RetrogeneDB ID: retro_mdom_1590

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 6:62432836..62433535(+)
• Located in intron of: ENSMODG00000008055

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000019803
• Aliases: None
• Description: None

Sequence

>retro_mdom_1590
GTGAGAGACTCCCAAACAAAATATTACTGAGGCTTTAGGTTTGTTACTTATTTTTGTATTGAAGAGACAGCTGTGGCGAT
GTGTGCTCAGCCACATTAGGTTGATGAGCATGTAGCAGAACAAAAGAAAGCTGTTTTCTTAAAAAGATCCTATAAAATCT
GGTGCACATCTAACTGTGAAGAAAGTTTTTGTTGGTGGTATTAAAGATACAAAAAAATATAACATAAGAGCATACTTTGA
AAAGTATGGCAAGACCAAAACTATAGAAGTTATGCAAGATTGATAGAGTGGAAAGAAGAGAGGATTTGCTTTTGTAATTT
TTAGTAATAATTATATAATTAGAAAAATTATTGTTCAGAAATATCATACTATTAATGGGCATAACTGTGAAGTGAAAAGG
ATCCTTTTGAAGCAAGAGATACAATCTGCTGGCTCACAAAGAGGTCATTGGAGGTACCTCAGGCAATTTTATAGGTTGAG
GAAGAAATTGGAGGTGGTAAAAGAAACTTTGGCCATGGTGGAAACTTTGGTGGAAGATGAAGTGATGGTGGTAGCAGAAA
AGGCAGTTATGGAGGTAGAATTGGTGAATATAATGGATTTGGTGGAGATGGTTGCAACTATGGAAGTGGTCCTGGCTACA
GTAGTAGAGGGAGTTATAGTTGTGGCAGTGGACCTGGATATGAAAACCAAGGCAGTGGA

Alignment

ORF - retro_mdom_1590 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.07 %
• Parental protein coverage: 91.73 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MRDPQTKRSRGFGFVTYSCVEEVDAAMCARPHKVDGRVVEPKRAV-SREDSVKPGAHLTVKKIFVGGIKE
          .RD.QTK...GF.FVTY.C.EE...AMCA.PH.VD..V.E.K.AV.S..D..K.GAHLTVKK.FVGGIK.
Retrocopy VRDSQTKYY*GFRFVTYFCIEETAVAMCAQPH*VDEHVAEQKKAV>S*KDPIKSGAHLTVKKVFVGGIK-

Parental  DTEEYNLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTFDDHDTVDKIVVQKYHTINGHNCEVKKALSKQ
          DT..YN.R.YFEKYGK..TIEVM.D..SGKKRGFAF.............VQKYHTINGHNCEVK..L.KQ
Retrocopy DTKKYNIRAYFEKYGKTKTIEVMQD**SGKKRGFAFXXXXXXXXXXXXXVQKYHTINGHNCEVKRILLKQ

Parental  EMQSAGSQRGR-GGGSGNFMGRGGNF-GGGGGNFGRGGNFGGR--DGGYNGFGGDGKTFSCCNYGGSG-N
          E.QSAGSQRG..GG.SGNF.G.G.N..GG...NFG.GGNFGGR..DGG.......G........GG.G.N
Retrocopy EIQSAGSQRGH>GGTSGNFIG*GRNW>GG-KRNFGHGGNFGGR*SDGGSRKGSYGGRIGEYNGFGGDGCN

Parental  YNDFGNYSGQQQSNYGPMKGGSFGGRSSG
          Y.....YS......Y....G.......SG
Retrocopy YGSGPGYS--SRGSYSCGSGPGYENQGSG

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_1590 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1590 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 18 parental genes, and 53 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011920	4 retrocopies	retro_amel_1407, retro_amel_557, retro_amel_715, retro_amel_765,
Cavia porcellus	ENSCPOG00000004251	3 retrocopies	retro_cpor_1516, retro_cpor_1543, retro_cpor_65,
Ficedula albicollis	ENSFALG00000003215	1 retrocopy	retro_falb_15,
Gallus gallus	ENSGALG00000009250	1 retrocopy	retro_ggal_10,
Monodelphis domestica	ENSMODG00000011916	6 retrocopies	retro_mdom_1496, retro_mdom_1789, retro_mdom_1951, retro_mdom_2017, retro_mdom_546, retro_mdom_981,
Monodelphis domestica	ENSMODG00000019803	1 retrocopy	retro_mdom_1590 ,
Mustela putorius furo	ENSMPUG00000014103	6 retrocopies	retro_mputfur_1141, retro_mputfur_1336, retro_mputfur_1545, retro_mputfur_603, retro_mputfur_674, retro_mputfur_779,
Oryctolagus cuniculus	ENSOCUG00000002743	2 retrocopies	retro_ocun_994, retro_ocun_995,
Otolemur garnettii	ENSOGAG00000025948	3 retrocopies	retro_ogar_1685, retro_ogar_3010, retro_ogar_3175,
Pongo abelii	ENSPPYG00000012967	1 retrocopy	retro_pabe_450,
Pelodiscus sinensis	ENSPSIG00000003011	1 retrocopy	retro_psin_16,
Pan troglodytes	ENSPTRG00000012676	5 retrocopies	retro_ptro_1059, retro_ptro_2430, retro_ptro_2966, retro_ptro_683, retro_ptro_872,
Rattus norvegicus	ENSRNOG00000001556	11 retrocopies	retro_rnor_1510, retro_rnor_1665, retro_rnor_1869, retro_rnor_2053, retro_rnor_2659, retro_rnor_2669, retro_rnor_2713, retro_rnor_2776, retro_rnor_2809, retro_rnor_348, retro_rnor_959,
Sarcophilus harrisii	ENSSHAG00000018255	1 retrocopy	retro_shar_518,
Tarsius syrichta	ENSTSYG00000012949	2 retrocopies	retro_tsyr_1480, retro_tsyr_2122,
Tursiops truncatus	ENSTTRG00000014225	3 retrocopies	retro_ttru_1459, retro_ttru_675, retro_ttru_9,
Xenopus tropicalis	ENSXETG00000001806	1 retrocopy	retro_xtro_11,
Xiphophorus maculatus	ENSXMAG00000000439	1 retrocopy	retro_xmac_2,