RetrogeneDB ID: retro_mdom_388

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:362430798..362431180(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C8orf33
• Ensembl ID: ENSMODG00000028791
• Aliases: None
• Description: chromosome 8 open reading frame 33 [Source:HGNC Symbol;Acc:26104]

Sequence

>retro_mdom_388
CAGTCTCTGGATCAGGATAAGCAGCTACAGCTCCTAGAGCTGGACTGGTGTGTAGAATAGCTAGAGTTGGGCCTGAGGAC
TTGAAATCCACCCCAAAACAGGTCAAACAGGCAGCTTGATCTGGAAAGACACTTTGGAGTAATCAAGCTAAGTTGCCCAA
GAAACATCAAGTGATGCTGTCACTGTTTGGGTACTATGGGGCACACATATCAGAAGATCAAAAAGCAGCACTGAAAGCCA
TGGAAACTGCTGCTCATTCTGCCTGGTTCTGCCTGATGAAGAGGCTGTGGGAAGGAAAAGTAGTCCCATCTGCAGGCATC
ACTCAAGTGGAAGAATGATTTCTGTTTCTTCTCCAAAGGAAGAAATTAGGTTTAACTTCTTT

Alignment

ORF - retro_mdom_388 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.23 %
• Parental protein coverage: 58.64 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RSLDEDEQMRLQRELDWCVEQLELGLRT-QKSTPKQAEQAARAVKTLRSNRAELPKKRQVMRSLFGDYRA
          .SLD.D.Q..L..ELDWCVE.LELGLRT..KSTPKQ..QAA...KTL.SN.A.LPKK.QVM.SLFG.Y.A
Retrocopy QSLDQDKQLQLL-ELDWCVE*LELGLRT<LKSTPKQVKQAA*SGKTLWSNQAKLPKKHQVMLSLFGYYGA

Parental  RMEEDRKAALKAMEVAARSA-RVLPVEEAVRRKSSRICRHRGGGGMISISSPKEEFRFNFF
          ...ED.KAALKAME.AA.SA..VLP.EEAV.RKSS.ICRH...G.MIS.SSPKEE.RFNFF
Retrocopy HISEDQKAALKAMETAAHSA<LVLPDEEAVGRKSSPICRHHSSGRMISVSSPKEEIRFNFF

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	0.12 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_388 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_388 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 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000015805	3 retrocopies	retro_dnov_1578, retro_dnov_406, retro_dnov_521,
Macaca mulatta	ENSMMUG00000016084	1 retrocopy	retro_mmul_1436,
Monodelphis domestica	ENSMODG00000028791	2 retrocopies	retro_mdom_1056, retro_mdom_388 ,
Mustela putorius furo	ENSMPUG00000005972	1 retrocopy	retro_mputfur_1096,
Rattus norvegicus	ENSRNOG00000034107	1 retrocopy	retro_rnor_436,