RetrogeneDB ID: retro_shar_251

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL835059.1:51872..52155(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCDC12
• Ensembl ID: ENSSHAG00000003265
• Aliases: None
• Description: coiled-coil domain containing 12 [Source:HGNC Symbol;Acc:28332]

Sequence

>retro_shar_251
AGAGAAAATATTAGACACAAGAATAAGGAAGATGAGGAAGAAAGAAGTGAGAAACACAAGGAACTCAAATTGTGGAACTA
TAGCCCTAAAGATGTGGAGCTAAAAAAGAGGAAGTCCAAACCAGCCTCAGTGAAAGAGAAAGTAAAAGACTAGTTGAAAG
AAGCAAAGTCAGCCCATCGTTGAGGAAGTGGATTTTGCCAACCTTACTAATCTTGCCCTCAGAAAGCCAGATTGGAATTT
AAAGAGAGATGTGGAAAAGAAATTGGAAAGGCCAAAGAAAAGG

Alignment

ORF - retro_shar_251 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.4 %
• Parental protein coverage: 60.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KEDEEPKNKVLKEEEGGEKHRELKLRNYVPEDEELKKRKVPQAKPASVEEKV-KDQLEAAK-PEPIIEEV
          .E....KNK...EEE..EKH.ELKL.NY.P.D.ELKKRK....KPASV.EKV.K...E..K...PI.EEV
Retrocopy RENIRHKNKE-DEEERSEKHKELKLWNYSPKDVELKKRK---SKPASVKEKV<KRLVERSK<SQPIVEEV

Parental  DLA---NLAPRKPDWDLKRDVAKKLEKLEKR
          D.A...NLA.RKPDW.LKRDV.KKLE...KR
Retrocopy DFANLTNLALRKPDWNLKRDVEKKLERPKKR

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Sarcophilus harrisii was not studied using RNA-Seq expression data.

ChIP-Seq

Sarcophilus harrisii was not studied using ChIP-Seq data.

EST

Sarcophilus harrisii was not studied using EST data.

TSS

Sarcophilus harrisii was not studied using FANTOM5 data.

Lab

retro_shar_251 was not experimentally validated.

Homology

Retrocopy orthology:

Sarcophilus harrisii 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 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002280	3 retrocopies	retro_cjac_1212, retro_cjac_2317, retro_cjac_3225,
Dipodomys ordii	ENSDORG00000016567	1 retrocopy	retro_dord_303,
Echinops telfairi	ENSETEG00000000030	2 retrocopies	retro_etel_1445, retro_etel_2038,
Homo sapiens	ENSG00000160799	1 retrocopy	retro_hsap_2257,
Macaca mulatta	ENSMMUG00000019810	1 retrocopy	retro_mmul_1025,
Mus musculus	ENSMUSG00000019659	1 retrocopy	retro_mmus_1275,
Nomascus leucogenys	ENSNLEG00000006219	1 retrocopy	retro_nleu_1282,
Ochotona princeps	ENSOPRG00000005086	1 retrocopy	retro_opri_746,
Pongo abelii	ENSPPYG00000013924	2 retrocopies	retro_pabe_1957, retro_pabe_2033,
Pan troglodytes	ENSPTRG00000014862	1 retrocopy	retro_ptro_1597,
Sarcophilus harrisii	ENSSHAG00000003265	1 retrocopy	retro_shar_251 ,