RetrogeneDB ID: retro_chof_1372

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_27548:6571..6988(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNF8
• Ensembl ID: ENSCHOG00000013760
• Aliases: None
• Description: SNF8, ESCRT-II complex subunit [Source:HGNC Symbol;Acc:17028]

Sequence

>retro_chof_1372
ATAACTCTGGAGGAACTACATTAACAGGTGTTAAAGGGAAGGGGCAAGTTTGCCCAAGACATCAACCAAGACAACCTGAT
TGGGACCATCAGGAAATCAAAGGCACTTGGCACTGGCTTTAGCATCATTCTTGTGGGCAAATGGAACTTACCCCATTCGG
TCTGGTCCAGCTGAGCTCAGTATGGTCATGTCGTGGTGCTGCAGCTGGCAGAGAACAGTGAATGCATGACTGTCAGTGAA
ATCAAAGCTGGTCTTAAATGGGAGGCACAGCAAGAGGGGCAAATGCTGGAACATCTGCTGAAGGGGGGGCTGGCCTCGCT
GGACTTGCAGACCCCCAGGGAGGCCCACTGCTGGCTGCCCACTCTCTTCACTGGCCTCTCCTCCCAGGAGGTGACAGCCG
AAGAGACCAGAGACGCC

Alignment

ORF - retro_chof_1372 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.91 %
• Parental protein coverage: 53.49 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ITLEELHQQVLKGRGKFAQDVSQDDLIRAIKKLKALGTGFGIIPVGGTYLIQSVPAE-LNMDHTVVLQLA
          ITLEELH.QVLKGRGKFAQD..QD.LI..I.K.KALGTGF.II.VG...L..SV........H.VVLQLA
Retrocopy ITLEELH*QVLKGRGKFAQDINQDNLIGTIRKSKALGTGFSIILVGKWNLPHSVWSS*AQYGHVVVLQLA

Parental  EKNGCVTVSEIKASLKWETERARQVLEHLLKEGLAWLDLQAPGEAHYWLPALFTDLYSQEITAEEAREA
          E...C.TVSEIKA.LKWE.....Q.LEHLLK.GLA.LDLQ.P.EAH.WLP.LFT.L.SQE.TAEE.R.A
Retrocopy ENSECMTVSEIKAGLKWEAQQEGQMLEHLLKGGLASLDLQTPREAHCWLPTLFTGLSSQEVTAEETRDA

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_1372 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 15 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005062	1 retrocopy	retro_amel_164,
Canis familiaris	ENSCAFG00000016893	1 retrocopy	retro_cfam_1488,
Choloepus hoffmanni	ENSCHOG00000013760	1 retrocopy	retro_chof_1372 ,
Callithrix jacchus	ENSCJAG00000007322	2 retrocopies	retro_cjac_1175, retro_cjac_1922,
Echinops telfairi	ENSETEG00000000758	1 retrocopy	retro_etel_709,
Felis catus	ENSFCAG00000008944	2 retrocopies	retro_fcat_1291, retro_fcat_574,
Homo sapiens	ENSG00000159210	1 retrocopy	retro_hsap_2394,
Gorilla gorilla	ENSGGOG00000025290	1 retrocopy	retro_ggor_1816,
Macropus eugenii	ENSMEUG00000016638	1 retrocopy	retro_meug_663,
Mustela putorius furo	ENSMPUG00000015356	1 retrocopy	retro_mputfur_1425,
Mus musculus	ENSMUSG00000006058	1 retrocopy	retro_mmus_1050,
Nomascus leucogenys	ENSNLEG00000002743	1 retrocopy	retro_nleu_2520,
Oryctolagus cuniculus	ENSOCUG00000009156	2 retrocopies	retro_ocun_814, retro_ocun_996,
Pongo abelii	ENSPPYG00000008911	1 retrocopy	retro_pabe_2161,
Tarsius syrichta	ENSTSYG00000004576	1 retrocopy	retro_tsyr_843,