RetrogeneDB ID: retro_chof_1150

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_212233:247..1161(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCHOG00000011251
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PABPC4
• Ensembl ID: ENSCHOG00000005327
• Aliases: None
• Description: poly(A) binding protein, cytoplasmic 4 (inducible form) [Source:HGNC Symbol;Acc:8557]

Sequence

>retro_chof_1150
GAATGGGCTCTGAACACCATGAATTTTGATTTGATTAATGGCAAACAATTCCGCCTCATGTGGTCTCAGCCAGATGACCG
CTTAAGAAAGTCTGGAGTTGGAAACATCTTCATCAAAAACCTGGACAAATCCATAGACAATAGGTCCCTTTTTTATTTAT
TTTCTGCTTTTGGGAACATTCTCTCTTGCAAAGTCGTATGCGATGATAAAGGCTCAAAAGGTTATGCCTATGTGCACTTT
GACACCCTGGCTGCAGCCAACAGAGCAATCTGGCATATGAATGGAGTGCGACTCAACAACCGTCAGGTGTACGTTGGCAG
ATTCAAATTCCCGGAAGAGCGGGCAGCAGAAGTCAGAACCAGGGATAGAGCAAGTTTCACCAACGTTTTCATTAAAAACT
TTGGCGAGGACATGGATGAAGAAAAACTGAAGGAACTTTTCAGTGAATATGGGCCAACTGAGAGTGTTAAGGTGATAAAA
GATGCCAGCGGGAAATCCAAAGGTTTTGGATTTGTGAAATATGAGACACACGAGGCTGCCCAAAAGTCTGTGCTAGAACT
GCACGGGAAGTCCATTGGTGGGAAAGCGCTTTATGTGGGGCGAGCGCAGAAGAAAATTGAACGCCTGGTTGAGTTAAGGC
GGAGATTTGAACGTTTGCGATTAAAGGAAAAAAGGCCTCCAGGGGTGCCTATCTATATTAAGAATCTGGATGAGACCATA
GATGATGAAAAACTGAAGGAGGAATTTTCTTCCTTTGGATCAATTAGACGGGCCAAGGTGATGACGGAAGTGCAGCAAGG
CAAAAGGGTTTGGTGTGGTCTGCTTTTCCTCTTTTGAAGAGGCTACCAAAGCAGTAGATGAGATGATGGTCACATAGTGG
GCTCCAGCCCCTGCATGTTACCCTGGCCAGGCAA

Alignment

ORF - retro_chof_1150 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.4 %
• Parental protein coverage: 51.35 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ERALDTMNFDVIKGKPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN
          E.AL.TMNFD.I.GK..R.MWSQ.D..LRKSGVGN.FIKNLDKSIDN..L...FSAFGNILSCKVVCD..
Retrocopy EWALNTMNFDLINGKQFRLMWSQPDDRLRKSGVGNIFIKNLDKSIDNRSLFYLFSAFGNILSCKVVCDDK

Parental  GSKGYAFVHFETQEAADKAIEKMIGMLLNDRKVFVGRFKSRKEREAELGAKAK-EFTNVYIKNFGEEVDD
          GSKGYA.VHF.T..AA..AI..M.G..LN.R.V.VGRFK...ER.AE........FTNV.IKNFGE..D.
Retrocopy GSKGYAYVHFDTLAAANRAIWHMNGVRLNNRQVYVGRFKFPEERAAEVRTRDRASFTNVFIKNFGEDMDE

Parental  ESLKELFIQFGKTLSVKVMRDPSGKSKGFGFVSYEKHEDANKAVEEMNGKEISGKVIFVGRAQKKVERQA
          E.LKELF...G.T.SVKV..D.SGKSKGFGFV.YE.HE.A.K.V.E..GK.I.GK...VGRAQKK.ER..
Retrocopy EKLKELFSEYGPTESVKVIKDASGKSKGFGFVKYETHEAAQKSVLELHGKSIGGKALYVGRAQKKIERLV

Parental  ELKRKFEQLKQERISRYQGVNLYIKNLDDTIDDEKLRKEFSPFGSITSAKVMLE-DGRSKGFGFVCFSSP
          EL.R.FE.L......R..GV..YIKNLD.TIDDEKL..EFS.FGSI..AKVM.E.....KGFG.VCFSS.
Retrocopy ELRRRFERLRLKE-KRPPGVPIYIKNLDETIDDEKLKEEFSSFGSIRRAKVMTE>CSKAKGFGVVCFSSF

Parental  EEATKAVTEM-NGRIVGS-KPLYVALAQR
          EEATKAV.EM..G.IVGS..PL.V.LA..
Retrocopy EEATKAVDEM<DGHIVGS<QPLHVTLARQ

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_1150 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 43 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011535	2 retrocopies	retro_amel_107, retro_amel_676,
Bos taurus	ENSBTAG00000017125	3 retrocopies	retro_btau_1492, retro_btau_28, retro_btau_656,
Canis familiaris	ENSCAFG00000003081	2 retrocopies	retro_cfam_45, retro_cfam_837,
Choloepus hoffmanni	ENSCHOG00000002464	1 retrocopy	retro_chof_1943,
Choloepus hoffmanni	ENSCHOG00000005327	3 retrocopies	retro_chof_1150 , retro_chof_1182, retro_chof_1274,
Choloepus hoffmanni	ENSCHOG00000006810	2 retrocopies	retro_chof_2564, retro_chof_44,
Choloepus hoffmanni	ENSCHOG00000008178	1 retrocopy	retro_chof_2531,
Equus caballus	ENSECAG00000009396	2 retrocopies	retro_ecab_2, retro_ecab_502,
Felis catus	ENSFCAG00000015254	2 retrocopies	retro_fcat_116, retro_fcat_545,
Loxodonta africana	ENSLAFG00000000151	3 retrocopies	retro_lafr_1144, retro_lafr_390, retro_lafr_597,
Microcebus murinus	ENSMICG00000016633	1 retrocopy	retro_mmur_675,
Myotis lucifugus	ENSMLUG00000012068	2 retrocopies	retro_mluc_228, retro_mluc_397,
Monodelphis domestica	ENSMODG00000017657	2 retrocopies	retro_mdom_1090, retro_mdom_1805,
Mustela putorius furo	ENSMPUG00000014414	2 retrocopies	retro_mputfur_152, retro_mputfur_546,
Mus musculus	ENSMUSG00000011257	7 retrocopies	retro_mmus_2006, retro_mmus_2326, retro_mmus_2327, retro_mmus_798, retro_mmus_801, retro_mmus_803, retro_mmus_805,
Rattus norvegicus	ENSRNOG00000015642	2 retrocopies	retro_rnor_175, retro_rnor_92,
Sarcophilus harrisii	ENSSHAG00000018139	1 retrocopy	retro_shar_823,
Sus scrofa	ENSSSCG00000003660	3 retrocopies	retro_sscr_1210, retro_sscr_974, retro_sscr_975,
Tursiops truncatus	ENSTTRG00000014340	2 retrocopies	retro_ttru_1117, retro_ttru_246,