RetrogeneDB ID: retro_shar_382

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL841551.1:845049..845379(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GINS2
• Ensembl ID: ENSSHAG00000015249
• Aliases: None
• Description: GINS complex subunit 2 (Psf2 homolog) [Source:HGNC Symbol;Acc:24575]

Sequence

>retro_shar_382
GTTGAAAAATTGGAGGTGATATGAGATCAAGAGAGAAAGGAGGAACTATTTATTGCAATGCCTAGTCTTTACTACATGGA
ACTTATCAAATTGTTGTCATATCATGCCTTGGATAGCATTCCCAAAGCAGATGAGATCCGGACCCTGATTAAGGATATGT
GGAATATTCAAGTAGCTAAATTCTAGGTATATGTAGACAGTTTTGTCAGATAGTAGAAGGCATGTAACAACTTGGATAAC
TTTACCTTGACCAACTTACATTACCTTATGGGAGAATTTCCCACAGAAGACCTAAAACATAAGTACAGACTCTGCATAAA
CTTCCATCCT

Alignment

ORF - retro_shar_382 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.0 %
• Parental protein coverage: 78.99 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LEKLEEIRDQERKEETFTPMPSPYYMELTKLLLNHASDNIPKADEIRTLIKDMWDTRIAKLRVSADSFVK
          .EKLE.I.DQERKEE.F..MPS.YYMEL.KLL..HA.D.IPKADEIRTLIKDMW....AK..V..DSFV.
Retrocopy VEKLEVI*DQERKEELFIAMPSLYYMELIKLLSYHALDSIPKADEIRTLIKDMWNIQVAKF*VYVDSFVR

Parental  QQEAHAKLDNLTLMEIN-TTGAFLTEALNHMYKLRTNLHP
          ...A...LDN.TL.......G.F.TE.L.H.Y.L..N.HP
Retrocopy **KACNNLDNFTLTNLHYLMGEFPTEDLKHKYRLCINFHP

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_382 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 14 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017303	1 retrocopy	retro_cjac_3309,
Dasypus novemcinctus	ENSDNOG00000008760	4 retrocopies	retro_dnov_1034, retro_dnov_166, retro_dnov_2424, retro_dnov_604,
Homo sapiens	ENSG00000131153	1 retrocopy	retro_hsap_2477,
Gallus gallus	ENSGALG00000028131	1 retrocopy	retro_ggal_22,
Gorilla gorilla	ENSGGOG00000009069	2 retrocopies	retro_ggor_1542, retro_ggor_960,
Macropus eugenii	ENSMEUG00000014703	1 retrocopy	retro_meug_1479,
Microcebus murinus	ENSMICG00000016691	1 retrocopy	retro_mmur_342,
Macaca mulatta	ENSMMUG00000020594	1 retrocopy	retro_mmul_596,
Pongo abelii	ENSPPYG00000007616	2 retrocopies	retro_pabe_1826, retro_pabe_896,
Pan troglodytes	ENSPTRG00000008430	1 retrocopy	retro_ptro_1433,
Pteropus vampyrus	ENSPVAG00000004944	1 retrocopy	retro_pvam_762,
Sarcophilus harrisii	ENSSHAG00000015249	1 retrocopy	retro_shar_382 ,
Sus scrofa	ENSSSCG00000002663	1 retrocopy	retro_sscr_883,
Tupaia belangeri	ENSTBEG00000006220	1 retrocopy	retro_tbel_1328,