RetrogeneDB ID: retro_mdom_1512

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 5:79758080..79758848(-)
• Located in intron of: ENSMODG00000004698

Retrocopy information

• Ensembl ID: ENSMODG00000025092
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SLC25A33
• Ensembl ID: ENSMODG00000003059
• Aliases: None
• Description: solute carrier family 25 (pyrimidine nucleotide carrier), member 33 [Source:HGNC Symbol;Acc:29681]

Sequence

>retro_mdom_1512
ATCACATCAACATCCCGATTACCGGAAGTCGTGAAGGTTCTGAAGTTGATTCTGGAGAAGGAGGGAGTAAAGACACTTTT
TCGCGGCTTCGGCCCTAACTTGATCGGAGTAGCCCCTTCAAGGGCTGTATACTTTGCCTGCTACTCCAAGGCCAAAGACC
ACCTGAATGGCATTTTCATGCCTAACAGCTATACTGTTCACATTATCTCCGCTGGCTCCGCGGGTTTTGTCACAAATACC
TTGATGAATCCTCTATGGATGATCAAAAGTCGCATGCAGTTAGGACTGCAAGAAAAGGGTTCCAAAGGGATAAACACTGT
CCAGTGTGCTCGTTACATTTACCAGGAAAACGGCATTTCTGGATTCTATAGAGGATTAACTGCCTCATATTTTGGCATTT
TTGAGACGGTGATCTGTTTTACTATTTATGAAAGATTAAAGAAATGGCTAACGGAGACCCCATTAAGCCTTTCTGCAAAC
GGGACTAACAAAAACAGTGCCAGCGCCAACTTTTTTAAATATATGGCTGCTGCTGCTATTGCCAGGATGCTCGCCTCCTT
CGTTGGTTATCCCCATGAAGTTTTGAGAACCCGGCTTCGGGAAGAGGGCAACAAGTATAGGTCCTTCACTCAAACAGTCT
ACCTGATAGCACAAGAAGAAGGCTTGCTAGGCTTCTACAGAGGACTCTGTGCTCAGCTCATCTGGCAGGTGCCAAATACT
GGGATTGTGTTGTCCACCTACGAGCTAATTGTGTTATTATTGAAGGAC

Alignment

ORF - retro_mdom_1512 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.14 %
• Parental protein coverage: 79.01 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VRPTSVSPGLLQVLKSILEKEGPRSLFRGLGPNLVGVAPSRAVYFACYSKAKEQFNGIFVPNSNIVHIFS
          ...TS..P....VLK.ILEKEG...LFRG.GPNL.GVAPSRAVYFACYSKAK...NGIF.PNS..VHI.S
Retrocopy ITSTSRLPEVVKVLKLILEKEGVKTLFRGFGPNLIGVAPSRAVYFACYSKAKDHLNGIFMPNSYTVHIIS

Parental  SGSAAFITNTLMNPIWMVKTRMQLERKVRGSKQMNTVQCARYVYQTEGIRGFYRGLTASYAGISETIICF
          .GSA.F.TNTLMNP.WM.K.RMQL.....GSK..NTVQCARY.YQ..GI.GFYRGLTASY.GI.ET.ICF
Retrocopy AGSAGFVTNTLMNPLWMIKSRMQLGLQEKGSKGINTVQCARYIYQENGISGFYRGLTASYFGIFETVICF

Parental  AIYESLKKWLKEAPLTPSANGTEISRNSTNFFGLMAAAAISKGCASCIAYPHEVIRTRLREEGTKYKAFI
          .IYE.LKKWL.E.PL..SANGT.....S.NFF..MAAAAI....AS...YPHEV.RTRLREEG.KY..F.
Retrocopy TIYERLKKWLTETPLSLSANGTNKNSASANFFKYMAAAAIARMLASFVGYPHEVLRTRLREEGNKYRSFT

Parental  QTARLIAREEGYLAFYRGLFAQLIRQIPNTAIVLSTYELIVYLLED
          QT..LIA.EEG.L.FYRGL.AQLI.Q.PNT.IVLSTYELIV.LL.D
Retrocopy QTVYLIAQEEGLLGFYRGLCAQLIWQVPNTGIVLSTYELIVLLLKD

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_1512 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1512 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.

---

Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000424	1 retrocopy	retro_cjac_2186,
Dasypus novemcinctus	ENSDNOG00000014396	1 retrocopy	retro_dnov_2369,
Homo sapiens	ENSG00000171612	1 retrocopy	retro_hsap_873,
Gorilla gorilla	ENSGGOG00000006766	1 retrocopy	retro_ggor_709,
Monodelphis domestica	ENSMODG00000003059	1 retrocopy	retro_mdom_1512 ,
Otolemur garnettii	ENSOGAG00000007103	1 retrocopy	retro_ogar_2098,