RetrogeneDB ID: retro_eeur_370

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_272796:244..886(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PTPN2
• Ensembl ID: ENSEEUG00000005636
• Aliases: None
• Description: protein tyrosine phosphatase, non-receptor type 2 [Source:HGNC Symbol;Acc:9650]

Sequence

>retro_eeur_370
AGTGGTGAAGCCAGAACCATCTCTCACTTCCATTACACTACCTGGCCAGATTTTGGAGTCCCTGAGTCACCAGCTTCATT
TCTCAATTTCTTATTTAAAGTGAGAGAATATGGCTCCCTGAATCCTGAGCATGGGCCTGCTGTGATCCACTGTAGTGCAG
GCATTGGGCGGTCAGGCACGTTTTCCCTAGTAGATACCTCTCTTGTTCTGATGGAAAAGGGAGATGAAATTAATATTAAA
CAACTATTACTGAATATGAGAAAGTACTGAATGGGACTTATTCAGACACCAGATCAACTCAGATTTTCGTATATGACTAT
TATAGAAGGAGCAAAATTCATAAAGGGAGGTCCAAGTATACAGAAAATGTGGAAAGAACTGTCTAAAGAAGACTTACATC
CTGCTTTTGATCACTCACCAGCCAGAATAATAACTGAAAAGTACAATGGCAACAGGGTAGGCCTAGAAGAAGGAAAGACG
ACAGGCGACAGACATACAGGATCATCCTCTAAAACTCAAGATCCTGTGGAGGAGAAAACAGAAAGTGTTCTGCGTATCTG
AGAGGACAGAAAAGCTATCACGGCTCAGAGAGTGCAGCAGATGAAGCAGAGGCTAAATGAGACTGAAAGAAAAAGAAAAA
GG

Alignment

ORF - retro_eeur_370 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.91 %
• Parental protein coverage: 52.05 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SGEARTISHFHYTTWPDFGVPESPASFLNFLFKVRESGSLNPEHGPAVIHCSAGIGRSGTFSLVDTSLVL
          SGEARTISHFHYTTWPDFGVPESPASFLNFLFKVRE.GSLNPEHGPAVIHCSAGIGRSGTFSLVDTSLVL
Retrocopy SGEARTISHFHYTTWPDFGVPESPASFLNFLFKVREYGSLNPEHGPAVIHCSAGIGRSGTFSLVDTSLVL

Parental  MEKGDEINIKQLLLNMRKYRMGLIQTPDQLRFSYMTIIEGAKFIKGGPSXXKMWKELSKEDLHPAFDHSP
          MEKGDEINIKQLLLNMRKY.MGLIQTPDQLRFSYMTIIEGAKFIKGGPS..KMWKELSKEDLHPAFDHSP
Retrocopy MEKGDEINIKQLLLNMRKY*MGLIQTPDQLRFSYMTIIEGAKFIKGGPSIQKMWKELSKEDLHPAFDHSP

Parental  ARIITEKYNGSRVSLEEGKTTGDRHTGLSSRTQDPVEEKTESVLRKRIREDRKAITAQRVQQMKQRLNET
          ARIITEKYNG.RV.LEEGKTTGDRHTG.SS.TQDPVEEKTESVL..RI.EDRKAITAQRVQQMKQRLNET
Retrocopy ARIITEKYNGNRVGLEEGKTTGDRHTGSSSKTQDPVEEKTESVL--RI*EDRKAITAQRVQQMKQRLNET

Parental  ERKRKR
          ERKRKR
Retrocopy ERKRKR

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	1.13 RPM	5.64 RPM
SRP017611_kidney	1.50 RPM	7.31 RPM
SRP017611_liver	2.25 RPM	3.22 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_370 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 14 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000867	1 retrocopy	retro_chof_2231,
Callithrix jacchus	ENSCJAG00000005102	1 retrocopy	retro_cjac_1577,
Dasypus novemcinctus	ENSDNOG00000016588	1 retrocopy	retro_dnov_1466,
Erinaceus europaeus	ENSEEUG00000005636	1 retrocopy	retro_eeur_370 ,
Echinops telfairi	ENSETEG00000005577	2 retrocopies	retro_etel_1743, retro_etel_1942,
Homo sapiens	ENSG00000175354	2 retrocopies	retro_hsap_1186, retro_hsap_480,
Gorilla gorilla	ENSGGOG00000010259	2 retrocopies	retro_ggor_453, retro_ggor_925,
Loxodonta africana	ENSLAFG00000011818	1 retrocopy	retro_lafr_701,
Macropus eugenii	ENSMEUG00000005156	1 retrocopy	retro_meug_653,
Monodelphis domestica	ENSMODG00000021422	1 retrocopy	retro_mdom_1225,
Nomascus leucogenys	ENSNLEG00000009074	3 retrocopies	retro_nleu_2112, retro_nleu_351, retro_nleu_894,
Otolemur garnettii	ENSOGAG00000028605	1 retrocopy	retro_ogar_3429,
Pongo abelii	ENSPPYG00000008983	3 retrocopies	retro_pabe_1077, retro_pabe_1144, retro_pabe_989,
Pan troglodytes	ENSPTRG00000009884	2 retrocopies	retro_ptro_361, retro_ptro_813,