RetrogeneDB ID: retro_chof_2212

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_58682:6414..7457(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SGK1
• Ensembl ID: ENSCHOG00000006626
• Aliases: None
• Description: serum/glucocorticoid regulated kinase 1 [Source:HGNC Symbol;Acc:10810]

Sequence

>retro_chof_2212
TCTACCTCACAGAACATCAACCTGGGACCATCTGGAAATCCTCATGCCAAACCAACAGATTTTGATTTCTTAAAAGTTAT
TGGAAAAAGAAGCTTTGGCAAAGTTCTTCTTGCAAAACGGAAACTGGATGGAAAATTTTATGCTGTTAAAGTGTTACAGA
AAAAAATAGTACTCAACAGAAAAGAGCAAAAACATATTATGGCTGAACGTAATGTACTCTTGAAAAATGTGAAGCATCCA
TTTTTGGTTTGATTACATTATTCTTTCCAAACAACTGAAAAGCTTTATTTTGTTCTGGATTTTGTTAATGGAGGGGAGCT
CTTCTTTCATTTACAAAGAGAAGGGTCCTTTCCTGAGCACAGAGCTAGGTTTTATGCTGCTGAAATTGCTAGTGCATTGG
GTTACTTGCACTCCATCAAAATAGTGTACAGAGACTTAAAACCAGAAAATATTCTTTTGGATTCAGTAGGACATGTTGTC
TACAGATTTGGCTTGTAAAGAAGGAATTGCTATTCGACACACACAACATTTTGTGGGACAGCAGAGTACTTTGCTCTGAA
GTCATCAGAAAACAGCCCTACGAGAACACAATAGACTGGTGGTGCGTGGGTGCTGTTCTGTATGAAATGCTCTATGGGTT
GCCTCTTTTTTATTGTCGAGATGTTTCTGAAATGTATGACAATATTCTTCACAAGCCTCTGAGTTTGAGGCCAGGAGTGA
GCCTCACAGCCTGGTCCATTCTGGAAGAACTCCTAGATAAAGACAGGCAAAATCGACTCAGTGCCAAAGAAGACTTTCTC
GAAATTCAGAATCATCCTTTTCTTGAATCTCTAAGCTGGATTGACCTTGTGCAAAAGAAGATTCCACCACCATTTAATCC
TAATGTGGCTGGACCAGATGATATCAAGAACTTTGATGCAGCATTTACAGAAGAAACCGTTCCATACTCTGTGTGTGTGT
CTTCTGACTACTCGATAGTGAACGCCAGTGTAATGGAAGTGGATGACACATTCCTTGGTTTCTCTTATGCACCTCCTTCA
GAA

Alignment

ORF - retro_chof_2212 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.34 %
• Parental protein coverage: 66.73 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SPSQQINLGPSSNPHAKPSDFHFLKVXXXXXXXXVLLARHKVEEAFYAVKVLQKKAILKKKEEKHIMSER
          S.SQ.INLGPS.NPHAKP.DF.FLKV........VLLA..K....FYAVKVLQKK..L..KE.KHIM.ER
Retrocopy STSQNINLGPSGNPHAKPTDFDFLKVIGKRSFGKVLLAKRKLDGKFYAVKVLQKKIVLNRKEQKHIMAER

Parental  NVLLKNVKHPFLVGLHFSFQTADKLYFVLDYINGGELFYHLQRERFFLEPRARFYAAEIASALGYLHSLN
          NVLLKNVKHPFLV.LH.SFQT..KLYFVLD..NGGELF.HLQRE..F.E.RARFYAAEIASALGYLHS..
Retrocopy NVLLKNVKHPFLV*LHYSFQTTEKLYFVLDFVNGGELFFHLQREGSFPEHRARFYAAEIASALGYLHSIK

Parental  IVYRDLKPENILLDSQGHIVLTDFGLCKENIEHNGTTSTFCGTPEY-LAPEVLHKQPYDRTVDWWCLGAV
          IVYRDLKPENILLDS.GH.V...FGL...N.....T..TFCGT.EY.L..EV..KQPY..T.DWWC.GAV
Retrocopy IVYRDLKPENILLDSVGHVVYR-FGL*RRNC--YSTHTTFCGTAEY<LCSEVIRKQPYENTIDWWCVGAV

Parental  LYEMLYGLPPFYSRNTAEMYDNILNKPLQLKPNITNSARHLLEGLLQKDRTKRLGAKDDFMEIKNHIFFS
          LYEMLYGLP.FY.R...EMYDNIL.KPL.L.P.....A...LE.LL.KDR..RL.AK.DF.EI.NH.F..
Retrocopy LYEMLYGLPLFYCRDVSEMYDNILHKPLSLRPGVSLTAWSILEELLDKDRQNRLSAKEDFLEIQNHPFLE

Parental  LINWDDLINKKITPPFNPNVSGPSDLRHFDPEFTEEPVPNSIGRSPDSILITASVKEAAEAFLGFSYAPP
          ...W.DL..KKI.PPFNPNV.GP.D...FD..FTEE.VP.S...S.D.....ASV.E....FLGFSYAPP
Retrocopy SLSWIDLVQKKIPPPFNPNVAGPDDIKNFDAAFTEETVPYSVCVSSDYSIVNASVMEVDDTFLGFSYAPP

Parental  MD
          ..
Retrocopy SE

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Choloepus hoffmanni was not studied using RNA-Seq expression data.

ChIP-Seq

Choloepus hoffmanni was not studied using ChIP-Seq data.

EST

Choloepus hoffmanni was not studied using EST data.

TSS

Choloepus hoffmanni was not studied using FANTOM5 data.

Lab

retro_chof_2212 was not experimentally validated.

Homology

Retrocopy orthology:

Choloepus hoffmanni 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.

---

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,