RetrogeneDB ID: retro_shar_554

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL849902.1:549395..549788(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000014470
• Aliases: None
• Description: None

Sequence

>retro_shar_554
GGGCTGCTCAGGGATAACAACAAATGTTTTGAGCAGGAAGGATTCCAACTCACGGGCATGAAGTTCCTTAGGACCCCAGA
GGAACATCTGAAACAGTATTATGCTGACCCAAAGGACAATTTTTTCCTAAGCTCATGAAATACATCAACTCAGGACTTGT
GGCCCTGTTTCGGGGGGATTTGAATATGGTGAAAGCAGCAGAATGATGCTGGGAAGGACCAACCCAGATGGTTCCTTAAG
CACCATTTGTAGAGACTTCCTCATTCAAGTCAGCAGGAACATCCTTTACCACAGAGATTCTGTAAAAAGTACTGAAAAGG
AAATAAAGCCTGTGGTCTAAGCCCTGAGATTTGGTCAACTAAATTGTCTTCTGTTCATGACTGGGTCTATGAA

Alignment

ORF - retro_shar_554 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.14 %
• Parental protein coverage: 50.19 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  GLVGDIIKRFEQKGFRLVGMKFLRASEEHLKQHYADLKDRPFF-PGLVKYMNSGPVVAMVWEGLNVVK-T
          GL..D..K.FEQ.GF.L.GMKFLR..EEHLKQ.YAD.KD..FF.P.L.KY.NSG..VA.....LN.VK..
Retrocopy GLLRDNNKCFEQEGFQLTGMKFLRTPEEHLKQYYADPKDN-FF<PKLMKYINSG-LVALFRGDLNMVK<S

Parental  GRVMLGETNPADSKPGTIRGDFCIQVGRNIIHGSDSVKSAEKEI-SLWFKPEELVD-YKSCAHDWVYE
          .R.MLG.TNP.D....TI..DF.IQV.RNI....DSVKS.EKEI.SLW.KP..LV....S..HDWVYE
Retrocopy SRMMLGRTNP-DGSLSTICRDFLIQVSRNILYHRDSVKSTEKEI>SLWSKP*DLVN>KLSSVHDWVYE

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_554 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 13 parental genes, and 44 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008022	3 retrocopies	retro_amel_1573, retro_amel_390, retro_amel_538,
Callithrix jacchus	ENSCJAG00000018395	5 retrocopies	retro_cjac_1765, retro_cjac_2517, retro_cjac_2642, retro_cjac_3940, retro_cjac_471,
Erinaceus europaeus	ENSEEUG00000003783	2 retrocopies	retro_eeur_156, retro_eeur_5,
Homo sapiens	ENSG00000011052	1 retrocopy	retro_hsap_1063,
Myotis lucifugus	ENSMLUG00000016929	3 retrocopies	retro_mluc_1422, retro_mluc_1882, retro_mluc_637,
Macaca mulatta	ENSMMUG00000001940	1 retrocopy	retro_mmul_1827,
Mus musculus	ENSMUSG00000020857	1 retrocopy	retro_mmus_221,
Oryctolagus cuniculus	ENSOCUG00000024946	1 retrocopy	retro_ocun_418,
Otolemur garnettii	ENSOGAG00000025331	9 retrocopies	retro_ogar_1326, retro_ogar_1875, retro_ogar_1997, retro_ogar_2373, retro_ogar_2393, retro_ogar_2779, retro_ogar_3299, retro_ogar_483, retro_ogar_95,
Rattus norvegicus	ENSRNOG00000002671	8 retrocopies	retro_rnor_1129, retro_rnor_1610, retro_rnor_1708, retro_rnor_1784, retro_rnor_1966, retro_rnor_2646, retro_rnor_2951, retro_rnor_628,
Sarcophilus harrisii	ENSSHAG00000014470	3 retrocopies	retro_shar_130, retro_shar_554 , retro_shar_781,
Sus scrofa	ENSSSCG00000017591	1 retrocopy	retro_sscr_854,
Tupaia belangeri	ENSTBEG00000013053	6 retrocopies	retro_tbel_1271, retro_tbel_1386, retro_tbel_2497, retro_tbel_294, retro_tbel_4620, retro_tbel_820,