RetrogeneDB ID: retro_mdom_1002

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:179489934..179490306(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PBDC1
• Ensembl ID: ENSMODG00000009685
• Aliases: None
• Description: polysaccharide biosynthesis domain containing 1 [Source:HGNC Symbol;Acc:28790]

Sequence

>retro_mdom_1002
GGAAAGCTGTTGTTGGTGGCTTACTCACTTTCCCTGATAGCTGAGGTCTAGGGCAATAATCACAATATTGAGATTGTTTT
GGCCATGAAGGCTATGCAGAATGCTGAGATTTATTACAATTTGATTTCCCAAGTTAACCTCATGTTCTTAAGACTCACTA
AAGTGGATGACCAGATCTATTTAGGTTCCCGGGAGAGCTTTGGGAAACTCAAGATAGATGTGTTGAACCCAGAAGAATTC
AAATCAGAACCAGCTAAAGAAAAGTGGAGACCATTTTGCATGAAGTTCAGTGGTATCTTGGAAGATTAAAACTATGGTAC
GTTGCTGCAACTGGACTGTACTCAGGGGTATAGTGAAGAAAGCACTGTCTTT

Alignment

ORF - retro_mdom_1002 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.81 %
• Parental protein coverage: 99.2 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GELLSAAHALSLPAEAYGNDPNIEMVWAMKAMQHAEVYYNLISSVDPLFLRLTKVDDQIYSEFRENFGKL
          G.LL..A..LSL.AE..GN..NIE.V.AMKAMQ.AE.YYNLIS.V...FLRLTKVDDQIY...RE.FGKL
Retrocopy GKLLLVAYSLSLIAEV*GNNHNIEIVLAMKAMQNAEIYYNLISQVNLMFLRLTKVDDQIYLGSRESFGKL

Parental  KIDVLDPEELKSEPAKEKWRPFCMKFNGIVEDYNYGTLLRLDCTQGYSEENTIF
          KIDVL.PEE.KSEPAKEKWRPFCMKF.GI.ED.NYGTLL.LDCTQGYSEE.T.F
Retrocopy KIDVLNPEEFKSEPAKEKWRPFCMKFSGILED*NYGTLLQLDCTQGYSEESTVF

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	71.88 RPM
SRP007412_cerebellum	0.00 RPM	79.33 RPM
SRP007412_heart	0.00 RPM	62.80 RPM
SRP007412_kidney	0.00 RPM	72.43 RPM
SRP007412_liver	0.00 RPM	63.44 RPM
SRP007412_testis	0.00 RPM	56.18 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1002 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1002 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 11 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000017228	2 retrocopies	retro_cfam_1588, retro_cfam_944,
Callithrix jacchus	ENSCJAG00000018571	1 retrocopy	retro_cjac_1880,
Equus caballus	ENSECAG00000009882	1 retrocopy	retro_ecab_532,
Erinaceus europaeus	ENSEEUG00000001116	1 retrocopy	retro_eeur_377,
Monodelphis domestica	ENSMODG00000009685	2 retrocopies	retro_mdom_1002 , retro_mdom_572,
Mus musculus	ENSMUSG00000031226	1 retrocopy	retro_mmus_1569,
Oryctolagus cuniculus	ENSOCUG00000001088	3 retrocopies	retro_ocun_1017, retro_ocun_1402, retro_ocun_595,
Otolemur garnettii	ENSOGAG00000015205	1 retrocopy	retro_ogar_3063,
Rattus norvegicus	ENSRNOG00000002662	3 retrocopies	retro_rnor_1703, retro_rnor_1705, retro_rnor_826,
Sarcophilus harrisii	ENSSHAG00000017872	1 retrocopy	retro_shar_132,
Tupaia belangeri	ENSTBEG00000003411	3 retrocopies	retro_tbel_3448, retro_tbel_494, retro_tbel_979,