RetrogeneDB ID: retro_shar_566

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL849963.1:198590..199122(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TAF1D
• Ensembl ID: ENSSHAG00000005874
• Aliases: None
• Description: TATA box binding protein (TBP)-associated factor, RNA polymerase I, D, 41kDa [Source:HGNC Symbol;Acc:28759]

Sequence

>retro_shar_566
ATGGCTTTAATTGGTTCATTGGTACACAGTGAAACTGATGACCCAGATTCTAGCAGCAGTTTATTTAAAACAATGTGATC
CCACCTCACCCAATCAAAAACCAAGAAATATATCTCCCTTAATTGTGGAACAGTCACCTGTAAATACTCAGTTGAGAGAT
GATTCAAACCAGTACTCTTCAAAACCAAAACTATTTCATTTGTGGGTTGTTTTTGAAAATTGGAAGAAAAGGAAAAGAGA
GAGAATATACAAACCAACTGGAAGGCCAAAGGGAAGGCCAAAAAGAAGCTTAAAAACAAAACAAAACCAGTCAGGCATTG
TACTGACAAAGGACTCATTCAAAGACAAAGGTTTCTGATTCCCTTTGATTGAATCAGAGAATGGAAGGAAATGATTATAT
TGGAAGAAAATTTTAGGCTATGAGCAAGCAGTTGTAAGAGGATTTTTCAACTATGTTAAGGAAAAGAAATGTGAATCCCA
CATCAGAGAAGTTTTGAAGCATCTGGATGTTAGTGAGAATTTAGAAAAAGAA

Alignment

ORF - retro_shar_566 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.56 %
• Parental protein coverage: 73.25 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MASTDSLVNNETDDSDSSSS-LFKTQCDPISPKRRPRNLSTSIVIQSPAKTQLRDDSSESSSELEPFNLR
          MA...SLV..ETDD.D.SSS.....QCDP.SP...PRN.S..IV.QSP..TQLRDDS...SS....F.L.
Retrocopy MALIGSLVHSETDDPD-SSS>VYLKQCDPTSPNQKPRNISPLIVEQSPVNTQLRDDSNQYSSKPKLFHLW

Parental  VIFENWKKKKRRKRKYKPTGRPRGRPKGSFKAKQSLR-IRPKKDLFRDKGFQFPLVESENGRKPLLWKKI
          V.FENWKK.KR..R.YKPTGRP.GRPK.S.K.KQ....I...KD.F.DKGF.FPL.ESENGRK.L.WKKI
Retrocopy VVFENWKKRKR-ERIYKPTGRPKGRPKRSLKTKQNQSGIVLTKDSFKDKGF*FPLIESENGRK*LYWKKI

Parental  LGYEQAVARGFFNYIKEKKCESHLGEALKQLDVGEDLEKD
          LGYEQAV.RGFFNY.KEKKCESH..E.LK.LDV.E.LEK.
Retrocopy LGYEQAVVRGFFNYVKEKKCESHIREVLKHLDVSENLEKE

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_566 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 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013436	1 retrocopy	retro_chof_405,
Myotis lucifugus	ENSMLUG00000011431	1 retrocopy	retro_mluc_2033,
Monodelphis domestica	ENSMODG00000008546	1 retrocopy	retro_mdom_1216,
Oryctolagus cuniculus	ENSOCUG00000001096	2 retrocopies	retro_ocun_101, retro_ocun_23,
Otolemur garnettii	ENSOGAG00000002521	1 retrocopy	retro_ogar_1139,
Sarcophilus harrisii	ENSSHAG00000005874	1 retrocopy	retro_shar_566 ,
Tarsius syrichta	ENSTSYG00000014258	1 retrocopy	retro_tsyr_1107,