOG00000010744	1 retrocopy	retro_ggor_2968,
Monodelphis domestica	ENSMODG00000005378	2 retrocopies	retro_mdom_1716, retro_mdom_299,
Mustela putorius furo	ENSMPUG00000014707	1 retrocopy	retro_mputfur_44,
Mus musculus	ENSMUSG00000022507	1 retrocopy	retro_mmus_3460,
Nomascus leucogenys	ENSNLEG00000010106	1 retrocopy	retro_nleu_2348,
Otolemur garnettii	ENSOGAG00000003909	1 retrocopy	retro_ogar_74,
Pongo abelii	ENSPPYG00000007088	1 retrocopy	retro_pabe_163,
Pan troglodytes	ENSPTRG00000007751	1 retrocopy	retro_ptro_3172,
Rattus norvegicus	ENSRNOG00000002545	2 retrocopies	retro_rnor_156, retro_rnor_1928,
Sus scrofa	ENSSSCG00000028454	1 retrocopy	retro_sscr_1177 ,
Ictidomys tridecemlineatus	ENSSTOG00000009324	1 retrocopy	retro_itri_137,