RetrogeneDB ID: retro_sscr_301

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 12:16345592..16346163(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000025295
• Aliases: None
• Description: Sus scrofa Nedd4 family interacting protein 1 (NDFIP1), mRNA. [Source:RefSeq mRNA;Acc:NM_001243361]

Sequence

>retro_sscr_301
GAACCTGAACAGGCTTCAGGTGACAGTCCTCTACCTAACAACAGCATCTCTGCAGAGAGTACAGAATAATTTAAGTACAA
AGATGGATTGGAGTTTGCAGAGCCTCCATATTTATAATGTAGCTACAACACTGCCCAGTTATGATGTAGGGAAGAGAATC
AAAGCTGAAGCAACTATCCCTTTGGTTTCTAGAAGAGATGAGGATTTTGTGGATCAGGATGACTTTGGGGATGCTCACCA
ACTAGGATGGGAAACAGTGGGATTTTCATGTTAATTTTTTTCATGACATTCTTCTTTAACTGGACTGGATTTTTCCTGTC
CTCTTGCCTGACCACCTCAGTTGCAAGAAGGTTTGGGGGTATTTCAGGATTTGGTCTCTCTCTAATTAAGTGGATCCTTA
TTGTCAGTTTTCCACAGATTTCCCTGAATATTCTGATGGCCAGAACTGCCTCTGGTTTGTGCTCCTTGTTTAGGTTTTCT
CCTGTTTCTCAGAGAATTTGTTAATTATTTCAAAGTTTGGAAAATGCAAAAACTCTCAAATTTCTGCAGGATCAGAGTTG
TCTGTATTTTT

Alignment

ORF - retro_sscr_301 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.35 %
• Parental protein coverage: 96. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  EPEQAAGDAPPPYSSISAESAVYFDYKDESGFPKPPS-YNVATTLPSYDEAERTKAEATIPLVPGRDEDF
          EPEQA.GD.P.P..SISAES...F.YKD...F..PP..YNVATTLPSYD...R.KAEATIPLV..RDEDF
Retrocopy EPEQASGDSPLPNNSISAESTE*FKYKDGLEFAEPPY>YNVATTLPSYDVGKRIKAEATIPLVSRRDEDF

Parental  VGRDDFDDADQM-RIGNDGVFMLTFFMAFLFNWIGFFLSFCLTTSAAGRYGAISGFGLSLIKWILIV-RF
          V..DDF.DA.Q..R.GN.G.FML.FFM.F.FNW.GFFLS.CLTTS.A.R.G.ISGFGLSLIKWILIV..F
Retrocopy VDQDDFGDAHQL<RMGNSGIFMLIFFMTFFFNWTGFFLSSCLTTSVARRFGGISGFGLSLIKWILIV<QF

Parental  STYFPGYFDGQYWLWWVFLV-LGFLLFLRGFINYAKVRKMPETFSNLPRTRVLFIY
          ST.FP.Y.DGQ..LW.V.LV.LGFLLFLR.F.NY.KV.KM....SN..R.RV..I.
Retrocopy STDFPEYSDGQNCLWFVLLV<LGFLLFLREFVNYFKVWKM-QKLSNFCRIRVVCIF

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	58.53 RPM
SRP014902_testis	0.00 RPM	138.48 RPM
SRP018288_heart	0.00 RPM	58.62 RPM
SRP018288_kidney	0.00 RPM	127.17 RPM
SRP018288_liver	0.00 RPM	96.91 RPM
SRP018288_lung	0.00 RPM	61.60 RPM
SRP018856_adipose	0.00 RPM	114.73 RPM
SRP035408_brain	0.00 RPM	843.68 RPM
SRP035408_liver	0.00 RPM	105.80 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_301 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_301 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_301 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000047747	1 retrocopy	retro_btau_766,
Callithrix jacchus	ENSCJAG00000018271	1 retrocopy	retro_cjac_3175,
Equus caballus	ENSECAG00000021907	1 retrocopy	retro_ecab_261,
Homo sapiens	ENSG00000131507	1 retrocopy	retro_hsap_1091,
Gorilla gorilla	ENSGGOG00000004879	1 retrocopy	retro_ggor_859,
Macaca mulatta	ENSMMUG00000016787	1 retrocopy	retro_mmul_846,
Pongo abelii	ENSPPYG00000015896	1 retrocopy	retro_pabe_908,
Pan troglodytes	ENSPTRG00000017358	1 retrocopy	retro_ptro_743,
Sarcophilus harrisii	ENSSHAG00000002466	1 retrocopy	retro_shar_738,
Sus scrofa	ENSSSCG00000025295	1 retrocopy	retro_sscr_301 ,
Ictidomys tridecemlineatus	ENSSTOG00000005153	1 retrocopy	retro_itri_1454,