RetrogeneDB ID: retro_chof_1784

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_383414:1..591(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000006468
• Aliases: None
• Description: None

Sequence

>retro_chof_1784
ATGGATGATCTGTCACCGGAAGAAATTCAGCTGAGGGCTCACCAGGTTACTGATGAATCTCTGGAAAGTACAAGGAGAAT
CCTGGGTTTAGCCATTGAGTCTCAGGATACAGGAATCAAAACTATCACTATGCTGGATGAACAAGGGAAACAACTAAACT
GCATTGAAGAAGGCATGGACCAAATAAATAAAGACATGAGGGAAGCAGAAAAGACTTTAACAGAACTCAACAATTGCTGA
GGTCTTTGTGTCTGCCAATGTAATAGGACAAAGAACTTTGAGTCTGGTAAGGCCTATAAGGCAACATGGGGCAATGGTGG
AGACAATTCATCTAGCAATGTAATGTCTAAGCAGCCAGGCCGGGTGACAGTCAGCCTCAGCAAGCAGCAACAGGAACAGC
CTCTGGAGGATACATTTAATGTATAACTAATGATGCCAGAGAAGATGAAATGGAGGGGAACCTGACTCAGGTGGGTAGTA
TCCTGGGAAATCTAAAAAACATGGCCCTGGGCATGGGCAATGAGATTGAGGCTCAAAATCAACAAAAACATTGGATTACA
GAAAAGGCTGACACCAACAAAGATTGTATT

Alignment

ORF - retro_chof_1784 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.93 %
• Parental protein coverage: 93.84 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MDDLSPEEIQLRAHQVTDESLESTRRILGLAIESQDTGIKTITMLDEQGEQLNRIEEGMDQINKDMREAE
          MDDLSPEEIQLRAHQVTDESLESTRRILGLAIESQDTGIKTITMLDEQG.QLN.IEEGMDQINKDMREAE
Retrocopy MDDLSPEEIQLRAHQVTDESLESTRRILGLAIESQDTGIKTITMLDEQGKQLNCIEEGMDQINKDMREAE

Parental  KTLTELNKCCGLCVCPCNRTKNFESGKAYKATWGDGGDNSSSNVIYKQPGRVT-NGQPQQAATGATSGGY
          KTLTELN.C.GLCVC.CNRTKNFESGKAYKATWG.GGDNSSSNV..KQPGRVT.....Q.A...A..G.Y
Retrocopy KTLTELNNC*GLCVCQCNRTKNFESGKAYKATWGNGGDNSSSNVMSKQPGRVT<SQPQQAATGTASGG-Y

Parental  IKRITNDAREDEMEENLTQVGSILGNLKNMALDMGNEIEAQNQQIQRITEKADTNKDRI
          I..ITNDAREDEME.NLTQVGSILGNLKNMAL.MGNEIEAQNQQ...ITEKADTNKD.I
Retrocopy I*CITNDAREDEMEGNLTQVGSILGNLKNMALGMGNEIEAQNQQKHWITEKADTNKDCI

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_1784 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 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000015685	1 retrocopy	retro_acar_38,
Ailuropoda melanoleuca	ENSAMEG00000015774	1 retrocopy	retro_amel_206,
Bos taurus	ENSBTAG00000005661	2 retrocopies	retro_btau_1622, retro_btau_371,
Canis familiaris	ENSCAFG00000011105	2 retrocopies	retro_cfam_1073, retro_cfam_1780,
Choloepus hoffmanni	ENSCHOG00000006468	3 retrocopies	retro_chof_1, retro_chof_1652, retro_chof_1784 ,
Cavia porcellus	ENSCPOG00000003638	1 retrocopy	retro_cpor_862,
Felis catus	ENSFCAG00000013387	1 retrocopy	retro_fcat_1114,
Loxodonta africana	ENSLAFG00000005462	1 retrocopy	retro_lafr_839,
Microcebus murinus	ENSMICG00000000813	2 retrocopies	retro_mmur_1188, retro_mmur_377,
Monodelphis domestica	ENSMODG00000017889	1 retrocopy	retro_mdom_1772,
Mustela putorius furo	ENSMPUG00000009856	3 retrocopies	retro_mputfur_1181, retro_mputfur_692, retro_mputfur_915,
Mus musculus	ENSMUSG00000027287	1 retrocopy	retro_mmus_2570,
Rattus norvegicus	ENSRNOG00000050552	2 retrocopies	retro_rnor_1505, retro_rnor_2389,
Tarsius syrichta	ENSTSYG00000006589	2 retrocopies	retro_tsyr_1020, retro_tsyr_715,
Tursiops truncatus	ENSTTRG00000002561	1 retrocopy	retro_ttru_658,