RetrogeneDB ID: retro_sscr_77

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: X:122225985..122226639(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000030606
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: CCDC169
• Ensembl ID: ENSSSCG00000026564
• Aliases: None
• Description: coiled-coil domain containing 169 [Source:HGNC Symbol;Acc:34361]

Sequence

>retro_sscr_77
CGTGACACTATGGGAGATGCAAGAGGTGACGACCTGAAAGGTATGAGCACCGACCGCCTTAAACTGGAATTATTGGAAGA
AATCCATATGAAAGACTTAGTACAAATCTCAATACTTGAAATGAGACAAAAGATAGTGGAACTGGAAGCCAAACTCAAAA
ATGACAATGAAAGCAATGAATGGAGAATCCGTTATGAGACCCAACTTGAACTGAATGAAGAACTAGAAAAGCAAATTGTT
ACTCTCAGAGAGAAACTGGAAAAAATCCGTGGAAATCCTTCAGACAGACTATCTTCTATTCGTGTCTATGAGCAGATGCC
AGTGGAATCCTTAAGTGCATTACTTAAACAGCTAGAAAAAGAAAAAAGGAGCCTTGAAAGTGAAGTGAAAGACTATGCAC
TTAGACTGGAACGAGAATCGAAGGCTCACCACCAGACCAATGAGGAACGCCGTATAATCCTAGCTAAAATGACCCAGGTC
TCTGGCTCATACCAAGTCTCTAAAAAACAACCAGTGAATCACCTGCAGAGACCGAAAGAGAATCCAGCAAAAACAGGAAG
ATATAATCCACCCAATCAAAAGATCGTAAATGCCAAGAGAGAACCAGCAAAAAAGACTACAAGATCAACTCATCTTCCAA
AACTCAATCCATGA

Alignment

ORF - retro_sscr_77 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.18 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEEGRSDTFDGVSTDRLKLELLEEIHLKDIVQLSVLEIEHKVAELEAKLSTDDEGGEWKTRYETQLELND
          M...R.D...G.STDRLKLELLEEIH.KD.VQ.S.LE...K..ELEAKL..D.E..EW..RYETQLELN.
Retrocopy MGDARGDDLKGMSTDRLKLELLEEIHMKDLVQISILEMRQKIVELEAKLKNDNESNEWRIRYETQLELNE

Parental  QLEKQIVSLKEKLEKICGTPSDRLSSIQVYEQMPVESLNAVLKQLEKEKRSLESQVKDYALRLEQESKAY
          .LEKQIV.L.EKLEKI.G.PSDRLSSI.VYEQMPVESL.A.LKQLEKEKRSLES.VKDYALRLE.ESKA.
Retrocopy ELEKQIVTLREKLEKIRGNPSDRLSSIRVYEQMPVESLSALLKQLEKEKRSLESEVKDYALRLERESKAH

Parental  HKTSNERRTYLAETSQVSGSNQVSKRQQMD
          H.T..ERR..LA...QVSGS.QVSK.Q...
Retrocopy HQTNEERRIILAKMTQVSGSYQVSKKQPVN

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	0.00 RPM
SRP014902_testis	0.00 RPM	0.28 RPM
SRP018288_heart	0.00 RPM	0.03 RPM
SRP018288_kidney	0.00 RPM	0.10 RPM
SRP018288_liver	0.00 RPM	0.00 RPM
SRP018288_lung	0.00 RPM	0.61 RPM
SRP018856_adipose	0.00 RPM	1.04 RPM
SRP035408_brain	0.00 RPM	1.81 RPM
SRP035408_liver	0.00 RPM	0.47 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_77 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_77 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_77 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Equus caballus	retro_ecab_111

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004615	1 retrocopy	retro_amel_120,
Equus caballus	ENSECAG00000011446	1 retrocopy	retro_ecab_111,
Felis catus	ENSFCAG00000008786	1 retrocopy	retro_fcat_39,
Oryctolagus cuniculus	ENSOCUG00000026427	1 retrocopy	retro_ocun_406,
Otolemur garnettii	ENSOGAG00000010367	2 retrocopies	retro_ogar_1996, retro_ogar_957,
Sus scrofa	ENSSSCG00000026564	1 retrocopy	retro_sscr_77 ,