RetrogeneDB ID: retro_sscr_65

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 7:18656733..18657420(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000001083
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: HDGF
• Ensembl ID: ENSSSCG00000006468
• Aliases: None
• Description: hepatoma-derived growth factor [Source:HGNC Symbol;Acc:4856]

Sequence

>retro_sscr_65
ATGTCGCGGTTCTGTCGGCGCAAGTACAAGAACGGGGACCTGGTGTTCGCCAAGTTAAAGGGCTATGCCCACTGGCCGGC
CAGGATCGAGCAAACGGCCGAAGCCAACCGCTACCAAGTGTTTTTCTTCGGGACCCACGAGACAGCCTTCCTGGGCCCCA
AGCATCTCTTCCCATATGAGGAGTGCAAGGAGAAGTTCGGCAAACCCAACAAGAGAAGGGGCTTCAGCGAGGGGCTGTGG
GAGATCGAGAACAACCCCACCGTCCAGGCTTCCGATTACCAGTTTGCGCAGAAGAGTGGCACTGAGGAGCTCGAGCCAGA
GGCCACCGAGGGCTTTGAGGACCTGAAGAGCCTCACCGATGGCAGCGGCGGAACCAAGCAAGGGCGGCGGGGCCTGGACC
CACCAGCCTTGCAGAAGAAGGAGCGGCTGAAGAGGAGTGCGGGGGACCCACCAGAAGGCATCCCCAAACGTCCCAGGGAG
GCCAATCCGGAAGCAGGGAAGGAGATGGAGGAGGCCGCGGCCGCGGAGGATGCGAGGCCACCACTCCCGGAGGCGGAGAT
CAACCACGCAGTGACCCAGTGGGGACCCACTTGGGAGCCGCCGGTGGAGGAGGAGTGGGAGTGGGAGGAAGAGGCTGCTG
AGAGAGAGGCTGAGGCTGCAGGCTTCGGACGCCCAGAGAGCCAGTAG

Alignment

ORF - retro_sscr_65 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.98 %
• Parental protein coverage: 76.54 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ANKYQVFFFGTHETAFLGPKDLFPYEESKEKFGKPNKRKGFSEGLWEIENNPTVKASGYQSSQKKSCVEE
          AN.YQVFFFGTHETAFLGPK.LFPYEE.KEKFGKPNKR.GFSEGLWEIENNPTV.AS.YQ..Q.KS..EE
Retrocopy ANRYQVFFFGTHETAFLGPKHLFPYEECKEKFGKPNKRRGFSEGLWEIENNPTVQASDYQFAQ-KSGTEE

Parental  PEPKADAAEGDGDKKGNAEGS-SDEEGKLVIDEPTKEKNEKGALKRRAGDLLEDSPKRPKEAEDPEGEE-
          .EP...A.EG..D.K....GS.....G....D.P...K.E...LKR.AGD..E..PKRP.EA....G.E.
Retrocopy LEP--EATEGFEDLKSLTDGSGGTKQGRRGLDPPALQKKER--LKRSAGDPPEGIPKRPREANPEAGKEM

Parental  KEVATLEGERPLPVEAEKNSTPSEPSSGRGPPPEEEEEEEEEEEEEEA
          .E.A..E..RP...EAE.N...........PP.EEE.E.EEE..E.EA
Retrocopy EEAAAAEDARPPLPEAEINHAVTQWGPTWEPPVEEEWEWEEEAAEREA

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	179.45 RPM
SRP014902_testis	0.71 RPM	143.00 RPM
SRP018288_heart	0.00 RPM	57.91 RPM
SRP018288_kidney	0.00 RPM	130.72 RPM
SRP018288_liver	0.00 RPM	124.25 RPM
SRP018288_lung	0.00 RPM	166.59 RPM
SRP018856_adipose	0.06 RPM	138.25 RPM
SRP035408_brain	0.00 RPM	185.83 RPM
SRP035408_liver	0.00 RPM	179.92 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_65 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_65 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_65 has 6 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_33
Pan troglodytes	retro_ptro_1
Pongo abelii	retro_pabe_6
Callithrix jacchus	retro_cjac_338
Bos taurus	retro_btau_216
Equus caballus	retro_ecab_5

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000039793	1 retrocopy	retro_btau_216,
Callithrix jacchus	ENSCJAG00000006157	2 retrocopies	retro_cjac_338, retro_cjac_4022,
Dasypus novemcinctus	ENSDNOG00000010231	1 retrocopy	retro_dnov_4,
Equus caballus	ENSECAG00000011178	1 retrocopy	retro_ecab_5,
Echinops telfairi	ENSETEG00000005243	1 retrocopy	retro_etel_1899,
Homo sapiens	ENSG00000143321	1 retrocopy	retro_hsap_33,
Myotis lucifugus	ENSMLUG00000010413	1 retrocopy	retro_mluc_257,
Mus musculus	ENSMUSG00000004897	1 retrocopy	retro_mmus_3647,
Pongo abelii	ENSPPYG00000000703	1 retrocopy	retro_pabe_6,
Pan troglodytes	ENSPTRG00000001474	1 retrocopy	retro_ptro_1,
Sus scrofa	ENSSSCG00000006468	1 retrocopy	retro_sscr_65 ,