RetrogeneDB ID: retro_mdom_1402

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:312158250..312159205(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCT4
• Ensembl ID: ENSMODG00000002882
• Aliases: None
• Description: chaperonin containing TCP1, subunit 4 (delta) [Source:HGNC Symbol;Acc:1617]

Sequence

>retro_mdom_1402
ATGCTGGAGAACATGGGTCCCAGGAACAATGGGCCTACCGGAGGTTCCGGCAATGGAGGGAGAGGCGCTTACCAGGATCG
GGACAAACCGGCCCAGATCCGCTTCAGCAACATCTCTGCCGTCAAAGCGATTACAGATGCTATTAGAACTAACCTTGGAC
CAAAAGGAATGGACAAAATGATTCAAGATGGAAAAGGTGATGTGACTATTACCAATGATGGTGCTACAATTTTGAAACAA
ATGCAGGTCTTGCATCCAGCAGCTAGGATGTTGGTGGAGCTCTCAAAAGCACAAGATATTGAAGCTGGTGATAGTACCAC
ATCTGTTGTTATCATTGCTGGATCTCTTTTGGACTCTTGTACCAAACTTCTTCAAAAGGGGATTCACCCCAACCATCATT
TCTGAATCATTCCAAAAAGCTGTGCATCGAGGTGTTGAAGTCTTAACTAAAATGTCACAGCCAGTGGAACTGAGTGACAG
AGAAACATTACTAAATAGGGCAACCACTTCACTAAACTCAAAGGTTGTATCTCAGTACTCAAGCCTGCTTTCTCCAATGA
GTGTAGATGCTGTGATGAAGGTGATTGACCCAACAACAGCTACTAGTGTAGATCTTCGAGACATTAAAATAGTTAAGAAA
CTTGGTGGGACAATTGACGACTGTGAACTGGTGGAAGGATTGGTCCCAACTCAGAAAGTGGCAAATACTGGCATAACCAG
AGTTGAGAAAGCTAAGATTGGTCTCATTCAGTTTTGTTTATCAGCTCCTAAAACAGATATGGATAATCAAATTGTAGTTT
CTGACTACGCTCAAATGGACAGAGTACTGCGGGAAGAGAGAGCTTATATTCTCAATTTAGTGAAGCAGATTAAGAAATCT
GGATGTAATGTACTCCTTATACAGAAATCTATTCTAAGGGATGCCCTCAGTGATCTTGCATTACATTTCCTAAAC

Alignment

ORF - retro_mdom_1402 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.75 %
• Parental protein coverage: 59.07 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPENMGPRNNGPAGGSGNRGRGAYQDRDKPAQIRFSNISAAKAVTDAIRTSLGPKGMDKMIQDGKGDVTI
          M.ENMGPRNNGP.GGSGN.GRGAYQDRDKPAQIRFSNISA.KA.TDAIRT.LGPKGMDKMIQDGKGDVTI
Retrocopy MLENMGPRNNGPTGGSGNGGRGAYQDRDKPAQIRFSNISAVKAITDAIRTNLGPKGMDKMIQDGKGDVTI

Parental  TNDGATILKQMQILYLGSINSLVELSKAQDIEAGDGTTSVVIIAGSLLDSCTKLLQKGIHP-TIISESFQ
          TNDGATILKQMQ.L.......LVELSKAQDIEAGD.TTSVVIIAGSLLDSCTKLLQKGIHP.TIISESFQ
Retrocopy TNDGATILKQMQVLHPAA-RMLVELSKAQDIEAGDSTTSVVIIAGSLLDSCTKLLQKGIHP>TIISESFQ

Parental  KAVDQGVEVLTKMSQPVELSDRETLLNSATTSLNSKVVSQYSSLLSPMSVDAVMKVIDPTTATSVDLRDI
          KAV..GVEVLTKMSQPVELSDRETLLN.ATTSLNSKVVSQYSSLLSPMSVDAVMKVIDPTTATSVDLRDI
Retrocopy KAVHRGVEVLTKMSQPVELSDRETLLNRATTSLNSKVVSQYSSLLSPMSVDAVMKVIDPTTATSVDLRDI

Parental  KIVKKLGGTIDDCELVEGLVLTQKVANTGITRVEKAKIGLIQFCLSAPKTDMDNQIVVSDYAQMDRVLRE
          KIVKKLGGTIDDCELVEGLV.TQKVANTGITRVEKAKIGLIQFCLSAPKTDMDNQIVVSDYAQMDRVLRE
Retrocopy KIVKKLGGTIDDCELVEGLVPTQKVANTGITRVEKAKIGLIQFCLSAPKTDMDNQIVVSDYAQMDRVLRE

Parental  ERAYILNLVKQIKKSGCNVLLIQKSILRDALSDLALHFLN
          ERAYILNLVKQIKKSGCNVLLIQKSILRDALSDLALHFLN
Retrocopy ERAYILNLVKQIKKSGCNVLLIQKSILRDALSDLALHFLN

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	280.47 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	362.22 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1402 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1402 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 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003083	2 retrocopies	retro_cfam_2093, retro_cfam_590,
Callithrix jacchus	ENSCJAG00000008703	1 retrocopy	retro_cjac_724,
Equus caballus	ENSECAG00000016982	1 retrocopy	retro_ecab_148,
Microcebus murinus	ENSMICG00000015263	1 retrocopy	retro_mmur_344,
Macaca mulatta	ENSMMUG00000013973	1 retrocopy	retro_mmul_2500,
Monodelphis domestica	ENSMODG00000002882	1 retrocopy	retro_mdom_1402 ,
Otolemur garnettii	ENSOGAG00000003974	2 retrocopies	retro_ogar_1041, retro_ogar_1931,
Sorex araneus	ENSSARG00000010539	1 retrocopy	retro_sara_7,