RetrogeneDB ID: retro_shar_160

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL834502.1:983873..984441(+)
• Located in intron of: ENSSHAG00000012085

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC25A4
• Ensembl ID: ENSSHAG00000000932
• Aliases: None
• Description: solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator), member 4 [Source:HGNC Symbol;Acc:10990]

Sequence

>retro_shar_160
CTTGACAAGTACACACAATTTTGGAGGTATTTTACTGGTAATCTTGCTCTGGTGGTGCTACTGGAACTACTTCTCTCTGC
ATCTACCCCTTGGTTTTTGCAAAAACCCACTTGGCCGCTGATGACAATCTGGCACTGAGAGAATTCAAAGGCCTGGGAGA
TTGCCTTGTGAAAATCACCAAGTCTGATGGAACTCATGGCTTGTATTAAGCTTTCATTGTCTCAGTTTAGGGTATCATTA
TCTATAGAGCAGCCTACTTTGGGATCTGTGATAAAGAAAAAGGTATACTCCCAGGTCATAAGAACACTGGTATTGTGTTA
ATTTAGACAATTGCACAAATAGTGACTGCTGTAGCAGATGTACTCTCCTATCTTTTTGATGCAGTAAGGTAATGAATGAT
GATGTAGTCTGGGTGAAAAGGAATTGATATCATGTACACGGGACATTGACTGCTGGAGGTAGATAGCTAAAGATGAGGGT
AGTAAAACTTTTTTTAAGAATTCCTAGTCCAGTTTTCTTAGAGCTTTTGGTTGCAGTTTTATTGCTTGTCCTGTCTGATG
AATTAAAG

Alignment

ORF - retro_shar_160 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.45 %
• Parental protein coverage: 64.77 %
• Number of stop codons detected: 9
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  VDRHKQFWRYFAGNLA-SGGAAGATSLCFVYPLDFARTRLAADVGKGATQREFSGLGDCLTKIFKSDGLK
          .D...QFWRYF.GNLA.SGGA.G.TSLC..YPL.FA.T.LAAD.......REF.GLGDCL.KI.KSDG..
Retrocopy LDKYTQFWRYFTGNLA<SGGATGTTSLC-IYPLVFAKTHLAAD--DNLALREFKGLGDCLVKITKSDGTH

Parental  GLYQGFSVSVQGIIIYRAAYFGVYDTAKGMLPDPKNVHIIVSWMIAQSVTAVAGLVSYPFDTVRRRMMMQ
          GLY..F.VSV.GIIIYRAAYFG..D..KG.LP..KN..I.....IAQ.VTAVA...SY.FD.VR..MMM.
Retrocopy GLY*AFIVSV*GIIIYRAAYFGICDKEKGILPGHKNTGIVLI*TIAQIVTAVADVLSYLFDAVR**MMM*

Parental  SGRKGADIMYT-GT-IDCWRKIAKDEGAKAFFKGAWSNVLRGMGGAFV-LVLYDEIK
          SG.KG.DIMYT.GT.IDCWR.IAKDEG.K.FFK...S..LR..G..F..LVL.DE.K
Retrocopy SG*KGIDIMYT<GT<IDCWR*IAKDEGSKTFFKNS*SSFLRAFGCSFI>LVLSDELK

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_160 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 13 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013208	1 retrocopy	retro_btau_1592,
Choloepus hoffmanni	ENSCHOG00000010542	3 retrocopies	retro_chof_1117, retro_chof_1777, retro_chof_807,
Dasypus novemcinctus	ENSDNOG00000007258	3 retrocopies	retro_dnov_1531, retro_dnov_1800, retro_dnov_390,
Dipodomys ordii	ENSDORG00000013787	1 retrocopy	retro_dord_268,
Erinaceus europaeus	ENSEEUG00000001021	2 retrocopies	retro_eeur_274, retro_eeur_36,
Macropus eugenii	ENSMEUG00000008508	4 retrocopies	retro_meug_222, retro_meug_549, retro_meug_6, retro_meug_921,
Microcebus murinus	ENSMICG00000010865	1 retrocopy	retro_mmur_1356,
Oryctolagus cuniculus	ENSOCUG00000002594	1 retrocopy	retro_ocun_102,
Ochotona princeps	ENSOPRG00000005957	6 retrocopies	retro_opri_1154, retro_opri_146, retro_opri_377, retro_opri_517, retro_opri_543, retro_opri_685,
Pan troglodytes	ENSPTRG00000016646	9 retrocopies	retro_ptro_146, retro_ptro_1588, retro_ptro_2143, retro_ptro_2364, retro_ptro_2388, retro_ptro_2517, retro_ptro_2525, retro_ptro_2819, retro_ptro_2882,
Pteropus vampyrus	ENSPVAG00000015279	1 retrocopy	retro_pvam_892,
Sarcophilus harrisii	ENSSHAG00000000932	1 retrocopy	retro_shar_160 ,
Tarsius syrichta	ENSTSYG00000004233	1 retrocopy	retro_tsyr_27,