RetrogeneDB ID: retro_eeur_81

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: GeneScaffold_4950:83059..83839(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CENPK
• Ensembl ID: ENSEEUG00000005831
• Aliases: None
• Description: centromere protein K [Source:HGNC Symbol;Acc:29479]

Sequence

>retro_eeur_81
GATAGTACTACAGAAGTGGAAAATAATCAAAATGCTGAAGAAGAACTTTTTAAAGAATGTGAAGAGATGTGGAAAGATAT
GGAAGAATGTCAGAATAAATTATCTCTTGTTGGAACTGAGACCCTTACTGATTCAAATGCTCAGCTATCATTACTAATTA
TACAAGCAAAATGCTTGACTGCTGGGCTCAGTCAATGGCAGAACGAAACTCCTGAAATAATTCCACTCAGTGAAGAAATT
CTGGTATCACTGGGAAAAGAGCAGTTCACAAAATTGAAACATGATCTTGAACTGGTGCTATCTACTGTTCAATCAAAGAA
TGAAAAGTTAAAGGAAGACCTGGAAAGGGAGCAGCAGTGGTTACGTGAACAGCAGCAGATAATGGAATCTCTTAATGCAC
TACATAACAAAATGAAAGAGCAGATTGTGACCTTTTCTGAGTCAAGAGTCATCAGTGAACTTAAAACTAAGTTGCATGAT
ATAAAAGAATATAGAAAGAAACTCTTAATTACCATGGGTGAATTTCTAGAAGACCATTTTCCTTTGCCTGACAGAAATGC
TAAAAAGAAAAAGAAAAACAAAGAAACAACTGAACATCTGATAACACTGCACGAGATTTTGGAGATTCTTTTGAATAGAT
TGTTTGATGTTCCACATGACCCATATGTCAAAATTAGAGATTCTTTTTGGCCACCTTATATTTAACTGCTCTTACGTAAT
GGAATTGCCTTGAGACATCCAGAAGATCCAACCAGAATAAGATTAGAAGCTTTCCATCAG

Alignment

ORF - retro_eeur_81 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.23 %
• Parental protein coverage: 95.24 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DSTTEVENNQNAEEELFKECEEMWKDMEECQNKLSLVGTETLTDSNAQLSLLIMQAKCLTAELSQWQNET
          DSTTEVENNQNAEEELFKECEEMWKDMEECQNKLSLVGTETLTDSNAQLSLLI.QAKCLTA.LSQWQNET
Retrocopy DSTTEVENNQNAEEELFKECEEMWKDMEECQNKLSLVGTETLTDSNAQLSLLIIQAKCLTAGLSQWQNET

Parental  PEXXXXXXXXXXXXXXXXFTKLKHDLELVLSTVQSKNEKLKEDLEREQQWLREQQQIMESLNALHNKMKE
          PE................FTKLKHDLELVLSTVQSKNEKLKEDLEREQQWLREQQQIMESLNALHNKMKE
Retrocopy PEIIPLSEEILVSLGKEQFTKLKHDLELVLSTVQSKNEKLKEDLEREQQWLREQQQIMESLNALHNKMKE

Parental  QIVTFSESRVISELKTKLHDIKEYRKKLLITMGEFLEDHFPLPDRNAKKKKKNKETTEHLITLHEILEIL
          QIVTFSESRVISELKTKLHDIKEYRKKLLITMGEFLEDHFPLPDRNA.........TEHLITLHEILEIL
Retrocopy QIVTFSESRVISELKTKLHDIKEYRKKLLITMGEFLEDHFPLPDRNAXXXXXXXXXTEHLITLHEILEIL

Parental  LNRLFDVPHDPYVKIRDSFWPPYIELLLRNGIALRHPEDPTRIRLEAFHQ
          LNRLFDVPHDPYVKIRDSFWPPYI.LLLRNGIALRHPEDPTRIRLEAFHQ
Retrocopy LNRLFDVPHDPYVKIRDSFWPPYI*LLLRNGIALRHPEDPTRIRLEAFHQ

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	3.06 RPM	3.71 RPM
SRP017611_kidney	1.31 RPM	3.00 RPM
SRP017611_liver	0.32 RPM	0.32 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_81 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 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013993	1 retrocopy	retro_chof_1252,
Dipodomys ordii	ENSDORG00000007357	1 retrocopy	retro_dord_787,
Equus caballus	ENSECAG00000019165	1 retrocopy	retro_ecab_181,
Erinaceus europaeus	ENSEEUG00000005831	1 retrocopy	retro_eeur_81 ,
Monodelphis domestica	ENSMODG00000019645	1 retrocopy	retro_mdom_1446,
Oryctolagus cuniculus	ENSOCUG00000011568	2 retrocopies	retro_ocun_1199, retro_ocun_74,
Tursiops truncatus	ENSTTRG00000006527	1 retrocopy	retro_ttru_1310,