RetrogeneDB ID: retro_mdom_1705

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 7:6886255..6886903(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000013487
• Aliases: None
• Description: None

Sequence

>retro_mdom_1705
GAAAAGCCTTCCCAGATTCATTGTAAACCCCAAAATACACCTGCAGAACCATAAAATAAAAATCTCCCCTGCACTAACAA
GATAAACAGATAGAAAATTTCTACTGTCATCTTTAATAATGACAGTGATATAGAAGAACAAAGTGAATAAGAAAAGGAAT
ATTTCTATAATCGCACAGAAGAGAGGTTGTATAAATAGTCTGCACTGTCTGAAGATAGCAATAGAGATGCTGATTTCTTC
ACTGGTAAAATTAAGTGGGACAGAAAGAAGGAAAATAGTTGTTGTTCTTCAATTAAGGACCAAAAGACTCTCAAGAAAGC
ACTTCCTAAAAAGAAAAGTTTGAGACTCTGAAGAGTGTGGAAAAAATGAGGGCAACTACAAAAGCAAGGAGACTAGAATC
AACATTTTTTTCCTTCTTTATCTGAATCCAGAAGGAAAACAAGAAATGTCAGAGAATATCCTCCTAAAAATGGAATTCCA
GTATTTCAATAAAATGAAACTCAGATCAAGAAACACCTTGACAGGAGTGTATATACAAAGCCTGAAAATAAGAAGTCACA
GTTGCATCAGGCCCTTTATCCTTCTTGGGAAGCAAGCCAGAAATGAGAAGAACAAATGTCTAAAATTCTAGTATTTCAAG
GAAAAAAA

Alignment

ORF - retro_mdom_1705 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.94 %
• Parental protein coverage: 50.35 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QKSSQIDCETQNTPVEPEKKNLPSANKINRSKCSTVITNNDSDLEEQSEEEKEYFDDSTEERFYKQSSLS
          .K.SQI.C..QNTP.EP..KNLP..NKINR.K.STVI.NNDSD.EEQSE.EKEYF...TEER.YK.S.LS
Retrocopy EKPSQIHCKPQNTPAEP*NKNLPCTNKINR*KISTVIFNNDSDIEEQSE*EKEYFYNRTEERLYK*SALS

Parental  EDSDSDDDFFIGKIKRTRKKENSCSSSFKDQKTPKKSFPE-QEKLETLKSVEKTRPTTKARRLESTFFS-
          EDS..D.DFF.GKIK..RKKENSC.SS.KDQKT.KK..P...EK.ETLKSVEK.R.TTKARRLESTFFS.
Retrocopy EDSNRDADFFTGKIKWDRKKENSCCSSIKDQKTLKKALPK<KEKFETLKSVEKMRATTKARRLESTFFS>

Parental  SLSESRRTRRNAREHPPKNRIPAFQQNETQIKNHVDRGVHAKPENKKPQLQQPLHPSWEASRKRKEQMSK
          SLSESRR..RN.RE.PPKN.IP.FQ.NETQIK.H.DR.V..KPENKK.QL.Q.L.PSWEAS.K..EQMSK
Retrocopy SLSESRRKTRNVREYPPKNGIPVFQ*NETQIKKHLDRSVYTKPENKKSQLHQALYPSWEASQK*EEQMSK

Parental  ITVFQGKK
          I.VFQGKK
Retrocopy ILVFQGKK

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_1705 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1705 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017177	1 retrocopy	retro_cjac_1132,
Monodelphis domestica	ENSMODG00000013487	2 retrocopies	retro_mdom_1304, retro_mdom_1705 ,
Otolemur garnettii	ENSOGAG00000032423	1 retrocopy	retro_ogar_1270,
Tarsius syrichta	ENSTSYG00000006869	1 retrocopy	retro_tsyr_1456,