RetrogeneDB ID: retro_eeur_605

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_360726:137849..138499(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM118B
• Ensembl ID: ENSEEUG00000007898
• Aliases: None
• Description: family with sequence similarity 118, member B [Source:HGNC Symbol;Acc:26110]

Sequence

>retro_eeur_605
CCAACAAAAAAACCCAGAAAGCTGCTTCCAAGTTTAAAAACAAAGGAGCCCTGGGAACTGTGCTCCTGATTGGAACAGGC
ACCAGTGCTCAAGTTGTACCTCACGTTCTAGCCCTAAGATCTTGTAAGGGCTTAATTCAGGCATTACTGGATGATGCCAC
TGTCTTTGATCTTCTAGAAGATGAGGAGAACAAGAAGTTTCAGAAATGTCCTCATGAAGACAAGAACCTTGTCCATGTTG
CCCATGGCCTCACCCAGAAACTCTTTCCTCGTACCAGTTATGTTTGATCCACATTTTTCAATGACTGTTTATATGAAGTA
TTTGATAATTTGGAGTCAAAGATGGAAGATTCTGGAAAATAGTTACTTCAGTCAATTCTCCACGTAATGGAAAATGGATC
CCTGGTACTCACTACAAATTTTGACAATCTTCTAGAACTGCATACAGCAGGTCATGGAAAACGGCTTGAATCCTTTGACC
TTACTGATGAGAAAAAGGTCTTCGAGTGGGCTCAGGAGAAGTGGAAGCTGAGTGTGTTGCATATCCATAGGGTCTACACT
AATCCGAGTGGCACTGTCCTTCATCCTGCTGTGTATCAGAATATCCTGAATGTGCTCAGGAACACTGACGTATCACAATG
TGCTCAGGAA

Alignment

ORF - retro_eeur_605 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.44 %
• Parental protein coverage: 60.8 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PTKKPRKLLPSLKTKKPREL-VLVIGTGISAAVAPQVPALKSWKGLIQALLDAAIDFDLLEDEESKKFQK
          PTKKPRKLLPSLKTK.P.EL.VL.IGTG.SA.V.P.V.AL.S.KGLIQALLD.A..FDLLEDEE.KKFQK
Retrocopy PTKKPRKLLPSLKTKEPWEL<VLLIGTGTSAQVVPHVLALRSCKGLIQALLDDATVFDLLEDEENKKFQK

Parental  CLHEDKNLVHVAHDLIQKLSPRTSNVRSTFFKDCLYEVFDDLESKMEDSGKQLLQSVLHLMENGALVLTT
          C.HEDKNLVHVAH.L.QKL.PRTS.V.STFF.DCLYEVFD.LESKMEDSGK.LLQS.LH.MENG.LVLTT
Retrocopy CPHEDKNLVHVAHGLTQKLFPRTSYV*STFFNDCLYEVFDNLESKMEDSGK*LLQSILHVMENGSLVLTT

Parental  NFDNLLELYAADQGKQLESLDLTDEKKVLEWAQEKRKLSVLHIHGVYTNPSGIVLHPAGYQN---VLRNT
          NFDNLLEL..A..GK.LES.DLTDEKKV.EWAQEK.KLSVLHIH.VYTNPSG.VLHPA.YQN...VLRNT
Retrocopy NFDNLLELHTAGHGKRLESFDLTDEKKVFEWAQEKWKLSVLHIHRVYTNPSGTVLHPAVYQNILNVLRNT

Parental  EVMREIQK
          .V....Q.
Retrocopy DVSQCAQE

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	14.50 RPM
SRP017611_kidney	0.00 RPM	13.69 RPM
SRP017611_liver	0.00 RPM	7.56 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_605 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000016718	1 retrocopy	retro_dord_554,
Erinaceus europaeus	ENSEEUG00000007898	1 retrocopy	retro_eeur_605 ,
Myotis lucifugus	ENSMLUG00000017329	1 retrocopy	retro_mluc_1535,
Oryctolagus cuniculus	ENSOCUG00000017049	1 retrocopy	retro_ocun_1272,
Otolemur garnettii	ENSOGAG00000008923	1 retrocopy	retro_ogar_1659,