RetrogeneDB ID: retro_eeur_109

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: GeneScaffold_7048:77889..78726(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LPCAT2
• Ensembl ID: ENSEEUG00000014277
• Aliases: None
• Description: lysophosphatidylcholine acyltransferase 2 [Source:HGNC Symbol;Acc:26032]

Sequence

>retro_eeur_109
AAATCCTTGTACCCGCCAGCTGTGGTCAATCCCTTTGTACAGAAGACGCACCTTAATGCTTGGCGCTGGGCCTACACCAT
CATCATGGGAACCGTGCTGCTGCCGTTGCGGGTGTCCTGCATCGCTTTCCTCTTCATCTTCCTCTGGCCAGCAGTCATGC
TTTACACCATAGGCCGCTCAACCCAACAATCCACGCCCACCAAGAGCTGGAGAAAAATATTGGTACAACCAGCCCTTAGG
TTCATGTTTCAGGCTGTGTTCTTTTTTGCAGGGTTCTTAGTAAGAGTAAGAGGGAAAAGGGCAACCCATGAAGAGGCCCC
CATCTTTGTGACAGCACCACACTCCTCTTTCTTCGACGCAATCGCCTGTGTGGTGGCGGGGTTACCCTCAGTGGTATCGG
CCTTACACAATGCACAAATCCCAATGATTGGCAGAATCCTCTTGACAACTCAGCCAGTGTTTGTGAACCGAGAAGATCTC
AATTCCAGGAGGAACACCCGGAACGAAATCGTGAAGCGAGTTACTTCTAATAGGAAGTGGCCACAGATCCTGATTTTCCC
GGAAGGAGTGTGTACCAACCGCACCTGTCTGATCACTTTCAGATTAGGTGCCTTCACTCCAGGTGTCCCTGTGCAACCAG
TGCTACTCAGGTACCCAAATGCCCTGGACACAGTCACGTGGACCTGGCAAGGGTTTTCAGCACTGCAAGCCTGTATGTTG
ACACTAAGCCAGCTCTTCACCAGGGTAGAAGTTGAGTTTATGCCTGTTTATATACCAAATGACATAGAAAAAAAAGACCC
TGTCCTTTTTGCCAACGCAGTGAGAGTCAGTATGGCA

Alignment

ORF - retro_eeur_109 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.99 %
• Parental protein coverage: 53.15 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QSFFPPPVCNPFVQQMRMGAVRMQI-FLLGIILLPIRALLVALIIVLAWPFAAISTACCPEKLTHPITGW
          .S..PP.V.NPFVQ.....A.R.......G..LLP.R....A......WP.....T.........P...W
Retrocopy KSLYPPAVVNPFVQKTHLNAWRWAYTIIMGTVLLPLRVSCIAFLFIFLWPAVMLYTIGRSTQQSTPTKSW

Parental  RRKITQPVMKFMGRAMFFSMGFVVTVKGKIASPVEAPIFVVAPHSTFFDGIACVLTGLPSIVSRCENVQV
          R....QP...FM..A.FF..GF.V.V.GK.A...EAPIFV.APHS.FFD.IACV..GLPS.VS...N.Q.
Retrocopy RKILVQPALRFMFQAVFFFAGFLVRVRGKRATHEEAPIFVTAPHSSFFDAIACVVAGLPSVVSALHNAQI

Parental  PLIGRLLRALQPVLVSRVDPDSRRNTINEIVKRATSGGEWPQILVFPEGTCTNRSCLITFKPGAFIPGVP
          P.IGR.L...QPV.V.R.D..SRRNT.NEIVKR.TS...WPQIL.FPEG.CTNR.CLITF..GAF.PGVP
Retrocopy PMIGRILLTTQPVFVNREDLNSRRNTRNEIVKRVTSNRKWPQILIFPEGVCTNRTCLITFRLGAFTPGVP

Parental  VQPVLLRYPNELDTVTWTWQGYTFIQLCMLTFCQPFTKVEVEFMPVQVPSDEEKHDPVLFAGRVRNLMA
          VQPVLLRYPN.LDTVTWTWQG....Q.CMLT..Q.FT.VEVEFMPV..P.D....DPVLFA..VR..MA
Retrocopy VQPVLLRYPNALDTVTWTWQGFSALQACMLTLSQLFTRVEVEFMPVYIPNDIXXXDPVLFANAVRVSMA

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	3.06 RPM	14.02 RPM
SRP017611_kidney	0.00 RPM	3.75 RPM
SRP017611_liver	0.80 RPM	2.89 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_109 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 20 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019272	1 retrocopy	retro_btau_64,
Callithrix jacchus	ENSCJAG00000012902	1 retrocopy	retro_cjac_2945,
Dasypus novemcinctus	ENSDNOG00000006859	1 retrocopy	retro_dnov_1735,
Dipodomys ordii	ENSDORG00000013193	1 retrocopy	retro_dord_399,
Equus caballus	ENSECAG00000009649	1 retrocopy	retro_ecab_865,
Erinaceus europaeus	ENSEEUG00000014277	1 retrocopy	retro_eeur_109 ,
Homo sapiens	ENSG00000087253	1 retrocopy	retro_hsap_185,
Gorilla gorilla	ENSGGOG00000005144	1 retrocopy	retro_ggor_266,
Loxodonta africana	ENSLAFG00000003965	1 retrocopy	retro_lafr_66,
Myotis lucifugus	ENSMLUG00000004008	1 retrocopy	retro_mluc_88,
Macaca mulatta	ENSMMUG00000004478	1 retrocopy	retro_mmul_392,
Mus musculus	ENSMUSG00000033192	1 retrocopy	retro_mmus_270,
Nomascus leucogenys	ENSNLEG00000001258	1 retrocopy	retro_nleu_994,
Pongo abelii	ENSPPYG00000007358	1 retrocopy	retro_pabe_445,
Pan troglodytes	ENSPTRG00000008124	2 retrocopies	retro_ptro_171, retro_ptro_2928,
Pteropus vampyrus	ENSPVAG00000007801	1 retrocopy	retro_pvam_173,
Rattus norvegicus	ENSRNOG00000016643	1 retrocopy	retro_rnor_309,
Sorex araneus	ENSSARG00000011914	1 retrocopy	retro_sara_88,
Sarcophilus harrisii	ENSSHAG00000012383	1 retrocopy	retro_shar_116,
Tursiops truncatus	ENSTTRG00000001182	1 retrocopy	retro_ttru_188,