RetrogeneDB ID: retro_eeur_341

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_264464:4985..5338(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSEEUG00000002782
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CHCHD1
• Ensembl ID: ENSEEUG00000015523
• Aliases: None
• Description: coiled-coil-helix-coiled-coil-helix domain containing 1 [Source:HGNC Symbol;Acc:23518]

Sequence

>retro_eeur_341
ATGGTGGTTCCCAGCCTGTGGGGCTGGCTAATGCAGCTTGGAAACTCACAGAAGCCTGTACTAAAACCCAGCAGACCCCT
CATTCTAACCAAGCAAGTGGGAGAACAGCATCAGGAGAGAGGTGAGGCAACGTGTGTCATGGAGATGCCATTGATGATGG
CTTGCTGGAAGCAGAATGAATTCCACGATGAAGAGTGTGGAAAAGAAATCAAGAACTTCTTCGATTGTGCTTCAGAGGCT
GAGCATCCCGAAAAATGAGATTAACACAGGATATCATGGGAGAGTTTGGGAGTTTACACCCCAAGAAGTTGAATAAATTA
TTACAGAGGTTTCCTAGTAAATCTTATATCCTC

Alignment

ORF - retro_eeur_341 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.35 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAVPNLRGRLARLGNSQKPVLKPSRPLILANRVGERRRERGEATCVMEMSLMMACWKQNEFHDEACGKEI
          M.VP.L.G.L..LGNSQKPVLKPSRPLIL...VGE...ERGEATCVMEM.LMMACWKQNEFHDE.CGKEI
Retrocopy MVVPSLWGWLMQLGNSQKPVLKPSRPLILTKQVGEQHQERGEATCVMEMPLMMACWKQNEFHDEECGKEI

Parental  KNFFDCASKAE-ASRKMKSTQEIMGELGSLHPKKLNKLLQRFPSKSYVL
          KNFFDCAS.AE.ASRKM..TQ.IMGE.GSLHPKKLNKLLQRFPSKSY.L
Retrocopy KNFFDCASEAE<ASRKMRLTQDIMGEFGSLHPKKLNKLLQRFPSKSYIL

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	0.32 RPM	11.44 RPM
SRP017611_kidney	0.56 RPM	11.44 RPM
SRP017611_liver	0.16 RPM	10.13 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_341 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000015523	1 retrocopy	retro_eeur_341 ,
Echinops telfairi	ENSETEG00000018904	1 retrocopy	retro_etel_27,
Monodelphis domestica	ENSMODG00000000361	1 retrocopy	retro_mdom_914,