RetrogeneDB ID: retro_eeur_174

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_143326:214..822(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CD9
• Ensembl ID: ENSEEUG00000009313
• Aliases: None
• Description: CD9 molecule [Source:HGNC Symbol;Acc:1709]

Sequence

>retro_eeur_174
CTGGCTGGGATCGCAGTCCTTGCCATTGGACTATGGTTGTGGTTCGACACTCAGACCAAAAGCATCTTGGAGCAGGACGA
TAACCACTCCAGCTTCCACACAGGAGTGTACATTCTGGTGGGCACTGGTGTTCTCATGACGCTGGTGGGGTTCCTGAGCT
GCTGTGGTGCTGTGCAAGAGTCCTAGTGCATGCTGGGACTGTTCTTCACCTTCCTCTTAGTGATATTCACCATTAAGATA
GTGCGGCCATCTGGGGATACTCTCACAAAGAAGAGGTGATTAAGGAAGTCCAGAAATTCTACCAGGACCCCTATACCAAG
ATGAAGAACAAGGATGAGCTGCAGAAGGAGACATTGAAGGCCATCCACTCCATATTGAACTGCTACAGGATGACCAGAGC
ACTTGAACAATTTCTCACTGACATCTGCCCTGAAAAGAAACTAATGAAAAGCATCACTACAAAGCCCTGCCCTCAAGCCA
TACAGGAGGTCTTCGACAAGTTCCACATCATCCGCGCCCTGGGCATCAGGATCTCTGTGGTGACTATATACGGCATGATC
TTCAGTATGATCCTGTTCTGTGCCATTCATAGAAGCAGAGAGATGGTC

Alignment

ORF - retro_eeur_174 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.9 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LAGIAVLAIGLWLRFDTQTKSIFEQENNHSSFYTGVYILIGAGALMMLVGFLGCCGAVQESQCMLGLFFT
          LAGIAVLAIGLWL.FDTQTKSI.EQ..NHSSF.TGVYIL.G.G.LM.LVGFL.CCGAVQES.CMLGLFFT
Retrocopy LAGIAVLAIGLWLWFDTQTKSILEQDDNHSSFHTGVYILVGTGVLMTLVGFLSCCGAVQES*CMLGLFFT

Parental  FLLVIFAIEI-AAAIWGYSHKEEVIKEVQKFYQDTYTKLKNKDELQKETLKAIHFALNCCGMTGALEQFL
          FLLVIF.I.I..AAIWGYSHKEEVIKEVQKFYQD.YTK.KNKDELQKETLKAIH..LNC..MT.ALEQFL
Retrocopy FLLVIFTIKI<SAAIWGYSHKEEVIKEVQKFYQDPYTKMKNKDELQKETLKAIHSILNCYRMTRALEQFL

Parental  TDICPEKKLMEGITTKPCPQAIQEVFDNKFHIIGAVGIGIAVVMIFGMIFSMILCCAIRRSREMV
          TDICPEKKLM..ITTKPCPQAIQEVFD.KFHII.A.GI.I.VV.I.GMIFSMIL.CAI.RSREMV
Retrocopy TDICPEKKLMKSITTKPCPQAIQEVFD-KFHIIRALGIRISVVTIYGMIFSMILFCAIHRSREMV

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	0.32 RPM	76.87 RPM
SRP017611_kidney	0.56 RPM	138.22 RPM
SRP017611_liver	0.16 RPM	57.08 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_174 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 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000009313	1 retrocopy	retro_eeur_174 ,
Felis catus	ENSFCAG00000006863	1 retrocopy	retro_fcat_1098,
Myotis lucifugus	ENSMLUG00000006901	1 retrocopy	retro_mluc_2384,
Monodelphis domestica	ENSMODG00000018053	3 retrocopies	retro_mdom_1490, retro_mdom_226, retro_mdom_872,
Mus musculus	ENSMUSG00000030342	1 retrocopy	retro_mmus_3022,
Ictidomys tridecemlineatus	ENSSTOG00000001348	1 retrocopy	retro_itri_768,