RetrogeneDB ID: retro_mdom_315

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:99084262..99084848(+)
• Located in intron of: ENSMODG00000010289

Retrocopy information

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

Parental gene information

• Parental gene symbol: THOC7
• Ensembl ID: ENSMODG00000003009
• Aliases: None
• Description: THO complex 7 homolog (Drosophila) [Source:HGNC Symbol;Acc:29874]

Sequence

>retro_mdom_315
GAAGATGAAGTCATGAGGAAGTGTCTCTTAACTGATGGTGCTGGTGCTGATCAAAGAATCAATCTATTAGGAAAGAGCTT
CATTAAATGGTATGATGATGGATCTCAGGAAGAGGGGTATAGCCAGTACCAGCACATGCTGAGTGCATTGTCTCAGTGTG
AATTTTCAATTGGAAAAACCCAGCTTGTATATGATATGAATCTCAGAGAAATGGAGAACTATGAAAACATTTACAAAGAC
AGAAAATAGCATAGCTGGAGCACATGAAAAAATTGCTGAGTGCAAAAAGCAGATCCTTCAAGCAAAAGGAATACAAAAAA
AATCGCCAGGAATATGATGCTTTGCCAAAAGTCATACAGCACCACCCAGACAGGCACAAGCCATTAAAGGAACTAGATGC
TTTGGGGGAAGAATTACAACACCTTTCTCATATAAAAGAAAATGTTGAAGATAAGCTGGAACTAAGGCAAAAACATTTCC
ATGTTCTTAGTACCATTCATGAACTTCAGCAGACATTAGAAAATGACAAAAACTCTCAGAAGAGGAAGAGGTTCAGGAAG
CAGGTATGGAAACAGAGACTAAACAG

Alignment

ORF - retro_mdom_315 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.26 %
• Parental protein coverage: 92.99 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DDEVIRKRLLIDGDGAGDDRRINLLVKSFIKWCNAGSQEEGYSQYQRMLSTLSQCE-FSMGKTLLVYDMN
          .DEV.RK.LL.DG.GA..D.RINLL.KSFIKW...GSQEEGYSQYQ.MLS.LSQCE.F...K..L.Y...
Retrocopy EDEVMRKCLLTDGAGA--DQRINLLGKSFIKWYDDGSQEEGYSQYQHMLSALSQCE>FQLEKPSL-YMI*

Parental  LREMENYEKIYKDIENSIAGAHEKIAECKKQILQAKRIRKN-RQEYDALAKVIQHHPDRHETLKELDALG
          ..E.....K.....ENSIAGAHEKIAECKKQILQAK.I....RQEYDAL.KVIQHHPDRH..LKELDALG
Retrocopy ISEKWRTMKTFTKTENSIAGAHEKIAECKKQILQAKGIXXX>RQEYDALPKVIQHHPDRHKPLKELDALG

Parental  KELQHLSHIKENVEDKLELRRKQFHVLLSTIHELQQTLEND-EKLSEVEEAQEAGMETETKQ
          .ELQHLSHIKENVEDKLELR.K.FHV.LSTIHELQQTLEND..KLSE.EE.QEAGMETETKQ
Retrocopy EELQHLSHIKENVEDKLELRQKHFHV-LSTIHELQQTLEND<QKLSEEEEVQEAGMETETKQ

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	0.12 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	1.18 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_315 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_315 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 10 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000034899	2 retrocopies	retro_cjac_354, retro_cjac_398,
Echinops telfairi	ENSETEG00000015076	3 retrocopies	retro_etel_1093, retro_etel_1858, retro_etel_85,
Macropus eugenii	ENSMEUG00000006342	4 retrocopies	retro_meug_1481, retro_meug_1524, retro_meug_1599, retro_meug_1861,
Myotis lucifugus	ENSMLUG00000012060	1 retrocopy	retro_mluc_369,
Monodelphis domestica	ENSMODG00000003009	1 retrocopy	retro_mdom_315 ,
Oryctolagus cuniculus	ENSOCUG00000021860	1 retrocopy	retro_ocun_124,
Sorex araneus	ENSSARG00000013894	1 retrocopy	retro_sara_41,
Sarcophilus harrisii	ENSSHAG00000011615	1 retrocopy	retro_shar_240,
Tupaia belangeri	ENSTBEG00000007069	1 retrocopy	retro_tbel_49,
Tursiops truncatus	ENSTTRG00000013618	3 retrocopies	retro_ttru_1365, retro_ttru_23, retro_ttru_957,