RetrogeneDB ID: retro_eeur_342

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_264593:620..960(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSEEUG00000000428
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TSPAN31
• Ensembl ID: ENSEEUG00000006647
• Aliases: None
• Description: tetraspanin 31 [Source:HGNC Symbol;Acc:10539]

Sequence

>retro_eeur_342
CTGGCTATTAACCATAGCACACAGACAGATGTCATCAGTGCTTCTTGGCGGGTTATGAGCAACAAAAACCCAGCATGAAC
TTGAAAGAAGTTTTGATTGTTGTGGCTTGTTCAAACTCACAACCCTACATCAACAAGATTATGCTTTCTGCGCGGCAAGC
TGCAAAAAGTGGAACATGTGCCGATTGTGTGGAGAGAAGCTTCTGAGACATTCAGATGAAGCCCTGAAAATCCTGGGAGG
TGTCAGACTCTTCTTTAGCTTTACAGAGATCTTTGGTGTTTGGGTAGCAATGAGATTCTGGAATCAGAAGGATCCTCACG
CCAACCCCAGTGCCTTTCTA

Alignment

ORF - retro_eeur_342 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.96 %
• Parental protein coverage: 54.07 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LAINQNTQTDVINASWRVMSN-KTQHELERSFDCCGLFNLTTLHQQDYAFCAASCRKWKTCQLCGEKFLK
          LAIN..TQTDVI.ASWRVMSN.KTQHELERSFDCCGLF.LTTLHQQDYAFCAASC.KW..C.LCGEK.L.
Retrocopy LAINHSTQTDVISASWRVMSN>KTQHELERSFDCCGLFKLTTLHQQDYAFCAASCKKWNMCRLCGEKLLR

Parental  HSDEALKILGGVGLFFSFTEILGVWLAMRFRNQKDPRANPSAFL
          HSDEALKILGGV.LFFSFTEI.GVW.AMRF.NQKDP.ANPSAFL
Retrocopy HSDEALKILGGVRLFFSFTEIFGVWVAMRFWNQKDPHANPSAFL

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	0.81 RPM	30.62 RPM
SRP017611_kidney	0.38 RPM	41.82 RPM
SRP017611_liver	0.16 RPM	20.10 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_342 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.

---

Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000006647	1 retrocopy	retro_eeur_342 ,
Ictidomys tridecemlineatus	ENSSTOG00000001138	1 retrocopy	retro_itri_1256,