RetrogeneDB ID: retro_eeur_448

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_307851:12352..12815(+)
• 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_448
ATCATCAAGGTATTCAATGACATGAAGGTGCACAAGTCCTCCACACCCGAGAAAGTGAAGAAGCAAGAATGAGAGCTCTT
CTGCCTGAGGGAAGACAAGAATATCATCCTGGAGGAGGGCAAAGAGATCTTGCTGGGCGACGTGGGCCAGACCGTGGATG
ACCCATAGGCCACCTTTGTCAAGATGCTGCAGGATATGGACTACAGCTATGCCCTCTACGATGCCACCTACGAGATCAAG
GAGAGCAAGAAGGATGACCTGGTTTTCATCTTCGGGGCTCGAAAGTGTGTGCCCCTTAAGAAAAAAAATGATCTGCACCA
GTTCCAAGGACGCCATCAAGAAGAAACTGACAGGAATCAAGTACAAATTACAAGCTAACTCCTCCGAGGAGGTCAAGAAC
CGCTGCACCCTGGCAGAGAAGCTGGGCTGCAGTGCTGTCATCTTCCTGGAGGGCAAGCCTTTG

Alignment

ORF - retro_eeur_448 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.15 %
• Parental protein coverage: 94.55 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VIKVFNDMKVRKSSTQEEIKKRKKAVLFCLSDDKRQIIVEEAKQILVGDIGDTVEDPYTAFVKLLPLNDC
          .IKVFNDMKV.KSST.E..KK.....LFCL..DK..II.EE.K.IL.GD.G.TV.DP...FVK.L...D.
Retrocopy IIKVFNDMKVHKSSTPEKVKKQE*E-LFCLREDKN-IILEEGKEILLGDVGQTVDDP*ATFVKMLQDMDY

Parental  RYALYDATYETKESKKEDLVFIFWAPESAPLK-SKMIYASSKDAIKKKFTGIKHEWQVNGLDDIKDRSTL
          .YALYDATYE.KESKK.DLVFIF.A....PLK....I..SSKDAIKKK.TGIK...Q.N.....K.R.TL
Retrocopy SYALYDATYEIKESKKDDLVFIFGARKCVPLK>XXXICTSSKDAIKKKLTGIKYKLQANSSEEVKNRCTL

Parental  GEKLGGNVVVSLEGKPL
          .EKLG...V..LEGKPL
Retrocopy AEKLGCSAVIFLEGKPL

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	0.64 RPM	26.59 RPM
SRP017611_kidney	0.56 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_448 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,