RetrogeneDB ID: retro_mdom_550

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:269653672..269653933(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNRPF
• Ensembl ID: ENSMODG00000008091
• Aliases: None
• Description: small nuclear ribonucleoprotein polypeptide F [Source:HGNC Symbol;Acc:11162]

Sequence

>retro_mdom_550
ACAATGTGTTTACGCCTCAACTGCAAACTATTCCTGAACAGGTTGTCTGGGAAGCTACTAATAGTGAAGCTTAAGTGCAG
AATAGAGTACAAAGGTTACCTGATATCCATGGATGGATACATGAACATTCAACTTGTGAATACAGAAAAGTACATAGATG
GGACATTATGTCAACATCTTGGTGAAATGTTAATAAGGTGCAAAAATGTCCTTTGGATGAAAAGTGTCTAAGAGGAGGAA
GAAGATGGGGAAATGTGAGAA

Alignment

ORF - retro_mdom_550 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.82 %
• Parental protein coverage: 76.32 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TMSLPLNPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDGALSGHLGEVLIRCNNV
          TM.L.LN.K.FLN.L.GK...VKLK...EYKGYL.S.DGYMN.QL.NTE.YIDG.L..HLGE.LIRC.NV
Retrocopy TMCLRLNCKLFLNRLSGKLLIVKLKCRIEYKGYLISMDGYMNIQLVNTEKYIDGTLCQHLGEMLIRCKNV

Parental  LYIRGVEEEEEDGEMRE
          L....V.EEEEDGEM.E
Retrocopy LWMKSV*EEEEDGEM*E

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_550 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_550 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 7 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002166	3 retrocopies	retro_amel_1239, retro_amel_42, retro_amel_883,
Canis familiaris	ENSCAFG00000006395	6 retrocopies	retro_cfam_110, retro_cfam_1975, retro_cfam_372, retro_cfam_619, retro_cfam_742, retro_cfam_763,
Callithrix jacchus	ENSCJAG00000002705	2 retrocopies	retro_cjac_1705, retro_cjac_3039,
Felis catus	ENSFCAG00000029966	4 retrocopies	retro_fcat_280, retro_fcat_66, retro_fcat_77, retro_fcat_861,
Monodelphis domestica	ENSMODG00000000526	4 retrocopies	retro_mdom_1027, retro_mdom_1383, retro_mdom_1983, retro_mdom_621,
Monodelphis domestica	ENSMODG00000008091	3 retrocopies	retro_mdom_550 , retro_mdom_780, retro_mdom_811,
Tarsius syrichta	ENSTSYG00000006837	4 retrocopies	retro_tsyr_1239, retro_tsyr_1782, retro_tsyr_192, retro_tsyr_2115,