RetrogeneDB ID: retro_chof_2002

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_449969:16..741(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000001101
• Aliases: None
• Description: None

Sequence

>retro_chof_2002
GGAATTCCTCTCAGCCAGGGTGGCATCCACGGGTGCATCTCTGCCACCGGCCGCGGGGTTTTCCACAGGATTGAAAACGT
CATCAATGAAGCCTCCTACATGAGCATTTTAGGAATGACCCCAGGCTTCAGAGATAAAACCTTCCTTGCTCAGGAATTTG
GTAACGTGGGTCTGCATTCCATGAGATATTTATCTCATTTTAGTGCTAAATGTATTGCTGTCGTGAATCTGATGGGAGCA
CCTGGAATCCAGATGGTACTGACCCAAAGGAACTGGAAGACTTCAAACTGCAACATGGATCAATCCTGGGCTTCCCCAAG
GCAAAGTGCTACCAAGGGAGCATCTTGGAAGCAGATTGTGACATACTGATCCCTGCTGCCAGTGAGAAGCAGCTGACCAA
ATCCAATGCACCCAGGGTCAAAGCCAAGATCATTGCTGAAGGTGCCAACAGGCCCACAACTCCAGAAGCTGGTAAGATTT
TCCTGGAGAGGAACATTATAGTTATTCCTGATCTCTACTTGAATGCTGGAAGAGTGACAGTGTCTTACTTTGAGTGGGTG
AAGAATCTAAATCATGTCAGCTATGGCCATCTGACCTTCAAATATGAACAGGATTCTAACTACCACTTGCTCATGTCTGT
TCAAGAGAGTTTGGAAAGAAAATTTGCAAAGCACGGTGGAACGATTCCCATTGTACCCACAGCAGAGTTCCAAGACAGGA
TATCG

Alignment

ORF - retro_chof_2002 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.48 %
• Parental protein coverage: 57.62 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GKPISQGGIHGRISATGRGVFHGIENFINEASYMSILGMTPGFGDKTFAVQGFGNVGLHSMRYLHRFGAK
          G.P.SQGGIHG.ISATGRGVFH.IEN.INEASYMSILGMTPGF.DKTF..Q.FGNVGLHSMRYL..F.AK
Retrocopy GIPLSQGGIHGCISATGRGVFHRIENVINEASYMSILGMTPGFRDKTFLAQEFGNVGLHSMRYLSHFSAK

Parental  CIAV-GESDGSIWNPDGIDPKELEDFKLQHGSILDFPKAKRYEGSILEADCDILIPAASEKQLTKSNAPR
          CIAV..ESDGS.WNPDG.DPKELEDFKLQHGSIL.FPKAK.Y.GSILEADCDILIPAASEKQLTKSNAPR
Retrocopy CIAV<RESDGSTWNPDGTDPKELEDFKLQHGSILGFPKAKCYQGSILEADCDILIPAASEKQLTKSNAPR

Parental  VKAKIIAEGANGPTTPEADKIFLERNILVIPDLYLNAGGVTVSYFEWLKNLNHVSYGRLTFKYERDSNYH
          VKAKIIAEGAN.PTTPEA.KIFLERNI.VIPDLYLNAG.VTVSYFEW.KNLNHVSYG.LTFKYE.DSNYH
Retrocopy VKAKIIAEGANRPTTPEAGKIFLERNIIVIPDLYLNAGRVTVSYFEWVKNLNHVSYGHLTFKYEQDSNYH

Parental  LLMSVQESLERKFGKHGGTIPVVPTAEFQDRIS
          LLMSVQESLERKF.KHGGTIP.VPTAEFQDRIS
Retrocopy LLMSVQESLERKFAKHGGTIPIVPTAEFQDRIS

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_2002 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 20 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007540	2 retrocopies	retro_btau_1413, retro_btau_1741,
Canis familiaris	ENSCAFG00000016095	1 retrocopy	retro_cfam_747,
Choloepus hoffmanni	ENSCHOG00000001101	1 retrocopy	retro_chof_2002 ,
Callithrix jacchus	ENSCJAG00000011633	1 retrocopy	retro_cjac_2830,
Dipodomys ordii	ENSDORG00000009767	1 retrocopy	retro_dord_400,
Equus caballus	ENSECAG00000007371	2 retrocopies	retro_ecab_886, retro_ecab_919,
Echinops telfairi	ENSETEG00000019638	2 retrocopies	retro_etel_141, retro_etel_2024,
Homo sapiens	ENSG00000148672	1 retrocopy	retro_hsap_31,
Gorilla gorilla	ENSGGOG00000015770	1 retrocopy	retro_ggor_2954,
Loxodonta africana	ENSLAFG00000012059	1 retrocopy	retro_lafr_504,
Microcebus murinus	ENSMICG00000016526	1 retrocopy	retro_mmur_524,
Monodelphis domestica	ENSMODG00000002756	1 retrocopy	retro_mdom_124,
Nomascus leucogenys	ENSNLEG00000011658	1 retrocopy	retro_nleu_36,
Otolemur garnettii	ENSOGAG00000003641	1 retrocopy	retro_ogar_2757,
Procavia capensis	ENSPCAG00000008662	1 retrocopy	retro_pcap_11,
Pongo abelii	ENSPPYG00000002827	3 retrocopies	retro_pabe_3109, retro_pabe_3213, retro_pabe_79,
Pan troglodytes	ENSPTRG00000002711	4 retrocopies	retro_ptro_3162, retro_ptro_3283, retro_ptro_3285, retro_ptro_3290,
Ictidomys tridecemlineatus	ENSSTOG00000012843	1 retrocopy	retro_itri_737,
Tarsius syrichta	ENSTSYG00000001578	1 retrocopy	retro_tsyr_313,
Tursiops truncatus	ENSTTRG00000008145	1 retrocopy	retro_ttru_950,