RetrogeneDB ID: retro_chof_2250

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_60671:3009..3585(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NRBF2
• Ensembl ID: ENSCHOG00000004648
• Aliases: None
• Description: nuclear receptor binding factor 2 [Source:HGNC Symbol;Acc:19692]

Sequence

>retro_chof_2250
CTCATCAACAGAGCAGACAGAAGAGCAGACCGTTTATTAGCTACAGGGAAATGCGAAGAGGCTATTTCTTATCACAAGAA
AGCTGTGGCATATCTTTCTGAAGCCATGAAGCTGACCCAGTCTGAGCAGGCTCATTTATCACTGGAATTGCAAAGGGATA
GCCACATGAAACAGCTCCTCCTCATCCAGGAGAGGTGGAAAAGGCAAAGCGTGAGGAAAGATTGAAAGCCCAGCAGAACA
CAAACAAGGATGTAGTTACCCATCTTCAGGCATCTCACAAACCCTCTGCTGAGGATGCAGAGGGTCAGAGTCCCCTTCTT
ACTCAGAAGTACAACCCTTCCACAAAGAAACATCCGCCTGAAATTCAGGGGGTCTTTGACAGGGATCCAGACACACTACT
ATTTTTACTTAAGCAAAAGAGTGAGACCAACAGAGGCATGCATTGGAAGCAAAGCCCCAAAAGATGATAAAACAATTATA
GAGGAGCAGGCAACCAAAATTGTACATTTGAAGAGGCATGTGGAGTTCCTTGTGGCTGAGAATGAAAGATTAAGGAAAGA
AAATAAACAGTTAAAG

Alignment

ORF - retro_chof_2250 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.66 %
• Parental protein coverage: 92.23 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LAHQQSRRADRLLATGKYEEAISCHKKAAAYLSEAMKLTQSEQAHLSLELQRDSHMKQLLLIQERWKR-A
          L.....RRADRLLATGK.EEAIS.HKKA.AYLSEAMKLTQSEQAHLSLELQRDSHMKQLLLIQERWKR.A
Retrocopy LINRADRRADRLLATGKCEEAISYHKKAVAYLSEAMKLTQSEQAHLSLELQRDSHMKQLLLIQERWKR<A

Parental  KREERLKAQQNTDKDVATHLQASHKPSAEDAEGQSPLLTQKYSPSTEKHLPEIQGVFDRDPDTLLFLLQQ
          KREERLKAQQNT.KDV.THLQASHKPSAEDAEGQSPLLTQKY.PST.KH.PEIQGVFDRDPDTLLFLL.Q
Retrocopy KREERLKAQQNTNKDVVTHLQASHKPSAEDAEGQSPLLTQKYNPSTKKHPPEIQGVFDRDPDTLLFLLKQ

Parental  KSE-PTEACIGSKAPKDDKTIIEEQATKIADLKRHVEFLVAEER--RKENKQLK
          KSE.PTEACIGSKAPKDDKTIIEEQATKI..LKRHVEFLVAE....RKENKQLK
Retrocopy KSE>PTEACIGSKAPKDDKTIIEEQATKIVHLKRHVEFLVAENERLRKENKQLK

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_2250 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 13 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004648	3 retrocopies	retro_chof_1032, retro_chof_2250 , retro_chof_2568,
Homo sapiens	ENSG00000148572	3 retrocopies	retro_hsap_2643, retro_hsap_3999, retro_hsap_433,
Gorilla gorilla	ENSGGOG00000013016	2 retrocopies	retro_ggor_1846, retro_ggor_2685,
Macropus eugenii	ENSMEUG00000010849	3 retrocopies	retro_meug_1385, retro_meug_2049, retro_meug_671,
Macaca mulatta	ENSMMUG00000017726	1 retrocopy	retro_mmul_1523,
Monodelphis domestica	ENSMODG00000017183	1 retrocopy	retro_mdom_1995,
Mus musculus	ENSMUSG00000075000	2 retrocopies	retro_mmus_1278, retro_mmus_1279,
Otolemur garnettii	ENSOGAG00000005856	1 retrocopy	retro_ogar_2110,
Pongo abelii	ENSPPYG00000002411	3 retrocopies	retro_pabe_2327, retro_pabe_3285, retro_pabe_3286,
Pan troglodytes	ENSPTRG00000002539	3 retrocopies	retro_ptro_1780, retro_ptro_194, retro_ptro_2715,
Rattus norvegicus	ENSRNOG00000000641	2 retrocopies	retro_rnor_1681, retro_rnor_994,
Sarcophilus harrisii	ENSSHAG00000004744	1 retrocopy	retro_shar_427,
Ictidomys tridecemlineatus	ENSSTOG00000011341	1 retrocopy	retro_itri_183,