RetrogeneDB ID: retro_mdom_1277

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:252483612..252484074(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C1orf131
• Ensembl ID: ENSMODG00000009357
• Aliases: None
• Description: chromosome 1 open reading frame 131 [Source:HGNC Symbol;Acc:25332]

Sequence

>retro_mdom_1277
CTAATACCTCCCAAGAATGAGGATGCAAAAACCAAAGTCAAGATCCCTTAGAAGGGATCAGATATGCAAAAATTTAATTT
GGAAAAGGCTCATTTGGAAGTGCATCAACTTAGGATCATTGGATAGGAAGGGGAAAGAATGGATTCTTGAATGGGAGATA
GCATTCATCCTGTGTGTCATGTCCTCCCCCAAAAAATATTGCATTAATTACAAAGTTTCGTAGAAGCAGATGGGGGGAGG
GGAGCAGCAAAAGAAGAAGAAAATAGAGTGGCTACGGTTAGAGACTTTCAGAAAAGAAAGAATAGAAAAGGTTCAGAGAA
TCATTAGAAGTCCAAAAAGAAGAAATCAGCTCCCAGTATTTTGTCAACAACATCAATAGGGCAAATTGAAAAATTCAAAA
TTGGGACACTGATTCCTAGTAGTATGGATATCAAGAAAATAAATTCATTCAAAGAAATTAAA

Alignment

ORF - retro_mdom_1277 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.39 %
• Parental protein coverage: 52.92 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LEPPKDEDTKTKANIPEKESDMQEFNLEKARLEVHRFGITG-YGKG-KERILEQERAIMLGA-KPPKNNY
          L.PPK.ED.KTK..IP.K.SDMQ.FNLEKA.LEVH...I.G..G.G.KE.ILE.E.A..L.....PK...
Retrocopy LIPPKNEDAKTKVKIP*KGSDMQKFNLEKAHLEVHQLRIIG<IGRG<KEWILEWEIAFILCVMSSPKKYC

Parental  VNYKVLQEQI-KGKKAAMEEEKRMAQITDAFRKKKRKGSEDSRKSKKKKSAPSILSTGSAGQIGKFKNGT
          .NYKV...Q...G..AA.EEE.R.A...D....K.RKGSE...KSKKKKSAPSILST.S.GQI.KFK.GT
Retrocopy INYKVS*KQM<GGRGAAKEEENRVATVRDFQKRKNRKGSENH*KSKKKKSAPSILSTTSIGQIEKFKIGT

Parental  LILSSVDIKKINSSKGIK
          LI.SS.DIKKINS.K.IK
Retrocopy LIPSSMDIKKINSFKEIK

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_1277 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1277 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000009357	1 retrocopy	retro_mdom_1277 ,
Oryctolagus cuniculus	ENSOCUG00000005657	1 retrocopy	retro_ocun_308,