RetrogeneDB ID: retro_etel_2070

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_47047:136..511(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000019910
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PAM16
• Ensembl ID: ENSETEG00000006416
• Aliases: None
• Description: presequence translocase-associated motor 16 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:29679]

Sequence

>retro_etel_2070
GCCAAGTACCTAGCCCAGATCATGGGGATGAGTGTGCCAGGGGGTGGGCAGAGCCTTTGCCCGGGCCTTGCAGCAGGAGT
TTGCGGCCAGCCAGGCAGCTGCTGATGCCCAGGGCCAGGCCGGTCACCAGTCAGCTGCTGCCTCCAACCCATAGGGGCCT
CAGCTTGCTGGAAGCCCAGCAGATCCTCAGCGTCGCCAAGCTGAGTCCTGTGGACATCGAAAAGAATTATGAACATTTGT
TAAAGGTAAACGACAAAACGGTGGGCGACTTCTTCTACCTGTAGTCCAACGTGGTCCATACAAAGGAGCGTCTTGACAAG
GAGCTCGAGATCCAGGCCCAGGGAGGACAAAGAGAAAAAACAGGCGTCCTGGACG

Alignment

ORF - retro_etel_2070 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.44 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  AKYLAQIIVMSV-QVVGRAFARALRQEFAASRAAADARGRAGHQS-AAAS-NLGLSVQEAQQILNVAKIS
          AKYLAQI..MSV.Q.VGRAFARAL.QEFAAS.AAADA.G.AGHQS.AA.....GLS..EAQQIL.VAK.S
Retrocopy AKYLAQIMGMSV>QGVGRAFARALQQEFAASQAAADAQGQAGHQSAAASN>HRGLSLLEAQQILSVAKLS

Parental  PEDIQKNYEHLFKVNDKSVGGSFYLQSKVVRAKERLEEELKIQAQ-EDREKEQASRT
          P.DI.KNYEHL.KVNDK.VG..FYL.S.VV..KERL..EL.IQAQ.ED.EK.QAS.T
Retrocopy PVDIEKNYEHLLKVNDKTVGDFFYL*SNVVHTKERLDKELEIQAQ>EDKEKKQASWT

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_2070 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 16 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009200	1 retrocopy	retro_btau_1664,
Canis familiaris	ENSCAFG00000019226	1 retrocopy	retro_cfam_1967,
Callithrix jacchus	ENSCJAG00000019772	1 retrocopy	retro_cjac_1148,
Dasypus novemcinctus	ENSDNOG00000010921	2 retrocopies	retro_dnov_1361, retro_dnov_8,
Dipodomys ordii	ENSDORG00000014888	1 retrocopy	retro_dord_81,
Equus caballus	ENSECAG00000019387	1 retrocopy	retro_ecab_302,
Erinaceus europaeus	ENSEEUG00000007432	7 retrocopies	retro_eeur_138, retro_eeur_171, retro_eeur_213, retro_eeur_234, retro_eeur_273, retro_eeur_440, retro_eeur_673,
Echinops telfairi	ENSETEG00000006416	1 retrocopy	retro_etel_2070 ,
Felis catus	ENSFCAG00000027971	1 retrocopy	retro_fcat_520,
Myotis lucifugus	ENSMLUG00000008921	6 retrocopies	retro_mluc_2446, retro_mluc_2447, retro_mluc_2448, retro_mluc_2516, retro_mluc_2517, retro_mluc_429,
Mus musculus	ENSMUSG00000014301	1 retrocopy	retro_mmus_73,
Rattus norvegicus	ENSRNOG00000004608	1 retrocopy	retro_rnor_713,
Sus scrofa	ENSSSCG00000007947	2 retrocopies	retro_sscr_1090, retro_sscr_468,
Ictidomys tridecemlineatus	ENSSTOG00000003461	1 retrocopy	retro_itri_1732,
Tupaia belangeri	ENSTBEG00000001347	1 retrocopy	retro_tbel_3190,
Tarsius syrichta	ENSTSYG00000009306	1 retrocopy	retro_tsyr_282,