RetrogeneDB ID: retro_chof_876

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_16002:1700..2159(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SRGN
• Ensembl ID: ENSCHOG00000000448
• Aliases: None
• Description: serglycin [Source:HGNC Symbol;Acc:9361]

Sequence

>retro_chof_876
ATACAGAGGATCCTCCAGTGCGTTAGGCTTGTCCTGGCTGTCTCATTCACCCTGATTTGGGAATCTTCAGTTCAAGGTTA
TCCCATGCAGAGAGCCAGGTACCAGGGGGTGTGCTGCAGCCCAGACAGTATTTCTGCAAACTGTGTTGAGGAGAAGGGAC
CAGTGTTCAATCTGCATCCTGATGAATCTAGCAGGATCCTCCCTCCAAGGATTGACCCTTTATCAATGATGAGGTTCCCG
AACATGCACGATGTGTTCCCTCTTCCTGAGGACTAGTCTGGATCAGGCTCTGGCTCTGGATCGGGCCTTGGAAGTGGATT
CCTATCTGAGATGGAACAAGAACATGAACCAATAGATGAGGATGATGCTCTCCATTACAATGTTCAGCCTTTCAATAGGA
ATCTGCCTTCAGACTAACAGGACTTGGGTCAAGATGGATCAGAAGATTATTTTATTATG

Alignment

ORF - retro_chof_876 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.9 %
• Parental protein coverage: 99.35 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VEFFLQCGRLVLALSI-LIGESSVQGYPMRRARYQWVRCSPDSNSANCIEEKGPVFNLPPGESNRLLPPR
          ....LQC.RLVLA.S..LI.ESSVQGYPM.RARYQ.V.CSPDS.SANC.EEKGPVFNL.P.ES.R.LPPR
Retrocopy IQRILQCVRLVLAVSFTLIWESSVQGYPMQRARYQGVCCSPDSISANCVEEKGPVFNLHPDESSRILPPR

Parental  TDSLPMKSLLNVQEVFPLSEDYSGSGSGSGSGSGGGFLTEMEQEYEPVDGDDALQYNVQPFKRNLPSDYQ
          .D.L.M....N...VFPL.ED.SGSGSGSGSG.G.GFL.EMEQE.EP.D.DDAL.YNVQPF.RNLPSD.Q
Retrocopy IDPLSMMRFPNMHDVFPLPED*SGSGSGSGSGLGSGFLSEMEQEHEPIDEDDALHYNVQPFNRNLPSD*Q

Parental  DLDQDGSEDDFMI
          DL.QDGSED.F..
Retrocopy DLGQDGSEDYFIM

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_876 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 3 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017969	1 retrocopy	retro_amel_82,
Choloepus hoffmanni	ENSCHOG00000000448	9 retrocopies	retro_chof_1085, retro_chof_1907, retro_chof_1936, retro_chof_1950, retro_chof_227, retro_chof_2572, retro_chof_403, retro_chof_876 , retro_chof_935,
Dasypus novemcinctus	ENSDNOG00000006889	2 retrocopies	retro_dnov_1745, retro_dnov_544,