RetrogeneDB ID: retro_shar_252

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL835145.1:52764..53444(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CXADR
• Ensembl ID: ENSSHAG00000005309
• Aliases: None
• Description: coxsackie virus and adenovirus receptor [Source:HGNC Symbol;Acc:2559]

Sequence

>retro_shar_252
AAGCCTTCAAGAACAAGATGTTACCTTGATAGATCATCAGAGATTGGCAGTGACTTTAAACTAAAATGTAAATCAGAAGA
TTCACTTCCTTTACATTATGAATGGCAAAAAGCTTCCCAAGGCAGAAAAAATGTCTGCCTGTCTCATTTTTTATCAGATC
TCAACCCATAAATTATTTTGTACAAAATCCCACTCCAGAGTACTCTAGCACATAGAGTTGTACAGTTAAAAACAGAGTCA
GTGTTGATAAATGGATTTTGATGTGAATGTCGTTCCTCCTTCAAACGCTGCTGGTACAATTGTTGGAGCTATCATAGGAA
CTTTTTGTGGCCTGTTACTACTGGGTCTTCTCATCTTTTGCTACTATAAAAAACACAAGGAGGACAAATATGAAAAAGAA
GATTCACCATGATATCAGAAAGGACATTCTTCCTTAAAGTACCGCAGATCTCCAGCCAGAAACTACATTGGTAGCAGTCT
TTTACCTCTGGGATCGATGTCTCTTTCCAACAGAGAAGACTATTCCAAACTTCAGTGTAGCTAAGAACCAAGTGAAGACT
TTGATCCTACTTCACAAAAGCCCAAGTTTTCTACCAGCTAAAGTAGCAGCATCTAATCTAAGTAAAATGGAAACTATTCC
TCTGATGATAGCAGAAAAAAGCAAAGATAGGTCAGCAGTA

Alignment

ORF - retro_shar_252 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.24 %
• Parental protein coverage: 61.81 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  KPSGTKCYLDGSSEIGSDFKLRCESEGSLPLYYEWQKFPNTEKFPPVS--LSDLNPAIIS-VRNATPEYS
          KPS.T.CYLD.SSEIGSDFKL.C.SE.SLPL.YEWQK.....K....S..LSDLNP.II..V.N.TPEYS
Retrocopy KPSRTRCYLDRSSEIGSDFKLKCKSEDSLPLHYEWQKASQGRKNVCLSHFLSDLNP*IIL<VQNPTPEYS

Parental  GTYSCTVKNRVGFDKCILT-VTVIPPSNTAGTIAGAIVGTLCGLLLLGLLIFCCCKKRKEEKYEKE-VHH
          .T.SCTVKNRV..DK.IL..V.V.PPSN.AGTI.GAI.GT.CGLLLLGLLIFC..KK.KE.KYEKE..HH
Retrocopy ST*SCTVKNRVSVDKWILM<VNVVPPSNAAGTIVGAIIGTFCGLLLLGLLIFCYYKKHKEDKYEKE>IHH

Parental  DIREDVPP-PKSRTSTARSYIGSNHSSLGSMSPSNIEGYSKAQYNQVPSEDFDRTPQ-SPSFPPAKVAAS
          DIR.D..P..K.R.S.AR.YIGS....LGSMS.SN.E.YSK.Q....PSEDFD.T.Q.SPSF.PAKVAAS
Retrocopy DIRKDILP<LKYRRSPARNYIGSSLLPLGSMSLSNREDYSKLQCS*EPSEDFDPTSQ>SPSFLPAKVAAS

Parental  NLSRMGAIPVMIPAQSKDGSIV
          NLS.M..IP.MI...SKD.S.V
Retrocopy NLSKMETIPLMIAEKSKDRSAV

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_252 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.

---

Parental genes homology:

Parental genes homology involve 6 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000012975	1 retrocopy	retro_dnov_990,
Homo sapiens	ENSG00000154639	6 retrocopies	retro_hsap_1533, retro_hsap_1535, retro_hsap_1918, retro_hsap_2492, retro_hsap_4322, retro_hsap_4323,
Nomascus leucogenys	ENSNLEG00000002063	2 retrocopies	retro_nleu_138, retro_nleu_58,
Pongo abelii	ENSPPYG00000011295	2 retrocopies	retro_pabe_1273, retro_pabe_2776,
Pan troglodytes	ENSPTRG00000013795	4 retrocopies	retro_ptro_1244, retro_ptro_1444, retro_ptro_801, retro_ptro_995,
Sarcophilus harrisii	ENSSHAG00000005309	1 retrocopy	retro_shar_252 ,