RetrogeneDB ID: retro_etel_427

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: GeneScaffold_7095:8991..9392(-)
• Located in intron of: ENSETEG00000013206

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM60A
• Ensembl ID: ENSETEG00000002888
• Aliases: None
• Description: family with sequence similarity 60, member A [Source:HGNC Symbol;Acc:30702]

Sequence

>retro_etel_427
GTGTTTGCTTTTCACAAGCCAAAGATGTATGGAAGTATGAGGGCTGCTGTGTTTGCAGAGCTAAGTCTTCCAGTTCTGGG
TTCACGACAGTCAATGCTATAAAAAGGACTTCCAGAGCTGTTTTGGTCACTGAGACATATTCAGGAGATAACTGCAGTGC
TTGCGTCCTGCTTATGAATAGGCGGAAGAAGCGGCCAGCAGAATCAAAGAAAAACTGGAATCATGTGGTAGATGTGAGGA
CAGGGTCCAGTCTAAAGACTACATTTAAACCAAAGAAAGTGAAAACTTTATCTGGAAACAGGGTAAAAATCAACCAGATC
AGTAAGCTTCAGAAGGAATTTAAATGTCCTAATTCTGATGCTCCCAGCGCCACCTCAAATGCCTCCTTGTTACAGTAGCC
A

Alignment

ORF - retro_etel_427 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.64 %
• Parental protein coverage: 80.36 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MFRFHKPKMYRSI-EGCCICRAKSSSSRFT-DSKRYEKDFQSCFGLH-ETRSGDICNACVLLVKRWKKLP
          .F.FHKPKMY.S..EGCC.CRAKSSSS.FT.DS..Y.KDFQSCFG.H.ET.SGD.C.ACVLL..R.KK.P
Retrocopy VFAFHKPKMYGSM<EGCCVCRAKSSSSGFT<DSQCYKKDFQSCFG-H>ETYSGDNCSACVLLMNRRKKRP

Parental  AGSKKNWNHVVDARAGPSLKTTLKPKKVKTLSGNRIKSNQISKLQKEFKRQNSDAHSTTSSASPAQSP
          A.SKKNWNHVVD.R.G.SLKTT.KPKKVKTLSGNR.K.NQISKLQKEFK..NSDA.S.TS.AS..Q.P
Retrocopy AESKKNWNHVVDVRTGSSLKTTFKPKKVKTLSGNRVKINQISKLQKEFKCPNSDAPSATSNASLLQ*P

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_427 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 13 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000010685	4 retrocopies	retro_cfam_1120, retro_cfam_1552, retro_cfam_1692, retro_cfam_1837,
Callithrix jacchus	ENSCJAG00000001215	3 retrocopies	retro_cjac_1072, retro_cjac_3154, retro_cjac_3289,
Dasypus novemcinctus	ENSDNOG00000016873	2 retrocopies	retro_dnov_1674, retro_dnov_2668,
Equus caballus	ENSECAG00000009655	2 retrocopies	retro_ecab_287, retro_ecab_385,
Erinaceus europaeus	ENSEEUG00000012617	2 retrocopies	retro_eeur_350, retro_eeur_372,
Echinops telfairi	ENSETEG00000002888	2 retrocopies	retro_etel_1087, retro_etel_427 ,
Felis catus	ENSFCAG00000008955	4 retrocopies	retro_fcat_1311, retro_fcat_1339, retro_fcat_58, retro_fcat_965,
Microcebus murinus	ENSMICG00000003460	2 retrocopies	retro_mmur_1176, retro_mmur_409,
Otolemur garnettii	ENSOGAG00000008927	4 retrocopies	retro_ogar_1253, retro_ogar_1762, retro_ogar_2117, retro_ogar_251,
Rattus norvegicus	ENSRNOG00000046048	1 retrocopy	retro_rnor_2858,
Rattus norvegicus	ENSRNOG00000049943	2 retrocopies	retro_rnor_1121, retro_rnor_2917,
Sarcophilus harrisii	ENSSHAG00000006261	1 retrocopy	retro_shar_670,
Ictidomys tridecemlineatus	ENSSTOG00000007097	1 retrocopy	retro_itri_16,