RetrogeneDB ID: retro_chof_1979

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_442159:41..894(-)
• 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_1979
GAAGAGGAGCAGATCCAGGAGGAGATGCTGCAGGGTCCACTGATGAGGTGAAGCGCTTGGAGGAAATGTCAAGCATGTTT
CAGAGCTCCGGAGTCGAGTGCCATCCCCAGAACCAAAATCCCAAACAGAAGGGAATGAAAATTCAGGCAGCCAAGAGCAG
CCATGGGAAATGGCGATGGATAAGAAACATTTTAAGCCGTTGAGGCGCCCAATTACAGGCACCCACCTTTACCAGTATCG
AGTTTTTGGAACCTACGCGATTGTGACACCCCGGCAGTTCGTCAGTGTTCAGCTGGATACAGAGTATTGAAAAAAGCAGG
ACGCCCTGGTAAACAAGCTGGAGGTGGTGGAGAGAGTCGCGGTTAGTGGTTCTGAGGTTCTCCACTGGGTAACCCATTTT
CCTTATCTGACGTACTCGCGGGATTATGTTTATGTTCGGCGGTGTAGTGTGGATGAGGAAAACAATGTGATGGTATTAGC
GTCACGAGCTGTGGAGCGCCCAGTTTGCCAGTCTCTGGAATTCGTCAGGGTCAGATCATATGAATCCCAAATGGTTATCG
ATCCCCACAAGTCATTTGATGAGAATAGCTTTGACTACTTGCTGATACACAGTGACTATCCACAGGCTGTGTTTCCTCGC
TACTGTGTTAGTTGGCTGGTTTCCAGTGGCATGCCCGATTTCCTGGAGAAGCTGCACATGGCCACTCTGGAAGCCAAGAA
TATTAAGATCAAAGTAAAGGACTACATCTCAGCTAAGCCTCTGGAAACGGGTAGTGAAGCCAAGGCCACTGTCCAGTCCT
TTGAGAGGAAGGGTGATGGTGGTAGTCGGAGCCCTTCCCCAATTGAGTATGCC

Alignment

ORF - retro_chof_1979 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.31 %
• Parental protein coverage: 92.53 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DEERIQEEELQR-SIDEMKRLEEMSRMFQSSGVECHPA-ETKSQTEGNENPDSQEQPWEMVMDKKHFKLW
          .EE.IQEE.LQ..S.DE.KRLEEMS.MFQSSGVECHP..E.KSQTEGNEN..SQEQPWEM.MDKKHFK..
Retrocopy EEEQIQEEMLQG<STDEVKRLEEMSSMFQSSGVECHPQ<EPKSQTEGNENSGSQEQPWEMAMDKKHFKPL

Parental  RRPITGTHLYQYRVFGTYTDVTPRQFFNVQLDTEYRKKWDALVIKLEVVERDAVSGSEVLHWVTHFPYPM
          RRPITGTHLYQYRVFGTY..VTPRQF..VQLDTEY.KK.DALV.KLEVVER.AVSGSEVLHWVTHFPY..
Retrocopy RRPITGTHLYQYRVFGTYAIVTPRQFVSVQLDTEY*KKQDALVNKLEVVERVAVSGSEVLHWVTHFPYLT

Parental  YSRDYVYVRRYSVDQENNVMVLVSRAVEHPSVPESPEFVRVRSYESQMVIRPHKSFDENGFDYLLTYSDN
          YSRDYVYVRR.SVD.ENNVMVL.SRAVE.P.V..S.EFVRVRSYESQMVI.PHKSFDEN.FDYLL..SD.
Retrocopy YSRDYVYVRRCSVDEENNVMVLASRAVERP-VCQSLEFVRVRSYESQMVIDPHKSFDENSFDYLLIHSDY

Parental  PQTVFPRYCVSWMVSSXXXXXXXXXXXXXXXXXXMEIKVKDYISAKPLEMGGEAKSAAQPSERKSE-GSR
          PQ.VFPRYCVSW.VSS....................IKVKDYISAKPLE.G.EAK...Q..ERK...GSR
Retrocopy PQAVFPRYCVSWLVSSGMPDFLEKLHMATLEAKNIKIKVKDYISAKPLETGSEAKATVQSFERKGDGGSR

Parental  GPARIEYA
          .P..IEYA
Retrocopy SPSPIEYA

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_1979 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,