RetrogeneDB ID: retro_chof_2217

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_59047:2894..3765(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNF2
• Ensembl ID: ENSCHOG00000011199
• Aliases: None
• Description: ring finger protein 2 [Source:HGNC Symbol;Acc:10061]

Sequence

>retro_chof_2217
GAACTCAGTTTATATGAATTACAACCAATACCTCAGGAGGCAATAATGGATGGTCTGGAAACTGCAGTTTCACCCTGAGT
TTACACAGTCAGCTAAGGTGCCCACTCTGGATATGTTGAAAAACACCATGACTACAAAGGAGTGCTTGCATTGTTTTGGT
GCAGACTGCATTATCACAGCCCTCAGAATTTGCAAGCAAGTAAGTCCTACTTATTGTAAAAAACTAGTTTTCAAAAGATT
ACTAAGATCAGACCCAAACTTTGATGCACTGATCAGCAAAATTTATACAAGTTGTGCTGAATATGAAACTCATCAAGACA
GATTATTAGCCAGGACCAAAAAGCACAATAATCAGCTAGCACTCAGTCACAGCCTTGAGGAAGGACTGAAGATACAGGCC
ATGAAGAGACTCCAGTGAGGAAAGACACAACAGATTGAAAATGGTAGTGGAGCAGATGGTAATGGCAACAGTTCTCACTG
TAGTAATGCACCCATACCTAGAAATCAGGAAGCAGGACCTAATAGCAAACAGAAAGAATTATCTGATGATTCTGGGCTTG
AGCTTGATTATAACAATGCAACAATGTCCACTGACCCTGTAATGGATGGTGCTAGTGAAACTGAATTTGTATTCGAGCTT
CATCCCACACTTATGCAAAAAGACAGCAGTACACAGACAAGATACATAAAAACTTCAAGCAACACCACTGTTGATCACTT
AGCCAAATATTTGGCTGTGAGGTTAGTTTTAGAAGAACTCTGGGGCAAAAGAGAATGAAACCAGATGAACCTTCCTACAG
CTAGTGAGAAGCAGCATACTATTTACACAGTAACAGCCAAAGGCCAATTCACTGTACTAAATGGCACTTTT

Alignment

ORF - retro_chof_2217 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.16 %
• Parental protein coverage: 86.71 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ELSLYELQRTPQEVITDGLEIGVLP-RSLHSELMCLICL-DLLKNMTTKECLHPFCADCIFTALRSGNKE
          ELSLYELQ..PQE.I.DGLE..V.P..SLHS.L.C......L...MTTKECLH.F.ADCI.TALR.....
Retrocopy ELSLYELQPIPQEAIMDGLETAVSP<LSLHSQLRCPLWI<MLKNTMTTKECLHCFGADCIITALRICKQV

Parental  CPMCRKQLVSKRSLRPDPNFDALISKIYPSHDEYEAH-ERVLARINKHNIQKVLSHSIEEGLKIQAMNRL
          .P...K.LV.KR.LR.DPNFDALISKIY.S..EYE.H..R.LAR..KHN.Q..LSHS.EEGLKIQAM.RL
Retrocopy SPTYCKKLVFKRLLRSDPNFDALISKIYTSCAEYETHQDRLLARTKKHNNQLALSHSLEEGLKIQAMKRL

Parental  Q-GKKQQIENGGGAEDNGDTSHCSNASTHSKWEAGPRNKWTKTSDDSGLELDNNNVTVTIDPVMDGASEI
          Q.GK.QQIENG.GA..NG..SHCSNA......EAGP..K....SDDSGLELD.NN.T...DPVMDGASE.
Retrocopy Q*GKTQQIENGSGADGNGNSSHCSNAPIPRNQEAGPNSKQKELSDDSGLELDYNNATMSTDPVMDGASET

Parental  ELVFKPQPTLTEKDDSAQTRYIKTSGNATVDHLSKYLAMKLALEALQSK-ESNQMKPDTVSEKQCTIYTA
          E.VF...PTL..KD.S.QTRYIKTS.N.TVDHL.KYLA..L.LE.L..K.E.NQM...T.SEKQ.TIYT.
Retrocopy EFVFELHPTLMQKDSSTQTRYIKTSSNTTVDHLAKYLAVRLVLEELWGKRE*NQMNLPTASEKQHTIYTV

Parental  TVNGQFT-FNGSF
          T..GQFT..NG.F
Retrocopy TAKGQFTVLNGTF

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_2217 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 17 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011199	3 retrocopies	retro_chof_1450, retro_chof_2217 , retro_chof_2251,
Callithrix jacchus	ENSCJAG00000005442	1 retrocopy	retro_cjac_4198,
Erinaceus europaeus	ENSEEUG00000014091	1 retrocopy	retro_eeur_88,
Echinops telfairi	ENSETEG00000015824	1 retrocopy	retro_etel_2081,
Felis catus	ENSFCAG00000009609	1 retrocopy	retro_fcat_1725,
Homo sapiens	ENSG00000121481	2 retrocopies	retro_hsap_4056, retro_hsap_4226,
Gorilla gorilla	ENSGGOG00000014400	1 retrocopy	retro_ggor_2724,
Loxodonta africana	ENSLAFG00000021357	1 retrocopy	retro_lafr_407,
Myotis lucifugus	ENSMLUG00000001129	1 retrocopy	retro_mluc_2187,
Monodelphis domestica	ENSMODG00000007422	1 retrocopy	retro_mdom_857,
Nomascus leucogenys	ENSNLEG00000018029	2 retrocopies	retro_nleu_1042, retro_nleu_554,
Oryctolagus cuniculus	ENSOCUG00000004892	1 retrocopy	retro_ocun_838,
Pongo abelii	ENSPPYG00000000417	2 retrocopies	retro_pabe_3331, retro_pabe_3374,
Pan troglodytes	ENSPTRG00000001775	2 retrocopies	retro_ptro_2749, retro_ptro_2871,
Ictidomys tridecemlineatus	ENSSTOG00000006625	3 retrocopies	retro_itri_1646, retro_itri_1794, retro_itri_410,
Tupaia belangeri	ENSTBEG00000016387	4 retrocopies	retro_tbel_1757, retro_tbel_3368, retro_tbel_3892, retro_tbel_4061,
Tarsius syrichta	ENSTSYG00000006109	6 retrocopies	retro_tsyr_1344, retro_tsyr_1647, retro_tsyr_2063, retro_tsyr_2083, retro_tsyr_227, retro_tsyr_474,