RetrogeneDB ID: retro_chof_984

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_1804:6299..6829(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: STARD3NL
• Ensembl ID: ENSCHOG00000008990
• Aliases: None
• Description: STARD3 N-terminal like [Source:HGNC Symbol;Acc:19169]

Sequence

>retro_chof_984
TTTGTCACCTTTGACCCCTTATTTGTAACATTACTGTGGATGATAGAGTTGAATATGAATGGAAGCATTTAGAACACATG
AGAGAAGGAGGTGCTGCAGTATGACTACCATGCTTCTTATTGTGATTTATGTCTTTTAGCAGTTTTTTTATTTAATGTAT
TAATACATGCACATGTTGTGTGCAAACTGCACCATTGGTGGGCAACAATGTTAATGACAAAAGTGACCAGTGCCTTTTTA
TTAGCAAAAATGACCCACTCAAAGCTTTTCTTTTGAGGGGCTTTTGAGTAAGTGCTACCCATCATTTCATTCATCCTTGC
CTGGATTGAGACCTGGTCCTGGAATTCAAAGTGTTACCTCAAGAAACAGAGAAAGAAAACAGACTCCAGATAGTTCCAGA
TGCTTCAAAGAGCGCAGCACTTAAACCTGGTGGTCTTTCCTATGATCATTTTTATGCTCCTGAATCTGAAACAGGATCTG
AAGAAGAAGCTGAAGAAAAACAAGTATGAGAGAAACCACTCCTAGAACTG

Alignment

ORF - retro_chof_984 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.83 %
• Parental protein coverage: 76.19 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FVTFD-LF-TLLXXXXXXVNGGIENTLEKEVVQYDYYSSYFDIFLLAVFRFKVLILAYAVCRLRHWWAIA
          FVTFD.LF.TLL.......NG.I.NT.EKEV.QYDY..SY.D..LLAVF.F.VLI.A..VC.L.HWWA..
Retrocopy FVTFDPLFVTLLWMIELNMNGSI*NT*EKEVLQYDYHASYCDLCLLAVFLFNVLIHAHVVCKLHHWWATM

Parental  LTTAVTSAFLLAKVILSKLFSQGAFGYVLPIISFILAWIETW-FLDFKVLPQEAEEENRLRIVQDASERA
          L.T.VTSAFLLAK...SKLF..GAF..VLPIISFILAWIETW..L.FKVLPQE.E.ENRL.IV.DAS..A
Retrocopy LMTKVTSAFLLAKMTHSKLFF*GAFE*VLPIISFILAWIETW<VLEFKVLPQETEKENRLQIVPDASKSA

Parental  ALIPGGLSDGQFYSPPESEAGSEEEAEEKQGNEKPLLEL
          AL.PGGLS...FY..PESE.GSEEEAEEKQ..EKPLLEL
Retrocopy ALKPGGLSYDHFYA-PESETGSEEEAEEKQV*EKPLLEL

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_984 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 10 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000038795	1 retrocopy	retro_btau_264,
Choloepus hoffmanni	ENSCHOG00000008990	1 retrocopy	retro_chof_984 ,
Callithrix jacchus	ENSCJAG00000012622	1 retrocopy	retro_cjac_3042,
Cavia porcellus	ENSCPOG00000004394	1 retrocopy	retro_cpor_1237,
Dasypus novemcinctus	ENSDNOG00000017960	1 retrocopy	retro_dnov_2389,
Equus caballus	ENSECAG00000005250	1 retrocopy	retro_ecab_709,
Microcebus murinus	ENSMICG00000000945	1 retrocopy	retro_mmur_388,
Macaca mulatta	ENSMMUG00000023659	1 retrocopy	retro_mmul_2643,
Ictidomys tridecemlineatus	ENSSTOG00000014750	1 retrocopy	retro_itri_286,
Tursiops truncatus	ENSTTRG00000004099	1 retrocopy	retro_ttru_864,