RetrogeneDB ID: retro_mdom_1951

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 8:290507992..290508865(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000011916
• Aliases: None
• Description: None

Sequence

>retro_mdom_1951
CATACAACACACTGGAGTTGTAATTCCCTCTCCTTGCCATCTGCTGAGCCACACCACCAATACTACTGCCAGTAGCCCAC
CTCCATGGAGGATGGGAATAAGTACAGCAATGTGGAGGAGTTTGCTGAAGCCTTTAAAATCATCACCATCAAGAACCAGT
AGGAAAAACAGTAAAAGTTTATTGAAACTCTAAGCTGGTATATGAGCAAAAAAGATCTCACTGAATACCTATCTCATTCA
GGAGAAGTTGTAGATGCACAATTAAAACAAATCCCATAAAGAGAAGTTCAAGGGGATTCGGATTTGTGCTTTTCAAAGAT
GCTGCTGGTGTTGATAAAGTTCTGGAACTTAAAGAACAGAAGGTGGATGGCATGTTGATAGACCCCAAAAGGATAATGCT
TTAAAGGGAAGGAAGTTCCTCCCAAAAAGTATTTGTTAGCTGACTGATCCCAGATATTTTGGGGAAAGAAATCAAAAGAA
TATTTTAGAGCATTTGAAGAGAATATTGAACTTCTTATAGACACAAAAACAAATGAAAGGAGAGGATTTCCTTTTATCAC
AAATATAGATGAAGAATCAATAAAGAAATTATTGGAAAACAGATATCTTCAGAATGGTTCTGGAAAGTGTAAAATCAAAG
TTGCCCAGTCCAGAGAGCTATAAGGAGTAACAGCAACAACAGAAAGGAGGGAAGGGTGCTGCAGCTGGCTAGAGAAGGAG
GTGGGACTAGGGGTCAGTGTCCAGGGGTAGGGCCAAAACTGGAACTATGGCTTTAATATCTATTATGATCAAGGATTTGG
AAATTATAAAAGTGTCTATGGTGGTGATCCAAACCATAGAGGCTATGGCAGATATCATTATTCTGTCTATAAC

Alignment

ORF - retro_mdom_1951 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.87 %
• Parental protein coverage: 70.02 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  HFKSGSIHRAAAATPSPRHLPPADSPAAMEDVNEYSNMEEFAEGSKINASKNQQDDGKMFIGGLSWDTSK
          H....S..........P.H......P..MED.N.YSN.EEFAE..KI...KNQ......FI..LSW..SK
Retrocopy HTTHWSCNSLSLPSAEPHHQYYCQ*PTSMEDGNKYSNVEEFAEAFKIITIKNQ*EKQ*KFIETLSWYMSK

Parental  KDLTEYLSRFGEVVD-CTIKTDPVTGRSRGFGFVLFKDAASVDKVLELKEHKLDGKLIDPKRAKALKGKE
          KDLTEYLS..GEVVD.CTIKT.P....SRGFGFVLFKDAA.VDKVLELKE.K.DG.LIDPKR........
Retrocopy KDLTEYLSHSGEVVD<CTIKTNPIKRSSRGFGFVLFKDAAGVDKVLELKEQKVDGMLIDPKRIML*REGS

Parental  PPKKVFVGGLSPDTSEEQI-KEYFGAFGEIENIELPMDTKTNERRGFCFITYTDEEPVKKLLENRYHQIG
          ...KVFV..L.PD.....I.KEYF.AF...ENIEL..DTKTNERRGF.FIT..DEE..KKLLENRY.Q.G
Retrocopy SSQKVFVS*LIPDILGKEI>KEYFRAFE--ENIELLIDTKTNERRGFPFITNIDEESIKKLLENRYLQNG

Parental  SGKCEIKVAQPKEV-YRQQQQQQK-GGRGAAAGGR-GG-TRGR-GRGQGQNWNQGFNNYYDQGYGNYNSA
          SGKC.IKVAQ..E...R......K.GG.GAAAG.R.GG.TRG....G.GQNWN.GFN.YYDQG.GNY.S.
Retrocopy SGKCKIKVAQSREL<IRSNSNNRK<GGKGAAAG*R>GGGTRGQ>VQG*GQNWNYGFNIYYDQGFGNYKSV

Parental  YGGDQNYSGYGGYDYTGYN
          YGGD.N..GYG.Y.Y..YN
Retrocopy YGGDPNHRGYGRYHYSVYN

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_1951 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1951 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 11 parental genes, and 40 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015197	1 retrocopy	retro_cjac_2589,
Dasypus novemcinctus	ENSDNOG00000003887	7 retrocopies	retro_dnov_1175, retro_dnov_1182, retro_dnov_144, retro_dnov_1603, retro_dnov_31, retro_dnov_723, retro_dnov_930,
Felis catus	ENSFCAG00000000455	1 retrocopy	retro_fcat_1568,
Macropus eugenii	ENSMEUG00000011454	7 retrocopies	retro_meug_1252, retro_meug_1378, retro_meug_1491, retro_meug_1971, retro_meug_2165, retro_meug_249, retro_meug_766,
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,
Otolemur garnettii	ENSOGAG00000002501	4 retrocopies	retro_ogar_2717, retro_ogar_2791, retro_ogar_437, retro_ogar_693,
Sarcophilus harrisii	ENSSHAG00000013616	3 retrocopies	retro_shar_297, retro_shar_527, retro_shar_625,
Ictidomys tridecemlineatus	ENSSTOG00000013979	1 retrocopy	retro_itri_1177,
Tupaia belangeri	ENSTBEG00000002817	7 retrocopies	retro_tbel_2079, retro_tbel_2283, retro_tbel_2608, retro_tbel_2874, retro_tbel_3344, retro_tbel_4302, retro_tbel_4405,
Tursiops truncatus	ENSTTRG00000001793	2 retrocopies	retro_ttru_1486, retro_ttru_744,