RetrogeneDB ID: retro_eeur_548

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_342493:94284..94987(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCNB1
• Ensembl ID: ENSEEUG00000005724
• Aliases: None
• Description: cyclin B1 [Source:HGNC Symbol;Acc:1579]

Sequence

>retro_eeur_548
CAACTACCAAAACCTGTGTAAAAGGAACCCCATACCTTTGGTGGAGCGAGAGCCCAAACCTGAACTATTACCTGAGCTCC
CTAGAGAAGAAAGGCTTTCACCTGAGCCTATTTTGTTGGATACTCCCTCTGTGAGCTCAATGGAAACACCTGAGTGTGCT
CCAGCAGAAGAAGATCTGTGCCAAGCTTTGTTGCAATTCTCTGATGTAATTCTTGCTGTGAGTGATGTGGATGCAGAAAA
TGGAGCTGACCCAAACCTCTGTAGTGAATACGTGAAAGATATCTATGCCTATCTGAGACAACTTGAGGAAGAGCAAGCAG
TTAAGCCAAGATACCTACTGGGTCATGAAGTCACTGGAAACATGAGAGTCATCTTAATTGACTAGCTAGTGCAGGTTCAA
ATGAAATTCAGGTTGTTGCAGGAGACTATGTATAAGACTGTTTCTATTATTGATCGGTTCATGCAGAACAACTAGGTGCC
CAAGAAGATGCTGCAGCCGGTTGGTGCTACTGCTATGTTTATTGCAAGCAAATATAAAGAGATGTACCTGCCAGAAATCA
GCGACTTTGCCTTTGTGACTGATAATACTTGCACTAAACACCAGGTCAGACAGATGGAAATAAATATTCTAAGAGCTTTA
AATTTTTGTTTGGGTTGCCCTCTGCCTCTGCACTTCCTTCATAGAGTGTCTAAGATCGGAGAG

Alignment

ORF - retro_eeur_548 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.4 %
• Parental protein coverage: 58.38 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KLPKPVEKEP-MPL-ERESKPELEPEPPREEKLSPEPILVDTPSASPMETSGCAPAEEDLCQA---FSDV
          .LPKPV.KEP..PL.ERE.KPEL.PE.PREE.LSPEPIL.DTPS.S.MET..CAPAEEDLCQA...FSDV
Retrocopy QLPKPV*KEP>IPLVEREPKPELLPELPREERLSPEPILLDTPSVSSMETPECAPAEEDLCQALLQFSDV

Parental  ILAVSDVDAEDGADPNLCSEYVKDIYVYLRQLEEEQAVKPKYLLGREVTGNMRAILIDWLVQVQMKFRLL
          ILAVSDVDAE.GADPNLCSEYVKDIY.YLRQLEEEQAVKP.YLLG.EVTGNMR.ILID.LVQVQMKFRLL
Retrocopy ILAVSDVDAENGADPNLCSEYVKDIYAYLRQLEEEQAVKPRYLLGHEVTGNMRVILID*LVQVQMKFRLL

Parental  QETMYMTVSIIDRFMQNNCVPKKMLQLVGVTAMFVASKYEEMYPPEIGDFAFVTDNTYTKHQIRQMEMKI
          QETMY.TVSIIDRFMQNN.VPKKMLQ.VG.TAMF.ASKY.EMY.PEI.DFAFVTDNT.TKHQ.RQME..I
Retrocopy QETMYKTVSIIDRFMQNN*VPKKMLQPVGATAMFIASKYKEMYLPEISDFAFVTDNTCTKHQVRQMEINI

Parental  LRALNFGLGRPLPLHFLRRASKIGE
          LRALNF.LG.PLPLHFL.R.SKIGE
Retrocopy LRALNFCLGCPLPLHFLHRVSKIGE

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	0.00 RPM	1.61 RPM
SRP017611_kidney	0.00 RPM	0.94 RPM
SRP017611_liver	0.00 RPM	0.16 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_548 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 10 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014239	2 retrocopies	retro_btau_1317, retro_btau_600,
Canis familiaris	ENSCAFG00000007705	1 retrocopy	retro_cfam_213,
Callithrix jacchus	ENSCJAG00000016075	1 retrocopy	retro_cjac_4137,
Cavia porcellus	ENSCPOG00000014629	1 retrocopy	retro_cpor_13,
Erinaceus europaeus	ENSEEUG00000005724	2 retrocopies	retro_eeur_386, retro_eeur_548 ,
Mustela putorius furo	ENSMPUG00000014648	1 retrocopy	retro_mputfur_58,
Procavia capensis	ENSPCAG00000002451	1 retrocopy	retro_pcap_176,
Sarcophilus harrisii	ENSSHAG00000007685	1 retrocopy	retro_shar_290,
Tupaia belangeri	ENSTBEG00000011817	4 retrocopies	retro_tbel_1185, retro_tbel_3200, retro_tbel_4185, retro_tbel_4531,
Tarsius syrichta	ENSTSYG00000008928	1 retrocopy	retro_tsyr_232,