RetrogeneDB ID: retro_eeur_8

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_244792:2809..4351(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSEEUG00000008014
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSEEUG00000012704
• Aliases: None
• Description: None

Sequence

>retro_eeur_8
ATGAAGGAGACTGCAGAGGCTTTCTTGGGTCACCCTATCAGCCATGCAGTGATCACTGTGCCTGCCTATTTCAATGATTC
ACAGCGCCAGGCCACCAAGGATGCAGGGGTGATTGCAGGTCTTAATGTTCTAAGAATTATCAATGAACCCACAGCAGCAG
CCATTGCCTACGGCTTAGATAAATCAGGTCAGGGGGAGCGACATGTCCTGATCTTTGATCTGGGTGGAGGCACATTTGAT
GTGTCCATCCTGACCATAGATGATGGGATCTTCGAGGTGAAGGCCACGGCAGGCGACACGCACCTGGGTGGCGAGGACTT
CGACAACCGGCTGGTGAGCCACTTTGTGGAGGAGTTCAAGAGGAAGCACAAGAAGGATATCAGCCAGAACAAGCGCGCCG
TGCGGCGGCTGCGCACAGCCTGCGAGAGGGCCAAGCGTACCCTGTCCTCCAGCACCCAGGCCAACCTGGAAATAGACTCC
TTGTATGAGGGTATTGACTTCTATACGTCCATCACCAGGGCGCGCTTTGAGGAGCTGTGCGCAGACCTATTTAGGGGCAC
TCTGGAGCCTGTGGAGAAGGCTCTTCGGGATGCTAAGATGGATAAAGCCAAAATTCATGACATTGTTTTAGTAGGAGGCT
CCACTCGTATTCCTAAGGTGCAGAAGCTGCTGCAGGACTACTTTAATGGCCGTGAACTCAACAAAAGCATCAACCCTGAT
GAGGCAGTAGCCTATGGGGCAGCAGTGCAGGCGGCCATCCTGATGGGGGACAAGTCGGAGAAGGTGCAGGACCTGCTGCT
GCTGGACGTGGCCCCGCTGTCGCTGGGGCTGGAGACGGCGGGCGGCGTGATGACGGCGCTCATCAAGCGCAACTCCACCA
TCCCCACCAAGCAGACACAGATTTTCACCACCTATTCAGATAACCAGCCTGGGGTGCTGATCCAGGTGTACGAGGGTGAG
CGGGCCATGACACGGGACAACAACCTGCTGGGGCGCTTTGACCTAACTGGAATCCCTCCTGCACCCCGAGGTATTCCTCA
GATCGAGGTGACTTTTGACATAGATGCCAATGGTATTCTAAATGTTACAGCTATGGATAAGAGCACTGGCAAGGCCAACA
AAATCACCATCACCAATGACAAGGGCCGGCTGAGCAAGGAGGACATCGAGCGCATGGTGCAGGATGCTGAGAAATATAAA
GCAGAGGATGAGATCCAGAGAGACAAAATTGCTGCAAAAAATGCTTTAGAATCCTATGCTTTTAACATGAAGAGTGCTGT
GAGTGATGAAGGCTTGAAGGACAAAATTAGTGAGTCTGATAAACAGAAAATATTGGACAAATGCAATGAGGTCCTTGCAT
GGCTGGAGACCAATCAACTGGCTGAGAAAGATGAGCTGGAGCATAAGAGAAAGGAATTGGAGCAGTTGTGTAACCCAATA
ATCTCCAACCTCTACCAGGGAGGGTGCACTGGCCCTACTTGTGCAACAGGAAACATACCTGGAAGGGCTGCCACAGGCCC
CACCATTGAAGAAGTAGATTAA

Alignment

ORF - retro_eeur_8 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.57 %
• Parental protein coverage: 94.36 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKEIAEAYLGKTVTNAVVTVPAYFNDSQRQATKDAGTIAGLNVLRIINEPTAAAIAYGLDKKVGAERNVL
          MKE.AEA.LG.....AV.TVPAYFNDSQRQATKDAG.IAGLNVLRIINEPTAAAIAYGLDK....ER.VL
Retrocopy MKETAEAFLGHPISHAVITVPAYFNDSQRQATKDAGVIAGLNVLRIINEPTAAAIAYGLDKSGQGERHVL

