RetrogeneDB ID: retro_mdom_1216

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:503252005..503252479(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TAF1D
• Ensembl ID: ENSMODG00000008546
• Aliases: None
• Description: TATA box binding protein (TBP)-associated factor, RNA polymerase I, D, 41kDa [Source:HGNC Symbol;Acc:28759]

Sequence

>retro_mdom_1216
CCATCTGGAAGGCCAAAGGGAAGGCCAAAAGGAAGCACTAAAACAACTCAATCTTTAGCCATTATGCCGAAAAAGGACCT
TTTCAAAGATAAAGGTTTACAGTTCCCTTTGGTAGAATCAGAGAATGGAAGGAAACCATTACTTTGGAAGAAAATTTTAG
GCTTTGAGCAAGCAGTTGCAAGAGGGTTTTTCAACTATGTTAAGGAACAGAAATATGAATCCCACCTCAGAGAGGCTTTG
AAGCATCTGGGTGCTGGTGAAGATTTAGTCAAAGAAGACTTTGGTGTACGGAGATATAAATATTTAGAAGATGATGATGA
ATCTATTTCTCCTATAGAAGAACCCAATGCAGAAAACAACCAGTTGGATGATCAATATGACTGTGATGTCAAATTAGTGG
ACAATAGTTGTTTCATAATAAGTACTAAATTCCCCAAGAAGACAAAGTCAAAGATGAAAAAGAGAAGACTAGAC

Alignment

ORF - retro_mdom_1216 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.81 %
• Parental protein coverage: 61.72 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PSGRPKGRPKGSTKTTQSLAVMSKKDLFKDKGLQFPLVESENGRKPLLWKKILGFEQAVARGFFNYVKEQ
          PS..........TKTTQSLA.M.KKDLFKDKGLQFPLVESENGRKPLLWKKILGFEQAVARGFFNYVKEQ
Retrocopy PSXXXXXXXXXXTKTTQSLAIMPKKDLFKDKGLQFPLVESENGRKPLLWKKILGFEQAVARGFFNYVKEQ

Parental  KYESHLREALKHLGASEDLDKEDFGVRRYKYLEDDDESISPIEDSNAEYNQLDDQDDCDVKLVDNSCFII
          KYESHLREALKHLGA.EDL.KEDFGVRRYKYLEDDDESISPIE..NAE.NQLDDQ.DCDVKLVDNSCFII
Retrocopy KYESHLREALKHLGAGEDLVKEDFGVRRYKYLEDDDESISPIEEPNAENNQLDDQYDCDVKLVDNSCFII

Parental  STELPEKTKSKMKKTAKD
          ST..P.KTKSKMKK...D
Retrocopy STKFPKKTKSKMKKRRLD

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain	0.00 RPM	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.00 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1216 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1216 was not experimentally validated.

Homology

Retrocopy orthology:

Monodelphis domestica 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 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,