RetrogeneDB ID: retro_sscr_1146

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: X:29031486..29031977(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000030768
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TRPT1
• Ensembl ID: ENSSSCG00000013040
• Aliases: None
• Description: tRNA phosphotransferase 1 [Source:HGNC Symbol;Acc:20316]

Sequence

>retro_sscr_1146
CAGTCGGGGGACCCCAGCATGTGCCCTCTCACCTGGGCCCATCTGAGTCATTCCCTGCAAGTACTTGAGTTGGAAGTGAT
GCCATTGGAGACCCCACAGACCCTACACATAATGCTCATTCATGGCACATACTGGTAGCACTGGCCATCCATCCTGCTCA
GAGGTCTGTCCTGCTGGGGAAGGATGCACATCCACCTGGCCTCAGGACTGCCTGGGGACCATGATGTTATCAGTGGCATG
CAGCCAAATTGCAAGGTGGCCGTGTTCATCAATGGGCCCCAGGCCCTGGCAGATGAAACCCCCTTCTTCTATTCTGTCAG
TGGGGTGATCCTGATTCCAGAGAATGCTGATGGTTTCCTACTTCCCAAGTCCTTCAAGAAGGTCTGCAGCTATGCCTTAC
CTGAAAGCCCCTCTCCTTGGCTGGTAATGAAGAGACAGATTGTTAGAGTAACCCTAAGCATGGCTCCAGAGGGTGAAGGA
TGATCCAACAA

Alignment

ORF - retro_sscr_1146 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.7 %
• Parental protein coverage: 65.08 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QPGDPSTGPLIRANQGHSLQVPALELIPLETPQALPLMLVHGTFWRHWPSILLKGLSRQGRTHIHLAPGL
          Q.GDPS..PL..A...HSLQV..LE..PLETPQ.L..ML.HGT.W.HWPSILL.GLS..GR.HIHLA.GL
Retrocopy QSGDPSMCPLTWAHLSHSLQVLELEVMPLETPQTLHIMLIHGTYW*HWPSILLRGLSCWGRMHIHLASGL

Parental  PGDPGVISGMRPNCEVAVFINGPQALADGIPFFRSANGVILTPGNADGVLLPKYFK-EALQLRPTRKPLS
          PGD..VISGM.PNC.VAVFINGPQALAD..PFF.S..GVIL.P.NADG.LLPK.FK.E.LQL..T.KPLS
Retrocopy PGDHDVISGMQPNCKVAVFINGPQALADETPFFYSVSGVILIPENADGFLLPKSFK<EGLQLCLT*KPLS

Parental  LAGNEETECQHGPKHSSRGRRTTPQ
          LAGNEET.C...PKH.SRG.R...Q
Retrocopy LAGNEETDC*SNPKHGSRG*RMIQQ

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	3.98 RPM
SRP014902_testis	0.00 RPM	4.81 RPM
SRP018288_heart	0.00 RPM	4.43 RPM
SRP018288_kidney	0.00 RPM	9.06 RPM
SRP018288_liver	0.00 RPM	5.12 RPM
SRP018288_lung	0.00 RPM	2.24 RPM
SRP018856_adipose	0.00 RPM	7.81 RPM
SRP035408_brain	0.00 RPM	4.80 RPM
SRP035408_liver	0.00 RPM	8.19 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_1146 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_1146 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_1146 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000009917	1 retrocopy	retro_ecab_1055,
Sus scrofa	ENSSSCG00000013040	1 retrocopy	retro_sscr_1146 ,
Tursiops truncatus	ENSTTRG00000010252	1 retrocopy	retro_ttru_1283,