RetrogeneDB ID: retro_chof_2539

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_83731:7634..8649(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HSPA9
• Ensembl ID: ENSCHOG00000013579
• Aliases: None
• Description: heat shock 70kDa protein 9 (mortalin) [Source:HGNC Symbol;Acc:5244]

Sequence

>retro_chof_2539
ATGATAACTGCCAGCCGAGCCACAGCTGCCCGTCTTGTCCACTCCCCAGCCTCCCAGAGTTCCATGGCCACCCACCACCA
GGATGGCTGGAATGGCCTTAGTCACAAGGCTTTTAGAATTATTTCAAGGCGGGACTACACATCAGAAGCAATCAAGGGAG
CAGTTGTTGGTATTGATTTGGGTACTACAACTCCTGTGTGGCAGTTATGGAAGGTAAACAAGCAAAGGTGCTGGAGAATG
CCGAAGGTGCCAGAACCACCCCTTCAGTTGTGGCCTTCACAGCAGATGGTGAGTGTCTTGTTGGTATGCCAGCCAAGAGA
CAGGCGTCACCAACCCAAATAACACATTCTATGCCACCAAGCTTCTTATTGGCCGGCGATATGATGACCCTGAAGTACAG
AAAGATATTAAAAATGTTCCCTTTAAAATTGTTCGTGCCTCCAATGGTGATGCCTGGGTTGAAGCTCATGGAAAACTCTA
TTCTCCAAGTCAAATTGGAGCATTTGTGTTGATGAAGATGAAGGAGATTGCAGAAAATTACTTGGGACATACAGCAAAAA
ATGCTGTGATCACAGTCCCAGCTTATTTCAATGACTCTCAGAGACAGGCCACTAAGGATACTGGTCAGATATCTGGACTA
AATGTTCTTCGAGTGATTAATGAACCCACAGCTACTGCTCTGGCCTCTGGTCTAGACAAATCAGAAGATAAAATCATTGC
TGTATATGATTTAGGTGGTGGAACCTTTGATATTTTTATTCTGGAAATTCAAAAAGGAGTGTTTGAGAGAAAATCCACCA
ATGGAGATACTTTCTTAGGTGGTGAAGACTTTGACCAGGCCTTGCTACAACACATTGTGAAGGAGTTCAAGACAGACACA
GGGGTTGATTTGACCAAAGACAATATGGTGCTTCAGAGGGTGTGGGAAGCTGCTGAGAAGGCCAAGTGTGAACTCTCTTC
ATCTGTACAGACTGACATCAACTTGCCATATCTTACAATGGGCGCTTCTGGACCC

Alignment

ORF - retro_chof_2539 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.38 %
• Parental protein coverage: 50.15 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MISASRAAAARLVRSPASRSSTASRHQDGWNGLSHKAFRIISRRDYASEAIKGAVVGIDLGTT-NSCVAV
          MI.ASRA.AARLV.SPAS.SS.A..HQDGWNGLSHKAFRIISRRDY.SEAIKGAVVGIDLGTT.NSCVAV
Retrocopy MITASRATAARLVHSPASQSSMATHHQDGWNGLSHKAFRIISRRDYTSEAIKGAVVGIDLGTT<NSCVAV

Parental  MEGKQAKVLENAEGARTTPSVVAFTADGERLVGMPAKRQA-VTNPNNTFYA-KRLIGRRYDDSEVQKDIK
          MEGKQAKVLENAEGARTTPSVVAFTADGE.LVGMPAKRQA.VTNPNNTFYA.K.LIGRRYDD.EVQKDIK
Retrocopy MEGKQAKVLENAEGARTTPSVVAFTADGECLVGMPAKRQA<VTNPNNTFYATKLLIGRRYDDPEVQKDIK

Parental  NVPFKIVRASNGDAWVEAHGKLYSPSQIGAFVLMKMKETAENYLGHTAKNAVITVPAYFNDSQRQATKDA
          NVPFKIVRASNGDAWVEAHGKLYSPSQIGAFVLMKMKE.AENYLGHTAKNAVITVPAYFNDSQRQATKD.
Retrocopy NVPFKIVRASNGDAWVEAHGKLYSPSQIGAFVLMKMKEIAENYLGHTAKNAVITVPAYFNDSQRQATKDT

Parental  GQISGLNVLRVINEPTAAALAYGLDKSEDKIIAVYDLGGGTFDISILEIQKGVFEVKSTNGDTFLGGEDF
          GQISGLNVLRVINEPTA.ALA.GLDKSEDKIIAVYDLGGGTFDI.ILEIQKGVFE.KSTNGDTFLGGEDF
Retrocopy GQISGLNVLRVINEPTATALASGLDKSEDKIIAVYDLGGGTFDIFILEIQKGVFERKSTNGDTFLGGEDF

Parental  DQALLQHIVKEFKRETGVDLTKDNMALQRVREAAEKAKCELFSSVQTDINLPYLTMDASGP
          DQALLQHIVKEFK..TGVDLTKDNM.LQRV.EAAEKAKCEL.SSVQTDINLPYLTM.ASGP
Retrocopy DQALLQHIVKEFKTDTGVDLTKDNMVLQRVWEAAEKAKCELSSSVQTDINLPYLTMGASGP

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_2539 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 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013579	2 retrocopies	retro_chof_2539 , retro_chof_293,
Homo sapiens	ENSG00000113013	1 retrocopy	retro_hsap_2214,
Gorilla gorilla	ENSGGOG00000014154	1 retrocopy	retro_ggor_1747,
Mus musculus	ENSMUSG00000024359	1 retrocopy	retro_mmus_3624,
Pan troglodytes	ENSPTRG00000017290	1 retrocopy	retro_ptro_1680,
Rattus norvegicus	ENSRNOG00000019525	1 retrocopy	retro_rnor_1797,