RetrogeneDB ID: retro_eeur_523

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_337025:3983..4535(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCDC137
• Ensembl ID: ENSEEUG00000014878
• Aliases: None
• Description: coiled-coil domain containing 137 [Source:HGNC Symbol;Acc:33451]

Sequence

>retro_eeur_523
CAGGTGATCTTCAGAAAAACGTTGGAGAAGGAAGCCAAGGGAGTCCAGCCAGACATAGCTGTGCCCAAGTTCAAGCAGAG
TAAGCGGGAGACAGACAGAGCATACATCCAGCGCATGGAGCGGGAGACCCAGCACGTGCTGTTCCTCACTAAGAACCAGG
CTGACCAGCGGCCAGAGGTGCAGGTGGCACCCAAGAAGAATTCGGAGAGGAAGAAAGCGTACCAGAAGCGACGGCTGGAC
AAGATTCAGCAGAAGGAAGAGAAGGCAGCAGAAAGGCTGGAGCAGGAGCTACTTCAAGATACAGTAAAGTTTGGGGAGGT
TGCACTGCAGCCCCCAGAGCTGACTGCCAAGCCCAGGACAAGCGTGAGCAAGAACCAGCCCGCCAGGAGGTCGCTAATGC
TAATGAGAATGCTTTTGAGTCCTGGCGCCGGGTCCCAGTCTCCAAGCATCTCGCTAGCCCGGCAGCGTATCCTTGGGGAG
GAAAGAGAACGGGCTGTGCAGGCTTATCGGGTGCTGAAGAAGCAGTGGCAACAACAGCACTGGCAGCAGGGG

Alignment

ORF - retro_eeur_523 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.02 %
• Parental protein coverage: 65.83 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QVIFRKTLEKEAKGVQPDIAVPKFKQSKRETDRAYIQRMEQETQHVLFLSKNQTDQRPEVQVAPKKNSER
          QVIFRKTLEKEAKGVQPDIAVPKFKQSKRETDRAYIQRME.ETQHVLFL.KNQ.DQRPEVQVAPKKNSER
Retrocopy QVIFRKTLEKEAKGVQPDIAVPKFKQSKRETDRAYIQRMERETQHVLFLTKNQADQRPEVQVAPKKNSER

Parental  KKAYQKRRLDKIQQKKGEKAERLEQELLQDTVKFGEVALQPPELTAKPRTSVSKNQPARKSLMLMRMLLS
          KKAYQKRRLDKIQQK....AERLEQELLQDTVKFGEVALQPPELTAKPRTSVSKNQPAR.SLMLMRMLLS
Retrocopy KKAYQKRRLDKIQQKEEKAAERLEQELLQDTVKFGEVALQPPELTAKPRTSVSKNQPARRSLMLMRMLLS

Parental  PGAGSQSPNISLARQRIVGEERERAVQAYRVLKKQW-QQHWQQG
          PGAGSQSP.ISLARQRI.GEERERAVQAYRVLKKQW.QQHWQQG
Retrocopy PGAGSQSPSISLARQRILGEERERAVQAYRVLKKQWQQQHWQQG

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	3.55 RPM	5.32 RPM
SRP017611_kidney	5.81 RPM	9.19 RPM
SRP017611_liver	2.41 RPM	4.18 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_523 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 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000014878	1 retrocopy	retro_eeur_523 ,
Homo sapiens	ENSG00000185298	1 retrocopy	retro_hsap_2661,
Gorilla gorilla	ENSGGOG00000009333	1 retrocopy	retro_ggor_1857,
Macaca mulatta	ENSMMUG00000008831	1 retrocopy	retro_mmul_1511,
Monodelphis domestica	ENSMODG00000002713	1 retrocopy	retro_mdom_1355,
Mus musculus	ENSMUSG00000049957	1 retrocopy	retro_mmus_641,
Nomascus leucogenys	ENSNLEG00000013830	3 retrocopies	retro_nleu_1264, retro_nleu_1530, retro_nleu_586,
Pongo abelii	ENSPPYG00000008741	1 retrocopy	retro_pabe_2312,
Pan troglodytes	ENSPTRG00000009767	1 retrocopy	retro_ptro_1793,
Rattus norvegicus	ENSRNOG00000048712	1 retrocopy	retro_rnor_472,