RetrogeneDB ID: retro_chof_2172

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_554:28744..29592(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDC20
• Ensembl ID: ENSCHOG00000006680
• Aliases: None
• Description: cell division cycle 20 [Source:HGNC Symbol;Acc:1723]

Sequence

>retro_chof_2172
ATGGCACAGTTTCTGTTCCAGAGAGATCTGTACTCCCTGCTCCAAGTGGATGCATCCATCCCCAATGCAGCACCTGCTCA
CTGGCAGCTCAAAGCCAAGGACTCTGTGGGGCCAGCCCCCTCACCCCAGAGGTTAGCCTACCCATCCCACAGTGCCAGCA
GGACCTGAGCCCCAATTCCTGGAAAAATCCAGCTCCAAAGCTCAAACAGTTCCCAGCCAAGTGGGCAGTGACTGCTACAT
CCACCATCACAGTGATTCCCAGAGGGAGGTGGCCAGCTTCCTTCTAAGCTGAGAGAGTGAAACTGAACACAGCCAGACAC
CCACTATGAAAGATCTTCAGAAAGCCTGGGCCTTGAATCTGAATGGTTTCGATGCAGAAGCAGTCAAGATCCTTTGTCTC
AGTGGAAAACCCCAGAATGCCCCAGAGGGTCACCAGAACAGACTGAATATGCTTTATAGCTAGAGAGCAATGCCTGGCTC
CAGCTGAAAGACCTGCTGATACATTCCTTCCCTCCCAGGCCATATCCTCAATGCCCTGGATATCCAGGATGACTTCTGCC
TGAACCTCGTGGACAGAAGTTATGGGAGCTTACTGACTGTGGTGCTGGACAACAGTGTATACTTGTGGAGTGCTAACTCT
GGTGACATCCTGCAGCTGCTGCAAATGGAGCAGCCTGGGGTCTACATGTGCTCCATGGCCTGGGTCAAAGGGGACCAGTA
CCTGGCTGTGGGCACCAGCAGTGCTGAGGTGCAGCTATGGGATGTGCAGCAGCAGAAATGGCTTTGAAGCATGACCAGTC
ACTCTGCACAAGTGGGATCCCTTTTCTTGGAACAGCTATATCCCATCC

Alignment

ORF - retro_chof_2172 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.83 %
• Parental protein coverage: 56.51 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAQFVFESDLHSLLQLDAPIPNAPPARWQRKAKDSMGPAPSPMRAANRSHSAGRTPGRTPGK-SSSKAQT
          MAQF.F..DL.SLLQ.DA.IPNA.PA.WQ.KAKDS.GPAPSP.R.A..SHSA.RT....PGK.SSSKAQT
Retrocopy MAQFLFQRDLYSLLQVDASIPNAAPAHWQLKAKDSVGPAPSPQRLAYPSHSASRT*APIPGK>SSSKAQT

Parental  TPSKAGGDRYIPHRSASQMEVASFLLSKENQPENSQTPTKKEHQKAWALNLNGFDVEEAKILRLSGKPQN
          .PS..G.D.YI.H.S.SQ.EVASFLLS.E...E.SQTPT.K..QKAWALNLNGFD.E..KIL.LSGKPQN
Retrocopy VPSQVGSDCYIHHHSDSQREVASFLLS*ESETEHSQTPTMKDLQKAWALNLNGFDAEAVKILCLSGKPQN

Parental  APEGYQNRLKVLYSQKATPGSSRKTCRYIPSLPDRILDAPEIRNDYYLNLVDWSSGNVLAVALDNSVYLW
          APEG.QNRL..LYS..A.PGSS.KTC.YIPSLP..IL.A..I..D..LNLVD.S.G..L.V.LDNSVYLW
Retrocopy APEGHQNRLNMLYS*RAMPGSS*KTC*YIPSLPGHILNALDIQDDFCLNLVDRSYGSLLTVVLDNSVYLW

Parental  SASSGDILQLLQMEQPGEYVSSVAWIKEGNYLAVGTSSAEVQLWDVQQQKRLRNMTSHSARVGSL-CWNS
          SA.SGDILQLLQMEQPG.Y..S.AW.K...YLAVGTSSAEVQLWDVQQQK.L..MTSHSA.VGSL..WNS
Retrocopy SANSGDILQLLQMEQPGVYMCSMAWVKGDQYLAVGTSSAEVQLWDVQQQKWL*SMTSHSAQVGSL>SWNS

Parental  YILS
          YI.S
Retrocopy YIPS

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_2172 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 10 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006680	2 retrocopies	retro_chof_2172 , retro_chof_2286,
Callithrix jacchus	ENSCJAG00000003414	1 retrocopy	retro_cjac_1608,
Homo sapiens	ENSG00000117399	1 retrocopy	retro_hsap_4187,
Gorilla gorilla	ENSGGOG00000010419	1 retrocopy	retro_ggor_96,
Mus musculus	ENSMUSG00000006398	1 retrocopy	retro_mmus_1536,
Nomascus leucogenys	ENSNLEG00000013419	1 retrocopy	retro_nleu_2847,
Pongo abelii	ENSPPYG00000001448	1 retrocopy	retro_pabe_3428,
Pan troglodytes	ENSPTRG00000000634	1 retrocopy	retro_ptro_2843,
Tarsius syrichta	ENSTSYG00000012703	3 retrocopies	retro_tsyr_1560, retro_tsyr_442, retro_tsyr_938,
Tursiops truncatus	ENSTTRG00000010813	1 retrocopy	retro_ttru_1309,