RetrogeneDB ID: retro_mdom_1395

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:274415519..274416220(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000004507
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NFU1
• Ensembl ID: ENSMODG00000011805
• Aliases: None
• Description: NFU1 iron-sulfur cluster scaffold homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:16287]

Sequence

>retro_mdom_1395
CGATTTTGTAACATAAAGCTAAATACGAACGACATTAGGAAGCAATCTCTGCATCAATATGTACAAAGACAGTTTCTGCC
TCCATTCACAGCATTATATAACGCAGTGCGATGCATGTTTATTCAAACACAGGATACCCCCAACCCGAACAGTTTGAAGT
TTATTCCAGGAAATCAGTGCTTGGATCACAGACCATGGATTTTCCTACACCAGCTACAGCATTCCGCTCCCCTTTGGCTA
GGCAATTATTCAGGATTGAAGGGGTGAAAAGTGTCTTCTTAGGACCAGATTTCATCACAGTCACAAAGGAAAGTGAAGAT
TTAGATTGGAACTTACTGAAACCAGATATTTATGCAACAATAATGGATTTCTTTGCATCTGGTTTACCCATACTTACTGA
AGAAACACCTTCCTCAGAAACAGCAACTGAAGAGGATGATGAAGTTGTAACAATGATTAAAGAACTGTTGGATATGAGGA
AAAGGCCAACTGTGCAGGAGGATGGGGGTGACGTGATCTACAAAGGCTTTGAAGATGGCATTCTGCAGCTGAAACTGCAG
GGTTCCTGTACCAACTGCCCAAGCTCTATCATCACTTTGAAAAATGGAATCCAAAACATGCTTCAGTTTTATATTCCAGA
AGTAGAAGGTGTGGAGCAGGTTGTGGATGATGAACTAGAAGAGAAAGATGCAAACTCACCT

Alignment

ORF - retro_mdom_1395 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.6 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RFYNIKLNTNDIRKQSLHQYVQRQFLPPFTALYNTVRCMFIQTQDTPNPNSLKFIPG-KSVLGSQTMDFP
          RF.NIKLNTNDIRKQSLHQYVQRQFLPPFTALYN.VRCMFIQTQDTPNPNSLKFIPG.KSVLGSQTMDFP
Retrocopy RFCNIKLNTNDIRKQSLHQYVQRQFLPPFTALYNAVRCMFIQTQDTPNPNSLKFIPG<KSVLGSQTMDFP

Parental  TPATAFRSPLARQLFRIEGVKSVFLGPDFITVTKESEDLDWNLLKPDIYATIMDFFASGLPILTEETPSS
          TPATAFRSPLARQLFRIEGVKSVFLGPDFITVTKESEDLDWNLLKPDIYATIMDFFASGLPILTEETPSS
Retrocopy TPATAFRSPLARQLFRIEGVKSVFLGPDFITVTKESEDLDWNLLKPDIYATIMDFFASGLPILTEETPSS

Parental  ETATEEDDEVVAMIKELLDTRIRPTVQEDGGDVIYKGFEDGIVQLKLQGSCTSCPSSIITLKNGIQNMLQ
          ETATEEDDEVV.MIKELLD.R.RPTVQEDGGDVIYKGFEDGI.QLKLQGSCT.CPSSIITLKNGIQNMLQ
Retrocopy ETATEEDDEVVTMIKELLDMRKRPTVQEDGGDVIYKGFEDGILQLKLQGSCTNCPSSIITLKNGIQNMLQ

Parental  FYIPEVEGVEQVVDDELEEKDANSP
          FYIPEVEGVEQVVDDELEEKDANSP
Retrocopy FYIPEVEGVEQVVDDELEEKDANSP

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	33.73 RPM
SRP007412_cerebellum	0.00 RPM	66.60 RPM
SRP007412_heart	0.00 RPM	173.64 RPM
SRP007412_kidney	0.00 RPM	67.16 RPM
SRP007412_liver	0.00 RPM	59.41 RPM
SRP007412_testis	0.00 RPM	84.66 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1395 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1395 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 14 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005978	1 retrocopy	retro_chof_456,
Callithrix jacchus	ENSCJAG00000019156	1 retrocopy	retro_cjac_1573,
Echinops telfairi	ENSETEG00000019002	1 retrocopy	retro_etel_1371,
Homo sapiens	ENSG00000169599	1 retrocopy	retro_hsap_2638,
Macaca mulatta	ENSMMUG00000000435	1 retrocopy	retro_mmul_1524,
Monodelphis domestica	ENSMODG00000011805	1 retrocopy	retro_mdom_1395 ,
Mustela putorius furo	ENSMPUG00000006663	1 retrocopy	retro_mputfur_67,
Mus musculus	ENSMUSG00000029993	1 retrocopy	retro_mmus_1401,
Nomascus leucogenys	ENSNLEG00000010101	1 retrocopy	retro_nleu_646,
Ochotona princeps	ENSOPRG00000016760	2 retrocopies	retro_opri_380, retro_opri_48,
Pongo abelii	ENSPPYG00000012339	1 retrocopy	retro_pabe_2329,
Pan troglodytes	ENSPTRG00000012016	1 retrocopy	retro_ptro_1778,
Tupaia belangeri	ENSTBEG00000008616	1 retrocopy	retro_tbel_525,
Tarsius syrichta	ENSTSYG00000013765	1 retrocopy	retro_tsyr_108,