RetrogeneDB ID: retro_chof_2699

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_98469:1889..3189(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SGOL1
• Ensembl ID: ENSCHOG00000013948
• Aliases: None
• Description: shugoshin-like 1 (S. pombe) [Source:HGNC Symbol;Acc:25088]

Sequence

>retro_chof_2699
GTGGCCAAGGAAAGGTGCCTTAAAAATTCCTTTCAAGATATTCTCAAAGATACAGAGAAATGAATGAAAGAGAAAAGGAA
CAAAAAGTTGGCAAAAATTGGCAAACGCAAGTCTTTTGCCTCTGCACCATGTCAAATAACCACCAGGACTCCTATGCTGC
TGAAAAATTAGCAGGGCAGCAATAGAATGTTAGTTTTAGCTTTGGAAAATGAAAAATTGAAAGTGAGAGAGGCCCAAGAT
ACCATCCTACAGCTAAGAAAAGAATGTTACTACCTCCCATGTCAGCTCTATGCATTGAAAAAAAAACTTACTTCACAACA
AACAGAAGAAACTGCTCAACACCATCCCTCTGGAATGGACTCCAATAGTGATGACAACTCCAGGGAATTATTTGTAAAAG
GTTTACTGCAAATTCCTCTTCAGGAAGCTGACCTTCTGGGACAAGGCGAATCATTCCAAGTACAAGAGCAAATACCTACT
GTTCAAGACATATTGAGATTTGATTTTGGTCAGATGAAGATTAGCCTACCGATAATGCCTTACTTAGAACCGTATTGGTT
TGTCACAATTTAAAGAAACGTTTCAACAATCTATCTCAATTTGATACTATAGATAATTTTGAAACTAGTCATTTAACAGG
GGAATCTTTTGGATTGGAAAAAATGCAACTTTCAGACCCACTCATAAATGAACACATACCTGAAAATGTAGAACAAAATG
TTTGTCAATGGAACAAGGACCAAATTAACTTATTACCAAAGTTGATTTACCCAGCAAGCCTTAGTAAAACAAAAGAAATC
ATTTTAGAATCTAAATCTGAGCAAACTAAAACTAAGCATAGAGATGCACAAAGAAGAAAAAGATAAAAGAAAATAATAAT
TAATAGAAGAAGAAAATCAAAGTCTGTATCAGGGTATAAAGGGAGCAAGAGTGAAAGTAAAAAAACTGTTTCCCAAAAAA
ATTTAGGTGAATCTTTCAGTTACAATGATGCTTACCATTTTAATTTGGAAGAAGGTATTCATCTCACTCCTTTCTGGCAA
AATAAAAAGAGCAGTGATTCTAAAAGAAAAGAAAGCAAAAATGACTCAGAAGTAAGTATTTGTAAATCAAGTGAATCAGA
TGATTCTGATGACCTCTATTTGCCTTCTAAAAATACCTGCCAAGTACATTCAGAATCTCACCAGCGAATCAGATAGAAGC
CCAATCACCAGGCCGCAATCTAAAAGACCACTAAAATATACAGACGAAAAAGAAACCCAAGGTTCCAAGCCAAAAAAAAA
CTCCTACCAGCAAAACTCCT

Alignment

ORF - retro_chof_2699 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.36 %
• Parental protein coverage: 77.26 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAKERCLKKSFQDSLEDIKKRMKEKRNKNLAEIGKRKSFAAAPCQLITSTSTLLKNYQDNNRMLVLALEN
          .AKERCLK.SFQD.L.D..K.MKEKRNK.LA.IGKRKSFA.APCQ..T.T..LLKN.Q..NRMLVLALEN
Retrocopy VAKERCLKNSFQDILKDTEK*MKEKRNKKLAKIGKRKSFASAPCQITTRTPMLLKN*QGSNRMLVLALEN

Parental  EKFKVKEAQEIILQLRKECYYLTCQLYALKEKLTSQQTEETAQNQEVCPSGMDSNSGDNSRELFVKDLLQ
          EK.KV.EAQ..ILQLRKECYYL.CQLYAL...LTSQQTEETAQ.....PSGMDSNS.DNSRELFVK.LLQ
Retrocopy EKLKVREAQDTILQLRKECYYLPCQLYALXXXLTSQQTEETAQHH---PSGMDSNSDDNSRELFVKGLLQ

Parental  IPLQEAELSGQGKSFQIQEQISPVQETLRFDFE-SSEDKPTDNVLPRTVSVRHNLKKHCNNLYQFDTLDN
          IPLQEA.L.GQG.SFQ.QEQI..VQ..LRFDF..S.ED.PTDN.L.RTV.V.HNLKK..NNL.QFDT.DN
Retrocopy IPLQEADLLGQGESFQVQEQIPTVQDILRFDFG<SDED*PTDNALLRTVLVCHNLKKRFNNLSQFDTIDN

Parental  FETSRLTGELFELERIRLSDPLINVHIPENVEQNICQWNEDQINLLPKLIYPTSLSKTKK-ILESISEQT
          FETS.LTGE.F.LE...LSDPLIN.HIPENVEQN.CQWN.DQINLLPKLIYP.SLSKTK..ILES.SEQT
Retrocopy FETSHLTGESFGLEKMQLSDPLINEHIPENVEQNVCQWNKDQINLLPKLIYPASLSKTKEIILESKSEQT

Parental  KTKHRDAQRRKREKKRKINRKSKSKSISRYKGSKHENKKTV-QKSLNESFSSNDAYNFNLEEGIHLTPFW
          KTKHRDA.................KS.S.YKGSK.E.KKTV.QK.L.ESFS.NDAY.FNLEEGIHLTPF.
Retrocopy KTKHRDAXXXXXXXXXXXXXXXXXKSVSGYKGSKSESKKTVSQKNLGESFSYNDAYHFNLEEGIHLTPFX

Parental  QNKKSSDSEREESKNGSEVSICESSESGDDSDDLYLPSKTTC-KYIQNPTSKSDRSLITRPQSKRQLKYT
          ................SEVSIC.SSES.DDSDDLYLPSK.TC.KYIQN.TS.SDRS.ITRPQSKR.LKYT
Retrocopy XXXXXXXXXXXXXXXDSEVSICKSSES-DDSDDLYLPSKNTC>KYIQNLTSESDRSPITRPQSKRPLKYT

Parental  DEKETQDSE-PTKIPTSAPP
          DEKETQ.S......PTS..P
Retrocopy DEKETQGSK>XXXXPTSKTP

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_2699 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.

---

Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013948	1 retrocopy	retro_chof_2699 ,
Dasypus novemcinctus	ENSDNOG00000008694	1 retrocopy	retro_dnov_1045,
Equus caballus	ENSECAG00000012475	1 retrocopy	retro_ecab_846,
Mus musculus	ENSMUSG00000023940	2 retrocopies	retro_mmus_3486, retro_mmus_867,
Rattus norvegicus	ENSRNOG00000022499	1 retrocopy	retro_rnor_2440,