RetrogeneDB ID: retro_shar_752

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL861848.1:35244..35674(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNRNPD
• Ensembl ID: ENSSHAG00000013312
• Aliases: None
• Description: heterogeneous nuclear ribonucleoprotein D (AU-rich element RNA binding protein 1, 37kDa) [Source:HGNC Symbol;Acc:5036]

Sequence

>retro_shar_752
CTTTATATAGGAAGCCTTAGCTGGGAGACCACAAAGAAAGATTTGAAAAACTATGTTTCCAAATTTGGTGAACAAGAAGA
CTGCCCTATCACTGTAAAGTTACAGACAATCACATGGTGATCAAGGGGTTTTGGTTTTGTACTATTTAAAAAATCAGATA
GTATAGATAAGGTTATGGACCAGAAAAAAACACAAATTGATTTGCAAAATGATACAAGAGTCAAAGTCAAGGGGAAAAAA
AGAACATGTTAATCTTTGTTGTTGTTGGCTGCCTTTCTTCAGGTATCCTTGAGAAAATAAGGGAGTACTATAATGATTTT
GGTGAGGTGGAATCTGTAGAGTTCCTCCTCAAATACAACCCAAGATGTGGATTGTGCTTTACTAATTTTAAGGAAGAAGA
AATAATAAAGAAATGATGGAAAAGACATAT

Alignment

ORF - retro_shar_752 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.62 %
• Parental protein coverage: 52.71 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MFIGGLSWDTTKKDLKDYFSKFGEVVDC--TLKLDPITGRSRGFGFVLFKESESVDKVMDQKE-HKLNGK
          ..IG.LSW.TTKKDLK.Y.SKFGE..DC..T.KL..IT..SRGFGFVLFK.S.S.DKVMDQK..HKL..K
Retrocopy LYIGSLSWETTKKDLKNYVSKFGEQEDCPITVKLQTITW*SRGFGFVLFKKSDSIDKVMDQKK>HKLICK

Parental  VIDPKRAKAMKTKEPVKK-IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEE
          .I.....K....KE.V.....VG.LS.....EKIREY...FGEVES.E.....K.N.R.G.CF..FKEEE
Retrocopy MI--QESKSRGKKEHVNL>VVVGCLSSGIL-EKIREYYNDFGEVESVEFLL--KYNPRCGLCFTNFKEEE

Parental  PVKK-IMEKKY
          ..KK..MEK.Y
Retrocopy IIKK<MMEKTY

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_752 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 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015165	1 retrocopy	retro_cjac_2796,
Dipodomys ordii	ENSDORG00000012507	1 retrocopy	retro_dord_649,
Homo sapiens	ENSG00000138668	1 retrocopy	retro_hsap_4689,
Gorilla gorilla	ENSGGOG00000026760	1 retrocopy	retro_ggor_2916,
Loxodonta africana	ENSLAFG00000016483	1 retrocopy	retro_lafr_686,
Pan troglodytes	ENSPTRG00000016215	1 retrocopy	retro_ptro_3116,
Sarcophilus harrisii	ENSSHAG00000013312	1 retrocopy	retro_shar_752 ,
Sarcophilus harrisii	ENSSHAG00000013616	3 retrocopies	retro_shar_297, retro_shar_527, retro_shar_625,
Sarcophilus harrisii	ENSSHAG00000018255	1 retrocopy	retro_shar_518,
Tupaia belangeri	ENSTBEG00000002327	1 retrocopy	retro_tbel_2698,
Tarsius syrichta	ENSTSYG00000010395	3 retrocopies	retro_tsyr_1092, retro_tsyr_2070, retro_tsyr_269,
Tursiops truncatus	ENSTTRG00000007592	1 retrocopy	retro_ttru_1913,
Vicugna pacos	ENSVPAG00000004374	2 retrocopies	retro_vpac_484, retro_vpac_97,