RetrogeneDB ID: retro_chof_1006

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_183358:3438..3927(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL49
• Ensembl ID: ENSCHOG00000012855
• Aliases: None
• Description: mitochondrial ribosomal protein L49 [Source:HGNC Symbol;Acc:1176]

Sequence

>retro_chof_1006
ATGGCGATGACCATGTTCCTGGCTGCGCTGAGGGGCTAGAGAACCCGCGTCCGGCCGGGCTCGGGGCTACAGCGCATGAG
CCAGACCCAGGGACCTCCTGATTACCCCAGCTTTGCGGAGTCTGTGCTTGAATACCAGTTTGTGGAGCCCCTTATACCCC
TCACCAGCATTCCAAAGCCCCCAACGCATGAGCATATCCCACCCCCAGTGGCTGGCTAACCTTTTGAGACCCTCCGCCCA
ACCTGACTTACTTTGTGTCGCAGTCTCAATGCACAACATTCCTGTCTACGGGGACATCACACATGGCAACCATCAGATGA
CAGTGATCAGGAAGGTGGAGGGGAACAGCTGAGTCCTACAGAAAGATGTGGAGGATTCTCTGAGCCCACTTCTGGGCAAG
ACATCCAACACTCAGGTAAACAAAGCACCCTGCAGGTTAAGGGCTACGCTGACCAGCAGCTCAAAGCTTGGCTCCCGGAG
AAGGGCTTC

Alignment

ORF - retro_chof_1006 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.68 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAASVVRAVLWRWRTGVQPGRGLRHLSQTQGPPDYPSFVESAHEYQFVERLIPPTSIPKPPKHEQ-YHTP
          MA.....A.L...RT.V.PG.GL...SQTQGPPDYPSF.ES..EYQFVE.LIP.TSIPKPP.HE..Y.TP
Retrocopy MAMTMFLAALRG*RTRVRPGSGLQRMSQTQGPPDYPSFAESVLEYQFVEPLIPLTSIPKPPTHEH<YPTP

Parental  SGWQPPQDPPPNLPYFVRRSR-MHNIPVYRDITHGNRQMTVIRKVEGDIWALQKDVED-FLSPLLGKTPI
          SGW....DPPPNL.YFV..S..MHNIPVY.DITHGN.QMTVIRKVEG....LQKDVED.F..P..G....
Retrocopy SGWLTF*DPPPNLTYFVSQSQ<MHNIPVYGDITHGNHQMTVIRKVEGNS*VLQKDVED<FSEPTSGQD--

Parental  TQVNEVTGTLRVKGYVDQQLKAWLLEKGF
          .Q......TL.VKGY.DQQLKAWL.EKGF
Retrocopy IQHSGKQSTLQVKGYADQQLKAWLPEKGF

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_1006 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 11 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012855	1 retrocopy	retro_chof_1006 ,
Dasypus novemcinctus	ENSDNOG00000004494	6 retrocopies	retro_dnov_1396, retro_dnov_1488, retro_dnov_1941, retro_dnov_2272, retro_dnov_2473, retro_dnov_2686,
Dipodomys ordii	ENSDORG00000003613	1 retrocopy	retro_dord_196,
Homo sapiens	ENSG00000149792	1 retrocopy	retro_hsap_3180,
Macropus eugenii	ENSMEUG00000009437	1 retrocopy	retro_meug_1151,
Microcebus murinus	ENSMICG00000016604	1 retrocopy	retro_mmur_629,
Macaca mulatta	ENSMMUG00000018778	1 retrocopy	retro_mmul_2031,
Nomascus leucogenys	ENSNLEG00000005505	1 retrocopy	retro_nleu_1659,
Oryctolagus cuniculus	ENSOCUG00000014882	1 retrocopy	retro_ocun_316,
Pan troglodytes	ENSPTRG00000003867	1 retrocopy	retro_ptro_2263,
Tupaia belangeri	ENSTBEG00000007929	2 retrocopies	retro_tbel_1350, retro_tbel_3334,