RetrogeneDB ID: retro_etel_1899

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_312504:57332..57919(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000004170
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: HDGF
• Ensembl ID: ENSETEG00000005243
• Aliases: None
• Description: hepatoma-derived growth factor [Source:HGNC Symbol;Acc:4856]

Sequence

>retro_etel_1899
TCCAACCGATACCAGGTGTTCTTTTTCGGGACCCACGAGACGGCGTTCATGGGCCCCAAAAACCTTTTCCCGTATGAAGA
GTCCAAGGACAAGTTTGGCAAACCCAGCAAGAGGAGAGGGTTCAGCGAAGGGCTGTGGGAGATCGAGAACAACCTACTGT
CAAGGCTGCTGATGGCCACGTGTCCCAGGCGAAGAGCTGTGGGGACACCCCGGGGCCCAAGGCCGCAGAGGCCGCCAGGA
ATAGAAAGAGGGCCACCGATGGCGGAGGCGACAAGAAGGAGAAGCCAACCCTCCTGGAGACCACCGAGGGGGAGAAGGAG
AAAGCTGCGTCCAAAAGGAGCGCGGGCGACCAGCCCGAGGACTCCTCCAAACGTCCCAAAGGGGGTGAGCCCCACGGGGA
CGAGAAGGAAGAGGCTGGGGTCAGCCACGAGAAGGGCCCTTTGGTCGAGGCTGAGAACCACCACACCGCCTCGGGAGAGC
CCAGCCCCCACTGCAGGCCGCCCCTGGAGGAGCAGGGACCCGAGGCAGTGAAGGGTGCTTCGGAGGAGAAGGATGAGGCC
GAGGCCCCCATGGTCAGAGATCCGGAG

Alignment

ORF - retro_etel_1899 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.23 %
• Parental protein coverage: 94.29 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ANKYQVFFFGTHETAFLGPKDLFPYEESKEKFGKPNKRKGFSEGLWEIENN-PAVKASGCQSSQKKSRVA
          .N.YQVFFFGTHETAF.GPK.LFPYEESK.KFGKP.KR.GFSEGLWEIENN.P.VKA.....SQ.KS...
Retrocopy SNRYQVFFFGTHETAFMGPKNLFPYEESKDKFGKPSKRRGFSEGLWEIENN<PTVKAADGHVSQAKS--C

Parental  EPEPEPEAAEGDGDKKGNAEGSSDEEGKLVIDEPTKEKNEKGALKRRAGDLLEDSPKRPKEAEDLEGEEK
          ...P.P.AAE.....K....G..D...K....E.T....EK.A.KR.AGD..EDS.KRPK..E...G.EK
Retrocopy GDTPGPKAAEAARNRKRATDGGGDKKEKPTLLETTEGEKEKAASKRSAGDQPEDSSKRPKGGEP-HGDEK

Parental  EAAALEGEERPLSVEVEKNSTPS-EPGSGRGPPQEEE-EEEDEEEETAKEDAEAPGIRDHE
          E.A....E..PL.VE.E...T.S.EP.....PP.EE...E........K..AEAP..RD.E
Retrocopy EEAGVSHEKGPL-VEAENHHTASGEPSPHCRPPLEEQGPEAVKGASEEKDEAEAPMVRDPE

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Echinops telfairi was not studied using RNA-Seq expression data.

ChIP-Seq

Echinops telfairi was not studied using ChIP-Seq data.

EST

Echinops telfairi was not studied using EST data.

TSS

Echinops telfairi was not studied using FANTOM5 data.

Lab

retro_etel_1899 was not experimentally validated.

Homology

Retrocopy orthology:

Echinops telfairi does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 13 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 ,
Echinops telfairi	ENSETEG00000010466	1 retrocopy	retro_etel_1234,
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,