RetrogeneDB ID: retro_ocun_1114

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 2:113032634..113033392(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SGK1
• Ensembl ID: ENSOCUG00000014367
• Aliases: SGK1, SGK
• Description: serum/glucocorticoid regulated kinase 1 (SGK1), mRNA [Source:RefSeq mRNA;Acc:NM_001082056]

Sequence

>retro_ocun_1114
AGGCTGCAAGGGGCAATGGTAGCAATCCTCATCACTTTCATGAAGCAGAGGATGGGCCTGAATGACTTTATTCAGAAGAT
GGCCAATAATTCCTCTATGTGCAAACACCCTGAAGTTCAGTCCATTTTGAAAATCTCCCAACCTCAGGAGCCCAAGCTTA
TGAATGCCAACCCTTCTTCTCTACCAAGTCCATCTCAACAAATCAACCTTGGCCCATCATCAAATCCTCATGCTAAACCG
TCAGACTCACTTCTTAAAGTGATTGGAAAGGGCAATTTTGGCAAAATTCTTCCAGCGAGACACGAAGCAGAGGAAGCCTT
CTATGCAGTCAAGGTTTTGCAGAAGAAAGCAATTCTGAGAAGGAGGAGAAGCATATTATGTCTGAGTGGAATGTGCTGCT
GAATGTGAAACACCCTTTCCTGGTGGGCCTGCACTTCTGCCAGACTGCTGACAAACTGTACTTTGTCCTAGACTATGTTA
ACAGTGGAGAGTTGTTCTACCATCTCCAGAGGGAGCGCTGCTTCCTGGAACCACAGGTGCTTTTCTATGCTGCTGAGATA
GCCAGTGCCTGGGGTTACCTGAACATCATTTATAGAGATTTGAAGCTGGAGAATACTTTACTAGATTTACAGGGACACAT
CGTCCTTGCTGACTTTGGACTGTGCAAGGGGAACACTGAACACAACGGCATGATGTCCACCTTCTGTGGCACACCTGAGT
ATCTTGCACCTGAGGTGCTTCACAAGGTGCCTTATGAT

Alignment

ORF - retro_ocun_1114 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.06 %
• Parental protein coverage: 60.32 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RMRG-MVAILIAFMKQRRMGLNDFIQKIANNSYACKHTEVQSILKISQPQEPELMNANPSPPPSPSQQIN
          R..G.MVAILI.FMKQR.MGLNDFIQK.ANNS..CKH.EVQSILKISQPQEP.LMNANPS..PSPSQQIN
Retrocopy RLQGAMVAILITFMKQR-MGLNDFIQKMANNSSMCKHPEVQSILKISQPQEPKLMNANPSSLPSPSQQIN

Parental  LGPSSNPHAKPSDFHFLKVIGKGSFGKVLLARHKAEEAFYAVKVLQKKAILK-KKEEKHIMSERNVLLKN
          LGPSSNPHAKPSD...LKVIGKG.FGK.L.ARH.AEEAFYAVKVLQKKAIL..K.E..HIMSE.NVLL.N
Retrocopy LGPSSNPHAKPSD-SLLKVIGKGNFGKILPARHEAEEAFYAVKVLQKKAILR<KEEK-HIMSEWNVLL-N

Parental  VKHPFLVGLHFSFQTADKLYFVLDYINGGELFYHLQRERCFLEPRARFYAAEIASALGYLHSLNIVYRDL
          VKHPFLVGLHF..QTADKLYFVLDY.N.GELFYHLQRERCFLEP...FYAAEIASA.GYL...NI.YRDL
Retrocopy VKHPFLVGLHFC-QTADKLYFVLDYVNSGELFYHLQRERCFLEPQVLFYAAEIASAWGYL---NIIYRDL

Parental  KPENILLDSQGHIVLTDFGLCKENIEHNGTTSTFCGTPEYLAPEVLHKQPYD
          K.EN.LLD.QGHIVL.DFGLCK.N.EHNG..STFCGTPEYLAPEVLHK.PYD
Retrocopy KLENTLLDLQGHIVLADFGLCKGNTEHNGMMSTFCGTPEYLAPEVLHKVPYD

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	73.62 RPM
SRP017611_kidney	0.00 RPM	113.92 RPM
SRP017611_liver	0.00 RPM	102.36 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1114 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1114 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1114 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 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	ENSOCUG00000006428	1 retrocopy	retro_ocun_830,
Oryctolagus cuniculus	ENSOCUG00000014367	1 retrocopy	retro_ocun_1114 ,
Tursiops truncatus	ENSTTRG00000009699	1 retrocopy	retro_ttru_22,