RetrogeneDB ID: retro_mdom_250

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 7:240809847..240810558(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000024645
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000004277
• Aliases: None
• Description: None

Sequence

>retro_mdom_250
TTAAGCATGCTCATTTGGGAGACCAACTTGAAAGCTCTCTCAAGGATTCCCCACATCAGCCCGGTAAGCCAGAAGCACCT
GAAGAATGTCTATGCCAGCCTGACCCTCTGCATGCTTGTGGCAGCCACAGGAGCCCATCTCAATGTGGTTGCCCATTTCT
TCCAGGCTGGCTTTATCTCGATCTTATGTTCTCTCGGAGTGTTAATATGGCTCCTGAACATACCCCACAGAAAGGAAACT
GAGCCAAAGAGACTGTTTCTGCTGGCAGGATTTGCTTTCCTCATAGGGATTGACTTGGGCCCTGACCTGGACACGTGCAT
TGACATCGACCCCAGCATTATCCCTTCCTCCTTCCTGGGCACAACAGCGACCTTCAGCTCTTTCACCTTGAGCTCAATCT
TTGGCCATTGCCTTAGCTACATCTACCTCAGCGCCATCTTGGGAGCAGCCCTGATACTGATACTCATCTCTTATCTTGGG
AACCTCTTCTTCATATCTACATGGCTTTATCAGGCAAACCTGTACTTTGGGCTGGCATTCATGTGTGGACTTGTTCTTTT
TGATACACAACTCATCATTGTTAAGGCAGAGAAAAAGGATGAAGATTATATTGGGCATAGCATGGACCTTTTCCTGGATT
TTGTGACCCTCTTCAGGAAATTCATGGTGATCCTTGAAATGAATGAAAAAAACAAGCTGAAAAATCAATGA

Alignment

ORF - retro_mdom_250 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.59 %
• Parental protein coverage: 96.72 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNMFDRKINLDALLKFSHITPSTQQHLKKVYASFALCMFVAAAGAYVHVVTHFIQVGLLSGLGSLGLMIW
          ..M.....NL.AL....HI.P..Q.HLK.VYAS..LCM.VAA.GA...VV.HF.Q.G..S.L.SLG..IW
Retrocopy LSMLIWETNLKALSRIPHISPVSQKHLKNVYASLTLCMLVAATGAHLNVVAHFFQAGFISILCSLGVLIW

Parental  LMATPHSHETEKKRLGLLTGFAFLTGVGLGPALELCIAINPSIIPTSFLGTAMIFSCFTLSALYARRRSY
          L...PH..ETE.KRL.LL.GFAFL.G..LGP.L..CI.I.PSIIP.SFLGT...FS.FTLS.......SY
Retrocopy LLNIPHRKETEPKRLFLLAGFAFLIGIDLGPDLDTCIDIDPSIIPSSFLGTTATFSSFTLSSIFGHCLSY

Parental  LFLGGILMSAMSLMLFSSLGNLFFGSIWLFQANLYVGLVVMCGFVLFDTQLIIEKAENGDKDYIWHCVDL
          ..L..IL..A..L.L.S.LGNLFF.S.WL.QANLY.GL..MCG.VLFDTQLII.KAE..D.DYI.H..DL
Retrocopy IYLSAILGAALILILISYLGNLFFISTWLYQANLYFGLAFMCGLVLFDTQLIIVKAEKKDEDYIGHSMDL

Parental  FLDFVTLFRKLMMILAMNEKDKKKEK
          FLDFVTLFRK.M.IL.MNEK.K.K..
Retrocopy FLDFVTLFRKFMVILEMNEKNKLKNQ

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_250 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_250 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 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000018588	1 retrocopy	retro_btau_762,
Canis familiaris	ENSCAFG00000008400	2 retrocopies	retro_cfam_1220, retro_cfam_876,
Callithrix jacchus	ENSCJAG00000021032	1 retrocopy	retro_cjac_272,
Dasypus novemcinctus	ENSDNOG00000007882	2 retrocopies	retro_dnov_164, retro_dnov_857,
Macropus eugenii	ENSMEUG00000015590	4 retrocopies	retro_meug_1076, retro_meug_1706, retro_meug_2157, retro_meug_48,
Monodelphis domestica	ENSMODG00000004277	2 retrocopies	retro_mdom_210, retro_mdom_250 ,
Otolemur garnettii	ENSOGAG00000005137	2 retrocopies	retro_ogar_1074, retro_ogar_3470,
Pteropus vampyrus	ENSPVAG00000016821	1 retrocopy	retro_pvam_755,
Sarcophilus harrisii	ENSSHAG00000010366	1 retrocopy	retro_shar_622,
Ictidomys tridecemlineatus	ENSSTOG00000001165	2 retrocopies	retro_itri_1273, retro_itri_564,
Tarsius syrichta	ENSTSYG00000002427	1 retrocopy	retro_tsyr_916,