RetrogeneDB ID: retro_eeur_666

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_378358:14739..15275(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NUP35
• Ensembl ID: ENSEEUG00000008469
• Aliases: None
• Description: nucleoporin 35kDa [Source:HGNC Symbol;Acc:29797]

Sequence

>retro_eeur_666
ATGGCTGCCTTCACTGTGGAACCCCAGGTGCTGAGGTTAGGTTCTGAACCAATGATGCCAGGTTCATCCATATCTACAAA
ACCAGGGGTTAATACACAATTCCTAACTGGATTTTTAATGGGGGATTTGCCAGAGCTGGTGACCCCATAACCTTGATCAA
TTAGTGATCCTTCAGCTGTAGTAATGGAGATGAGATCAGATGGTTCAGGTGGTTCACCACCGCAAATAGTTGTCCCAGCA
CATAAGGATAAAAGTGCAGCTCCACCAGTTACAAGCATATATGATGACATTTCCAGCCCAGGAAATGCATGTCTTCTTTA
GCTTCAAGAAGACAGCCAAACATTTCAGTAATGCAGAGCCCCCTTGTTGGAGTTATGTCAACTACTCCTGGAACAGGGCA
AAGTACATTTAGTTCAACAGGCATTGGTCAACCACGAAAAACAGCATTATCACCTGCCGAGCTGGATCCTTTTTATACTC
AAGGAGATTCTCTGACTTCAGAAAAACATATTGATGACATTAGGGTGACTGTGTTT

Alignment

ORF - retro_eeur_666 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.69 %
• Parental protein coverage: 55.56 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAAFAVEPQALTLGSEPMMLGSPTSPKPGVNAQFLPGFLMGDLPAPATPQPRSISGPAVGVMEMRSPVLA
          MAAF.VEPQ.L.LGSEPMM.GS..S.KPGVN.QFL.GFLMGDLP...TP.P.SIS.P...VMEMRS....
Retrocopy MAAFTVEPQVLRLGSEPMMPGSSISTKPGVNTQFLTGFLMGDLPELVTP*P*SISDPSAVVMEMRSDG-S

Parental  GGSPPQPVVPAHKDKSGAPPVRSIYDDISSPALGS-TPLTSRRQPNISVMQSPLVGVMTTTPGTGQSMFS
          GGSPPQ.VVPAHKDKS.APPV.SIYDDISSP.......L.SRRQPNISVMQSPLVGVM.TTPGTGQS.FS
Retrocopy GGSPPQIVVPAHKDKSAAPPVTSIYDDISSPGNAC<SSLASRRQPNISVMQSPLVGVMSTTPGTGQSTFS

Parental  PASIGQPRKTTLSPAQLDPFYTQGDSLTSEDHLDDTWVTVF
          ...IGQPRKT.LSPA.LDPFYTQGDSLTSE.H.DD..VTVF
Retrocopy STGIGQPRKTALSPAELDPFYTQGDSLTSEKHIDDIRVTVF

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	9.99 RPM
SRP017611_kidney	0.19 RPM	14.25 RPM
SRP017611_liver	0.00 RPM	3.05 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_666 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 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000008469	1 retrocopy	retro_eeur_666 ,
Homo sapiens	ENSG00000163002	1 retrocopy	retro_hsap_551,
Gorilla gorilla	ENSGGOG00000009919	1 retrocopy	retro_ggor_500,
Macaca mulatta	ENSMMUG00000004140	1 retrocopy	retro_mmul_2387,
Nomascus leucogenys	ENSNLEG00000006423	1 retrocopy	retro_nleu_2019,
Pongo abelii	ENSPPYG00000012998	1 retrocopy	retro_pabe_508,
Pan troglodytes	ENSPTRG00000012711	1 retrocopy	retro_ptro_414,
Ictidomys tridecemlineatus	ENSSTOG00000000711	2 retrocopies	retro_itri_755, retro_itri_760,