RetrogeneDB ID: retro_chof_522

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_117221:3474..4953(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000005172
• Aliases: None
• Description: None

Sequence

>retro_chof_522
CATGTTGATACAAGCCCAGAAGGGTCATCTCAGAGTTCACTTTCTCCTGTAGCCATCAGTGGAAACCATTTGATCAGTGC
AAGTGTGCAAAGACAAAGTAAAAGGATTGCAGACAAAAAAGTTTGCAGGGTGGAATCAGGAAAAGCAGGCTGCTTCTCTC
CTAAAATCAGTCATAAAGAAAAGGTTCGAAGATCTCTTCATTTGAAATTTAGTCTGGGGAAAAGTAACAGAGATGATGGA
TGTTCTGATGTCAATAGATATGAAAATGTTGGTCGGCGACTTGCAAGTCAACAAAATTTTTAAAATAGAATTGAATCTGT
AAAAACAGGTCTACTTTTTAGCCCAGATATTGAAAGATTAACAAAGAAAGGTTCAAAAAAGATCAGTAAGTCTGAGGAAT
ACTTATCAACTCCAGAGCAGCTGGATGGAACAAATTACCACATGTCTTGAACAGGACCTACTAATTCAAGTTTTCAGGAA
ATAGACGCAAATGAAACATCTCCGATAGAGGGAAATCTTGAGGTGGAAAACTCTTCTTTGGATCCTGATCTTATGGTTGA
AAAGTCACCTGTTACTTCATATGCGCTTACCCCTTCTACTGTACACAATAAGCATAATAGCAACCTAACTGGAAACTCTC
CTAATGGGGATGAAGATAACTTGACCACAGAGACTTTGGTGAAAATTCAGAAAGCATTTTCTGAATCTGGAAGTAATCTT
CACACATTGATAAATCATGGGCAGTCCTCAATAACTAATATGGTGAAAGCAAAATTAAATGAAACATCATATACAGAATA
TAGCCCAAAGGAAAATTTATTTGAAACTAATGATTTGACTGTGATAGAATCGAAGAAAAAGTACGAACACCAAGCTAGTA
AAGATGAAAATAGTTTCTCAGAAAGACACTTCTCACTACATCAAACTCAAGAATTAGGTAGAGAAGCAACTACAAAATGT
TACTCAACTCAGATGAAGGTGGAACATGAAAAAACCATTTATTCAAATATAGCAAAAGATTATTTAAGCATGCAAGAGTT
CCCCAGTGAAGAACAAATAAAGAAACAGGAGTCCGCAAGGAATAAACTAAATACTAAATTAAAGGAGAATGAGAGTGTGA
TTGAAGAGAATTTATTGAAATGCACAGCTTCTGGGGAGGACATGTCTAAATCATCATCTTCAAAGCAGATTACCTGTAAT
ATAACAACTTTGTCAAAACCTAGGCCTATGAGAATTGTTAAACAGCAGTCTCTGGTAGAAAAATGTGATAAAATGGTTTC
AGAAAGTTTACAAATGACAGAGCATGGAAAGGTTTCAGACCACATACAGTGGTTTAACAAACTTTCCTTAAATGAACCAA
ATAGAACAAAAATTAAATCACCTCTTAAGTTTCAGCGTACTCCTGTCCGTCAGTCTGTCAGAAGAATTAATTCTTTATCG
GAGTATAACCGACAACCTGTAAGGTGTAAGTTGGCAAGT

Alignment

ORF - retro_chof_522 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.36 %
• Parental protein coverage: 57.04 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  HVDTSPEGSSQSSLSPVAISGNHLISASVQRQSKRIADKKVCRVESGKAGCFSPKISRKEKVRRSLRLKF
          HVDTSPEGSSQSSLSPVAISGNHLISASVQRQSKRIADKKVCRVESGKAGCFSPKIS.KEKVRRSL.LKF
Retrocopy HVDTSPEGSSQSSLSPVAISGNHLISASVQRQSKRIADKKVCRVESGKAGCFSPKISHKEKVRRSLHLKF

Parental  SLGKSNRDVNGCSDVNRYENVGRRLASQQNFKNRIESVKTGLLFSPDIERLTKKGSKKISKSEEYLSTPE
          SLGKSNRD..GCSDVNRYENVGRRLASQQNF.NRIESVKTGLLFSPDIERLTKKGSKKISKSEEYLSTPE
Retrocopy SLGKSNRD-DGCSDVNRYENVGRRLASQQNF*NRIESVKTGLLFSPDIERLTKKGSKKISKSEEYLSTPE

Parental  QLDGTNYCMSWTGPTNSSFQEIDANETSPIEGNLEVENSSLDPDLMVEKSPVTSYALTPSIVDNKHNSNL
          QLDGTNY.MS.TGPTNSSFQEIDANETSPIEGNLEVENSSLDPDLMVEKSPVTSYALTPS.V.NKHNSNL
Retrocopy QLDGTNYHMS*TGPTNSSFQEIDANETSPIEGNLEVENSSLDPDLMVEKSPVTSYALTPSTVHNKHNSNL

Parental  TGNSPNGDEDNLTTETLVKIQ-AFSESGSNLHTL-NHGQSSITNMVKAKLNETSYTEYSPKENLFETNDL
          TGNSPNGDEDNLTTETLVKIQ.AFSESGSNLHTL.NHGQSSITNMVKAKLNETSYTEYSPKENLFETNDL
Retrocopy TGNSPNGDEDNLTTETLVKIQKAFSESGSNLHTLINHGQSSITNMVKAKLNETSYTEYSPKENLFETNDL

Parental  TVIESKKKYEHQASKDDNSFSERDFSLHQTQELGREATTKCYSTQMKVEHEKTIYSNIAKDYLSMQKFPS
          TVIESKKKYEHQASKD.NSFSER.FSLHQTQELGREATTKCYSTQMKVEHEKTIYSNIAKDYLSMQ.FPS
Retrocopy TVIESKKKYEHQASKDENSFSERHFSLHQTQELGREATTKCYSTQMKVEHEKTIYSNIAKDYLSMQEFPS

Parental  EEQIKKQESTRNKLNTKLKENESVIEENLLKCTASGEDMSK-SSSEQITCNITTLSKPRPMRIVKQQSLV
          EEQIKKQES.RNKLNTKLKENESVIEENLLKCTASGEDMSK.SSS.QITCNITTLSKPRPMRIVKQQSLV
Retrocopy EEQIKKQESARNKLNTKLKENESVIEENLLKCTASGEDMSKSSSSKQITCNITTLSKPRPMRIVKQQSLV

Parental  EKCDKMVSESLQMTEHGKVSDHIQWFNKLSLNEPNRTKIKSPLKFQRTPVRQSVRRINSLSEYNRQPV-C
          EKCDKMVSESLQMTEHGKVSDHIQWFNKLSLNEPNRTKIKSPLKFQRTPVRQSVRRINSLSEYNRQPV.C
Retrocopy EKCDKMVSESLQMTEHGKVSDHIQWFNKLSLNEPNRTKIKSPLKFQRTPVRQSVRRINSLSEYNRQPVRC

Parental  KLAS
          KLAS
Retrocopy KLAS

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_522 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	ENSCHOG00000005172	1 retrocopy	retro_chof_522 ,