RetrogeneDB ID: retro_chof_1182

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_22047:3326..4359(+)
• Located in intron of: None

Retrocopy information

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

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_1182
CAGAAGGCCCTGGACACGATGAACTTTGACATGATCAAAGGCAAATCCATCCGTCTCATGTGGTCTCAACATGATGCCTA
CTTAAGGAAATCGGGAATTGGGAACGTGTTCATCAAGAATCTGGACAAATCCATAGACAACAAAGCCCTGTATGAACGTT
TTTCAGTTTTTGAGAAGATCCTGTCCTCCAAGGTGATGAGTGATGATAAAGGCTCCAAGGGCTATGCATTTGTGCACTTT
CAGAGCCAGAGTGCTGCAGACAGGGCCATTGAGGAGATGAATGGGATGTTGCTCAACGACTGCCGAGTATTTGTTGGCAG
GTTCAAAAGCCGCAAAGATCGGGAAGCTGAGTTCAGAAACAAAGCCAATGAATTCACCAATGTTTACATCAAAAACTTTG
GAGTTGACATGGATGATGAAAGACTGAAGGACGTTTTCAGTAAATATGGTAAAACCCTGAGTGTCAAGGTGATGACAGAT
TCTAGTGGGAAATCCAAAGGCTTTGGCTTTGTGAGTTTTGATAGCCATGAGGCTGCCAAAAAGGCTGTGGAAGAAATGAA
TGGAAAGGACATAAATGGGCAGCTGGTTTTTGTGGCCCGGGCACAAAAGAAAGTAGAGCGACAGGCTGAGTTAAAACATA
TGTTTGAGCAGCTGAAACAAGAACGAATTTTTCAGTGCCAGGGGGCGAAGCTCTACATTAAGAATCTTGATGATACTATT
GATGATGAAAAACTTTTGAAGGAATTTTCTTCATTTGGATCAATTAGTAGAGTTAAGGTAATGCAGGAAGAAGGGCGAAG
CAAAGGGTTTGGCTTGATCTGCTTTTCCTCTCAGGAGGAGGCTATTAAAGCAATGACTGAGATGAATGGCCGCATCTTGG
GCTCCAAGCCACTCAACATTGCCCTGGCCCAGAGGCAAAGGAGAGAAAAGCTGACCTCACCAGCCAGTGTTTACAGTAGG
TGGGGGAAGAACAGTGATCCTTGCCTGGATTGTTCTCAATGAATTTCAGACCTTGGCTAGTGGCAGCTTAGTT

Alignment

ORF - retro_chof_1182 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.18 %
• Parental protein coverage: 58.08 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ERALDTMNFDVIKGKPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN
          ..ALDTMNFD.IKGK.IR.MWSQ.D..LRKSG.GNVFIKNLDKSIDNKALY..FS.F..ILS.KV..D..
Retrocopy QKALDTMNFDMIKGKSIRLMWSQHDAYLRKSGIGNVFIKNLDKSIDNKALYERFSVFEKILSSKVMSDDK

Parental  GSKGYAFVHFETQEAADKAIEKMIGMLLNDRKVFVGRFKSRKEREAELGAKAKEFTNVYIKNFGEEVDDE
          GSKGYAFVHF..Q.AAD.AIE.M.GMLLND..VFVGRFKSRK.REAE...KA.EFTNVYIKNFG...DDE
Retrocopy GSKGYAFVHFQSQSAADRAIEEMNGMLLNDCRVFVGRFKSRKDREAEFRNKANEFTNVYIKNFGVDMDDE

Parental  SLKELFIQFGKTLSVKVMRDPSGKSKGFGFVSYEKHEDANKAVEEMNGKEISGKVIFVGRAQKKVERQAE
          .LK..F...GKTLSVKVM.D.SGKSKGFGFVS...HE.A.KAVEEMNGK.I.G...FV.RAQKKVERQAE
Retrocopy RLKDVFSKYGKTLSVKVMTDSSGKSKGFGFVSFDSHEAAKKAVEEMNGKDINGQLVFVARAQKKVERQAE

Parental  LKRKFEQLKQERISRYQGVNLYIKNLDDTIDDEKLRKEFSPFGSITSAKVMLEDGRSKGFGFVCFSSPEE
          LK..FEQLKQERI...QG..LYIKNLDDTIDDEKL.KEFS.FGSI...KVM.E.GRSKGFG..CFSS.EE
Retrocopy LKHMFEQLKQERIFQCQGAKLYIKNLDDTIDDEKLLKEFSSFGSISRVKVMQEEGRSKGFGLICFSSQEE

Parental  ATKAVTEMNGRIVGSKPLYVALAQRK-EERKAHLTNQYMQRV-AGMRALPANAILNQFQPAAGGYFV
          A.KA.TEMNGRI.GSKPL..ALAQR...ERKA.LT.Q..Q.V..G.....A...LN.FQ..A.G..V
Retrocopy AIKAMTEMNGRILGSKPLNIALAQRQ<KERKADLTSQCLQ*V<GGRTVILAWIVLNEFQTLASGSLV

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_1182 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,