RetrogeneDB ID: retro_eeur_526

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_338554:1129..1869(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NUDC
• Ensembl ID: ENSEEUG00000001291
• Aliases: None
• Description: nuclear distribution C homolog (A. nidulans) [Source:HGNC Symbol;Acc:8045]

Sequence

>retro_eeur_526
CTGATCACACAGCCCCTTAAGCCTTCACAACCAGTTGCCACAGAGGCTCGGAGAGAGAAGAGAGCTCGGCAGGAGACTGA
GCGGCGGGAGAAGGCAGAGCGGGGCAGCCAGGATGGTGAAGGGAGGCCAAGTCAGAGACCTCTGGACCCCAAATCAAAGA
GCTGACTGATGAGGAGGCAGAGAGGTTGCAGCTGGAGATTGACCAGAAAAAGGATGCTGAGAATCATGAGCTCCAGGTCA
AGAATGGCAGCCCTGACTCACCAGGAAAGCAGGATGCTGAGGAAGAGGAAGAAGAAGATGAGAAGGACAAAGGGAAACTA
ACGCCCAATCTTGGTAATGGAGCAGACCTGCCCAATTACCGCTGGACGCAGACCCTGTCAGAGCTGGATCTGGCAGTGCC
CTTTCGTGTGAATTTTCACCTGAAGGGGAAGGATGTGGTGGTGGACATCCAGCGGCGGCACCTCCGGGTGGGACTCAAGG
GCCAGCCGGCCATCATTGATGGGGAGCTGTACAACGAAGTGAAGGTGGAGGAGAGCTCGTGGCTCATTGAAGACGGCAAG
GTGGTGACTGTGCATTTAGAGAAGATCAACAAGATGGAGTGGTGGAGCCGCTTGGTGTCCAGTGAACCTGAGATCAATAC
TAAGAAGATTATCCTTGAAAATTCTAAGCTGTCGGATCTGGACAGCGAGACACGCAGCATGGTGGAAAAGATGATGTATG
ACCAGAGACAGAAGTCCATG

Alignment

ORF - retro_eeur_526 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.52 %
• Parental protein coverage: 74.32 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LITQTFSHHNQLAQKARREKRARQETERREKAER-AARMAK-EAKSETSGPQIKELTDEEAERLQLEIDQ
          LITQ........A..ARREKRARQETERREKAER.AARM.K.EAKSETSGPQIKELTDEEAERLQLEIDQ
Retrocopy LITQPLKPSQPVATEARREKRARQETERREKAER>AARMVK>EAKSETSGPQIKELTDEEAERLQLEIDQ

Parental  KKDAENHELQVKNGSLDSPGKQDAEEEEEEDEKDKGKLKPNLGNGADLPNYRWTQTLSELDLAVPFRVNF
          KKDAENHELQVKNGS.DSPGKQDAEEEEEEDEKDKGKL.PNLGNGADLPNYRWTQTLSELDLAVPFRVNF
Retrocopy KKDAENHELQVKNGSPDSPGKQDAEEEEEEDEKDKGKLTPNLGNGADLPNYRWTQTLSELDLAVPFRVNF

Parental  RLKGKDVVVDIQRRHLRVGLKGQPAIIDGELYNEVKVEESSWLIEDGKVVTVHLEKXXXXXXXSRLVSSD
          .LKGKDVVVDIQRRHLRVGLKGQPAIIDGELYNEVKVEESSWLIEDGKVVTVHLEK.......SRLVSS.
Retrocopy HLKGKDVVVDIQRRHLRVGLKGQPAIIDGELYNEVKVEESSWLIEDGKVVTVHLEKINKMEWWSRLVSSE

Parental  PEINTKKINPENSKLSDLDSETRSMVEKMMYDQRQKSM
          PEINTKKI..ENSKLSDLDSETRSMVEKMMYDQRQKSM
Retrocopy PEINTKKIILENSKLSDLDSETRSMVEKMMYDQRQKSM

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	8.22 RPM	69.13 RPM
SRP017611_kidney	4.88 RPM	55.14 RPM
SRP017611_liver	3.70 RPM	42.12 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_526 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 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000001291	1 retrocopy	retro_eeur_526 ,
Homo sapiens	ENSG00000090273	2 retrocopies	retro_hsap_2168, retro_hsap_2183,
Gorilla gorilla	ENSGGOG00000015314	2 retrocopies	retro_ggor_1720, retro_ggor_1730,
Microcebus murinus	ENSMICG00000015671	1 retrocopy	retro_mmur_457,
Mus musculus	ENSMUSG00000028851	1 retrocopy	retro_mmus_3181,
Nomascus leucogenys	ENSNLEG00000009404	2 retrocopies	retro_nleu_2545, retro_nleu_312,
Pongo abelii	ENSPPYG00000001673	2 retrocopies	retro_pabe_2055, retro_pabe_2064,
Pan troglodytes	ENSPTRG00000000395	2 retrocopies	retro_ptro_1655, retro_ptro_1661,
Pteropus vampyrus	ENSPVAG00000004408	1 retrocopy	retro_pvam_434,
Rattus norvegicus	ENSRNOG00000007399	2 retrocopies	retro_rnor_2009, retro_rnor_2108,