RetrogeneDB ID: retro_eeur_581

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_348560:43001..43298(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CNN2
• Ensembl ID: ENSEEUG00000015171
• Aliases: None
• Description: calponin 2 [Source:HGNC Symbol;Acc:2156]

Sequence

>retro_eeur_581
GCTAAAACAAAAGATTTCTACACAACCATTGATGTGAAGTATGCAGAAAAACAAAGAAGATATTTTGATGATGGCAAATT
AAAAGCTGGCCAAAGTATAACTAGTTTGCAGATGGGAACCAACCAATGTGCCAGCCAGGCAGGTATGATAGCCTATGAGA
CTAGGAGGCATCTATATGATCCCAAGATGCAAACTGACAAACCTTTTGACCAGACTATGATTAGTGAGCAGGTGTAAGCC
AACCAGGCAGGGAAGTTAGCATCAGGCACTAGAAGAGATATTTATGATCAGAAGTTG

Alignment

ORF - retro_eeur_581 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.1 %
• Parental protein coverage: 61.05 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AKTKGLHTGMDIGVKYSEKQQRNFDDATMKAGQCVIGLQMGTNKCASQSGMTAYGTRRHLYDPKNHILPP
          AKTK...T..D..VKY.EKQ.R.FDD...KAGQ....LQMGTN.CASQ.GM.AY.TRRHLYDPK.....P
Retrocopy AKTKDFYTTID--VKYAEKQRRYFDDGKLKAGQSITSLQMGTNQCASQAGMIAYETRRHLYDPKMQTDKP

Parental  MDHSTISLQMGTNKCASQVGMTAPGTRRHIYDTKL
          .D...IS.Q...N....Q.G..A.GTRR.IYD.KL
Retrocopy FDQTMISEQV*AN----QAGKLASGTRRDIYDQKL

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	0.16 RPM	0.48 RPM
SRP017611_kidney	0.75 RPM	3.94 RPM
SRP017611_liver	0.32 RPM	1.45 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_581 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 8 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000001141	1 retrocopy	retro_dord_672,
Erinaceus europaeus	ENSEEUG00000015171	1 retrocopy	retro_eeur_581 ,
Gorilla gorilla	ENSGGOG00000028153	9 retrocopies	retro_ggor_1199, retro_ggor_1271, retro_ggor_1555, retro_ggor_1612, retro_ggor_1646, retro_ggor_1922, retro_ggor_2370, retro_ggor_305, retro_ggor_762,
Macaca mulatta	ENSMMUG00000015306	1 retrocopy	retro_mmul_1131,
Nomascus leucogenys	ENSNLEG00000001161	2 retrocopies	retro_nleu_1757, retro_nleu_2893,
Otolemur garnettii	ENSOGAG00000010144	2 retrocopies	retro_ogar_1416, retro_ogar_1733,
Pongo abelii	ENSPPYG00000009302	12 retrocopies	retro_pabe_1299, retro_pabe_1397, retro_pabe_1838, retro_pabe_1920, retro_pabe_2171, retro_pabe_2249, retro_pabe_2900, retro_pabe_3512, retro_pabe_3515, retro_pabe_3543, retro_pabe_3823, retro_pabe_407,
Ictidomys tridecemlineatus	ENSSTOG00000028367	1 retrocopy	retro_itri_326,