RetrogeneDB ID: retro_chof_2533

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_83241:1324..2197(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AKTIP
• Ensembl ID: ENSCHOG00000013690
• Aliases: None
• Description: AKT interacting protein [Source:HGNC Symbol;Acc:16710]

Sequence

>retro_chof_2533
ATGAACCCATTCTGGAGCATCTCTACAAGCTCTCCCTGCAAACGAGGTGATGATGAAGAGAAGATGTTTATAGGGGATGT
GAAAGTCAGTCCTCCATACAGTGCTCTGAAGAAACACTTGCCTTCTATTCCCAAAATGCTTTGCCCATAACTAAGCCTAC
ATCTCCTGCTCCAGCAGCACAGTCAACCAACGGCACACATGCCTCTTCCGGACCCTTCCACCTGGAATGCACTCTTCTTG
CAGAGTTTACCTTGGTTTGAAACAGAAGTTACTTGAGGTTCTGTGCAGCCATCTTATCACTCTGTATTAATGTGGTTCAG
AGTAATATTCATACAGCATGGACTTTATCAGGATAGATATTTAAGTTTACAGTTTACATCCCTGAATAACTACCCAAATG
GTGACTTGTCCATGCCTAGTGTTTGATATTCCCATCTTTCACCCACTAGCTGATGATCCCACTTCAGGTATACTGGATGT
GAAGGGACCATTTACAAAATGGAGGCAGAACCATAGCCATATTTGGCAAGTATTAATGTATGGAAGGAGGATTTTCCACA
AGATTGATGTAGCAAGTCCCCTAAACCCACAGGCTTTAGTACTGTATGAAAAAGATGTTCAGCTTTTTAAAAATAAAGTG
GTTGGCAGCATTAAGGTATGCACTGCTCCTTCATTTGAACAACCGAAAATAGAGGACCCCTATGCAATTAGCTTTTCTCT
GTGGAATCCTGCTGTATGTGGTGACACCAGAGAGAAGAAGTGACTCAGAAAAAGTATGAAGAACAGTACAGTCAGAGCAT
TAATGTTGCTTCTCTGTCATAGGTAAAACTTGGCTTAGTACAACCTTTCAACAAAGAAGAGAAAGCAATAGCA

Alignment

ORF - retro_chof_2533 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.58 %
• Parental protein coverage: 99.66 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  MNPFWSMSTSS-VRRSDGEEKSLTGDVKTSPPRTAPKKQLPSIPK-NALPITKPTSPAPAAQSTNGTHAS
          MNPFWS.STSS...R.D.EEK...GDVK.SPP..A.KK.LPSIPK.NALPITKPTSPAPAAQSTNGTHAS
Retrocopy MNPFWSISTSSPCKRGDDEEKMFIGDVKVSPPYSALKKHLPSIPK<NALPITKPTSPAPAAQSTNGTHAS

Parental  YGPFYLEYSLLAEFTLV-VKQKLPGVY-VQPSYRSALMWFGVIFIRHGLYQDG-VFKFTVYIPD-NYPDG
          .GPF.LE..LLAEFTLV..KQKL..V..VQPSY.S.LMWF.VIFI.HGLYQD...FKFTVYIP..NYP.G
Retrocopy SGPFHLECTLLAEFTLV<LKQKLLEVL<VQPSYHSVLMWFRVIFIQHGLYQDR<IFKFTVYIPE>NYPNG

Parental  D-CPRLVFDIPVFHPLVD-PTSGELDVKRAFAKWRRNHNHIWQVLMYARRVFYKIDTASPLNPEAAVLYE
          D.CP.LVFDIP.FHPL.D.PTSG.LDVK..F.KWR.NH.HIWQVLMY.RR.F.KID.ASPLNP.A.VLYE
Retrocopy D>CPCLVFDIPIFHPLADDPTSGILDVKGPFTKWRQNHSHIWQVLMYGRRIFHKIDVASPLNPQALVLYE

Parental  KDVQLFKSKVVESVKMCTARLFDQPKIEDPYAISFSPWNPSVHEEARDKM-LTQKKPEEQHNKSVHVAGL
          KDVQLFK.KVV.S.K.CTA..F.QPKIEDPYAISFS.WNP.V....R.K...TQKK.EEQ...S..VA.L
Retrocopy KDVQLFKNKVVGSIKVCTAPSFEQPKIEDPYAISFSLWNPAVCGDTREKK<VTQKKYEEQYSQSINVASL

Parental  SWVKPGSVQPFSKEEKTVA
          S.VK.G.VQPF.KEEK..A
Retrocopy S*VKLGLVQPFNKEEKAIA

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_2533 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.

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016345	1 retrocopy	retro_amel_392,
Canis familiaris	ENSCAFG00000009500	1 retrocopy	retro_cfam_1826,
Choloepus hoffmanni	ENSCHOG00000013690	2 retrocopies	retro_chof_2533 , retro_chof_629,
Callithrix jacchus	ENSCJAG00000001498	1 retrocopy	retro_cjac_2895,
Cavia porcellus	ENSCPOG00000006523	1 retrocopy	retro_cpor_622,
Dasypus novemcinctus	ENSDNOG00000004906	4 retrocopies	retro_dnov_1376, retro_dnov_1776, retro_dnov_2080, retro_dnov_756,
Equus caballus	ENSECAG00000020381	1 retrocopy	retro_ecab_504,
Homo sapiens	ENSG00000166971	2 retrocopies	retro_hsap_1458, retro_hsap_3152,
Gorilla gorilla	ENSGGOG00000014821	1 retrocopy	retro_ggor_1122,
Microcebus murinus	ENSMICG00000010810	3 retrocopies	retro_mmur_124, retro_mmur_333, retro_mmur_985,
Microcebus murinus	ENSMICG00000016793	1 retrocopy	retro_mmur_1191,
Monodelphis domestica	ENSMODG00000025788	1 retrocopy	retro_mdom_1881,
Nomascus leucogenys	ENSNLEG00000001106	1 retrocopy	retro_nleu_2660,
Otolemur garnettii	ENSOGAG00000014495	1 retrocopy	retro_ogar_365,
Oryzias latipes	ENSORLG00000013747	1 retrocopy	retro_olat_30,
Pongo abelii	ENSPPYG00000007351	2 retrocopies	retro_pabe_1204, retro_pabe_1205,
Pan troglodytes	ENSPTRG00000008116	1 retrocopy	retro_ptro_2282,
Rattus norvegicus	ENSRNOG00000011956	1 retrocopy	retro_rnor_1611,
Tupaia belangeri	ENSTBEG00000017105	5 retrocopies	retro_tbel_1063, retro_tbel_2864, retro_tbel_3350, retro_tbel_4130, retro_tbel_853,
Tursiops truncatus	ENSTTRG00000012705	1 retrocopy	retro_ttru_348,