RetrogeneDB ID: retro_chof_2666

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_95517:5233..5704(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: STARD7
• Ensembl ID: ENSCHOG00000001391
• Aliases: None
• Description: StAR-related lipid transfer (START) domain containing 7 [Source:HGNC Symbol;Acc:18063]

Sequence

>retro_chof_2666
CCCAGCCATGCCTCGGCCTTGATGGGGGCTCTGGCCGGTGTCTTCATGTGGAAGAGGAGCAGATCCAGGAGGAGATGCTG
CAGGGTCCACTGATGAGGTGAAGCGCTTGGAGGAAATGTCAAGCATGTTTCAGAGCTCCGGAGTCGAGTGCCATCCCCAG
AACCAAAATCCCAAACAGAAGGGAATGAAAATTCAGGCAGCCAAGAGCAGCCATGGGAAATGGCGATGGATAAGAAACAT
TTTAAGCCGTTGAGGCGCCCAATTACAGGCACCCACCTTTACCAGTATCGAGTTTTTGGAACCTACGCGATTGTGACACC
CCGGCAGTTCGTCAGTGTTCAGCTGGATACAGAGTATTGAAAAAAGCAGGACGCCCTGGTAAACAAGCTGGAGGTGGTGG
AGAGAGTCGCGGTTAGTGGTTCTGAGGTTCTCCACTGGGTAACCCATTTTCCTTATCTGACGTACTCGCGG

Alignment

ORF - retro_chof_2666 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.5 %
• Parental protein coverage: 51.3 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  PAHALTLMAALTGVFAW-DEERIQEEELQR-SIDEMKRLEEMSRMFQSSGVECHPA-ETKSQTEGNENPD
          P.HA..LM.AL.GVF.W..EE.IQEE.LQ..S.DE.KRLEEMS.MFQSSGVECHP..E.KSQTEGNEN..
Retrocopy PSHASALMGALAGVFMW<EEEQIQEEMLQG<STDEVKRLEEMSSMFQSSGVECHPQ<EPKSQTEGNENSG

Parental  SQEQPWEMVMDKKHFKLWRRPITGTHLYQYRVFGTYTDVTPRQFFNVQLDTEYRKKWDALVIKLEVVERD
          SQEQPWEM.MDKKHFK..RRPITGTHLYQYRVFGTY..VTPRQF..VQLDTEY.KK.DALV.KLEVVER.
Retrocopy SQEQPWEMAMDKKHFKPLRRPITGTHLYQYRVFGTYAIVTPRQFVSVQLDTEY*KKQDALVNKLEVVERV

Parental  AVSGSEVLHWVTHFPYPMYSR
          AVSGSEVLHWVTHFPY..YSR
Retrocopy AVSGSEVLHWVTHFPYLTYSR

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_2666 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 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001391	3 retrocopies	retro_chof_1979, retro_chof_2666 , retro_chof_491,
Ictidomys tridecemlineatus	ENSSTOG00000016345	1 retrocopy	retro_itri_1242,