RetrogeneDB ID: retro_mdom_1082

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:27974845..27975754(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ACTR2
• Ensembl ID: ENSMODG00000003364
• Aliases: None
• Description: ARP2 actin-related protein 2 homolog (yeast) [Source:HGNC Symbol;Acc:169]

Sequence

>retro_mdom_1082
ACCTTTGGACCAGAAAAATTTAACATAGATACTAGAAATTGTAAAATCTTGCTCACGGAACCTCCTATGAACCCAACAAA
AAACAGGGAGAAGATTGTGGAGGTCATGTCTGAGACTTACCAGTTATCTGGTTTGTATGTAGCCATCAAGGCTGTTCTTG
CTTTGTATGCTCAAGGTTTATTGACTGGTGGTGTTGTGGACTCTGGTGATGGTGTAACTCATATTTGTCCAGTATATGAA
GGTTTTTCTCTTCCTCATCTTACCAGAAGACTAGATATTGCTGGGAGAGATACTACCAGTTACCTTATCAAGCTGGTTCT
GCTTCAAAGATATGCCTTCAACCATTCTGCTGATTTTGAAACTGTTTGCATGATTAAAGAAAAACTCTGTCATGTGGGGT
ACAATATTGAGCAGGAGCAGAAACTGGCCACAGAAACCACAGTTTTAGTTGAATCTTATACACTCCCAGTTGGCCAAATT
ATCAAAGTTGGTGGAGAGAGATTTGAAGCACCTGAAGCTTTATTTCAGCCTCTTTTGATCAACATGGAAGGAGTGGGTAT
TGCTGAACTGCTCTTTAACACAATCAAGGCTGCTGATATTGACACCAGATCTGAATTTTATAAGCACATTGTGCTTTCTG
GAGGATCCACCATGTACCCGGGGCTGCCATCTCATTTGGAACACAAACTTAAGCAACTGTACCTAGAATGAGTCTTAAAG
GGAGACTTGGAAAAACTTTTGAAATTTAAGATACATATTGAGGACCCGCCTCGATGAAAGCACACGGTGTTTCTGGGTGG
TGTGGTTCTGGCAGACATCATGAAAGACAAAGACAACTTTTGGAGGACCAGACAAGAATACCAGGAAAAGGGTGTTCCTG
TGCTGGAGAAACTTGGAATGATTGTTCGA

Alignment

ORF - retro_mdom_1082 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.45 %
• Parental protein coverage: 76.9 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TFGPEKLNIDTRNCKILLTEPPMNPTKNREKIVEVMFETYQFSGVYVAIQAVLTLYAQGLLTGVVVDSGD
          TFGPEK.NIDTRNCKILLTEPPMNPTKNREKIVEVM.ETYQ.SG.YVAI.AVL.LYAQGLLTG.VVDSGD
Retrocopy TFGPEKFNIDTRNCKILLTEPPMNPTKNREKIVEVMSETYQLSGLYVAIKAVLALYAQGLLTGGVVDSGD

Parental  GVTHICPVYEGFSLPHLTRRLDIAGRDITRYLIKLLLLRGYAFNHSADFETVRMIKEKLCYVGYNIEQEQ
          GVTHICPVYEGFSLPHLTRRLDIAGRD.T.YLIKL.LL..YAFNHSADFETV.MIKEKLC.VGYNIEQEQ
Retrocopy GVTHICPVYEGFSLPHLTRRLDIAGRDTTSYLIKLVLLQRYAFNHSADFETVCMIKEKLCHVGYNIEQEQ

Parental  KLALETTVLVESYTLPDGRIIKVGGERFEAPEALFQPHLINVEGVGVAELLFNTIQAADIDTRSEFYKHI
          KLA.ETTVLVESYTLP.G.IIKVGGERFEAPEALFQP.LIN.EGVG.AELLFNTI.AADIDTRSEFYKHI
Retrocopy KLATETTVLVESYTLPVGQIIKVGGERFEAPEALFQPLLINMEGVGIAELLFNTIKAADIDTRSEFYKHI

Parental  VLSGGSTMYPGLPSRLERELKQLYLERVLKGDVEKLSKFKIRIEDPPRRKHMVFLGGAVLADIMKDKDNF
          VLSGGSTMYPGLPS.LE..LKQLYLE.VLKGD.EKL.KFKI.IEDPPR.KH.VFLGG.VLADIMKDKDNF
Retrocopy VLSGGSTMYPGLPSHLEHKLKQLYLE*VLKGDLEKLLKFKIHIEDPPR*KHTVFLGGVVLADIMKDKDNF

Parental  WMTRQEYQEKGVRVLEKLGVTVR
          W.TRQEYQEKGV.VLEKLG..VR
Retrocopy WRTRQEYQEKGVPVLEKLGMIVR

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	279.04 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	69.54 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1082 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1082 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.

---

Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009761	1 retrocopy	retro_btau_707,
Callithrix jacchus	ENSCJAG00000006722	1 retrocopy	retro_cjac_429,
Homo sapiens	ENSG00000138071	1 retrocopy	retro_hsap_1978,
Gorilla gorilla	ENSGGOG00000008505	1 retrocopy	retro_ggor_1435,
Monodelphis domestica	ENSMODG00000003364	2 retrocopies	retro_mdom_1082 , retro_mdom_754,
Mus musculus	ENSMUSG00000020152	1 retrocopy	retro_mmus_2989,
Pongo abelii	ENSPPYG00000012359	1 retrocopy	retro_pabe_1877,
Pan troglodytes	ENSPTRG00000011990	1 retrocopy	retro_ptro_1320,