RetrogeneDB ID: retro_chof_12

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_138884:2..1598(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCHOG00000002575
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: ZNF782
• Ensembl ID: ENSCHOG00000012100
• Aliases: None
• Description: zinc finger protein 782 [Source:HGNC Symbol;Acc:33110]

Sequence

>retro_chof_12
AAATGTGACACTGTAGGACCTACTTACCTTGATCTAAGCGCATTGGCCTCACACTGTCAGTATTCAAAAGAGAGTGCTGA
TGAGGTTAATGTATTTGAGAAGTGGATCCACAGTATTGATGGCAGAACTCAAGCAGGAGAGGAATATTTTCATTGTAATA
AAAACATGAAAGCCTTCAGTCAGGAGGAGGAAGTTATTCAGAATCAGGCAGTTCAGAGTTTGGGGCAACCTTTTGAAGAT
GGTGAATGTGGAAAAGCTTTCCTACAGAAAGCTGCCTTTTTTGCATCTATGAATGCCCACCCAAGTATGAAATCGTATAA
ATGCAATGAAGGTGGGGAAAACATGCTTGAAAAATCTATTATTGTATCTCAGAACATTCCTAAAGAACATAAGAGTCACG
ATGAGCTTAATGAATATAAATCTAATGAAAATGGGATAAAGTTCAGTAGGATCATTCAACTTCGAAAAATTGATACGGGA
GGGAAGACTTTCAGCCATGATTCACATTTTAGAGAACATCACAGAATTCTTACAGAAGTGAAACCATTTGAATATGGAAA
ATTTTTTTGTCAGGATTCAGCCCTTCCAGTGCATCAGAGAACTCATACAACAGATAAGTCCTCTGATTATAACACATGTA
GAGAGACATTCAGTTACCAGTCATCTTGCAGTGTATATCAGAGAACTCACACAAGGGAAAAACCCTATGAGTGTAAGGGA
TTTGGAAAGTCCTGTCCTATGAATTTACGCCCAGTTAGTCCTCAAATAAGTTACTCAAAGAAGAAGCCCCATGAATGTCA
TGAATGTGGGAAAACTTTCAGTGAGAAATCACAGCTAAGGAAACATCAGAGAACCCACAAAGGAGAGAAACCGTATAAAT
GTGATACATGTGAGAAAGCTTCTAGTGTAAAGATAGGTCTCAGAGTACATCAGAGAACTCACAAATGCGATAGACTCTTT
GAATTCAGTGAGTGTGGGAAATCTTTCAACTATAAGTCAACCCTCATAGGACACCAGAGAACTCACACAGGGGAGAAACC
CTTTAAATGTAATGAATGTGAGAAATCTTTCAGTTTTAGATCACACCTAGGGAATCATGAGCAAACACACATAAGGGAAA
GACCATATAAATGTGATGAATGTGGAAAACATTTCAAACACAAGTCATCCCTTGGAAAACATCTTAGGAATCACACAATG
GAGAAACCGTATGAATGTAATGAATGTGGAAAAGCTTTCAATCAGAATTCACTTCTTAGTTCACATCAGAGAACTCACAC
AGGAGAGAAACCATATAATTGTAATCAGTATGCACAGTCTTTTAGCCAGAACTCAAGTCTCAGAAGACATGAGAGAATTC
ACACTGGTGAGAAACCCTATAAATGCGATGAATGTGGGAAATGTTTTAGATGGAAATCACACCTCACAGAACATCAGAGA
ACACACACAGGTGAGAAACTCGATGAATGTAATCAATGTGGAAAAGCTTTCAGTGAGCATTCACGTCTAAGAAAACATAA
GAGAACTCACACAGGTGAGAAACCCTATGAATGTAATCAATGTGGAAAAGCTTTCATGGACAAGTTGAGTCTAAAA

Alignment

ORF - retro_chof_12 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.72 %
• Parental protein coverage: 77.95 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IPKEHNSHDELNKYKYNENGSTFVGSANFQK-DTGRKSFSQKSHFRENQRILTEVKPSENGKIFCPDSAL
          IPKEH.SHDELN.YK.NENG..F.......K.DTG.K.FS..SHFRE..RILTEVKP.E.GK.FC.DSAL
Retrocopy IPKEHKSHDELNEYKSNENGIKFSRIIQLRKIDTGGKTFSHDSHFREHHRILTEVKPFEYGKFFCQDSAL

Parental  PVHQKSHTTEKFSDYNTCRETFSYQTALSVYQRTHIREKPYECKEFGKSCPMNLVSVRPQKSYRGEKPCE
          PVHQ..HTT.K.SDYNTCRETFSYQ...SVYQRTH.REKPYECK.FGKSCPMNL..V.PQ.SY...KP.E
Retrocopy PVHQRTHTTDKSSDYNTCRETFSYQSSCSVYQRTHTREKPYECKGFGKSCPMNLRPVSPQISYSKKKPHE

Parental  YHECGKAFSKKLQLRK-QRIHTAGKPYKCIGCEKAFSAKSGLRIHQRTHTGEKPFECNECGKSFDYKSHL
          .HECGK.FS.K.QLRK.QR.H...KPYKC..CEKA.S.K.GLR.HQRTH.....FE..ECGKSF.YKS.L
Retrocopy CHECGKTFSEKSQLRKHQRTHKGEKPYKCDTCEKASSVKIGLRVHQRTHKCDRLFEFSECGKSFNYKSTL

Parental  IIHQRTHTGEKPFKCNECGKSFSYISGLRNHQPTHTGERPYKCDECGKAFRLKSGLRKHHRTHTGEKPYK
          I.HQRTHTGEKPFKCNEC.KSFS..S.L.NH..TH..ERPYKCDECGK.F..KS.L.KH.R.HT.EKPY.
Retrocopy IGHQRTHTGEKPFKCNECEKSFSFRSHLGNHEQTHIRERPYKCDECGKHFKHKSSLGKHLRNHTMEKPYE

Parental  CSQCGIAYSQKSQLRGHQRIHT-EKPFKCSQCGESFSWKSYLRVHQRTHTGEKPYKCDECGKSFRQKSNL
          C..CG.A..Q.S.L..HQR.HT.EKP..C.Q...SFS..S.LR.H.R.HTGEKPYKCDECGK.FR.KS.L
Retrocopy CNECGKAFNQNSLLSSHQRTHTGEKPYNCNQYAQSFSQNSSLRRHERIHTGEKPYKCDECGKCFRWKSHL

Parental  SGHQRTHTGEKPYECNKCGKAFSQNSVLRIHQRTHTGEKPYNCNRCGESFRQKSTL
          ..HQRTHTGEK..ECN.CGKAFS..S.LR.H.RTHTGEKPY.CN.CG..F..K..L
Retrocopy TEHQRTHTGEKLDECNQCGKAFSEHSRLRKHKRTHTGEKPYECNQCGKAFMDKLSL

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_12 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 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010418	2 retrocopies	retro_chof_431, retro_chof_969,
Choloepus hoffmanni	ENSCHOG00000012100	1 retrocopy	retro_chof_12 ,