RetrogeneDB ID: retro_shar_666

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL856972.1:62874..63168(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CNBP
• Ensembl ID: ENSSHAG00000017132
• Aliases: None
• Description: CCHC-type zinc finger, nucleic acid binding protein [Source:HGNC Symbol;Acc:13164]

Sequence

>retro_shar_666
TGTGGTAAGTCTGGTCATCTTGCCAAGGATTGTAATCTTCAGAAGGATGCTTGCTATAACTGCGGTAGAGATGGCTACTT
TGCCAAGCACTGCAGGGAACCCAAGCAAGAAAGAGAGTAGTGTTGCTACAATGTAGCAAAGTTGGTCATTTGGCTCATGA
CTGTGACCATGCAGATAAAGTACAAGTGTTATTCATGTGGAAAGTTTGGGCACATTCAGAAAGATTGCACCAAAGTGAAA
TGCTGTATGTGTGGTGAAACTAGTCATGTAACCATCAACTGCAGCAAGATGAGT

Alignment

ORF - retro_shar_666 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77. %
• Parental protein coverage: 55.37 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  CGESGHLAKDCDLQEDACYNCGRGGHIAKDCKEPKREREQCCYN-CGKPGHLARDCDHAD-EQKCYSCGE
          CG.SGHLAKDC.LQ.DACYNCGR.G..AK.C.EPK.ERE.CCYN.C.K.GHLA.DCDHAD...KCYSCG.
Retrocopy CGKSGHLAKDCNLQKDACYNCGRDGYFAKHCREPKQERE*CCYN<CSKVGHLAHDCDHAD>KYKCYSCGK

Parental  FGHIQKDCTKVKCYRCGETGHVAINCSKTS
          FGHIQKDCTKVKC..CGET.HV.INCSK.S
Retrocopy FGHIQKDCTKVKCCMCGETSHVTINCSKMS

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_666 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 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012159	1 retrocopy	retro_btau_19,
Callithrix jacchus	ENSCJAG00000017430	1 retrocopy	retro_cjac_4079,
Equus caballus	ENSECAG00000009512	1 retrocopy	retro_ecab_1072,
Echinops telfairi	ENSETEG00000008408	5 retrocopies	retro_etel_12, retro_etel_1791, retro_etel_2192, retro_etel_237, retro_etel_583,
Felis catus	ENSFCAG00000028042	2 retrocopies	retro_fcat_1922, retro_fcat_2001,
Loxodonta africana	ENSLAFG00000002502	1 retrocopy	retro_lafr_49,
Oryctolagus cuniculus	ENSOCUG00000008696	2 retrocopies	retro_ocun_1626, retro_ocun_208,
Otolemur garnettii	ENSOGAG00000013898	1 retrocopy	retro_ogar_144,
Pteropus vampyrus	ENSPVAG00000015070	1 retrocopy	retro_pvam_908,
Sorex araneus	ENSSARG00000011874	1 retrocopy	retro_sara_397,
Sarcophilus harrisii	ENSSHAG00000017132	1 retrocopy	retro_shar_666 ,