RetrogeneDB ID: retro_eeur_633

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_371377:50193..50590(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PABPN1L
• Ensembl ID: ENSEEUG00000004747
• Aliases: None
• Description: poly(A) binding protein, nuclear 1-like (cytoplasmic) [Source:HGNC Symbol;Acc:37237]

Sequence

>retro_eeur_633
TCTATTTATGTGGACTCTGTGTACCATGAATCTCTGAGCTGAGAAGCTAGATGACCACTTCCACCACTGTGAGTACACCC
ACCAGCTCCCTAACTCTGTGACAAGTTCTCTGGACATCCCAAGGACTATGCCTACATAGAGTTTGACAGTGAGAATGTTG
TACAGGCTGTTGTGGGGCTGGACAGCAGTGTGTTCTGAGTCTGAATCGTTAAGGTACTGCTCAAAAGGACTAATTTCCCA
GGGATTAGCTATCTCCACAGATCAAGGAGCCACAGGGGCCACTTAAACACAAGAGGTGAGCCCTACCTCTGCAGTGGCCT
CCAAGTGGAGTTCCACTTCAAACTTCAGGGATGGAGCACTGGGCTGTGGAAAACTTTCACTATGGTACTCAATCTAT

Alignment

ORF - retro_eeur_633 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.74 %
• Parental protein coverage: 55.51 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SVYVGSVDYGGS-AEELEAHFNHCGNIHRVTI-LCDKFSGHPKGYAYIEFASESSVQAAVGLDSSVFRGR
          S.YV.SV......AE.L..HF.HC...H.....LCDKFSGHPK.YAYIEF.SE..VQA.VGLDSSVF...
Retrocopy SIYVDSVYHESL>AEKLDDHFHHCEYTHQLPN<LCDKFSGHPKDYAYIEFDSENVVQAVVGLDSSVF*V*

Parental  IIKVLPKRTNFPGISSTDRG-GPRSHLGTRGGPYLRNGLQAGAHFRFQGRNRGR-GKLSLWYSPY
          I.KVL.KRTNFPGIS...R....R.HL.TRG.PYL..GLQ...HF..QG...G..GKLSLWYS.Y
Retrocopy IVKVLLKRTNFPGISYLHRSRSHRGHLNTRGEPYLCSGLQVEFHFKLQGWSTGL>GKLSLWYSIY

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	0.48 RPM
SRP017611_kidney	0.00 RPM	0.00 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_633 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 4 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000023752	1 retrocopy	retro_btau_972,
Erinaceus europaeus	ENSEEUG00000004747	1 retrocopy	retro_eeur_633 ,
Ochotona princeps	ENSOPRG00000005597	2 retrocopies	retro_opri_1001, retro_opri_174,
Tursiops truncatus	ENSTTRG00000004691	3 retrocopies	retro_ttru_1488, retro_ttru_243, retro_ttru_822,