RetrogeneDB ID: retro_ecab_5

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 20:20744599..20745172(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000002747
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: HDGF
• Ensembl ID: ENSECAG00000011178
• Aliases: None
• Description: hepatoma-derived growth factor [Source:HGNC Symbol;Acc:4856]

Sequence

>retro_ecab_5
ATGTTTTTTTTCGGGACCCACGAGACGGCCTTCCTGAGCCCCCAACGCCTCTTCCCGTACGAGGAGGCCAAGGAGAAGTT
CGGCAGGCCCAACAAGAGGAGGGGGTTCAGCGCGGGGCTGTGGGAGATCGAGAACAATCCTACCGTCCAGGTCGCCGGCC
AGCCCCTGGCCCAAGAGCAGAGCTGCGCGGAAGGGCCACCGCCGGCGTCCGAGGCCACCGAGGGCGACGGGGACCAGGAG
AGCATCGCCGACGGCGACAGTGATGAGCAGGGGAAGCCCGGCGTCGACCAGACGGTCCAGGAGGCGGGCGAGAAGGGGCC
GCTGAAGAGGAGCGCGGGGGAGCTGCCGGAGGACGCCGCCAAGCGTCCCAAGGAGGCCGCGCCAGAAGCGGAGGAGGAGG
AGGCCGCCGGGGAGGCCGCGCTGCTGCTGGAGCCGGAGGAGGAGGACGCCAGCGCCACGGCCCAGCCAGGCCTGGCAGGA
GGGTCGCCCCCAGAGCAGCGGGAACCCAAGGAGGAGGCCGCCGAGAAAGACGTCGAGGCCCCAGGCGTTGGAGAAGGTCG
CGAGAGCCTGTAG

Alignment

ORF - retro_ecab_5 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.75 %
• Parental protein coverage: 89.05 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VFFFGTHETAFLGPKDLFPYEESKEKFGKPNKRKGFSEGLWEIENNPTVKASGYQSSQKKSSVEEPEPEP
          .FFFGTHETAFL.P..LFPYEE.KEKFG.PNKR.GFS.GLWEIENNPTV...G....Q..S..E.P.P..
Retrocopy MFFFGTHETAFLSPQRLFPYEEAKEKFGRPNKRRGFSAGLWEIENNPTVQVAGQPLAQEQSCAEGPPPAS

Parental  EATEGDGDKKGNAEGSSDEEGKLVIDEPTKEKNEKGALKRRAGDLLEDSPKRPKEAEDPEGEEKEAATLE
          EATEGDGD....A.G.SDE.GK...D....E..EKG.LKR.AG.L.ED..KRPKEA..PE.EE.EAA..E
Retrocopy EATEGDGDQESIADGDSDEQGKPGVDQTVQEAGEKGPLKRSAGELPEDAAKRPKEAA-PEAEEEEAAG-E

Parental  SERPLPVEVEKNSTRSEPGSGRGPPQEEEEEEEEEEAAKEDAEAPGI
          ....L..E.E..S....PG...G.P...E..E..EEAA..D.EAPG.
Retrocopy AALLLEPEEEDASATAQPGLAGGSP--PEQREPKEEAAEKDVEAPGV

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
SRP021940_articular_cartilage	0.00 RPM	80.40 RPM
SRP021940_cerebellum	0.10 RPM	150.81 RPM
SRP021940_embryo	0.08 RPM	222.56 RPM
SRP021940_placental_villous	0.14 RPM	124.85 RPM
SRP021940_synovial_membrane	0.00 RPM	101.44 RPM
SRP021940_testis	310.19 RPM	489.55 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_5 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_5 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_5 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
Sus scrofa	retro_sscr_65

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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,