RetrogeneDB ID: retro_mdom_1043

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:342159882..342160250(+)
• 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_1043
CAGCTCAGTGAATATACCCACAACAACCTCTTCCTAGCCCTATATCTAGCCAGAGACATGGGGGAAGACAGAGAGGACCC
CCAGTATGAGATTTTGCCCATGGTCCTGGACCAGGGCTAGTGAAAGCTTGTGCCCAGTTCCCTGTGCCAGAGGGACCAGA
TGTGGGGACAGATGGGCTATTGGGCAACTTTGAGCTGGCACTGATGTGAAGAGGTCATGGTCAACGAACTATCCCATTGT
TCTTGGACCAGAAAATGGTCAGTCTACCATGGGGAGCTCATCAAGAATCCCCCAAAGGGGACCAGAACTGTCCTTTTGTC
ATGTCCCAGGTCTCAAAGCTCTTTCTACTAGGCTGCTCTGTTTATGGC

Alignment

ORF - retro_mdom_1043 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.13 %
• Parental protein coverage: 55.66 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QLSEYTHSNLFLALYLANDMEEDREDPKYEILPWALGQGWRKLVPSFLRQRDQLWARMGYRAAVSRHCCE
          QLSEYTH.NLFLALYLA.DM.EDREDP.YEILP..L.QG..KLVPS.L.QRDQ.W..MGY.A..S.H.CE
Retrocopy QLSEYTHNNLFLALYLARDMGEDREDPQYEILPMVLDQG**KLVPSSLCQRDQMWGQMGYWATLSWH*CE

Parental  EVMAKEPSHWAWTRERPIHHG-GAQRSSLQGNQNCPSVMSHVSNLSPLGCSVCG
          EVM..E.SH..WTR.....HG.GA...S..G.QNCP.VMS.VS.L..LGCSV.G
Retrocopy EVMVNELSHCSWTRKWSVYHG<GAHQESPKGDQNCPFVMSQVSKLFLLGCSVYG

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_1043 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1043 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,