RetrogeneDB ID: retro_mdom_1686

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 6:201826027..201826388(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000013377
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RWDD1
• Ensembl ID: ENSMODG00000017837
• Aliases: None
• Description: RWD domain containing 1 [Source:HGNC Symbol;Acc:20993]

Sequence

>retro_mdom_1686
ATAACAAATTACAGTGAGGAGCAGCATAAGGAACTTGAGGCTCTGGAATCCAGCTATCTGAACTCCACAGTATAATCAAA
AAAATCCAACCAATTTCACTATTACTATGACATCTGAAGCAGGAGAAAATGATGAAACTGTCCAGATAACCCTTAAGTTT
ACTTATGGAGAGAAGTATCCAGATGAAATGCCTCGTTATGAAATATTTTCTGAGGAAAACCTAGAAGATAATGATGTTTC
AGATATATTAAAACTATTAGAGTTACAAACAGAAGAAAACCATGGCATGGTAATGATCTTCACTCTGGTATCAGCTGTTC
AAGAAAAACTCAATGAAATTGTAGATCAAATTAAAACTAGA

Alignment

ORF - retro_mdom_1686 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.25 %
• Parental protein coverage: 50.42 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MTDYSEEQRNELEALESIYPDSFTVLSE-NPTCFTITVTSEAGENDETVQTTLKFTYGEKYPDEMPRYEI
          .T.YSEEQ..ELEALES.Y..S.TV.S..NPT.FTIT.TSEAGENDETVQ.TLKFTYGEKYPDEMPRYEI
Retrocopy ITNYSEEQHKELEALESSYLNS-TV*SK>NPTNFTITMTSEAGENDETVQITLKFTYGEKYPDEMPRYEI

Parental  FSQENLEDNDVSDIVKLLELQAEENLGMVMIFTLVSAVQEKLNEIVDQIKTR
          FS.ENLEDNDVSDI.KLLELQ.EEN.GMVMIFTLVSAVQEKLNEIVDQIKTR
Retrocopy FSEENLEDNDVSDILKLLELQTEENHGMVMIFTLVSAVQEKLNEIVDQIKTR

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_1686 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1686 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 13 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005692	1 retrocopy	retro_amel_991,
Bos taurus	ENSBTAG00000009689	1 retrocopy	retro_btau_1004,
Callithrix jacchus	ENSCJAG00000004474	1 retrocopy	retro_cjac_1622,
Dasypus novemcinctus	ENSDNOG00000007516	1 retrocopy	retro_dnov_2467,
Equus caballus	ENSECAG00000006587	2 retrocopies	retro_ecab_216, retro_ecab_277,
Echinops telfairi	ENSETEG00000019085	3 retrocopies	retro_etel_140, retro_etel_1992, retro_etel_423,
Loxodonta africana	ENSLAFG00000008170	1 retrocopy	retro_lafr_813,
Monodelphis domestica	ENSMODG00000017837	1 retrocopy	retro_mdom_1686 ,
Oryctolagus cuniculus	ENSOCUG00000013592	1 retrocopy	retro_ocun_691,
Procavia capensis	ENSPCAG00000005016	1 retrocopy	retro_pcap_114,
Ictidomys tridecemlineatus	ENSSTOG00000020231	2 retrocopies	retro_itri_121, retro_itri_365,
Ictidomys tridecemlineatus	ENSSTOG00000022124	1 retrocopy	retro_itri_596,
Tupaia belangeri	ENSTBEG00000002543	2 retrocopies	retro_tbel_2986, retro_tbel_4366,