RetrogeneDB ID: retro_eeur_73

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: GeneScaffold_4407:75632..75947(-)
• Located in intron of: ENSEEUG00000004204

Retrocopy information

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

Parental gene information

• Parental gene symbol: TCEA1
• Ensembl ID: ENSEEUG00000009220
• Aliases: None
• Description: transcription elongation factor A (SII), 1 [Source:HGNC Symbol;Acc:11612]

Sequence

>retro_eeur_73
GTGCAGCAGGTTAAGGATGCAAAGAATCCAAATTTAAGGAAAAATGTATTGTGTGGGAATATTTCTCCTGACTTATTTGC
TAGAATGACAGCAAAGGAAATGGCTAGTGATGAGCTGAAAGAGATGCGGAAAAGCTTGACCAAAGAAGCCATCAGAGAAC
ATCAGATGGCCAAGACTGGTGGGACCCAGACTGACTTATTCACATGTGGCAAGTGTAAAAAGAGGAATTGTACTTATACA
CAGGTACAAACTTGCAGTGCTGATGAACCCATGACAACATTTGTTGTCTGTAATGAATGTGGAAATCGGTGGAAG

Alignment

ORF - retro_eeur_73 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.38 %
• Parental protein coverage: 91.3 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ISNLKDAKNPNLRKNVLCGNISPDLFARMTAEEMASDELKEMRKNLTKEAIREHQMAKTGGTQTDLFTCG
          ....KDAKNPNLRKNVLCGNISPDLFARMTA.EMASDELKEMRK.LTKEAIREHQMAKTGGTQTDLFTCG
Retrocopy VQQVKDAKNPNLRKNVLCGNISPDLFARMTAKEMASDELKEMRKSLTKEAIREHQMAKTGGTQTDLFTCG

Parental  KCKKKNCTYTQVQTRSADEPMTTFVVCNECGNRWK
          KCKK.NCTYTQVQT.SADEPMTTFVVCNECGNRWK
Retrocopy KCKKRNCTYTQVQTCSADEPMTTFVVCNECGNRWK

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	11.60 RPM	14.34 RPM
SRP017611_kidney	9.94 RPM	18.57 RPM
SRP017611_liver	7.72 RPM	14.95 RPM

ChIP-Seq

Erinaceus europaeus was not studied using ChIP-Seq data.

EST

Erinaceus europaeus was not studied using EST data.

TSS

Erinaceus europaeus was not studied using FANTOM5 data.

Lab

retro_eeur_73 was not experimentally validated.

Homology

Retrocopy orthology:

Erinaceus europaeus 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 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001247	1 retrocopy	retro_chof_458,
Callithrix jacchus	ENSCJAG00000014407	1 retrocopy	retro_cjac_2095,
Dasypus novemcinctus	ENSDNOG00000013799	4 retrocopies	retro_dnov_1315, retro_dnov_1853, retro_dnov_839, retro_dnov_952,
Erinaceus europaeus	ENSEEUG00000009220	1 retrocopy	retro_eeur_73 ,
Homo sapiens	ENSG00000187735	4 retrocopies	retro_hsap_2634, retro_hsap_4159, retro_hsap_4200, retro_hsap_4243,
Gorilla gorilla	ENSGGOG00000023652	3 retrocopies	retro_ggor_2794, retro_ggor_2814, retro_ggor_2844,
Macaca mulatta	ENSMMUG00000016022	1 retrocopy	retro_mmul_1146,
Mus musculus	ENSMUSG00000033813	2 retrocopies	retro_mmus_1369, retro_mmus_3559,
Nomascus leucogenys	ENSNLEG00000000981	3 retrocopies	retro_nleu_1028, retro_nleu_1374, retro_nleu_1384,
Oryctolagus cuniculus	ENSOCUG00000007474	3 retrocopies	retro_ocun_1382, retro_ocun_401, retro_ocun_852,
Pongo abelii	ENSPPYG00000018589	3 retrocopies	retro_pabe_3395, retro_pabe_3436, retro_pabe_3455,
Pan troglodytes	ENSPTRG00000020251	2 retrocopies	retro_ptro_2851, retro_ptro_2884,
Rattus norvegicus	ENSRNOG00000022323	1 retrocopy	retro_rnor_1089,
Sarcophilus harrisii	ENSSHAG00000013661	1 retrocopy	retro_shar_50,
Ictidomys tridecemlineatus	ENSSTOG00000021179	1 retrocopy	retro_itri_1745,
Tarsius syrichta	ENSTSYG00000001030	1 retrocopy	retro_tsyr_1624,