RetrogeneDB ID: retro_mdom_2017

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: X:37838314..37839104(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000005557
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_mdom_2017
GATCTCTTCCACTGCCATTTTAAATCCAGCTCCTTACAACACGCTGCCACTGTGACTACCTCTCTGCACCACATGCCTCC
AGCCAACAGCTCCACCGCTATGGAGGACGTGAATGAGTACAGCAATATGGAGAAGTTCACATTCAAAATCAACACCAGCA
AGAACCAGCAGGACGATGGTAAAATGTTTATTGGAGGGCGAAGCTGGGAAACAAATAAGAAAGATCTCACTGAATACCTG
TCTCGTTTTGGAGAGGTTATAGACTGCACAATTAAAACAGATCCCATCACGGGAACATTGACGGTATTTGGATTTGTGCT
TTTCAGAGATGCTGCCTGTGTTGATAAGGTTCTGGAACTTAAAGAACACAAGTTAGATGGCAAGTTGATAGACCCCAAAA
GGGCTAAAGCTTTAAAGGGAAAGGAGCCCCCCAAAAGTATCTGTCAGTGGATTGAACCCAGATACATGTGCAGAACAAAT
CAAAGAATATTTTGGAGCATTTGGAGAGATTAAGAATATTGAACTTTCTATAGACTAAAAAACAAATGAAAGAAGAGGAT
TCTGTTTTATCACATATACAGATGAAGTACCAGTAAAGAAATTATTAGAAAACCAATATCATCAGAATGGTTCTGGGGAG
TGTCAAATCAAAGTTGTCCAGCCCAAAGAGGTATACAGGCAGCAACAGCAACAACAGCAAGGAGGGAAGGGCACTATGGC
TGGTGGCCGAGGTGGCTGAGGTCAGGGCCAAAACTGGAACCAAGGATTTAATAACTATTATGATCAAGGA

Alignment

ORF - retro_mdom_2017 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.47 %
• Parental protein coverage: 64.99 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DLFRRHFKSGSIHRAAAATPSPRHLPPADSPAAMEDVNEYSNMEEFAEGSKINASKNQQDDGKMFIGGLS
          DLF..HFKS.S...AA..T.S..H.PPA.S..AMEDVNEYSNME.F....KIN.SKNQQDDGKMFIGG.S
Retrocopy DLFHCHFKSSSLQHAATVTTSLHHMPPANSSTAMEDVNEYSNMEKFT--FKINTSKNQQDDGKMFIGGRS

Parental  WDTSKKDLTEYLSRFGEVVDCTIKTDPVTGRSRGFGFVLFKDAASVDKVLELKEHKLDGKLIDPKRAKAL
          W.T.KKDLTEYLSRFGEV.DCTIKTDP.TG....FGFVLF.DAA.VDKVLELKEHKLDGKLIDPKRAKAL
Retrocopy WETNKKDLTEYLSRFGEVIDCTIKTDPITGTLTVFGFVLFRDAACVDKVLELKEHKLDGKLIDPKRAKAL

Parental  KGKE-PPKKVFVGGLSPDTSEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFITYTDEEPVKKLLENRY
          KGKE.PPK.V.V.GL.PDT..EQIKEYFGAFGEI.NIEL..D.KTNERRGFCFITYTDE.PVKKLLEN.Y
Retrocopy KGKE>PPK-VSVSGLNPDTCAEQIKEYFGAFGEIKNIELSID*KTNERRGFCFITYTDEVPVKKLLENQY

Parental  HQIGSGKCEIKVAQPKEVYRQQQQQQKGGRGAAAGGRGGTRGRGRGQGQNWNQGFNNYYDQG
          HQ.GSG.C.IKV.QPKEVYRQQQQQQ.GG.G..AGGRGG..G.G....Q....GFNNYYDQG
Retrocopy HQNGSGECQIKVVQPKEVYRQQQQQQQGGKGTMAGGRGG-*GQGQNWNQ----GFNNYYDQG

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_2017 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_2017 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,