RetrogeneDB ID: retro_chof_2119

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_51115:4136..4836(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM134B
• Ensembl ID: ENSCHOG00000009107
• Aliases: None
• Description: family with sequence similarity 134, member B [Source:HGNC Symbol;Acc:25964]

Sequence

>retro_chof_2119
ATTAATCAGAAGAAATATATGAGATCTGAAGCAGATAAAGAAAACAAGATGACAGTGAATTAGACTTTTCAGCTCTTTGT
CCTAAGATTAGCCTCAAAGTTGCTGCCAAAGAGCTATCTGTGTCTAGCATGGATATGGATGTATCAGAAGTCTACGGGAT
CAATAGTGGGACCTTCCACCTTTTAGAAGGGTACACTCCACAGACAGACACTTCTGATGATCTTAACCGACCTAGTGAAC
ATGAAGTTTTCTCTCGAGAACTTTCAGATTTTCCATCTGCAGGAAATAGTATGGGAACAAATGACAAAAATGAAGTAAGC
CTTCGGTTGTCCATTGAGTTCAAGAGAAAAAAAGGCACAGCTGTCCCAGACCAAGCAGAGAGAGGCAGTCAGCAGCTGGC
CCCACCCTTCCTCTGAACAGTGACCAAGCCTATTACTTGCTGAGCAATCTGTCTGGGGACATCATCACAGTTGTGGTAAT
TGCTGCTGTCAAAGACCAGATAGAGGGTGTGCAGTGAGCACTTTCTCCAGCAGCGCCCAGCCCAGGAGAGGACACAGACG
CTGAAGAAGGCGATGACTTTGAACTACTTGACCAGTCAGAGCTTGATCAAATTGAGAGTGAATTGGGACTTACACAAGAC
CAGGGAGCAGCAGCACAGCAAAATAAGTCATCAGGCTTCCTTCCAAATCTAATGGGAGGT

Alignment

ORF - retro_chof_2119 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.69 %
• Parental protein coverage: 61.56 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  INQKKRARSEADKEKSPK-DDSELDFSALCPKISLTVAAKELSVS--DTDVSEVSWTDNGTFNLSEGYTP
          INQKK..RS.....K..K.DDSELDFSALCPKISL.VAAKELSVS..D.DVSEV.....GTF.L.EGYTP
Retrocopy INQKKYMRS--EADKENK<DDSELDFSALCPKISLKVAAKELSVSSMDMDVSEVYGINSGTFHLLEGYTP

Parental  QTDTSDDLDRPSEREVFSRDLSDFPSVENGTGTNDEDEVSLGLPVELKR-KKEQLDSVPRPSQGRQSAAG
          QTDTSDDL.RPSE.EVFSR.LSDFPS..N..GTND..EVSL.L..E.KR.KK....S.PRPS..RQSAAG
Retrocopy QTDTSDDLNRPSEHEVFSRELSDFPSAGNSMGTNDKNEVSLRLSIEFKR<KKRH--SCPRPSRERQSAAG

Parental  LTLPLNSDQTFHLLSNLAGDVITAAVTAAVKDQLEGVQQALSQAAPSPGEDTDTEEGDDFELLDQSELDQ
          .TLPLNSDQ...LLSNL.GD.IT..V.AAVKDQ.EGVQ.ALS.AAPSPGEDTD.EEGDDFELLDQSELDQ
Retrocopy PTLPLNSDQAYYLLSNLSGDIITVVVIAAVKDQIEGVQ*ALSPAAPSPGEDTDAEEGDDFELLDQSELDQ

Parental  IENELGLTQDQEADAQQNKKSSGFLSNLLGG
          IE.ELGLTQDQ.A.AQQN.KSSGFL.NL.GG
Retrocopy IESELGLTQDQGAAAQQN-KSSGFLPNLMGG

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_2119 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000009107	1 retrocopy	retro_chof_2119 ,