RetrogeneDB ID: retro_etel_678

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_14138:473..761(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CBX5
• Ensembl ID: ENSETEG00000001220
• Aliases: None
• Description: chromobox homolog 5 [Source:HGNC Symbol;Acc:1555]

Sequence

>retro_etel_678
AGAAAAAATAGTATAAAAAGGACGTCTTCATCTAACAATGACTATGATGACAGCAAATCAAAGAGGAAAAGAGATGCTGT
TGACAAATCAAGGGTCTTTGTCAAAGGTCTTGATCCTGAACAAATAATTGGTGCTATTGACAGCAGTGGAGAATTAATGT
TTTTCGTTAAGTGGAAAGATTCAGATGAGGCAGACTTGGTGCTGGCAAAAGAGGCTAACATGAAATGCCCTCAAATTATA
ATTGCATTTTATGAAGAGAGACTAACTTGGCATTCTTGTCCAGAAGAT

Alignment

ORF - retro_etel_678 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.95 %
• Parental protein coverage: 50.79 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KSESNKRKSNFSNNTDEIKSKKKREQSNDIARGFERGLEPEKIIGATDSCGDLMFLMKWKDTDEADLVLA
          ...S.KR.S...N..D..KSK.KR....D..R.F..GL.PE.IIGA.DS.G.LMF..KWKD.DEADLVLA
Retrocopy RKNSIKRTSSSNNDYDDSKSKRKRD-AVDKSRVFVKGLDPEQIIGAIDSSGELMFFVKWKDSDEADLVLA

Parental  KEANVKCPQIVIAFYEERLTWHAYPED
          KEAN.KCPQI.IAFYEERLTWH..PED
Retrocopy KEANMKCPQIIIAFYEERLTWHSCPED

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_678 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 11 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018847	1 retrocopy	retro_cjac_2020,
Echinops telfairi	ENSETEG00000000203	7 retrocopies	retro_etel_1083, retro_etel_1572, retro_etel_1577, retro_etel_1611, retro_etel_2165, retro_etel_382, retro_etel_932,
Echinops telfairi	ENSETEG00000001220	1 retrocopy	retro_etel_678 ,
Homo sapiens	ENSG00000094916	1 retrocopy	retro_hsap_2811,
Gorilla gorilla	ENSGGOG00000000041	1 retrocopy	retro_ggor_1955,
Mus musculus	ENSMUSG00000009575	1 retrocopy	retro_mmus_650,
Nomascus leucogenys	ENSNLEG00000017671	1 retrocopy	retro_nleu_428,
Pongo abelii	ENSPPYG00000004599	1 retrocopy	retro_pabe_2307,
Pan troglodytes	ENSPTRG00000005034	1 retrocopy	retro_ptro_1905,
Rattus norvegicus	ENSRNOG00000036841	1 retrocopy	retro_rnor_1727,
Tursiops truncatus	ENSTTRG00000004524	1 retrocopy	retro_ttru_1859,