RetrogeneDB ID: retro_chof_2173

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_55426:8619..9416(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAD51AP1
• Ensembl ID: ENSCHOG00000010098
• Aliases: None
• Description: RAD51 associated protein 1 [Source:HGNC Symbol;Acc:16956]

Sequence

>retro_chof_2173
ATATCTTTAGATGACAAGCTCCACAAGAGAGACTTAGAAGTCACACTAGCATTATCAGTGAAGGAACTTCTGACAGCCAC
CATTGATGTGCAGGAGTCTCAAGATAAACACATTGAAAAACGTGGCAATAGTGAAACAGTAACAATGAATAAGTTTTCTC
ATATCTCTAACTGCAGTGTAGCCAGCAATTACTTATGTTTGGATAAGATTACTGAGGAAGATGATTTTCATGATGTTCAA
GGGAAAAGAAAAGCAGTATCTAAAGCTGTGGTATAACAGAGGAAGATTCTTTTGGAAGGCAGTGATGGCAATAGTATAAA
TGACTCCGAACCAGACTTTGCAACTAGTGAAGATGCTGAAGGATGATTTCCGATTTTGGTGAGAGTGAAGATAATGATGA
AAAGTTCACTATGAGAAAAAGTAAAACTAAAGAAATTAAAAAGAAAGAAGTGAAGGTAAAATTCCCAGTAGAAAAGAAAT
AGAAGAAATCTAAATCCAAATGTAATGCTTTGGTGACTTCAGAAGACTCTACACCAGCTGCCATCAAATTGGAATCTCAG
ACTTCATCAAAAATGGCTTCTCTTCCTTCAGTGGCCATTAGGAAACCATTACAAATGTGCAGTCCTTCGCTGAAAGCAAG
AGACCTAAGTGGGTCCCACCAGCGGTGTCTGGAAGTAGCAGCAACAGCAGCAGCCCATTGGCAGGAGTGTCCATTAAGTT
TCCAAGTCAGAGTCTCTGCCTTGGCTTATCCAGATTAGCGTCAGTTAAACTTTTGCATCCAAAATGCCACTGATAGC

Alignment

ORF - retro_chof_2173 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.58 %
• Parental protein coverage: 75.5 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MALDDKFYKRSLEVALALSVKEIPTVTIDGQESQDECIEKCGSTETETVKKSSHISNCSVANNYLGLDKI
          ..LDDK..KR.LEV.LALSVKE..T.TID.QESQD..IEK.G..ET.T..K.SHISNCSVA.NYL.LDKI
Retrocopy ISLDDKLHKRDLEVTLALSVKELLTATIDVQESQDKHIEKRGNSETVTMNKFSHISNCSVASNYLCLDKI

Parental  TEEDDFHDVQGKRKAASKAMVQRRKILLEGSDGDSVNDSEPDFATSEDAE-DD-SDFGESEDNDEEFTMR
          TEEDDFHDVQGKRKA.SKA.V..RKILLEGSDG.S.NDSEPDFATSEDAE.DD.SDFGESEDNDE.FTM.
Retrocopy TEEDDFHDVQGKRKAVSKAVV*QRKILLEGSDGNSINDSEPDFATSEDAE>DD>SDFGESEDNDEKFTMX

Parental  KSKTKEIKKKEVKVKSPVEKKEKKPKSKCNALVTSGDSTPAAIKSESQPSPKKASLPSVAVRKPLQMCSP
          ................PVEKK.KK.KSKCNALVTS.DSTPAAIK.ESQ.S.K.ASLPSVA.RKPLQMCSP
Retrocopy XXXXXXXXXXXXXXXXPVEKK*KKSKSKCNALVTSEDSTPAAIKLESQTSSKMASLPSVAIRKPLQMCSP

Parental  S-AESKRPKWVPPAVSGSSSNSSSPLAGVSVKSPSQSLRLGLSRLARVKPLHP-NATNS
          S.AESKRPKWVPPAVSGSSSNSSSPLAGVS.K.PSQSL.LGLSRLA.VK.LHP.NAT.S
Retrocopy S<AESKRPKWVPPAVSGSSSNSSSPLAGVSIKFPSQSLCLGLSRLASVKLLHP>NATDS

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_2173 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	ENSCHOG00000010098	1 retrocopy	retro_chof_2173 ,
Homo sapiens	ENSG00000111247	1 retrocopy	retro_hsap_2841,
Nomascus leucogenys	ENSNLEG00000003178	1 retrocopy	retro_nleu_1595,
Tupaia belangeri	ENSTBEG00000010089	1 retrocopy	retro_tbel_4671,