RetrogeneDB ID: retro_eeur_314

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_251432:3928..4301(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSEEUG00000012509
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SEC11A
• Ensembl ID: ENSEEUG00000015328
• Aliases: None
• Description: SEC11 homolog A (S. cerevisiae) [Source:HGNC Symbol;Acc:17718]

Sequence

>retro_eeur_314
CAGCTCTACTACCAGGTCTTGAACTTCACCATGATCGTGTCGTCAGTGCTCATGATCTGGAAAGGCCTGATTGTCCTCAG
CGAGAGCCCCATCGTGGTGGTGCTGAGTGGAAGCATGGAGCCAGCGCTCCACAGAGGAGACCTTCTGTTCCTGAAAAACT
TCGGGGAAGACCCCCATCAGAGCCGGAGAAATCGTCGTCTTCAAAGTTGAAGGCCTGGACATCCCAATCATTCACAGACT
GATAAAAGTTCATGAAAAAGGTAAAGGCAACATCAAATTTCTGACAAAAGGAGATAGTAATGAAGTTGATGGCCGAGGCT
TGTACAAGGAAGGCCAGAACTGGCTGGAGAAGGACTTGGCGGGGCGAGCTAGA

Alignment

ORF - retro_eeur_314 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.56 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QLYYQVLNFGMIVSSALMIWKGLMVVTGSESPIVVVLSGSMEPAFHRGDLLFLTNRVEDP-IRVGEIVVF
          QLYYQVLNF.MIVSS.LMIWKGL.V...SESPIVVVLSGSMEPA.HRGDLLFL.N..EDP.IR.GEIVVF
Retrocopy QLYYQVLNFTMIVSSVLMIWKGLIVL--SESPIVVVLSGSMEPALHRGDLLFLKNFGEDP>IRAGEIVVF

Parental  RIEGREIPIVHRVLKIHEKQNGNIKFLTKGDNNAVDDRGLYKQGQHWLEKKDVVGRAR
          ..EG..IPI.HR..K.HEK..GNIKFLTKGD.N.VD.RGLYK.GQ.WLE.KD..GRAR
Retrocopy KVEGLDIPIIHRLIKVHEKGKGNIKFLTKGDSNEVDGRGLYKEGQNWLE-KDLAGRAR

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	1.93 RPM	7.73 RPM
SRP017611_kidney	1.50 RPM	25.32 RPM
SRP017611_liver	2.25 RPM	13.18 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_314 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 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000015328	2 retrocopies	retro_eeur_314 , retro_eeur_412,
Macaca mulatta	ENSMMUG00000011486	1 retrocopy	retro_mmul_2343,
Monodelphis domestica	ENSMODG00000019364	1 retrocopy	retro_mdom_726,
Oryctolagus cuniculus	ENSOCUG00000008205	1 retrocopy	retro_ocun_849,
Otolemur garnettii	ENSOGAG00000007281	1 retrocopy	retro_ogar_3315,
Ictidomys tridecemlineatus	ENSSTOG00000019948	1 retrocopy	retro_itri_206,
Tupaia belangeri	ENSTBEG00000012320	3 retrocopies	retro_tbel_1139, retro_tbel_2280, retro_tbel_745,