RetrogeneDB ID: retro_eeur_145

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: GeneScaffold_9036:578..1416(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TTLL1
• Ensembl ID: ENSEEUG00000004854
• Aliases: None
• Description: tubulin tyrosine ligase-like family, member 1 [Source:HGNC Symbol;Acc:1312]

Sequence

>retro_eeur_145
CTGACCCGCAGGGATCTCATGGTGAAGAATATTAAGCGGTGCAGGAAAGAACCGGGAAAGGAAGGAAGTTCGCTTGCAGA
AAAAGACGAAAATGAAATACCTCTATTTGGACTTTCTTCGGATCACCTACATGCTGCCAGCTGACTACAGCCTGTTCGTG
GAGGAGTTCCGAAAGAGCCCCTCCAGCAAGTGGACTGTAAAGATATGTGGTAAAGCTCCGGGCAAGGGCATCTTTCTCAT
TAACAAGCTCTCACAAATCAAGAAGTTGTACTGGGACAGCAAAACTTCCTCATTTATGACTCAGTCAATAGAAGAAGCCT
ACGTGATCTCTCTGTACATCAACAATCTGCTGCTCATTGGCAGGAAGTTGGACCTGAGCTTGTATGTCCTGGTGTCCACC
TACCTCCCACTGGGCTGCTACATGTATAAACTTGGATTTCGTCGTTTTTGCACAGGAAAATACATTCCAAATAACAGTGA
GCTGGATAACATGTTTGTGCACTTCACCAATATTGCCATTCAGAAACACGGGGAGGACTACAACCATATCCACGGGAGCA
AGTGGACTGTCAACAACCTGTGGCTCTAACTGGAGAGCACCTAGGGCAGGGAGGTGACCAGCAAGCTGTTCGAGGAGATC
CACTGGATCATCATGCAATCACTGAAGGCTGTGGCACCGGAGATGAATAACAACAAGTGGTGCTTTGAGTGATATGGCTA
CAACATCATCATCGGCAACAAATGGAAGCCTCGGCTGATTGAGGTGAATGTATCACCGTCGCTCACCTCCAGCATTACCA
ATGATCTAATACTGAAGTACAACCTCATCAATGACAGC

Alignment

ORF - retro_eeur_145 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.95 %
• Parental protein coverage: 66.59 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LTRKDLMVKNIKRYR-KELEKEGSPLAEKDENGKYLYLDFVPITYMLPADYNLFVEEFRKSPSSTWIMKP
          LTR.DLMVKNIKR.R.K..E.....L..K....KYLYLDF..ITYMLPADY.LFVEEFRKSPSS.W..K.
Retrocopy LTRRDLMVKNIKRCR>KNRERKEVRLQKKTKM-KYLYLDFLRITYMLPADYSLFVEEFRKSPSSKWTVKI

Parental  CGKAQGKGIFLINKLSQIKKWSRDSKTSSFVTQSTKEAYVISLYINNPLLIGGRKFDLRLYVLVSTYRPL
          CGKA.GKGIFLINKLSQIKK...DSKTSSF.TQS..EAYVISLYINN.LLIG.RK.DL.LYVLVSTY.PL
Retrocopy CGKAPGKGIFLINKLSQIKKLYWDSKTSSFMTQSIEEAYVISLYINNLLLIG-RKLDLSLYVLVSTYLPL

Parental  RCYMYKLGFCRFCTVKYTPSTSELDNMFVHLTNVAIQKHGEDYNHIHGGKWTVSNLRLYLESTRGREVTT
          .CYMYKLGF.RFCT.KY.P..SELDNMFVH.TN.AIQKHGEDYNHIHG.KWTV.NL.L.LEST.GREVT.
Retrocopy GCYMYKLGFRRFCTGKYIPNNSELDNMFVHFTNIAIQKHGEDYNHIHGSKWTVNNLWL*LEST*GREVTS

Parental  KLFDEIHWIIVQSLKAVAPVMNNDKHCFECYGYDIIIDDKLKPWLIEVNASPSLTSSTANDRILKYNLIN
          KLF.EIHWII.QSLKAVAP.MNN.K.CFE.YGY.III..K.KP.LIEVN.SPSLTSS..ND.ILKYNLIN
Retrocopy KLFEEIHWIIMQSLKAVAPEMNNNKWCFE*YGYNIIIGNKWKPRLIEVNVSPSLTSSITNDLILKYNLIN

Parental  DT
          D.
Retrocopy DS

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	24.98 RPM
SRP017611_kidney	0.00 RPM	12.94 RPM
SRP017611_liver	0.00 RPM	2.41 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_145 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000004854	1 retrocopy	retro_eeur_145 ,
Oryctolagus cuniculus	ENSOCUG00000016224	1 retrocopy	retro_ocun_1952,
Drosophila melanogaster	FBgn0030823	1 retrocopy	retro_dmel_24,