RetrogeneDB ID: retro_mdom_1695

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 6:255141389..255141762(-)
• Located in intron of: None

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_1695
CTGCAGCTCAGTGTATACACCTACAGCAACCTCTTCTTAGCCCCGTATCTAGTGAATTACATAGAAGAAGACAGAGAAGA
CCCCAAGTATGAGATTTTTGTCCTGGGCCCTGGGCCAGGGCTGGTGGAAACTTGTGCCTAGCTTTTTGCACCAGGGGGAC
CAGTTGTGGGCATGTATGGGCTACAGGGCAGCTGTAAGGCAACACTGCTGTGAAGAGGTCATGGCAAAGGAACCGTCCCA
TTGGGCTTGGACAAGGGAGCGACCAGTCCACCATGGGGGTGCTCATCAAGGCTCCCCCCAGGAGCTCCAGAACTGCCCTT
CTGTCATGTCCCATGTCTCAAACCTCTCTCGACTGGGCTGCTTCCTTTGTGGC

Alignment

ORF - retro_mdom_1695 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.8 %
• Parental protein coverage: 56.11 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LQLSEYTHSNLFLALYLANDMEEDREDPKYEI-LPWALGQGWRKLVPSFLRQRDQLWARMGYRAAVSRHC
          LQLS.YT.SNLFLA.YL.N..EEDREDPKYEI.L.WALGQGW.KLVPSFL.Q.DQLWA.MGYRAAV..HC
Retrocopy LQLSVYTYSNLFLAPYLVNYIEEDREDPKYEI>LSWALGQGWWKLVPSFLHQGDQLWACMGYRAAVRQHC

Parental  CEEVMAKEPSHWAWTRERPIHHGGAQRSSLQGNQNCPSVMSHVSNLSPLGCSVCG
          CEEVMAKEPSHWAWTRERP.HHGGA...S.Q..QNCPSVMSHVSNLS.LGC..CG
Retrocopy CEEVMAKEPSHWAWTRERPVHHGGAHQGSPQELQNCPSVMSHVSNLSRLGCFLCG

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_1695 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1695 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,