RetrogeneDB ID: retro_eeur_256

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_225397:1667..2006(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HRSP12
• Ensembl ID: ENSEEUG00000014805
• Aliases: None
• Description: heat-responsive protein 12 [Source:HGNC Symbol;Acc:16897]

Sequence

>retro_eeur_256
CAAGCTGTGTTGGTCGGCAAGACAGTTTATGTTTGGGGACAAGTCGGTATGGACCCCTCAAGTGGACAGCTTGTGCCAGG
AGGGGTGACAGCAGAGACCAAACAAGCTCTTAAAAACATGGGTGAAATTCTGAAAGCAGCAGACTGTGACTTTTCTAATG
TGGTGAAAACAACTGTTTTGCTGGCTGACATAAATGACTTCGATACTGTCAATGAAATCTACAAGCAGTATTTCAAGGAT
TATTTTCCTGCTAGAGATGCATCCCAGGTTGCTGCTTTGCCCAAAGGAAGCCGTGTTGAGACTGAATCCATTGCTATTCA
AGGACCTTTCACATCGATG

Alignment

ORF - retro_eeur_256 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.06 %
• Parental protein coverage: 83.09 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QAVLVGKTVYVSGQVGMDPSSGQLVPGGVTAETKQXXXXXXXXXXXXXXXXXXXVKTTVLLADINDFNTV
          QAVLVGKTVYV.GQVGMDPSSGQLVPGGVTAETKQ...................VKTTVLLADINDF.TV
Retrocopy QAVLVGKTVYVWGQVGMDPSSGQLVPGGVTAETKQALKNMGEILKAADCDFSNVVKTTVLLADINDFDTV

Parental  NEIYKQXXXXXXXXXXXXXXXXXXXGRRVEIGGIAIQGPFTSM
          NEIYKQ...................G.RVE...IAIQGPFTSM
Retrocopy NEIYKQYFKDYFPARDASQVAALPKGSRVETESIAIQGPFTSM

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	9.83 RPM	4.51 RPM
SRP017611_kidney	334.57 RPM	141.78 RPM
SRP017611_liver	270.59 RPM	122.83 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_256 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 14 parental genes, and 39 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000030250	1 retrocopy	retro_cfam_668,
Choloepus hoffmanni	ENSCHOG00000001278	8 retrocopies	retro_chof_133, retro_chof_1972, retro_chof_2434, retro_chof_2503, retro_chof_2676, retro_chof_380, retro_chof_515, retro_chof_757,
Callithrix jacchus	ENSCJAG00000015560	2 retrocopies	retro_cjac_1702, retro_cjac_465,
Dasypus novemcinctus	ENSDNOG00000025138	3 retrocopies	retro_dnov_1155, retro_dnov_224, retro_dnov_793,
Erinaceus europaeus	ENSEEUG00000014805	1 retrocopy	retro_eeur_256 ,
Gorilla gorilla	ENSGGOG00000001185	1 retrocopy	retro_ggor_1153,
Loxodonta africana	ENSLAFG00000002078	1 retrocopy	retro_lafr_437,
Macaca mulatta	ENSMMUG00000011825	2 retrocopies	retro_mmul_558, retro_mmul_88,
Monodelphis domestica	ENSMODG00000006575	1 retrocopy	retro_mdom_319,
Mus musculus	ENSMUSG00000022323	1 retrocopy	retro_mmus_3584,
Ornithorhynchus anatinus	ENSOANG00000021532	1 retrocopy	retro_oana_33,
Otolemur garnettii	ENSOGAG00000001465	3 retrocopies	retro_ogar_2308, retro_ogar_2951, retro_ogar_552,
Ictidomys tridecemlineatus	ENSSTOG00000011452	4 retrocopies	retro_itri_1591, retro_itri_192, retro_itri_605, retro_itri_894,
Tupaia belangeri	ENSTBEG00000002602	10 retrocopies	retro_tbel_1543, retro_tbel_1602, retro_tbel_2450, retro_tbel_2868, retro_tbel_2995, retro_tbel_3589, retro_tbel_421, retro_tbel_621, retro_tbel_888, retro_tbel_953,