RetrogeneDB ID: retro_eeur_35

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: GeneScaffold_1947:92327..92769(+)
• Located in intron of: ENSEEUG00000006651

Retrocopy information

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

Parental gene information

• Parental gene symbol: NUDT21
• Ensembl ID: ENSEEUG00000003402
• Aliases: None
• Description: nudix (nucleoside diphosphate linked moiety X)-type motif 21 [Source:HGNC Symbol;Acc:13870]

Sequence

>retro_eeur_35
AGGACTGTAGAAGTGGTTCCAGTTGCACATGAATGCTGGCTACCTTATCTGCCGATGCTACACTTGGCAATGACCTTTCT
TAAATTACTGGATAGTGACCTTAACCCAGGAGATGATGAAGTTAAAGAGGGATCAGGATGCTTAAGGACAAACAGGCTGG
ACCATCAAGATGGAGTCCTGCAAGACTGGGTCATTGGTAACTAAGAGAGACCAAATTTTTGAGCCTTCTCAGTATCCATA
CATTCTTATACATGTTGCAAAACCTAAAGAACTCAAGAAGTTGTTTTGGGTTCAACTTCAAGAGAAAACCACATTTGCAG
TCCCTAAAAGTGACTAGCTGGCAGCTGCAACATTGTTCAAATTGTATGATAGTGTACCAAGATAAGGATCTAGCTCTTCT
AATCTCCCTTCACTTTTGAGCAGGTTCAATTTTAGATACAAC

Alignment

ORF - retro_eeur_35 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.53 %
• Parental protein coverage: 66.08 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RTVEGVLIVHEHRLPHVLLLQLGTTFFKLPGGELNPGEDEV-EGLKRLMTEILGRQDGVLQDWVIDDCIG
          RTVE.V...HE..LP....L.L..TF.KL....LNPG.DEV.EG...L.T..L..QDGVLQDWV....IG
Retrocopy RTVEVVPVAHECWLPYLPMLHLAMTFLKLLDSDLNPGDDEVKEGSGCLRTNRLDHQDGVLQDWV----IG

Parental  NWWRPNF-EPPQYPYIPAHITKPKEHKKLFLVQLQEKALFAVPKNYKLVAAPLFELYDNAPGYGPIISSL
          N..RPNF.EP.QYPYI..H..KPKE.KKLF.VQLQEK..FAVPK...L.AA.LF.LYD..P..G...S.L
Retrocopy N*ERPNF>EPSQYPYILIHVAKPKELKKLFWVQLQEKTTFAVPKSD*LAAATLFKLYDSVPR*GSSSSNL

Parental  PQLLSRFNFIYN
          P.LLSRFNF.YN
Retrocopy PSLLSRFNFRYN

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	0.16 RPM	34.16 RPM
SRP017611_kidney	0.38 RPM	33.01 RPM
SRP017611_liver	0.00 RPM	19.61 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_35 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 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016628	1 retrocopy	retro_amel_540,
Callithrix jacchus	ENSCJAG00000012724	3 retrocopies	retro_cjac_1121, retro_cjac_2211, retro_cjac_4100,
Equus caballus	ENSECAG00000001043	1 retrocopy	retro_ecab_292,
Erinaceus europaeus	ENSEEUG00000003402	1 retrocopy	retro_eeur_35 ,
Loxodonta africana	ENSLAFG00000028465	1 retrocopy	retro_lafr_610,
Myotis lucifugus	ENSMLUG00000004968	2 retrocopies	retro_mluc_1576, retro_mluc_999,
Mustela putorius furo	ENSMPUG00000003451	1 retrocopy	retro_mputfur_158,
Oryctolagus cuniculus	ENSOCUG00000017224	2 retrocopies	retro_ocun_154, retro_ocun_87,
Sarcophilus harrisii	ENSSHAG00000009651	1 retrocopy	retro_shar_469,
Sus scrofa	ENSSSCG00000029848	2 retrocopies	retro_sscr_117, retro_sscr_185,
Tupaia belangeri	ENSTBEG00000007664	1 retrocopy	retro_tbel_4003,
Vicugna pacos	ENSVPAG00000003701	2 retrocopies	retro_vpac_340, retro_vpac_605,