RetrogeneDB ID: retro_etel_1552

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_278073:37895..38346(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMCO1
• Ensembl ID: ENSETEG00000009382
• Aliases: None
• Description: transmembrane and coiled-coil domains 1 [Source:HGNC Symbol;Acc:18188]

Sequence

>retro_etel_1552
AGGATCACCATGTTCGCGACACACTCCTCATCGTCTTCATTTCCGGGTGCACGGCTCTGCTCGCGGAGGGCATGACTTGG
GTCCTGGTTTACAGGACCGACAGATACAAGAGATTGAAGGCAGAAGTGGAAAAACAGAGTAAAAAATTAGAAAAGAAGCA
AGAAACGGTAACAGTCAGCTGGTCGGCACCAGAAAAAGAAAATAGAGAGGCAAGAAGAGAAACTGAAAAACAACAACAGA
GCTCTATCAATGGTTCGAATGGAATCCATGTTGGCAACTGGCTTTTGTTTTACTGCTCTGATGGGAAGGTTCAATTCCAT
ATTTGATGGTCGGGTGGTGGCAAAGCTCCCTTTTACCCCCTTTCCTACATCCAAGGGCTGTCTCATCGGAACCTGCTGGG
GACAGCACCACTGACTGCTCCTTCATCTTCCTCTGTATTCTCTGCACCATG

Alignment

ORF - retro_etel_1552 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.54 %
• Parental protein coverage: 89.41 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  RITMFA-DTLLIVFISVCTALLAEGITWVLVYRTDKYKRLKAEVEKQSKKLEKKKETIT-ESAGRQQKKK
          RITMFA.DTLLIVFIS.CTALLAEG.TWVLVYRTD.YKRLKAEVEKQSKKLE.KK......SAGR.QKKK
Retrocopy RITMFA<DTLLIVFISGCTALLAEGMTWVLVYRTDRYKRLKAEVEKQSKKLE-KKQETV>QSAGRHQKKK

Parental  IERQEEKLKNNNRDLSMVRMKSMFAIGFCFTALMGMFNSIFDGRVVAKLPFT-PLSYIQGLSHRNLL-GD
          IERQEEKLKNNNR.LSMVRM.SM.A.GFCFTALMG.FNSIFDGRVVAKLPFT.PLSYIQGLSHRNLL.GD
Retrocopy IERQEEKLKNNNRALSMVRMESMLATGFCFTALMGRFNSIFDGRVVAKLPFT<PLSYIQGLSHRNLL<GD

Parental  DTTDCSFIFLYILCTM
          .TTDCSFIFL.ILCTM
Retrocopy STTDCSFIFLCILCTM

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_1552 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 7 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000010009	1 retrocopy	retro_btau_1441,
Canis familiaris	ENSCAFG00000013472	2 retrocopies	retro_cfam_1640, retro_cfam_833,
Echinops telfairi	ENSETEG00000009382	2 retrocopies	retro_etel_1552 , retro_etel_570,
Macropus eugenii	ENSMEUG00000011045	2 retrocopies	retro_meug_894, retro_meug_997,
Monodelphis domestica	ENSMODG00000001335	2 retrocopies	retro_mdom_1319, retro_mdom_334,
Oryctolagus cuniculus	ENSOCUG00000008441	2 retrocopies	retro_ocun_1148, retro_ocun_1642,
Sarcophilus harrisii	ENSSHAG00000016602	1 retrocopy	retro_shar_790,