RetrogeneDB ID: retro_eeur_317

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_252022:15217..15611(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSEEUG00000012151
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TMED4
• Ensembl ID: ENSEEUG00000007627
• Aliases: None
• Description: transmembrane emp24 protein transport domain containing 4 [Source:HGNC Symbol;Acc:22301]

Sequence

>retro_eeur_317
TCTGAGGGCTACTTCACCTTCACCCCCACACACCCGGGGACAATCAGATCTGCCACCACTCCAACTCCACCAAGCTGATG
CTCTTTGCCAGCCGCGGACTGCGTGTGCACCTAGACATTCGGGTTGGGGAACATGGCAGCAACTACCCAGAGATTGCTGC
CAAAGATAAACTGACAGAGCTGCAGCTCCGAGCCCACCAGTTGCTAGATCAGGTGGAACAAATCCAGAAGGAGCAGGACT
ACCAAAGGTACCGTGAAGAGCACTTCCAGCTGACCAGTGAAAGCACCAACCAGCTAGTGCTGTGGTGGTCCATCGCTCAG
ACGGTCACCTCATTCTCACTAGCATTTGGCAGATGCGTCACCTCAAGAGTTTCTTTGAGGCCAAGAAGTTGGTG

Alignment

ORF - retro_eeur_317 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.15 %
• Parental protein coverage: 57.76 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SEGRFTFTS-HTPGDHQICLHSNSTKMSLFAGGRLRVHLDIQVGEHANNYPEIAAKDKLTELQLRARQLL
          SEG.FTFT..HTPGD.QIC.HSNSTK..LFA...LRVHLDI.VGEH..NYPEIAAKDKLTELQLRA.QLL
Retrocopy SEGYFTFTP<HTPGDNQICHHSNSTKLMLFASRGLRVHLDIRVGEHGSNYPEIAAKDKLTELQLRAHQLL

Parental  DQVEQIQKEQDYQRVSYLERRFRLTSESTHQRVLWWPIAQTVI-LILTGIWQMRLLKSFFEAKKLV
          DQVEQIQKEQDYQR..Y.E..F.LTSEST.Q.VLWW.IAQTV..LILT.IWQMR.LKSFFEAKKLV
Retrocopy DQVEQIQKEQDYQR--YREEHFQLTSESTNQLVLWWSIAQTVT<LILTSIWQMRHLKSFFEAKKLV

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	3.87 RPM	14.18 RPM
SRP017611_kidney	14.44 RPM	69.01 RPM
SRP017611_liver	5.63 RPM	21.70 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_317 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 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000007627	2 retrocopies	retro_eeur_12, retro_eeur_317 ,
Macropus eugenii	ENSMEUG00000006810	1 retrocopy	retro_meug_1225,
Monodelphis domestica	ENSMODG00000016129	2 retrocopies	retro_mdom_256, retro_mdom_362,
Oryctolagus cuniculus	ENSOCUG00000003964	1 retrocopy	retro_ocun_1909,
Ictidomys tridecemlineatus	ENSSTOG00000014658	1 retrocopy	retro_itri_1499,