RetrogeneDB ID: retro_eeur_67

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: GeneScaffold_3912:56685..57180(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TXN2
• Ensembl ID: ENSEEUG00000010654
• Aliases: None
• Description: thioredoxin 2 [Source:HGNC Symbol;Acc:17772]

Sequence

>retro_eeur_67
ATGGCTCAGCCACTTCTCCTGAGAAGGTTCCTGGCCTCCATCTCCTGGAAGCCCCCTCAGGGTGGGTTGGCACCACTCTG
CTCCAGGCCCCTGCAGACCCCATGGCACAGTCCTAGTGGCCTGGCAGTCATACCCAGCCAAGTGCGGTCAGTATTCACCA
CCAAGGTCTCCACAACAACTTTTAACATCCAGGATGGACCTAATTTTCAAGACCGAGTTGTCGATAGTGAGAGCCCAGTG
GTTGTGGATTTCCACACACAGTGGTGTGGCCCCTGCAGGATCCTGAGCCCGAGGTTAGAGAAGATGGTGGCCAAGCAGCA
AGGAAAGGTGGTAATGGCCAAGGTGGACATCGACGACCACACAGACCTCGCCATGGAGTATGAGGTGTCGGCTGTGCCCA
CGGTTCTGGCCATGAAGAATGGGGACGTGGTAGACAAGTTTGTGGGCATCAAGGATGAGGACCAGCTGGAGGCCTTTCTC
AGGAAGTTAACTGAC

Alignment

ORF - retro_eeur_67 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.3 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAQRLLLRRFLASISWKPPQARLAPLCSRALPTPQHSPSGLAVIPSQVRSIFTTKVSTTTFNIQDGPDFQ
          MAQ.LLLRRFLASISWKPPQ..LAPLCSR.L.TP.HSPSGLAVIPSQVRS.FTTKVSTTTFNIQDGP.FQ
Retrocopy MAQPLLLRRFLASISWKPPQGGLAPLCSRPLQTPWHSPSGLAVIPSQVRSVFTTKVSTTTFNIQDGPNFQ

Parental  DRVVNSETPVVVDFHAQWCGPCKILGPRLEKMVAKQQGKVVMAKVDIDDHTDLAIEYEVSAVPTVLAMKN
          DRVV.SE.PVVVDFH.QWCGPC.IL.PRLEKMVAKQQGKVVMAKVDIDDHTDLA.EYEVSAVPTVLAMKN
Retrocopy DRVVDSESPVVVDFHTQWCGPCRILSPRLEKMVAKQQGKVVMAKVDIDDHTDLAMEYEVSAVPTVLAMKN

Parental  GDVVDKFVGIKDEDQLEAFLKKLID
          GDVVDKFVGIKDEDQLEAFL.KL.D
Retrocopy GDVVDKFVGIKDEDQLEAFLRKLTD

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	2.26 RPM	12.89 RPM
SRP017611_kidney	3.94 RPM	28.88 RPM
SRP017611_liver	2.89 RPM	27.49 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_67 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 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000013929	1 retrocopy	retro_ecab_229,
Erinaceus europaeus	ENSEEUG00000010654	2 retrocopies	retro_eeur_554, retro_eeur_67 ,
Homo sapiens	ENSG00000100348	1 retrocopy	retro_hsap_179,
Gorilla gorilla	ENSGGOG00000028091	1 retrocopy	retro_ggor_260,
Myotis lucifugus	ENSMLUG00000015841	1 retrocopy	retro_mluc_483,
Monodelphis domestica	ENSMODG00000000837	2 retrocopies	retro_mdom_1125, retro_mdom_13,
Pteropus vampyrus	ENSPVAG00000002012	1 retrocopy	retro_pvam_1431,
Sarcophilus harrisii	ENSSHAG00000000670	1 retrocopy	retro_shar_61,
Tursiops truncatus	ENSTTRG00000006612	1 retrocopy	retro_ttru_438,