RetrogeneDB ID: retro_chof_2426

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_74373:705..1682(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM175B
• Ensembl ID: ENSCHOG00000007635
• Aliases: None
• Description: family with sequence similarity 175, member B [Source:HGNC Symbol;Acc:28975]

Sequence

>retro_chof_2426
AAAGTTACTGGTTGGTACAGATTTTGATGAAACGCACAGCAGCAGATGTCGTACAGAGAGCAAGTCATCCACAAGCAGCT
TACCGGATCCTTGGCGTACCTGACCTTATCTTCCTTCTCTACAGCTTCATCTCCACCGCCAACAATTCTACTCATGCTTT
AGAATATGTTCTCTTTAGACCAAATCGAAGGTATAATCAAAGGATATCACTTGCTATTCCCAACCTAGGCAATACTAGCC
AGCAGGAGTACAAAGTGTCTTCAGTGCCAAATACTTCTCAGAGTTATGCCAAAGTTATTAAAGAACATGGTACCAACTTT
TTTGACAAGGATGGAGTAATGAAAGACATCAGGGCCATTTATCAGGTTTGTAACGCACTTCAGGAGAAAGTACAGGCAGT
GTGTGCAGGTGTAGAAAAGAGTGAGCAAGTTGTTGAATCTTGTCAGGCAGAAGTGAACAAATTAAAAAGACAAATCACTC
AAAGGAAAAATGAAAAGGGACAGGAAAGAAGATCGCAGCCGACGATGTTAAGCAGACAGATGCCACCTGAAAGTCTGGAA
CCAGTGTTCAGCCCTCGGATGCCCTATTCCGGGTTTGCAGCTGAAGGTGGAATTACACTTGGAGATGCAGAGGCCACCGA
TCCTCCTCCCCCTTATTCTGATTTTAACCCAAACAATCAAGAAAGTACTTTAAGCCATTCTCACGTGGAAAGTAGCGTCT
TTATGCCTCGACCTCAAGCCGTGGGCTCCTCCAGTGATGCTTCCACCGGTGCTGGACTGAAGCATCCTGGAAGTGGAGCA
GAGCTTCCTCCTTCCCAAAGAGCAGCTGGAGACAGTGTTGATGAATCAGACGACAGCGATTATGAAAATTCGATTAACCC
TACAGAGCCCTCCAATAGTGAATCCTCCCATCCGAGGGATCCACGGCCCACGACACATCCTGATGGAGACTCCAGGAACA
CTCAGGCCTCCCAGATT

Alignment

ORF - retro_chof_2426 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.83 %
• Parental protein coverage: 83.38 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KVIGWYRFRRNTQQQMSYREQVIHKQLT-RILGVPDLVFLLFSFISTANNSTHALEYVLFRPNRRYNQRI
          KV.GWYRF..N.QQQMSYREQVIHKQLT.RILGVPDL.FLL.SFISTANNSTHALEYVLFRPNRRYNQRI
Retrocopy KVTGWYRF**NAQQQMSYREQVIHKQLT<RILGVPDLIFLLYSFISTANNSTHALEYVLFRPNRRYNQRI

Parental  SLAIPNLGNTSQQEYKVSSVPNTSQSYAKVIKEHGTDFFDKDGVMKDIRAIYQVYNALQEKVQAVCADVE
          SLAIPNLGNTSQQEYKVSSVPNTSQSYAKVIKEHGT.FFDKDGVMKDIRAIYQV.NALQEKVQAVCA.VE
Retrocopy SLAIPNLGNTSQQEYKVSSVPNTSQSYAKVIKEHGTNFFDKDGVMKDIRAIYQVCNALQEKVQAVCAGVE

Parental  KSERVVESCQAEVNKLKRQITQRKNEKEQERRLQQTMLSRQMPPESLEPVFSPRMPYSGFAAEGRITLGD
          KSE.VVESCQAEVNKLKRQITQRKNEK.QERR.Q.TMLSRQMPPESLEPVFSPRMPYSGFAAEG.ITLGD
Retrocopy KSEQVVESCQAEVNKLKRQITQRKNEKGQERRSQPTMLSRQMPPESLEPVFSPRMPYSGFAAEGGITLGD

Parental  AEATDPPPPYSDFNPNNQESTLSHSRVESSVFMPRPQAVGSSNYASTSAGLNYPGYGAELSPSQRAAGDS
          AEATDPPPPYSDFNPNNQESTLSHS.VESSVFMPRPQAVGSS..AST.AGL..PG.GAEL.PSQRAAGDS
Retrocopy AEATDPPPPYSDFNPNNQESTLSHSHVESSVFMPRPQAVGSSSDASTGAGLKHPGSGAELPPSQRAAGDS

Parental  VDESDNSVYENLIDPTEPSNSESSHPRDSRPTTHSDGHSRNTQASQI
          VDESD.S.YEN.I.PTEPSNSESSHPRD.RPTTH.DG.SRNTQASQI
Retrocopy VDESDDSDYENSINPTEPSNSESSHPRDPRPTTHPDGDSRNTQASQI

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_2426 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000023840	1 retrocopy	retro_btau_729,
Choloepus hoffmanni	ENSCHOG00000007635	3 retrocopies	retro_chof_1691, retro_chof_2426 , retro_chof_2563,
Choloepus hoffmanni	ENSCHOG00000013241	1 retrocopy	retro_chof_2580,
Equus caballus	ENSECAG00000023340	1 retrocopy	retro_ecab_839,