RetrogeneDB ID: retro_chof_1398

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_28286:5948..6472(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBBP9
• Ensembl ID: ENSCHOG00000013286
• Aliases: None
• Description: retinoblastoma binding protein 9 [Source:HGNC Symbol;Acc:9892]

Sequence

>retro_chof_1398
ATTCCTGGGAATGGAGGCAGGGATGTGGCCACGCACAGCTGGTACGGCTGGGTGAGAATGGGGCTGGAGCAGATACCTGG
TTTCCAGTGTTTGGCTAAAAACATGCCTGACCCAATTTGGCTCAAGAGAGCATCTGGCTGCCCTTCTTGGAGACGGAGCT
CCACTGTGATGACAAGACCATCATCATAGGCTACGGTTCCAGGGCCACTGATGCCATGAGGTATGCAGAGACACATTGAG
TCTATGCTGTTATATTAGTGGCTGCCTACACATCAGACCCAGGGGATGAAAATGAGCGGGCAAGTGGATACTTCTACCGT
CCCTGGCAGTGGGAGAAGATCAAGGCCAACTGCCCTCACATTGTACAGTTTGGGTCTACAGATGATCCTTTCCTTCCCTG
GAAAGAGCAACAAGAAGTTGCTGATAGGCTGGAAGCCAAATTGTACAAATTCACTGATCGTGGCCACTTTCAGGTCACTG
AGTTTCACGAACTGATTAGCGTAGTGAAGTCTACGCTGAAAATA

Alignment

ORF - retro_chof_1398 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.55 %
• Parental protein coverage: 94.09 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VPGNGGGDVATHGWYGWVRKGLEQIPGFQCLAKNMPDPF-MARESIWLPFMETELHCDDKTIIIGHSSGA
          .PGNGG.DVATH.WYGWVR.GLEQIPGFQCLAKNMPDP...A.ESIWLPF.ETELHCDDKTIIIG..S.A
Retrocopy IPGNGGRDVATHSWYGWVRMGLEQIPGFQCLAKNMPDPI<LAQESIWLPFLETELHCDDKTIIIGYGSRA

Parental  IAAMXXXXXXXXXXXXXXXAYTSDLGNENERASGYFNRPWQWEKIKANCSHIVQFGSTDDPFLPWKEQQE
          ..AM...............AYTSD.G.ENERASGYF.RPWQWEKIKANC.HIVQFGSTDDPFLPWKEQQE
Retrocopy TDAMRYAETH*VYAVILVAAYTSDPGDENERASGYFYRPWQWEKIKANCPHIVQFGSTDDPFLPWKEQQE

Parental  VADRLEAKLYKFTDRGHFQNTEFHELISVVKSMLKV
          VADRLEAKLYKFTDRGHFQ.TEFHELISVVKS.LK.
Retrocopy VADRLEAKLYKFTDRGHFQVTEFHELISVVKSTLKI

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_1398 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013286	1 retrocopy	retro_chof_1398 ,
Callithrix jacchus	ENSCJAG00000005170	1 retrocopy	retro_cjac_768,
Macaca mulatta	ENSMMUG00000004146	1 retrocopy	retro_mmul_2604,
Rattus norvegicus	ENSRNOG00000007972	1 retrocopy	retro_rnor_1118,