RetrogeneDB ID: retro_chof_2106

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_49556:57..729(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: THUMPD2
• Ensembl ID: ENSCHOG00000000360
• Aliases: None
• Description: THUMP domain containing 2 [Source:HGNC Symbol;Acc:14890]

Sequence

>retro_chof_2106
GTTGAGTATATCTCAGGAAAGGTTTTCTTCACCACCTGTTCTTATTTGAATATGCTGATGAAATTAAAATCTGCAAAAAG
GTTATTTCTGCTGATAAAAAAGCAGTTTCCACTGACACTTTCTTCTGAAGTAAAGGAAAAATATTTAGTGATATGCAAAG
ACTTGTAAATGATGACCTAGGAAGTTGGTTGAATGCCCATTTCAATTGTGAAAAATCTTCTTGAACTTGATGCAAAAAGG
GAAGAACTTTCTCAAGGAGATTCTAACCCACTAAAAAGAAAAGCAGGAGAAAATGAAATCATTATGGCTAAAAAATTTAA
AACAGAACAAATGCAAGACATACCAGAGAACAGGGAATGTTGGCTGGAAAAACAAATAGAAGAAGAAACACTAGAGCAAA
AAGATTTTATCAATCAAAGAGACGATCTTCAAGAAGAATAGTTTCAGAGTGATGTAGAGAAAGCAAATGATACTCATAAC
TGGAGCGACTTGACTTTCAGGGTTTCTTGTTGCTGTAGTGGTGCTTTTGGAAGGACTGCACAGGAAGTAGGAAGAATAAT
TGGAATTGCTCTTAGGAAACAGCTTGGATGGAAAGCAGATTTGAGGAATCCAAATTTAGAGATCTTTATACATCTAAATG
ATGTTTACTCCATTGTGGGGATTTCTGTTTTC

Alignment

ORF - retro_chof_2106 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.19 %
• Parental protein coverage: 63.74 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VECISGKVFFTTCSDLNMLMKLKSAERLFLLIKKQFPLTVSSV-SKGKIFNEMQRLVNDDPGSWSNA-IS
          VE.ISGKVFFTTCS.LNMLMKLKSA.RLFLLIKKQFPLT.SS..SKGKIF..MQRLVNDD.GSW.NA.IS
Retrocopy VEYISGKVFFTTCSYLNMLMKLKSAKRLFLLIKKQFPLTLSSE<SKGKIFSDMQRLVNDDLGSWLNA>IS

Parental  IWKNLHELDAKREELSQGDSNPLKRKAGENEIIMAKKFKTEQMQDIPENGECQLEKQVEEETLEQKDCIG
          I.KNL.ELDAKREELSQGDSNP..................EQMQDIPEN.EC.LEKQ.EEETLEQKD.I.
Retrocopy IVKNLLELDAKREELSQGDSNPXXXXXXXXXXXXXXXXXXEQMQDIPENRECWLEKQIEEETLEQKDFIN

Parental  QRGDFQEE-FQSDAEKAIDTHNQCDLTFRVSCRCSGAIGRTFAAQEVGRIIGISLMKQFGWKADLRNPTL
          QR.D.QEE.FQSD.EKA.DTHN..DLTFRVSC.CSGA.GRT..AQEVGRIIGI.L.KQ.GWKADLRNP.L
Retrocopy QRDDLQEE*FQSDVEKANDTHNWSDLTFRVSCCCSGAFGRT--AQEVGRIIGIALRKQLGWKADLRNPNL

Parental  EIFIHLNDVYSIVGIPVF
          EIFIHLNDVYSIVGI.VF
Retrocopy EIFIHLNDVYSIVGISVF

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_2106 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	ENSCHOG00000000360	1 retrocopy	retro_chof_2106 ,