RetrogeneDB ID: retro_mdom_1025

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:276077860..276078182(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPIL3
• Ensembl ID: ENSMODG00000015037
• Aliases: None
• Description: peptidylprolyl isomerase (cyclophilin)-like 3 [Source:HGNC Symbol;Acc:9262]

Sequence

>retro_mdom_1025
CAGGAGAGAGATCTAATAGGTTCTGGGAAAGGAGGCAACAGCATCAGGGGCAGGAAATTTGAATATGAATACAGGAACTA
CCTTACAGGAGGAGTTACAACCATAGCTAATCATGACCCAAATACCAATGGATCACAGTTCTTCATTACTTATGGCAAGC
AGCTTCATTTGGATACAAAGTACGCAGTGTTTGAAAAGGTAGTAGATGATCTAGAGGCTTTGGATGAACTACAGAAGATC
CCAGTAAATGAAAAAAATATTTTAGTCTCTTAATAATGTACACATTAAAGATATTACCATTCATGCCAGCCCATTTGCTC
CA

Alignment

ORF - retro_mdom_1025 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.27 %
• Parental protein coverage: 68.32 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QTGDPTGSGKGGNSIWGRKFEDEYSEYLKHSVRGVVSMANNGPNTNGSQFFITYGKQPHLDMKYTVFGKV
          Q..D..GSGKGGNSI.GRKFE.EY..YL.....GV...AN..PNTNGSQFFITYGKQ.HLD.KY.VF.KV
Retrocopy QERDLIGSGKGGNSIRGRKFEYEYRNYL---TGGVTTIANHDPNTNGSQFFITYGKQLHLDTKYAVFEKV

Parental  IDGLETLDELEKLPVNEKT-FRPLNDVHIKDITIHANPFAP
          .D.LE.LDEL.K.PVNEK..F..LN.VHIKDITIHA.PFAP
Retrocopy VDDLEALDELQKIPVNEKN>F*SLNNVHIKDITIHASPFAP

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_1025 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1025 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 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005917	1 retrocopy	retro_amel_1458,
Bos taurus	ENSBTAG00000005416	1 retrocopy	retro_btau_1585,
Canis familiaris	ENSCAFG00000032245	1 retrocopy	retro_cfam_180,
Dasypus novemcinctus	ENSDNOG00000002364	1 retrocopy	retro_dnov_2477,
Dipodomys ordii	ENSDORG00000007389	1 retrocopy	retro_dord_575,
Monodelphis domestica	ENSMODG00000013502	2 retrocopies	retro_mdom_500, retro_mdom_997,
Monodelphis domestica	ENSMODG00000015037	1 retrocopy	retro_mdom_1025 ,
Tupaia belangeri	ENSTBEG00000000664	1 retrocopy	retro_tbel_4520,