RetrogeneDB ID: retro_eeur_648

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_374626:44822..45123(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SSU72
• Ensembl ID: ENSEEUG00000010799
• Aliases: None
• Description: SSU72 RNA polymerase II CTD phosphatase homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:25016]

Sequence

>retro_eeur_648
CCACTGATGGTGGCGGTGGTATACTCGAGCAACCAGAACAGAGCATGGAGGCACACAACATCCTCAGCAAATGAGGGTTT
AGCGTCCTGTCCTTTGCAACAGGAACTCATGTGAAGAAGCTTCCAGGGCCAGCACCCAACAAGCTAAATTGTTTAGGATT
TCAAAACCACCTATGATCAGATGTACAACAATATCCTTAGGAAAGACAAAGAACTCTACTCATAGAATGGCATTTTTATA
AATGCTGGACAGAAATAAGAGAATTAAGCCCCGACCAGAAAGATTCCAGAATTCCAGAAAT

Alignment

ORF - retro_eeur_648 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.55 %
• Parental protein coverage: 66.89 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  PLRVAVVCSSNQNR-SMEAHNILSKRGFSVRSFGTGTHVK-LPGPAPDKPN-VYDFKTTYDQMYNDLLRK
          PL.VAVV.SSNQNR.SMEAHNILSK.GFSV.SF.TGTHVK.LPGPAP.K.N.V.DFKTTYDQMYN..LRK
Retrocopy PLMVAVVYSSNQNR<SMEAHNILSK*GFSVLSFATGTHVKKLPGPAPNKLN>V*DFKTTYDQMYNNILRK

Parental  DKELYTQNGI-LHMLDRNKRIKPRPERFQNCRD
          DKELY..NGI.L.MLDRNKRIKPRPERFQN.R.
Retrocopy DKELYS*NGI>L*MLDRNKRIKPRPERFQNSRN

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	0.00 RPM	19.98 RPM
SRP017611_kidney	0.00 RPM	18.75 RPM
SRP017611_liver	0.00 RPM	12.22 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_648 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 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013736	3 retrocopies	retro_amel_1930, retro_amel_292, retro_amel_84,
Erinaceus europaeus	ENSEEUG00000010799	1 retrocopy	retro_eeur_648 ,
Felis catus	ENSFCAG00000003318	1 retrocopy	retro_fcat_54,
Microcebus murinus	ENSMICG00000011016	5 retrocopies	retro_mmur_1057, retro_mmur_1081, retro_mmur_1353, retro_mmur_890, retro_mmur_891,
Mustela putorius furo	ENSMPUG00000014394	2 retrocopies	retro_mputfur_108, retro_mputfur_1408,
Sarcophilus harrisii	ENSSHAG00000009747	1 retrocopy	retro_shar_32,
Tupaia belangeri	ENSTBEG00000010136	3 retrocopies	retro_tbel_1675, retro_tbel_2435, retro_tbel_2704,