RetrogeneDB ID: retro_eeur_564

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_345317:11584..12493(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SGK1
• Ensembl ID: ENSEEUG00000008758
• Aliases: None
• Description: serum/glucocorticoid regulated kinase 1 [Source:HGNC Symbol;Acc:10810]

Sequence

>retro_eeur_564
ACAGCCTTCATGAAACAGAAGAGAATGAATCAGAGCAACTTTATTCAGAAAAATTTTAGTAACTCCTATGCATGCAGACA
CCCTGAAGTTCAGTCTACTTATAAAATCTCCCAAATGCAACATCCTAAGCTTATGACTGCCAACGCTTACTCTGCAAGTC
TTTCTCAGCAAATCAACATTAGACCATCATCCAGTCCTCATGCTAAACCCTCTAACTTCAGTTCCTTGAATGTGACTGGA
AAGGGCAGTTTGGGAAATGTCCTTCTAGCAAGACACAAAGCATTGCAGGTAGTCAGTCTTAAAGAAGAAAATAATCCTGG
AAAAGGGGGGAGGAAACGCCCATTATGGCAGAAAGAAGTGCTCTACTGAAACGTGAAATGACATTTCCTGGTGGGCTTTC
ACTTCACTTTCTAAACTGCTGATAAACTGTACTTTGTCCTGGATGACCTTAATGGTGGAGAATTGTTCTACTACCTCCAG
AGGGAATGTTGCTTCCTGAAACCAAAGACTCACTGCTGAGGAGCTGAAATAGCCGGAATTGTGTTTTACCTGTGCTCTCT
GAATATCATTTACAGAGACTTAAAACTAGAGAATGGTTTTGATAGATTCACAGACACACACAGACATACTGGCTTTGGAC
TCTGCAGAGAGAACATTGAACAAAGAGTACTGAGTCCACCTCCTGCAGCACACCTGAGTACCTGGGAGCTAACATACTTC
CTCAGCTGTCTTATGATAGAACTGTGGACTGGTGGTGCTGGGAGCTGTCTCATGTGAGTTTCTGTATATCCTGCCTCATT
TTTATAGATGAAACAAGCTGAGGTATATGACAGCATTCTGGGCAAGCCCTTTTAGTTGAAGATAAGTATTACAAATTCTG
TAAGACACTTCCTGGAGGGCCTCCTGCAG

Alignment

ORF - retro_eeur_564 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.53 %
• Parental protein coverage: 60.77 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 8

Retrocopy - Parental Gene Alignment:

Parental  SAFMKQRRMGLNDFIQKIANNSYACKHPEVQSILKISQPQEPELMNANPSPPSLSQQINIRPSSSPHAKP
          .AFMKQ.RM....FIQK...NSYAC.HPEVQS..KISQ.Q.P.LM.AN....SLSQQINIRPSSSPHAKP
Retrocopy TAFMKQKRMNQSNFIQKNFSNSYACRHPEVQSTYKISQMQHPKLMTANAYSASLSQQINIRPSSSPHAKP

Parental  SNFSSLNVTGKGSLGNVLLARHKALQVV-VLKKKIILE-KGE-TPIMAERSALL-NVK-HFLVGFHFTF-
          SNFSSLNVTGKGSLGNVLLARHKALQVV.VLKKKIILE..GE.TPIMAERSALL.NVK.HFLVGFHFTF.
Retrocopy SNFSSLNVTGKGSLGNVLLARHKALQVV>VLKKKIILE>RGEETPIMAERSALL>NVK*HFLVGFHFTF*

Parental  TADKLYFVLDDLNGGELFYYLQRECCFLKPKTHC-GAEIAGIVFYLCSLNIIYRDLKPEN-ILLDSQGHI
          TADKLYFVLDDLNGGELFYYLQRECCFLKPKTHC.GAEIAGIVFYLCSLNIIYRDLK.EN..L.DSQ.H.
Retrocopy TADKLYFVLDDLNGGELFYYLQRECCFLKPKTHC*GAEIAGIVFYLCSLNIIYRDLKLEN>VLIDSQTHT

Parental  VL-TDFGLCKENIEH-NGTTSTFCGTPEYLAPEVLHKQPYDRTVDWWC-LGAVLYEMLYGLPPFYSRN-T
          ...T.FGLC.ENIE....T.ST.C.TPEYL....L....YDRTVDWWC.LGAV..E.LY.LP.FY..N..
Retrocopy DI<TGFGLCRENIEQ<KSTESTSCSTPEYLGANILPQLSYDRTVDWWC<LGAVSCEFLYILPHFYR*N<Q

Parental  AEMYDNILNKPLQLKPNITNSARHLLEGLLQ
          AE.YD.IL.KP..LK..ITNS.RH.LEGLLQ
Retrocopy AEVYDSILGKPF*LKISITNSVRHFLEGLLQ

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	27.56 RPM
SRP017611_kidney	0.00 RPM	122.09 RPM
SRP017611_liver	0.00 RPM	17.20 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_564 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006626	1 retrocopy	retro_chof_2212,
Erinaceus europaeus	ENSEEUG00000008758	1 retrocopy	retro_eeur_564 ,
Loxodonta africana	ENSLAFG00000012698	1 retrocopy	retro_lafr_875,
Microcebus murinus	ENSMICG00000007886	1 retrocopy	retro_mmur_401,
Oryctolagus cuniculus	ENSOCUG00000014367	1 retrocopy	retro_ocun_1114,
Tursiops truncatus	ENSTTRG00000009699	1 retrocopy	retro_ttru_22,