Parental  IFDLGGGTFDVSILTIEDGIFEVKSTAGDTHLGGEDFDNRMVNHFIAEFKRKHKKDISENKRAVRRLRTA
          IFDLGGGTFDVSILTI.DGIFEVK.TAGDTHLGGEDFDNR.V.HF..EFKRKHKKDIS.NKRAVRRLRTA
Retrocopy IFDLGGGTFDVSILTIDDGIFEVKATAGDTHLGGEDFDNRLVSHFVEEFKRKHKKDISQNKRAVRRLRTA

Parental  CERAKRTLSSSTQASIEIDSLYEGIDFYTSITRARFEELNADLFRGTLDPVEKALRDAKLDKSQIHDIVL
          CERAKRTLSSSTQA..EIDSLYEGIDFYTSITRARFEEL.ADLFRGTL.PVEKALRDAK.DK..IHDIVL
Retrocopy CERAKRTLSSSTQANLEIDSLYEGIDFYTSITRARFEELCADLFRGTLEPVEKALRDAKMDKAKIHDIVL

Parental  VGGSTRIPKIQKLLQDFFNGKELNKSINPDEAVAYGAAVQAAILSGDKSENVQDLLLLDVTPLSLGIETA
          VGGSTRIPK.QKLLQD.FNG.ELNKSINPDEAVAYGAAVQAAIL.GDKSE.VQDLLLLDV.PLSLG.ETA
Retrocopy VGGSTRIPKVQKLLQDYFNGRELNKSINPDEAVAYGAAVQAAILMGDKSEKVQDLLLLDVAPLSLGLETA

Parental  GGVMTVLIKRNTTISTKQTQTFTTYSDQQ-GVLIQXHESERAMTKGNNLLGKFELTGIPPAPCGVPQIEA
          GGVMT.LIKRN.TI.TKQTQ.FTTYSD.Q.GVLIQ..E.ERAMT..NNLLG.F.LTGIPPAP.G.PQIE.
Retrocopy GGVMTALIKRNSTIPTKQTQIFTTYSDNQPGVLIQVYEGERAMTRDNNLLGRFDLTGIPPAPRGIPQIEV

Parental  TFDIDANGILNVSSVDKSAGKENKITITNGKG-LSKENIEQMVQEAEKYKAEDEKQRDKVSSKNPFESYA
          TFDIDANGILNV...DKS.GK.NKITITN.KG.LSKE.IE.MVQ.AEKYKAEDE.QRDK...KN..ESYA
Retrocopy TFDIDANGILNVTAMDKSTGKANKITITNDKGRLSKEDIERMVQDAEKYKAEDEIQRDKIAAKNALESYA

Parental  FNIKVAVEDEKLQGKINDDYKQKILDKSNEINNWLDKNQTAAKEEFEHQQKELDKVCNPIITELYQSAGG
          FN.K.AV.DE.L..KI....KQKILDK.NE...WL..NQ.A.K.E.EH..KEL...CNPII..LYQ....
Retrocopy FNMKSAVSDEGLKDKISESDKQKILDKCNEVLAWLETNQLAEKDELEHKRKELEQLCNPIISNLYQGGCT

Parental  MPGGMPSGFPGGGA
          .P.......PG..A
Retrocopy GPTCATGNIPGRAA

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	0.16 RPM	895.48 RPM
SRP017611_kidney	0.75 RPM	1042.90 RPM
SRP017611_liver	0.00 RPM	396.63 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_8 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 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000012704	1 retrocopy	retro_eeur_8 ,
Microcebus murinus	ENSMICG00000004702	1 retrocopy	retro_mmur_7,
Sorex araneus	ENSSARG00000000161	1 retrocopy	retro_sara_31,
Tupaia belangeri	ENSTBEG00000011602	8 retrocopies	retro_tbel_1764, retro_tbel_344, retro_tbel_3488, retro_tbel_3524, retro_tbel_4348, retro_tbel_4412, retro_tbel_4490, retro_tbel_471,