RetrogeneDB ID: retro_shar_179

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL834547.1:45057..45372(+)
• Located in intron of: ENSSHAG00000001715

Retrocopy information

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

Parental gene information

• Parental gene symbol: KHDRBS3
• Ensembl ID: ENSSHAG00000000632
• Aliases: None
• Description: KH domain containing, RNA binding, signal transduction associated 3 [Source:HGNC Symbol;Acc:18117]

Sequence

>retro_shar_179
AAACTTTTCATTCAAACTGGAAATTCTTTACATTGTCTATAGGAGGAAACCTTAGCCAAAATGTCCATTCTTGGAAAAGG
TTTCTTACAGGATAAAAACAAAGAATTGAATTGTAAAGGAATTCAATTCTTCCACTTAAAAGATGATATGATTGTCCTTG
TTGATATTATTGCCCTATAAGCAAAAGGATGTGCTTAATTTGGGCATGCTTTGGAAGAAATTTAAAAGTTCCTTATCTCT
GCTTGTGATGATTAAAACCAGGCAAGAACAGCTTCAAGAATAATATACTTAAATGGTGGTTCACAAAATACAGAT

Alignment

ORF - retro_shar_179 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.45 %
• Parental protein coverage: 89.26 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KLLGPRGNSLKRLQEETLTKMSILGKGSMRDKTKEEELRKSGEAKYFHLNDDLHVLIEVFAPPAEAYARM
          KL....GNSL..L.EETL.KMSILGKG...DK.K..EL...G....FHL.DD..VL....A..A...A..
Retrocopy KLFIQTGNSLHCL*EETLAKMSILGKGFLQDKNK--ELNCKG-IQFFHLKDDMIVLVDIIAL*AKGCA*F

Parental  GHALEEIKKFLIPDYND-EIRQAQLQE-LTYLNGGSENAD
          GHALEEI.KFLI....D...RQ.QLQE...YLNGGS.N.D
Retrocopy GHALEEI*KFLISACDD>KTRQEQLQE<IIYLNGGSQNTD

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_179 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000010878	2 retrocopies	retro_dnov_1085, retro_dnov_1131,
Dipodomys ordii	ENSDORG00000014595	1 retrocopy	retro_dord_689,
Equus caballus	ENSECAG00000010194	1 retrocopy	retro_ecab_460,
Otolemur garnettii	ENSOGAG00000005150	3 retrocopies	retro_ogar_2456, retro_ogar_3114, retro_ogar_550,
Sarcophilus harrisii	ENSSHAG00000000632	1 retrocopy	retro_shar_179 ,
Tursiops truncatus	ENSTTRG00000001270	2 retrocopies	retro_ttru_1633, retro_ttru_1929,