RetrogeneDB ID: retro_chof_2504

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_81085:91..1097(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCNY
• Ensembl ID: ENSCHOG00000006201
• Aliases: None
• Description: cyclin Y [Source:HGNC Symbol;Acc:23354]

Sequence

>retro_chof_2504
ATGGGGAACACTACCTCATGCTGCGTGTCATGCAGCCCCAAGCTCAGGAGGAATGCCCACTCTCGGCTGGAGTCCTACTG
GCCCGACACTGATCTGAGCCGCGAGGACACAGGCTGCAACCTGCAGCACATCAGCGACCGGGAGAACATCGACAATTTGA
ACATGGAATTCAATCCTTCAGACCATCCTCGGGCTAGCACAATATTCCCCAGTAAATCTCAGACGGACGTGAGAGAAAAG
CGCAAGAGTCTCTTCATTAACCGTCATCCTCCAGGACAAATAGCAAGGAAATACAGCTCCTGCTCCACTATTTTTCTAGA
TGATAGCACAGTCAGTCAACCAAACCTCAAGTATACAATTAAATGTGTAGCTCTCACAATATATTATAACATAAAAAACA
GGGACCCAGATGGAAAGATGCTCTTAGATATTTTTGATGAAAACCTTCACCCTCTTTCAAAATCCGAAGTGCCACCAGAT
TATGACAAACGCAACCCAGAGCAGAAACAGATTTACCAGTTTGTTCAGACGCTCTTCAGTGCTGCTCAGCTGACAGCTGA
ATGTGCCGTTGTCACCCTGGTATACCTTGAAAGACTTTTAGCATATGCAGAGATAGATATCTGTCCAGCAAACTGGAAGT
GAATTGTACTAGGGGCGATTCTGCTGGCCTCCAAAGAGTGGGACGACCATGCGGTCTGGAATGTGGATTACTGCCAGATC
CTGAAAGATATCACGGTCGAAGACATGAACGAGCTAGAGCGACAGTTTCTGGAATTGCTCGAATTCAACATCAATGTTCC
TTCCAGTGTCTATGCCAAGTATAATTTTGATCTTCTTTCTCTGGCAGAAGCTTCCCCTTGGAACCCCTTAGCAGGGAGAG
AGCTCACAAACTTGAGGCCATCTCCCACCTCTGCGAGGACAAGTACAAGGACCTGAGAAGATCCATGAGGAAGCTGTCGG
CAAGCGCCAACAACTGACTCTGGCCAGGTGGTCTCCGGCCATCATC

Alignment

ORF - retro_chof_2504 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.64 %
• Parental protein coverage: 99.71 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MGNTTSCCVSSSPKLRRNAHSRLESYRPDTDLSREDTGCNLQHISDRENIDDLNMEFNPSDHPRASTIFL
          MGNTTSCCVS.SPKLRRNAHSRLESY.PDTDLSREDTGCNLQHISDRENID.LNMEFNPSDHPRASTIF.
Retrocopy MGNTTSCCVSCSPKLRRNAHSRLESYWPDTDLSREDTGCNLQHISDRENIDNLNMEFNPSDHPRASTIFP

Parental  SKSQTDVREKRKSLFINHHPPGQIARKYSSCSTIFLDDSTVSQPNLKYTIKCVALAIYYHIKNRDPDGRM
          SKSQTDVREKRKSLFIN.HPPGQIARKYSSCSTIFLDDSTVSQPNLKYTIKCVAL.IYY.IKNRDPDG.M
Retrocopy SKSQTDVREKRKSLFINRHPPGQIARKYSSCSTIFLDDSTVSQPNLKYTIKCVALTIYYNIKNRDPDGKM

Parental  LLDIFDENLHPLSKSEVPPDYDKHNPEQKQIYRFVRTLFSAAQLTAECAIVTLVYLERLLTYAEIDICPA
          LLDIFDENLHPLSKSEVPPDYDK.NPEQKQIY.FV.TLFSAAQLTAECA.VTLVYLERLL.YAEIDICPA
Retrocopy LLDIFDENLHPLSKSEVPPDYDKRNPEQKQIYQFVQTLFSAAQLTAECAVVTLVYLERLLAYAEIDICPA

Parental  NWKRIVLGAILLASKVWDDQAVWNVDYCQILKDITVEDMNELERQFLELLQFNINVPSSVYAKYYFDLRS
          NWK.IVLGAILLASK.WDD.AVWNVDYCQILKDITVEDMNELERQFLELL.FNINVPSSVYAKY.FDL.S
Retrocopy NWK*IVLGAILLASKEWDDHAVWNVDYCQILKDITVEDMNELERQFLELLEFNINVPSSVYAKYNFDLLS

Parental  LAEANNLSFPLEPL-SRERAHKLEAISRLCEDKYKDLRRSTRKRSASADN-LTLARWSPAII
          LAEA.....P..PL.SRERAHKLEAIS.LCEDKYKDLRRS.RK.SASA.N.LTLARWSPAII
Retrocopy LAEAS----PWNPL<SRERAHKLEAISHLCEDKYKDLRRSMRKLSASANN<LTLARWSPAII

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_2504 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006201	1 retrocopy	retro_chof_2504 ,
Echinops telfairi	ENSETEG00000005121	1 retrocopy	retro_etel_2021,
Loxodonta africana	ENSLAFG00000012820	1 retrocopy	retro_lafr_79,
Pan troglodytes	ENSPTRG00000002421	2 retrocopies	retro_ptro_1322, retro_ptro_3228,