RetrogeneDB ID: retro_mdom_1348

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:102181561..102181950(-)
• Located in intron of: ENSMODG00000018603

Retrocopy information

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

Parental gene information

• Parental gene symbol: SPDYC
• Ensembl ID: ENSMODG00000010068
• Aliases: None
• Description: speedy/RINGO cell cycle regulator family member C [Source:HGNC Symbol;Acc:32681]

Sequence

>retro_mdom_1348
TCCTGTCCCTCCTTCCCCTTCTTTCTTCTTTTCTTCCCTCCTTTCATAATGATAAACCAAGGTCAGGACTCTTATTTCTG
TCCTTCCTATGGTCACCAGCTGTGTGAAGCCTGGAGTCTGGGCTGACACTGGGTGCCTCCCTTCCCACCAGTGCCAGCAA
GTTTGAGCCTTACTCAGCCTTCTAGAGGACAGCTACCTTCAGTATTTCTTTTTCATAGATATATGTTTTCAAATCTCTGA
TAAGTATCTCTTCATAATGGCCCTGATTTATTCACAAAGAGTTGGCCTGCAGCTCAGTGAATACAATCACAGCAACCTCT
TTTTAGCTTTGTATCTAGTGAATAACATGGAAGAAGACAAAAGAGGATGCCAAGTATGAGATTTTGCCC

Alignment

ORF - retro_mdom_1348 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.66 %
• Parental protein coverage: 59.28 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SCRPFPI-LPPLPPSTMTSLSSRGQDSS-AALPAVTSWVKPGVWAGTGRLPSRQCQEVRAFLNLLEDSYL
          SC..FP..L...PP..M......GQDS....LP.VTS.VKPGVWA.TG.LPS.QCQ.V.A.L.LLEDSYL
Retrocopy SCPSFPFFLLFFPPFIMIN---QGQDSY>SVLPMVTSCVKPGVWADTGCLPSHQCQQV*ALLSLLEDSYL

Parental  QQFFATDLCFQISDKYLLAMALIYFQRAGLQLSEYTHSNLFLALYLANDMEED-REDPKYEILP
          Q.FF..D.CFQISDKYL..MALIY.QR.GLQLSEY.HSNLFLALYL.N.MEED..ED.KYEILP
Retrocopy QYFFFIDICFQISDKYLFIMALIYSQRVGLQLSEYNHSNLFLALYLVNNMEED>KEDAKYEILP

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_1348 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1348 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 3 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002403	2 retrocopies	retro_cjac_1136, retro_cjac_1851,
Monodelphis domestica	ENSMODG00000010068	3 retrocopies	retro_mdom_1043, retro_mdom_1348 , retro_mdom_1695,
Otolemur garnettii	ENSOGAG00000015020	1 retrocopy	retro_ogar_2812,