RetrogeneDB ID: retro_sscr_1023

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 9:37580915..37581658(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000002722
• Aliases: None
• Description: None

Sequence

>retro_sscr_1023
CCACGCAAGCAGATACCCCAGTGTCTGTGCTTCTCCCAAACTTAAGAGCTTGTCCTTCAAACAGGAAAAGTGATTTAGTG
GATGGGAAAATCTTACCCTGAACTTAAGCCAGCTTATGGTGTTCAAGTCAATAAACTGGAAAAAAGATCAGAAGGTCAGT
GAGCATGTTTTCATTGGCACCCCCTGGGGCCATTCTGGACTGCTGCTCCAAGCTTACGTTCATTGACTCCAAGAAGATCA
AGATTTGACCTGGATGAAACTGACATGGTGATAGCTACTCACCACCACCAAGATCAGAATATCTCCATCTAGAGGCTGCT
ACCCAGGAACTGCCAGATGCTGTTTTCCCCCGCCACCTTTGAAGACTGTGTGGAAATTTGCCCAGACAGTGGTCCCAGAC
CCAAATATTATTAAACTGAGATTAAACAGGAAACAGTGAACAACAAGAAGCACTACTACATCCTGTGCAATAATAGAAAT
GAGAAGTTCCAGGCCTTGAATAGCCTCTATGAGACCATCGCCATTGCTTAAGCAATGATCTTCTGCCATACTCCTAAAAC
ACCTGGCTGGCTGGCAGTTGATCTCTCAAAAGAAGGCCACCAGGTGGCTCTGCTGACTGGTGAAATGAGGTGGAGCAGAG
GGCTGTAGTGATTGAGAACTCCAGAGAGAACAAAGAGAAAGTTCTGGTGACCACCAACATACATGCCCAAATTGTTGATT
TTGAACACATGTCTCTCATACTT

Alignment

ORF - retro_sscr_1023 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.92 %
• Parental protein coverage: 51.77 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  PANRYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLER-GQKISEHIVIGTP-GTVLDWC
          P....PQCLC.S.T.EL.LQTGKVI..MGK.YPELK.AY.V..NKLE...QK.SEH..IGTP.G..LD.C
Retrocopy PRKQIPQCLCFSQT*ELVLQTGKVI*WMGKSYPELKPAYGVQVNKLEK>DQKVSEHVFIGTP>GAILDCC

Parental  SKLKFID-PKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATFED-SVWKFAQKVVPDPN
          SKL.FID.P.....F.LDE.D..IAT..HQDQ.I.I.R.LPRNCQM.LFS.......VWKFAQ.VVPDPN
Retrocopy SKLTFID>PRRSR-FDLDETDMVIATHHHQDQNISI*RLLPRNCQM-LFSPATFE>TVWKFAQTVVPDPN

Parental  IIKLKR-EEETLDTIKQYYVLCNNRDEKFQALCNLYGAITIAQAMIFCHTRKTASWLAAELSKEGHQVAL
          IIKL.....ET....K.YY.LCNNR.EKFQAL..LY..I.IA.AMIFCHT.KT..WLA..LSKEGHQVAL
Retrocopy IIKLRL<KQETVNNKKHYYILCNNRNEKFQALNSLYETIAIA*AMIFCHTPKTPGWLAVDLSKEGHQVAL

Parental  LSGEM-VVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVI
          L.GEM..VEQRA.VIE..RE.KEKVLVTTN..A...D.E..S...
Retrocopy LTGEM<EVEQRAVVIENSRENKEKVLVTTNIHAQIVDFEHMSLIL

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	3.45 RPM
SRP014902_testis	0.00 RPM	2.69 RPM
SRP018288_heart	0.00 RPM	3.69 RPM
SRP018288_kidney	0.00 RPM	5.91 RPM
SRP018288_liver	0.00 RPM	3.36 RPM
SRP018288_lung	0.10 RPM	7.54 RPM
SRP018856_adipose	0.00 RPM	5.34 RPM
SRP035408_brain	0.00 RPM	5.18 RPM
SRP035408_liver	0.00 RPM	6.02 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_1023 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_1023 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_1023 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010216	1 retrocopy	retro_chof_106,
Sus scrofa	ENSSSCG00000002722	1 retrocopy	retro_sscr_1023 ,