RetrogeneDB ID: retro_eeur_335

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_259634:191..688(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CFL2
• Ensembl ID: ENSEEUG00000013155
• Aliases: None
• Description: cofilin 2 (muscle) [Source:HGNC Symbol;Acc:1875]

Sequence

>retro_eeur_335
GCTTCTGGAGTAACAGTGAATGATAACATCATCAAAGGTTTAATGATATGAATGTAAGGAAATCTTCTACACAAGAGGAG
ATCTAAAGGAAAGAAAGAAAGCTGTTCTTTTCTGTTTATGCAAAGACAAAAGACAAATAATTGTAGAGGAAGCGAAGCAG
ATCTTGGTGGGTTACACTGGTGATACTGTAGAGGACCCCTACACACCTTTTGTGAAGTTGCTACCTCTAGATAATTGCCT
ACAAGCTTTGTGCAATGCCACATATGAAACAAAAGAGTCTATGAAGGAAAGCCTGGTATTTACATTCTGGGCCCCTGAGA
GTTCACCTTTAAAAAAGCAAGATGACTTACTCTAGCTCGAAAGATACCATTAAAAAGAAATTTACAGATATTAAACATGA
ATGGCAAGTAAATGGATTGAGTGACGTAAAGGGTTGTTCAACACTGGGAGAGAAACTGTGAGGCGATGTCGTAGTTTCAC
TTGAAGGAAACCCCTTA

Alignment

ORF - retro_eeur_335 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.15 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ASGVTVNDEVIKV-FNDMKV-RKSSTQE-EIKKRKKAVLFCLSDDKRQIIVEEAKQILVGDIGDTVEDPY
          ASGVTVND..IK..FNDM.V...S...E...K.RKKAVLFCL..DKRQIIVEEAKQILVG..GDTVEDPY
Retrocopy ASGVTVNDNIIKG<FNDMNVRKSSTQEE<DLKERKKAVLFCLCKDKRQIIVEEAKQILVGYTGDTVEDPY

Parental  TAFVKLLPLNDCRYALYDATYETKESKKEDLVFIFWAPESAPL-KSKMIYASSKDAIKKKFTGIKHEWQV
          T.FVKLLPL..C..AL..ATYETKES.KE.LVF.FWAPES.PL.KSKM.Y.SSKD.IKKKFT.IKHEWQV
Retrocopy TPFVKLLPLDNCLQALCNATYETKESMKESLVFTFWAPESSPL>KSKMTYSSSKDTIKKKFTDIKHEWQV

Parental  NGLDDIKDRSTLGEKLGGNVVVSLEGKPL
          NGL.D.K..STLGEKL.G.VVVSLEG.PL
Retrocopy NGLSDVKGCSTLGEKL*GDVVVSLEGNPL

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	26.59 RPM
SRP017611_kidney	0.00 RPM	8.25 RPM
SRP017611_liver	0.00 RPM	0.80 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_335 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 10 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000017048	7 retrocopies	retro_dnov_1072, retro_dnov_1379, retro_dnov_1697, retro_dnov_2195, retro_dnov_2691, retro_dnov_715, retro_dnov_905,
Erinaceus europaeus	ENSEEUG00000011893	1 retrocopy	retro_eeur_529,
Erinaceus europaeus	ENSEEUG00000013155	4 retrocopies	retro_eeur_335 , retro_eeur_448, retro_eeur_513, retro_eeur_578,
Echinops telfairi	ENSETEG00000006010	3 retrocopies	retro_etel_1579, retro_etel_1622, retro_etel_684,
Latimeria chalumnae	ENSLACG00000018011	1 retrocopy	retro_lcha_23,
Macropus eugenii	ENSMEUG00000000739	11 retrocopies	retro_meug_1026, retro_meug_1138, retro_meug_125, retro_meug_1266, retro_meug_1666, retro_meug_1791, retro_meug_2025, retro_meug_2062, retro_meug_210, retro_meug_321, retro_meug_668,
Monodelphis domestica	ENSMODG00000012949	1 retrocopy	retro_mdom_171,
Oryctolagus cuniculus	ENSOCUG00000009383	1 retrocopy	retro_ocun_1397,
Sarcophilus harrisii	ENSSHAG00000004732	1 retrocopy	retro_shar_528,
Tupaia belangeri	ENSTBEG00000000391	2 retrocopies	retro_tbel_29, retro_tbel_4131,