RetrogeneDB ID: retro_eeur_146

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: GeneScaffold_910:241775..242898(+)
• Located in intron of: ENSEEUG00000010560

Retrocopy information

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

Parental gene information

• Parental gene symbol: GPN1
• Ensembl ID: ENSEEUG00000013421
• Aliases: None
• Description: GPN-loop GTPase 1 [Source:HGNC Symbol;Acc:17030]

Sequence

>retro_eeur_146
ATGGCGGCGCCCACGGCTCCCGCTGTCGTGGCTGAGGAGCCGCAGGCTTCGGGAGGTCCCAGGCCCCCAGTGTGCCTGCT
GGTGTTGGGGATGGCGGGATCTGGGAACACTACCTTTGTGCAGAGGCTTACGGGACACCTGCATAGTCTAGGCTCTCCAC
CTTATGTGATCAGTCTGGACCCAGCAGTGCATGAAGTTCCCTTTCCTGCCAATATTGATATACGTGACACTGAAATATAA
AGAAGTTATAAAACAATATGGACTTGGGCCCAATGGTGGCATAGTGACCTCACTCAATCTCTTTGCTACCAGATTTGATC
AGGTAATGAAATTTATTGAGAAGGCCCAGAACATGTCTAAATATGTCTTGATCGACACACCTGGACAGATTGAGGTATTC
ACCTGGTCAGCTTCCAGGACAATCATCACTGAGGCCCTGGCATCCTCGTTCCCTACAGTTGTCATTTATGTAATGGACAC
ATCGAGAAGTACCAATCCGGTGACCTTCATGTCCAATATGCTCTATGCATGCAGCATCTTGTACAAAACCAAGCTGCCTT
TCATTGTGGTCATGAATAAAACTGATATCATTGATCACAGTTTTGCAGTGGAATGGATGCAGGATTTTGAGACTTTCCAA
AATGCTTTGAATCAAGAGACTACATACCTCAGCAACCTGACTCGCTCAATGAGCCTGGTGTTGGATGAGTTTTATAGCTC
ACTTAGGGTTGTGGGTGTCTCTGCGGTCCTGGGAACTGGCTTAGTTGAGCTATTTGTGCAAGTTACCAGTGCTGCTGAAG
AATATGAAAGGGAATATCATCCTGAATATGAACGTCTGAAGAAATCACTGGCCAGTGCACAGAGCCAGCAGCAGAAAGAG
CAGCTGGAGCGCCTTCGGAAGGACATGGGCTCCATAGCCTTGGACCCAGGGGCTGCTAAAGACAGGTTGTCTCCCGTGCT
GGACCCTTCTGACCTGATCCTGACACGGGGAACCTTGGGATGAAGAGGATGAAGAAGCAGACAGTGATACAGATGATACT
GACCACAGAGTTACAGGAGGAAAGTCACAAGAGCCAGCATTCCGGATTTCATGCAGGAATCAATGTCACAGTACTGAAAG
AGG

Alignment

ORF - retro_eeur_146 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.48 %
• Parental protein coverage: 99.21 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAAPTAPAVAAEEPQASGGPRPPVCLLVLGMAGSGKTTFVQRLTGHLHSQGSPPYVINLDPAVHEV-PFP
          MAAPTAPAV.AEEPQASGGPRPPVCLLVLGMAGSG.TTFVQRLTGHLHS.GSPPYVI.LDPAVHEV.PF.
Retrocopy MAAPTAPAVVAEEPQASGGPRPPVCLLVLGMAGSGNTTFVQRLTGHLHSLGSPPYVISLDPAVHEV>PF-

Parental  ANIDIRDTVKYKEVMKQYGLGPNGGIVTSLNLFATRFDQVMKFIEKAQNMSKYVLIDTPGQIEVFTWSAS
          ..I.I..T.KYKEV.KQYGLGPNGGIVTSLNLFATRFDQVMKFIEKAQNMSKYVLIDTPGQIEVFTWSAS
Retrocopy LPILIYVTLKYKEVIKQYGLGPNGGIVTSLNLFATRFDQVMKFIEKAQNMSKYVLIDTPGQIEVFTWSAS

Parental  GTIITEALASSFPTVVIYVMDTSRSTNPVTFMSNMLYACSILYKTKLPFIVVMNKTDIIDHSFAVEWMQD
          .TIITEALASSFPTVVIYVMDTSRSTNPVTFMSNMLYACSILYKTKLPFIVVMNKTDIIDHSFAVEWMQD
Retrocopy RTIITEALASSFPTVVIYVMDTSRSTNPVTFMSNMLYACSILYKTKLPFIVVMNKTDIIDHSFAVEWMQD

Parental  FETFQDALNQETTYVSNLTRSMSLVLDEFYSSLRVVGVSAVLGTGLDELFVQVTSAAEEYEREYRPEYER
          FETFQ.ALNQETTY.SNLTRSMSLVLDEFYSSLRVVGVSAVLGTGL.ELFVQVTSAAEEYEREY.PEYER
Retrocopy FETFQNALNQETTYLSNLTRSMSLVLDEFYSSLRVVGVSAVLGTGLVELFVQVTSAAEEYEREYHPEYER

Parental  LKKSLXXXXXQQQKEQLERLRKDMGSIALDPGAAKDRLSPVLDPSDLILTRGTL-DEEDEEADSDTDDID
          LKKSL.....QQQKEQLERLRKDMGSIALDPGAAKDRLSPVLDPSDLILTRGTL.DEEDEEADSDTDD.D
Retrocopy LKKSLASAQSQQQKEQLERLRKDMGSIALDPGAAKDRLSPVLDPSDLILTRGTL>DEEDEEADSDTDDTD

Parental  HRVTEESHEEPAFQ-NFMQESVAQYWKR
          HRVT.....EPAF...FMQES..QY.KR
Retrocopy HRVTGGKSQEPAFR<DFMQESMSQY*KR

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	1.93 RPM	29.33 RPM
SRP017611_kidney	1.69 RPM	31.32 RPM
SRP017611_liver	1.13 RPM	10.61 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_146 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000013421	1 retrocopy	retro_eeur_146 ,
Microcebus murinus	ENSMICG00000014941	1 retrocopy	retro_mmur_649,
Ictidomys tridecemlineatus	ENSSTOG00000006379	2 retrocopies	retro_itri_1428, retro_itri_1718,
Tupaia belangeri	ENSTBEG00000007425	1 retrocopy	retro_tbel_3907,