RetrogeneDB ID: retro_eeur_179

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_161690:1405..1953(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MAPRE1
• Ensembl ID: ENSEEUG00000004499
• Aliases: None
• Description: microtubule-associated protein, RP/EB family, member 1 [Source:HGNC Symbol;Acc:6890]

Sequence

>retro_eeur_179
GCAGTGAACATATATTCCACGTTAGTCACCAGTGATAACTTGAGTCATGATGACATGCGGCCTGGACCAATAAGTCCCTG
TCGTTGAATCAGACAAAGACTGAACAGTTATGCTTAGGGGCTGTCTATTGTCTGTTTATGAATATGCTGTTCTTTGATTC
CATTGCCTTGAAGAAAGTGAAGTTCCAAGCTAGACTAGAACATAAATACATCCAGAGCCTCAAAATACTACAAGCAGGTT
TTAAAAGGATGGGCGTTGACTAAATAATTCCTGTGGACAAATTGGTGAAAGGAAAGTTGAAGGACAACTTTGAGTTTGTT
CAGTGGTTCAAGAAGTTTTCTGATGCAAACTATTATGGGAAAGAATATGACCTTGTAGCTGTCAGTCAAGGTCAAGAAAC
TGCCATAGCTCCTTCTCTTGCTGCTCCAACTCTCAACAAGCCCAAGAAACCGCTCAGCTCCAGCAGTGCCACTCCACAGA
AGCCCATTGCTACACAGAGCACTACTGCAACTCCCATGGCTGCCTCAGGTGAGGTGTGAAAGAACCCT

Alignment

ORF - retro_eeur_179 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.26 %
• Parental protein coverage: 68.28 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AVNVYSTSVTSDNLSRHDM-LAWINESLQLNLTKIEQLCSGAAYCQFMDMLFPGSIALKKVKFQAKLEHE
          AVN.YST.VTSDNLS..DM..AW.N.SL.LN.TK.EQLC.GA.YC.FM.MLF..SIALKKVKFQA.LEH.
Retrocopy AVNIYSTLVTSDNLSHDDM<AAWTNKSLSLNQTKTEQLCLGAVYCLFMNMLFFDSIALKKVKFQARLEHK

Parental  YIQNFKILQAGFKRMGVDKIIPVDKLVKGKFQDNFEFVQWFKKFFDANYDGKEYDPVAARQGQETAVAPS
          YIQ..KILQAGFKRMGVD.IIPVDKLVKGK..DNFEFVQWFKKF.DANY.GKEYD.VA..QGQETA.APS
Retrocopy YIQSLKILQAGFKRMGVD*IIPVDKLVKGKLKDNFEFVQWFKKFSDANYYGKEYDLVAVSQGQETAIAPS

Parental  LVAPALNKPKKPLSSSSAAPQRPIATHRTTATPKAAPGVVRKNP
          L.AP.LNKPKKPLSSSSA.PQ.PIAT..TTATP.AA.G.V.KNP
Retrocopy LAAPTLNKPKKPLSSSSATPQKPIATQSTTATPMAASGEV*KNP

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	48.50 RPM
SRP017611_kidney	0.00 RPM	43.70 RPM
SRP017611_liver	0.00 RPM	9.81 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_179 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 12 parental genes, and 42 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013238	3 retrocopies	retro_amel_1187, retro_amel_1436, retro_amel_848,
Canis familiaris	ENSCAFG00000007306	13 retrocopies	retro_cfam_1338, retro_cfam_1554, retro_cfam_1665, retro_cfam_1804, retro_cfam_1808, retro_cfam_2084, retro_cfam_2163, retro_cfam_241, retro_cfam_547, retro_cfam_762, retro_cfam_774, retro_cfam_806, retro_cfam_913,
Callithrix jacchus	ENSCJAG00000015601	10 retrocopies	retro_cjac_1424, retro_cjac_1647, retro_cjac_1946, retro_cjac_2077, retro_cjac_2084, retro_cjac_2366, retro_cjac_2861, retro_cjac_3259, retro_cjac_3271, retro_cjac_3308,
Cavia porcellus	ENSCPOG00000023542	1 retrocopy	retro_cpor_194,
Erinaceus europaeus	ENSEEUG00000004499	1 retrocopy	retro_eeur_179 ,
Echinops telfairi	ENSETEG00000017922	4 retrocopies	retro_etel_1747, retro_etel_1778, retro_etel_2148, retro_etel_222,
Gorilla gorilla	ENSGGOG00000022496	1 retrocopy	retro_ggor_2765,
Monodelphis domestica	ENSMODG00000019445	3 retrocopies	retro_mdom_1213, retro_mdom_1946, retro_mdom_431,
Mus musculus	ENSMUSG00000027479	2 retrocopies	retro_mmus_3160, retro_mmus_3466,
Otolemur garnettii	ENSOGAG00000026557	2 retrocopies	retro_ogar_226, retro_ogar_2290,
Sorex araneus	ENSSARG00000002368	1 retrocopy	retro_sara_380,
Drosophila melanogaster	FBgn0027066	1 retrocopy	retro_dmel_83,