RetrogeneDB ID: retro_mdom_1220

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:14357995..14358545(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TBPL1
• Ensembl ID: ENSMODG00000017515
• Aliases: None
• Description: TBP-like 1 [Source:HGNC Symbol;Acc:11589]

Sequence

>retro_mdom_1220
ATGGATGCAGATAGTGATGCTGCATTGGACATTTTAATGACAAACGTAGTCTGCATTTTTAGAACCAGATGCCATTTGAA
CTTAAGGAAGATTGCTTCAGAGGGAGCAAATGTAATTTCAAGTGTGATGTTGGAAAAGTGTTAATGAAGCTAGAAAACCT
GGAATTACAGCTACAATTTGGTCCTCGTGAAAAATTATTTGCACAGGAGCTACAAGTGAAGAAGGAGCTAAATTTGGTGC
CAGGCGATTAGCCCCAAGTCCACAGAAACTTGGTTTTCAGGCAATATTTACAGATTTTAAAGTCGTTAATGTTTTGGCAT
TATGTAACATGCCCTTTGAAATCCGATTGCCAGATATCACAAAGAATGACAGGCTTCATGCCAGTTATGAACCTGAACTT
CATCTTGCAGTATGTTATAGTATAAAAGCTCTACGAGCTACATTACAGATTTTTTCAATAGGAAATATCACAGTAACAGG
GACAAATGTAAAGGTTGATGCTACTCCTGTGGAACAGATTTACCCATATGTGTTTGAAAGCAGAAAAGAA

Alignment

ORF - retro_mdom_1220 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.48 %
• Parental protein coverage: 98.92 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MDADSDVALDILITNVVCVFRTRCHLNLRKIALEGANVI-YKRDVGKVLMKL-RKPRITATIWSSGKIIC
          MDADSD.ALDIL.TNVVC.FRTRCHLNLRKIA.EGANVI..K.DVGKVLMKL.RKP.ITATIWSS.KIIC
Retrocopy MDADSDAALDILMTNVVCIFRTRCHLNLRKIASEGANVI<FKCDVGKVLMKL<RKPGITATIWSS*KIIC

Parental  TGATSEEEAKFGARRLARSLQKLGFQVIFTDFKVVNVLAVCNMPFEIRLPEFTKNNRPHASYEPELHPAV
          TGATSEE.AKFGARRLA.S.QKLGFQ.IFTDFKVVNVLA.CNMPFEIRLP..TKN.R.HASYEPELH.AV
Retrocopy TGATSEEGAKFGARRLAPSPQKLGFQAIFTDFKVVNVLALCNMPFEIRLPDITKNDRLHASYEPELHLAV

Parental  CYRIKALRATLQIFSTGSITVTGPNVKAVATAVEQIYPYVFESRKE
          CY.IKALRATLQIFS.G.ITVTG.NVK..AT.VEQIYPYVFESRKE
Retrocopy CYSIKALRATLQIFSIGNITVTGTNVKVDATPVEQIYPYVFESRKE

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_1220 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1220 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007544	1 retrocopy	retro_chof_469,
Cavia porcellus	ENSCPOG00000011899	1 retrocopy	retro_cpor_575,
Echinops telfairi	ENSETEG00000015892	1 retrocopy	retro_etel_1883,
Monodelphis domestica	ENSMODG00000017515	1 retrocopy	retro_mdom_1220 ,
Otolemur garnettii	ENSOGAG00000006622	2 retrocopies	retro_ogar_1508, retro_ogar_1509,