RetrogeneDB ID: retro_mdom_1319

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:4039407..4039913(-)
• Located in intron of: ENSMODG00000020980

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMCO1
• Ensembl ID: ENSMODG00000001335
• Aliases: None
• Description: transmembrane and coiled-coil domains 1 [Source:HGNC Symbol;Acc:18188]

Sequence

>retro_mdom_1319
CTGAGCACCATCTTTGCTGACACCCTCCTCATTGTTTTCATCTCTGTGTGTGTGGCGCTGCTAACTGAGGGTATAACTTG
GGTACCAGTTTACAGGCCAGTCAAGTTTAGGAGATTAAAAGCTGAAGTGGAAAAGCAGAGCAAAACATTGGAAAAGAAGA
AAGAAAACAAAAAAGTGGAATCACTTTGTCATCAGCAAAAGAAGAAAACAGAGAGGCAGGAGGAGAAGCCGAAGAATAAC
AACAGGGATCTGTGAATGGTTTGAATGAAATCGACATCTACAATTAGCTTTGGTTTTACTGCCCTGATGGGAATGTTCAA
CTCCATATCTGATGGCAGCGTGTTGGCAAAGCTTCCCTTCATGCCTCTTTCCTAATTCAAGGACTATTTCATCATAATCT
GTTGGGAGAAGATTATACAGACTGTTCCTTCATCATGCTCTCTAGCCTCTGTACCTTATTCAGAAGATGCTTGGTCTTGC
TCCTTCTTGGGCTGCCACCAAGCAAG

Alignment

ORF - retro_mdom_1319 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.29 %
• Parental protein coverage: 89.36 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSTMFADTLLIVFISVCTALLAEGITWVLVYRTDKYKRLKAEVEKQSKKLEKKKETITESAGRQQKK-KI
          .ST.FADTLLIVFISVC.ALL.EGITWV.VYR..K..RLKAEVEKQS.................Q.K.K.
Retrocopy LSTIFADTLLIVFISVCVALLTEGITWVPVYRPVKFRRLKAEVEKQSXXXXXXXXXXXXESLCHQQKKKT

Parental  ERQEEKLKNNNRDLSMVRMKSMFAIGFCFTALMGMFNSIFDGRVVAKLPFTPLS-YIQGLSHRNLLGEDY
          ERQEEK.KNNNRDL.MV.MKS...I.F.FTALMGMFNSI.DG.V.AKLPF.PLS..IQGL.H.NLLGEDY
Retrocopy ERQEEKPKNNNRDL*MV*MKSTSTISFGFTALMGMFNSISDGSVLAKLPFMPLS<LIQGLFHHNLLGEDY

Parental  TDCSFIFLYILCTMSIRQNIQKMLGLAPSR
          TDCSFI.L..LCT...R......LGL.PS.
Retrocopy TDCSFIMLSSLCTLFRRCLVLLLLGLPPSK

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_1319 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1319 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 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000010009	1 retrocopy	retro_btau_1441,
Canis familiaris	ENSCAFG00000013472	2 retrocopies	retro_cfam_1640, retro_cfam_833,
Echinops telfairi	ENSETEG00000009382	2 retrocopies	retro_etel_1552, retro_etel_570,
Macropus eugenii	ENSMEUG00000011045	2 retrocopies	retro_meug_894, retro_meug_997,
Monodelphis domestica	ENSMODG00000001335	2 retrocopies	retro_mdom_1319 , retro_mdom_334,
Oryctolagus cuniculus	ENSOCUG00000008441	2 retrocopies	retro_ocun_1148, retro_ocun_1642,
Otolemur garnettii	ENSOGAG00000011784	1 retrocopy	retro_ogar_2381,
Sarcophilus harrisii	ENSSHAG00000016602	1 retrocopy	retro_shar_790,