RetrogeneDB ID: retro_mdom_287

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:262980645..262981710(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000023959
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: TMEM30A
• Ensembl ID: ENSMODG00000018502
• Aliases: None
• Description: transmembrane protein 30A [Source:HGNC Symbol;Acc:16667]

Sequence

>retro_mdom_287
ATGGCCTGGAGTGCGACGTCGCCCGGGGCCAACCAGCCAGATAACACAGCCTTCACGCAGCAGCGCCTGCCAGCCTGGCA
GCCGCTGCTGTCGGCCGGCATCACCCTGCCGCTCTTTTTCTGCGTGGGCTTGGCCTTCATCGGCTTGGGCCTAGGCCTCT
ACTACTCCTCCAATGGCATTAAGGAGATAGAGTACGACTATACGGGCGAGCCAGGAATCGGCAACTGCACTGCCTGCGCC
AGGGTCGGGGAGCGAGTAGCCCCACCCCACCCCAACTGCACCTGCCAGTGGTGTTTCTCGCTGCCCGAGCTCTTCCAGGG
CCCCGTGTTCCTCTACTATGAATTATCTAACTTTTACCAGAATAACCGCCGCTACGTGGTCTCGCGAGACGATGAGCAGC
TCAGTGGGCTGGCGAGTGCACTGCGTCACCCTGCCAACGAGTGCGCGCCCTACCAGCGCACTCCCACCGGCCTGCCCATC
GCGCCGTGCGGCGCCATAGCCAACAGCCTCTTCAACGACTCATTCAAGCTGCTGTACCAGCGCCAGCCCAATGGCCCCTA
CGATGAGGTGCCGTTGGACCGCACCGGCATTGCCTGGTGGACAGACTACCACGTCAAGTTCCACAACCCGGCACCCATCA
ACGGCAGCCTGAAGCTGGCCTTCCATGGCACAGCCAAACCGCCCAACTGGCCTCGTCCAGTCTATGATCTAAGCCCGGAT
CCCAACAACACAGGCTTCGTGAACCAGGACTTCGTGGTGTGGATGCGCACGGCTGCGCTGCCCACGTTCCGCAAACTGTA
CGCCCGCATCCGCCACGTCAACTACTCGGCTGGGCTGCCACGTGGGACTTACTGCGTGAACATCACCTACAACTATCCGG
TCCTTGCCTTCGGGGGCCAGAAGCGCATCATCTTCAGCAGCATCTCGTGGATGGGGGGCAAGAATCCCTTCCTGGGCATC
GCCTACCTGACTTTTGGTTCCCTCTGCATCATCACTGGCTTTGTCATGCTCATCGTGTACATCCGGTATCAGGATGAGAA
TGGTGACGGAGATGAAGACGAGTGA

Alignment

ORF - retro_mdom_287 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.92 %
• Parental protein coverage: 68.36 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  CICEINFTLEQPFEGNVFMYYGLSNFYQNHRRYVKSRDDSQLNGDITALKNPSKECEPYRRDED-IPIAP
          C.C...F.L...F.G.VF.YY.LSNFYQN.RRYV.SRDD.QL.G...AL..P..EC.PY.R.....PIAP
Retrocopy CTCQWCFSLPELFQGPVFLYYELSNFYQNNRRYVVSRDDEQLSGLASALRHPANECAPYQRTPTGLPIAP

Parental  CGAIANSMFNDTLEL-FQMNGTTPMPIV-MHRTGIAWWTDKNVKFRNPPGDN--LTETFTGTTKPRNWPK
          CGAIANS.FND...L..Q.....P...V...RTGIAWWTD..VKF.NP...N..L...F.GT.KP.NWP.
Retrocopy CGAIANSLFNDSFKLLYQRQPNGPYDEVPLDRTGIAWWTDYHVKFHNPAPINGSLKLAFHGTAKPPNWPR

Parental  PVYMLDKDEENNGFINEDFIVWMRTAALPTFRKLYRLIERKNGLHPTLPVGQYLLKITYNYPVHTFDGRK
          PVY.L..D..N.GF.N.DF.VWMRTAALPTFRKLY..I...N.....LP.G.Y...ITYNYPV..F.G.K
Retrocopy PVYDLSPDPNNTGFVNQDFVVWMRTAALPTFRKLYARIRHVN-YSAGLPRGTYCVNITYNYPVLAFGGQK

Parental  RMILSTISWMGGKNPFLGIAYITVGSICFLFGVVLLVIHHKYGNRNNSAD
          R.I.S.ISWMGGKNPFLGIAY.T.GS.C...G.V.L.....Y...N...D
Retrocopy RIIFSSISWMGGKNPFLGIAYLTFGSLCIITGFVMLIVYIRYQDENGDGD

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	2.38 RPM	0.00 RPM
SRP007412_cerebellum	5.22 RPM	0.00 RPM
SRP007412_heart	1.20 RPM	0.00 RPM
SRP007412_kidney	102.71 RPM	0.00 RPM
SRP007412_liver	27.19 RPM	0.00 RPM
SRP007412_testis	10.21 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_287 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_287 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 15 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005100	1 retrocopy	retro_btau_72,
Canis familiaris	ENSCAFG00000002708	1 retrocopy	retro_cfam_26,
Callithrix jacchus	ENSCJAG00000010325	1 retrocopy	retro_cjac_801,
Cavia porcellus	ENSCPOG00000020712	1 retrocopy	retro_cpor_23,
Homo sapiens	ENSG00000112697	1 retrocopy	retro_hsap_12,
Myotis lucifugus	ENSMLUG00000011923	1 retrocopy	retro_mluc_1871,
Monodelphis domestica	ENSMODG00000018502	1 retrocopy	retro_mdom_287 ,
Mus musculus	ENSMUSG00000032328	1 retrocopy	retro_mmus_108,
Nomascus leucogenys	ENSNLEG00000004962	1 retrocopy	retro_nleu_69,
Otolemur garnettii	ENSOGAG00000015718	1 retrocopy	retro_ogar_22,
Pongo abelii	ENSPPYG00000016782	1 retrocopy	retro_pabe_204,
Pelodiscus sinensis	ENSPSIG00000007174	1 retrocopy	retro_psin_61,
Rattus norvegicus	ENSRNOG00000010895	1 retrocopy	retro_rnor_399,
Ictidomys tridecemlineatus	ENSSTOG00000002543	1 retrocopy	retro_itri_50,
Tarsius syrichta	ENSTSYG00000008211	1 retrocopy	retro_tsyr_928,