RetrogeneDB ID: retro_mdom_603

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:487906409..487906796(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TAF12
• Ensembl ID: ENSMODG00000010943
• Aliases: None
• Description: TAF12 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 20kDa [Source:HGNC Symbol;Acc:11545]

Sequence

>retro_mdom_603
CCCCACAATCTCAAAAAGAAACAGGATCTTCACAAGCTCCATGAACTGAAGGCCAAAGCCCAGCAGATTATGAACCAGTT
TGTCCCCTCAGCCTTGATCAACCTCTCGTCATCCATAAAATCTGAACCTTCCAGCACCCAGAGGTCTGTGGCCAACAGTA
CCACAGTGGGAAAGATGCCAGGCTCTCCTGGGGCAGGGGGTCATCTTAGTCCAGAAAGCAATCAGGTTTTGACCAAGAAG
AAATTACACCACCTGGTTAGAGAAGGAGGTCCCAATGAACAGCTGGATGAAGCCATAGAACAGATGCTACAACATTTTGC
TGATTACTTCATTGAAAATGTAGTGACGACAGTGTACCAACTAGGGTCAAAAATGTCCAGCTGCACT

Alignment

ORF - retro_mdom_603 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.44 %
• Parental protein coverage: 62.44 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PHNPKKKQDLDKLHELKAKARQIMNQFGPSALINLSNFSSIKPEPSSTPPQGSMANSTTVGKMPGPPGAG
          PHN.KKKQDL.KLHELKAKA.QIMNQF.PSALINLS..SSIK.EPSST..Q.S.ANSTTVGKMPG.PGAG
Retrocopy PHNLKKKQDLHKLHELKAKAQQIMNQFVPSALINLS--SSIKSEPSST--QRSVANSTTVGKMPGSPGAG

Parental  GRLSPESNQVLTKKKLQDLVREVDPNEQLDEDVEEMLLQIADDFIESVVTAACQLARHRKSNT
          G.LSPESNQVLTKKKL..LVRE..PNEQLDE..E.ML...AD.FIE.VVT...QL.....S.T
Retrocopy GHLSPESNQVLTKKKLHHLVREGGPNEQLDEAIEQMLQHFADYFIENVVTTVYQLGSKMSSCT

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	1.67 RPM	0.00 RPM
SRP007412_cerebellum	0.65 RPM	0.00 RPM
SRP007412_heart	0.20 RPM	0.00 RPM
SRP007412_kidney	1.32 RPM	0.00 RPM
SRP007412_liver	1.01 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_603 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_603 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 16 parental genes, and 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004366	4 retrocopies	retro_chof_1112, retro_chof_2145, retro_chof_2182, retro_chof_402,
Callithrix jacchus	ENSCJAG00000009742	1 retrocopy	retro_cjac_2398,
Cavia porcellus	ENSCPOG00000009044	3 retrocopies	retro_cpor_1211, retro_cpor_352, retro_cpor_895,
Dipodomys ordii	ENSDORG00000015036	1 retrocopy	retro_dord_384,
Echinops telfairi	ENSETEG00000012597	2 retrocopies	retro_etel_129, retro_etel_540,
Macropus eugenii	ENSMEUG00000000914	3 retrocopies	retro_meug_1305, retro_meug_1609, retro_meug_1730,
Myotis lucifugus	ENSMLUG00000012595	8 retrocopies	retro_mluc_1214, retro_mluc_2541, retro_mluc_2542, retro_mluc_2598, retro_mluc_403, retro_mluc_412, retro_mluc_415, retro_mluc_416,
Monodelphis domestica	ENSMODG00000010943	1 retrocopy	retro_mdom_603 ,
Mustela putorius furo	ENSMPUG00000015506	1 retrocopy	retro_mputfur_458,
Oryctolagus cuniculus	ENSOCUG00000003935	2 retrocopies	retro_ocun_510, retro_ocun_712,
Ochotona princeps	ENSOPRG00000001524	1 retrocopy	retro_opri_503,
Rattus norvegicus	ENSRNOG00000048288	1 retrocopy	retro_rnor_2638,
Sorex araneus	ENSSARG00000007568	5 retrocopies	retro_sara_243, retro_sara_35, retro_sara_358, retro_sara_441, retro_sara_570,
Tarsius syrichta	ENSTSYG00000005320	1 retrocopy	retro_tsyr_1288,
Tursiops truncatus	ENSTTRG00000005548	1 retrocopy	retro_ttru_1943,
Vicugna pacos	ENSVPAG00000006779	1 retrocopy	retro_vpac_362,