RetrogeneDB ID: retro_eeur_124

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: GeneScaffold_7689:75734..76220(+)
• Located in intron of: ENSEEUG00000007465

Retrocopy information

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

Parental gene information

• Parental gene symbol: NSMCE4A
• Ensembl ID: ENSEEUG00000014906
• Aliases: None
• Description: non-SMC element 4 homolog A (S. cerevisiae) [Source:HGNC Symbol;Acc:25935]

Sequence

>retro_eeur_124
ACCTTCCATTTCATGTTTAGTTCAGTCAAGACGGATTCCTCTGCACCCAAGCGCCGAGTGGAGTACAGGAGGAAGGCTCC
CAAGATGGAAGAAAGCGGGGATATGCCTACAAAGCTGAGGCGGATGGACCTGACTTGCAATCAAGAAGCGACCGAAAAAG
AAGTAGAGAGAATCCTGGGGCTGTTGCAAACATATTTCCGAAAGTACCCAGACACTCCCGTGTCCTATTTTGAGTTTGTG
ATTGATCCAACCTCTTTTTCTCGTACGGTGGAGAACATATTCTATGTTTCTTTCATTATAAGGGATGGTTTTGCAAGAAT
AAGGCTTGACCAAGACAGGCTGCCTATATTAGAACCCATTGACATTGACCAAATGGGTGAGGGCAGTGATTTCAGTTTCC
ATAGCCGTAAGCAGGGAATTATATCGTTGAGCTTACAGGACTGGAAAAATATCGTGGCCACCTTTGAAATTTCAGAGGCC
ATGATC

Alignment

ORF - retro_eeur_124 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.73 %
• Parental protein coverage: 56.1 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TFHFLLGSVQGEAPIPKPRTDRPRRVAAPEEQRAMPAQLKRMEES-HQEATEKEVERILGLLQTYFREDP
          TFHF...SV......PK.R....R.....EE...MP..L.RM.....QEATEKEVERILGLLQTYFR..P
Retrocopy TFHFMFSSVKTDSSAPKRRVEYRRKAPKMEESGDMPTKLRRMDLTCNQEATEKEVERILGLLQTYFRKYP

Parental  DTPMSFFDFVIDPHSFPRTVENIFHVSFIIRDGFARIRLDQDRLPIIEPININEASLVMDQNTQMRIQGI
          DTP.S.F.FVIDP.SF.RTVENIF.VSFIIRDGFARIRLDQDRLPI.EPI.I.......D.....R.QGI
Retrocopy DTPVSYFEFVIDPTSFSRTVENIFYVSFIIRDGFARIRLDQDRLPILEPIDIDQMGEGSDFSFHSRKQGI

Parental  IALISRDWEDIVKTFEISEPVI
          I.L...DW..IV.TFEISE..I
Retrocopy ISLSLQDWKNIVATFEISEAMI

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	16.28 RPM	11.44 RPM
SRP017611_kidney	2.81 RPM	28.51 RPM
SRP017611_liver	0.00 RPM	16.08 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_124 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 19 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010897	1 retrocopy	retro_amel_419,
Bos taurus	ENSBTAG00000019166	1 retrocopy	retro_btau_1387,
Canis familiaris	ENSCAFG00000012419	2 retrocopies	retro_cfam_1427, retro_cfam_379,
Choloepus hoffmanni	ENSCHOG00000003695	1 retrocopy	retro_chof_577,
Dipodomys ordii	ENSDORG00000003880	1 retrocopy	retro_dord_677,
Equus caballus	ENSECAG00000016651	2 retrocopies	retro_ecab_109, retro_ecab_465,
Erinaceus europaeus	ENSEEUG00000014906	1 retrocopy	retro_eeur_124 ,
Felis catus	ENSFCAG00000003647	1 retrocopy	retro_fcat_994,
Homo sapiens	ENSG00000107672	1 retrocopy	retro_hsap_43,
Loxodonta africana	ENSLAFG00000004214	1 retrocopy	retro_lafr_1051,
Macaca mulatta	ENSMMUG00000012044	1 retrocopy	retro_mmul_716,
Mustela putorius furo	ENSMPUG00000002960	1 retrocopy	retro_mputfur_396,
Nomascus leucogenys	ENSNLEG00000016919	1 retrocopy	retro_nleu_2073,
Otolemur garnettii	ENSOGAG00000010026	1 retrocopy	retro_ogar_280,
Pongo abelii	ENSPPYG00000002712	1 retrocopy	retro_pabe_878,
Pteropus vampyrus	ENSPVAG00000017186	2 retrocopies	retro_pvam_1163, retro_pvam_795,
Rattus norvegicus	ENSRNOG00000020452	1 retrocopy	retro_rnor_2515,
Ictidomys tridecemlineatus	ENSSTOG00000011112	1 retrocopy	retro_itri_36,
Vicugna pacos	ENSVPAG00000006534	1 retrocopy	retro_vpac_260,