RetrogeneDB ID: retro_chof_890

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_163090:3235..3991(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000000160
• Aliases: None
• Description: None

Sequence

>retro_chof_890
AAGCAAGAAAGATCTAACTATTTGTCTCGATTTGTAGACTGCACAATTAAAACAGATCCAGTCACTGGAAGTTCAAGAGG
ATTTAGATTTGTGCTTTTCAAAGATGCTGCTAGTGTTGATAAGGTTTTGGAACTGAAAGAACACAAACTGGATGGCATAT
TGGTAGATCCCAAAAGGGTGAAGGTTTTAAAAGGGAAAAAAAAACCCAAAAAAAGTTTCTGTGGGTATATTGAGCCCAGA
GACTTCTGAAGAGCAAATAAAAGAATATTTTGGAGCATTTGGAGAAATCAAAAATATTGAACTTCCCATGGATAAAAAAA
CAAATGAAAGAAGAGAATTTTGTTTTATCACATATACAGAAGAAGAGCCAATAAATTATTAGAAAGCAGATATCGTCAAA
TTGGTTCTGGGAAGTGTGAAATAAAAGTTGCACAACCCAAAGGGTATATAGGTAGGAACAGCAACAAAGGAAAGATGAAG
AAGAGCTGCAGCTGCTGGACAAGGTGGTACTAGGGGTCATGGACGAGGTCAGGGCCAAAACTGGAACCAAGGATTTAAAA
ACTATTATGATCAAGATCATGGAAATTATAATAGTGCCCATGGTGGTGATCAGAACTCTATTGGCTTGGCAGATATGATT
ATAGTGGGTATAACTATGGGAACTGTGGATATGGACAGGGATATGCAGACTACAGTGGCCAACAGAGCAAGGCATCTCAA
GCAGGTGGCAATCACCAAAACAATTACCAGCCATAC

Alignment

ORF - retro_chof_890 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.72 %
• Parental protein coverage: 89.04 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  KKDLTEYLSRFGEVVDCTIKTDPVTGRSRGFGFVLFKDAASVDKVLELKEHKLDGKLID-PKRAKALKGK
          K.....YLSRF...VDCTIKTDPVTG.SRGF.FVLFKDAASVDKVLELKEHKLDG.L.D.PK........
Retrocopy KQERSNYLSRF---VDCTIKTDPVTGSSRGFRFVLFKDAASVDKVLELKEHKLDGILVD>PKG*RFXXXX

Parental  EPPKKVFVGGLSPDTSEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFITYTDEEP-VKKLLESRYHQI
          .....V.VG.LSP.TSEEQIKEYFGAFGEI.NIELPMD.KTNERR.FCFITYT.EE....KLLESRY.QI
Retrocopy XXXXXVSVGILSPETSEEQIKEYFGAFGEIKNIELPMDKKTNERREFCFITYT-EEE<ANKLLESRYRQI

Parental  GSGKCEIKVAQPK-EVYRQQQQQQKGG-RGAAAAGRGGTRDRGRGQGQNWNQGFNNYYDQGYGNYNSAYG
          GSGKCEIKVAQPK..VYR..QQQ.K...R.AAAAG.GGTR..GRGQGQNWNQGF.NYYDQ..GNYNSA.G
Retrocopy GSGKCEIKVAQPK<RVYR*EQQQRKDE<RRAAAAGQGGTRGHGRGQGQNWNQGFKNYYDQDHGNYNSAHG

Parental  GDQNYSG-YGGYDYTGYNYGNYGYGQGYTDYSGQQSTYGKASRGGGNHQNNYQPY
          GDQN..G..G.YDY.GYNYGN.GYGQGY.DYSGQQS...KAS..GGNHQNNYQPY
Retrocopy GDQNSIG<LGRYDYSGYNYGNCGYGQGYADYSGQQS---KASQAGGNHQNNYQPY

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_890 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 19 parental genes, and 56 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014804	2 retrocopies	retro_btau_1827, retro_btau_461,
Canis familiaris	ENSCAFG00000008940	1 retrocopy	retro_cfam_1086,
Choloepus hoffmanni	ENSCHOG00000000160	8 retrocopies	retro_chof_115, retro_chof_1470, retro_chof_2108, retro_chof_2370, retro_chof_533, retro_chof_59, retro_chof_741, retro_chof_890 ,
Choloepus hoffmanni	ENSCHOG00000003275	2 retrocopies	retro_chof_1578, retro_chof_18,
Choloepus hoffmanni	ENSCHOG00000013832	15 retrocopies	retro_chof_1060, retro_chof_1191, retro_chof_1413, retro_chof_1460, retro_chof_1507, retro_chof_2062, retro_chof_2135, retro_chof_2235, retro_chof_2263, retro_chof_2404, retro_chof_2425, retro_chof_2473, retro_chof_2574, retro_chof_499, retro_chof_853,
Cavia porcellus	ENSCPOG00000015619	5 retrocopies	retro_cpor_1110, retro_cpor_1318, retro_cpor_264, retro_cpor_274, retro_cpor_567,
Dipodomys ordii	ENSDORG00000000968	1 retrocopy	retro_dord_145,
Equus caballus	ENSECAG00000022692	1 retrocopy	retro_ecab_1082,
Loxodonta africana	ENSLAFG00000008612	1 retrocopy	retro_lafr_650,
Microcebus murinus	ENSMICG00000001445	4 retrocopies	retro_mmur_1016, retro_mmur_1570, retro_mmur_1572, retro_mmur_557,
Myotis lucifugus	ENSMLUG00000014452	2 retrocopies	retro_mluc_1140, retro_mluc_1761,
Mustela putorius furo	ENSMPUG00000014753	2 retrocopies	retro_mputfur_1359, retro_mputfur_600,
Nomascus leucogenys	ENSNLEG00000008636	1 retrocopy	retro_nleu_673,
Oryctolagus cuniculus	ENSOCUG00000013805	1 retrocopy	retro_ocun_505,
Otolemur garnettii	ENSOGAG00000002501	4 retrocopies	retro_ogar_2717, retro_ogar_2791, retro_ogar_437, retro_ogar_693,
Ochotona princeps	ENSOPRG00000007178	3 retrocopies	retro_opri_1075, retro_opri_623, retro_opri_703,
Procavia capensis	ENSPCAG00000011543	1 retrocopy	retro_pcap_366,
Rattus norvegicus	ENSRNOG00000002270	1 retrocopy	retro_rnor_1365,
Sorex araneus	ENSSARG00000009961	1 retrocopy	retro_sara_421,