RetrogeneDB ID: retro_shar_211

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL834666.1:251550..251958(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ORC6
• Ensembl ID: ENSSHAG00000004207
• Aliases: None
• Description: origin recognition complex, subunit 6 [Source:HGNC Symbol;Acc:17151]

Sequence

>retro_shar_211
CTCTCTGTGTTAAACAAAAAGATGCATCAAAGCTGTTTTAAGTCAGTTGAGTGTTTGATGAATCTGAATTAAAATCTGAA
CATAAAATTCTTAGCTATAGAGTTTAGTTTCATGGAAGTAGTAAGTATAGCTTCCAAGATCTCTCAGAAGGATGAAATTC
TTCCCCAGATGCAGAAAGTAGGTCTAGATTGATCTACTACAATCTCTTTTCAAAATAGCTACTCTGTTCTCAATAGTTGG
GGTCCTAAAGCTAAAACTAGATAAAGACAAAATGGTGGCCACATCTGGTATAAAAAAAGCTGTTTTTGATTTGATTCTGT
AAACATCTGGGGGAAAAATGAACAGCAAGTTAAGGGAGGACCTAGTAAACCAACTAAAAGAGAAGTTAAACATTCCAAGA
AAGGAAAG

Alignment

ORF - retro_shar_211 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.11 %
• Parental protein coverage: 54.41 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LSGLNKKMYQSCLKSFECLLGLNSNLGIKDLAVQFNCVEAVNIASQI-LQRYEVSLPQIQK-VDLDLSKP
          LS.LNKKM.QSC.KS.ECL..LN.NL.IK.LA..F...E.V.IAS.I.L.R.....P...K.V..DL...
Retrocopy LSVLNKKMHQSCFKSVECLMNLN*NLNIKFLAIEFSFMEVVSIASKI>LRRMKF-FPRCRK*V*IDLLQS

Parental  LFTTAALFSACRVLKIKVNKDKIVATSGVKKAVFDRL-CKQL-EKFEQQVKGESSSSASPPAKRQKIIIE
          LF..A.LFS...VLK.K..KDK.VATSG.KKAVFD...CK.L..K.EQQVKG..S.....P.KR......
Retrocopy LFKIATLFSIVGVLKLKLDKDKMVATSGIKKAVFDLI>CKHL>GKNEQQVKGGPSK----PTKRE---VK

Parental  QSKKGE
          .SKKG.
Retrocopy HSKKGK

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_211 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 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002944	1 retrocopy	retro_chof_2302,
Dasypus novemcinctus	ENSDNOG00000010859	1 retrocopy	retro_dnov_838,
Erinaceus europaeus	ENSEEUG00000012122	1 retrocopy	retro_eeur_489,
Otolemur garnettii	ENSOGAG00000000688	1 retrocopy	retro_ogar_1426,
Sarcophilus harrisii	ENSSHAG00000004207	2 retrocopies	retro_shar_211 , retro_shar_759,
Tupaia belangeri	ENSTBEG00000000278	1 retrocopy	retro_tbel_3089,
Tarsius syrichta	ENSTSYG00000005205	2 retrocopies	retro_tsyr_1294, retro_tsyr_889,
Tursiops truncatus	ENSTTRG00000013294	1 retrocopy	retro_ttru_1528,