RetrogeneDB ID: retro_mdom_333

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:199582030..199582853(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000009436
• Aliases: None
• Description: None

Sequence

>retro_mdom_333
ATGGATTGGGTGTTGAAGCATACTGGTCAAATAGTCCTGGCACTGCCAATGATGGCTTTGTGTGCCTTAGAGACTCCCAT
TTGGCTGTAGCAAGGAAGAAACTGTCCCGTTTTTTTCAGAGTTGGAAATTATGTCAAACGGAATAACACTGCCGATGGAC
TTCCAGGGGACAAGTATGGGAGAGGCAATCGTGCAGTTTACTTCACAGGAAATAGTTGAAAAGGCTCTAAAGAAACACAA
GGAAAGAATAGGGCACAGGCGCATTGAAATCTTTGAGAGCATCCAGGTAAAAGTTCGTCCTCATGAGGTTCCTCCTGGAA
AGCTAATGTCTAGGCAGCGGCCAGGTCCTTATGACAGGCTAGGTGCTGGCAGAGGCTAAAACAGCACTGGGAGAGGAGCT
GGGTTTGAAAGAATGAGGCAAGGTGCCTAGAGTGGAGGCTGTGGAGGCTGTGATGACCACAATGGGTATAATGATGGATA
TGGCTTTGGGTCTGATAGATTTGGAAGACTTCAAAATTACTTTTTTTTCCGGAACGTCCGATTATAGATATGGAGATGGT
GGGTCTACTTTCCAAAGTACTACGGGCTGTTGAGTGCCCATGAGATGCCTTACAGAGCTAATGAAAGGGATATTTACAAT
TTTTTCTCACCACTCAACCTTGTTCAAATACTTGTTGAAATTGGACCCAATGGCTGAGTGACTAGAAATGCAAATGCTGA
ATTTACTACTCATCAAGATGCTGTGACAGCTATGTCAAAAGACAAAGCAAAGAGGCAGCACAGATATATAGAACTCTTCT
TGAATTCGACAGCAGGAGCAAGC

Alignment

ORF - retro_mdom_333 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.07 %
• Parental protein coverage: 62.87 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MDWVLKHTGP-NSPDTANDGFVRLRG-LPFGCSKEEIVQFFSGLEIVPNGITLPVDFQGRSTGEAFVQFA
          MDWVLKHTG..NSP.TANDGFV.LR..LPFGCSKEE.V.FFS.LEI..NGITLP.DFQG.S.GEA.VQF.
Retrocopy MDWVLKHTGQ<NSPGTANDGFVCLRD<LPFGCSKEETVPFFSELEIMSNGITLPMDFQGTSMGEAIVQFT

Parental  SQEIAEKALKKHKERIGHRYIEIFKSSRAEVRTHYDPPRKLMAMQRPGPYDRPGAGRGYNSIGRGAGFER
          SQEI.EKALKKHKERIGHR.IEIF.S....VR.H..PP.KLM..QRPGPYDR.GAGRG.NS.GRGAGFER
Retrocopy SQEIVEKALKKHKERIGHRRIEIFESIQVKVRPHEVPPGKLMSRQRPGPYDRLGAGRG*NSTGRGAGFER

Parental  MRRGAYGGGYGGYDDYNGYNDGYGFGSDRFGRDLNYCFS-GMSDHRYGDGGSTFQSTTGHC-VHMRGLPY
          MR.GA.........D.NGYNDGYGFGSDRFGR..NY....G.SD.RYGDGGSTFQ..T..C.......PY
Retrocopy MRQGA*XXXXXXXXDHNGYNDGYGFGSDRFGRLQNYXXX>GTSDYRYGDGGSTFQ-STTGC<LSAHEMPY

Parental  RATENDIYNFFSPLNPVRVHIEIGPDGRVTGEADVEFATHEDAVAAMSKDKANMQHRYVELFLNSTAGAS
          RA.E.DIYNFFSPLN.V....EIGP.G.VT..A..EF.TH.DAV.AMSKDKA..QHRY.ELFLNSTAGAS
Retrocopy RANERDIYNFFSPLNLVQILVEIGPNG*VTRNANAEFTTHQDAVTAMSKDKAKRQHRYIELFLNSTAGAS

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	1869.72 RPM
SRP007412_cerebellum	0.33 RPM	2881.62 RPM
SRP007412_heart	0.00 RPM	1119.36 RPM
SRP007412_kidney	0.00 RPM	2505.93 RPM
SRP007412_liver	0.00 RPM	1900.67 RPM
SRP007412_testis	0.00 RPM	1938.21 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_333 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_333 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 33 parental genes, and 54 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008888	2 retrocopies	retro_amel_57, retro_amel_9,
Bos taurus	ENSBTAG00000009389	1 retrocopy	retro_btau_130,
Bos taurus	ENSBTAG00000020513	1 retrocopy	retro_btau_42,
Canis familiaris	ENSCAFG00000000336	2 retrocopies	retro_cfam_200, retro_cfam_230,
Choloepus hoffmanni	ENSCHOG00000003841	4 retrocopies	retro_chof_1051, retro_chof_1235, retro_chof_1491, retro_chof_2650,
Callithrix jacchus	ENSCJAG00000009931	1 retrocopy	retro_cjac_127,
Cavia porcellus	ENSCPOG00000001485	5 retrocopies	retro_cpor_1065, retro_cpor_1094, retro_cpor_1095, retro_cpor_121, retro_cpor_711,
Dipodomys ordii	ENSDORG00000005453	1 retrocopy	retro_dord_3,
Equus caballus	ENSECAG00000014429	1 retrocopy	retro_ecab_94,
Erinaceus europaeus	ENSEEUG00000010991	1 retrocopy	retro_eeur_481,
Erinaceus europaeus	ENSEEUG00000013364	2 retrocopies	retro_eeur_478, retro_eeur_649,
Echinops telfairi	ENSETEG00000011303	1 retrocopy	retro_etel_50,
Felis catus	ENSFCAG00000001204	2 retrocopies	retro_fcat_131, retro_fcat_27,
Homo sapiens	ENSG00000169045	2 retrocopies	retro_hsap_3322, retro_hsap_4911,
Gorilla gorilla	ENSGGOG00000025844	2 retrocopies	retro_ggor_1299, retro_ggor_177,
Loxodonta africana	ENSLAFG00000015766	2 retrocopies	retro_lafr_366, retro_lafr_74,
Myotis lucifugus	ENSMLUG00000016625	1 retrocopy	retro_mluc_124,
Macaca mulatta	ENSMMUG00000010843	1 retrocopy	retro_mmul_2,
Monodelphis domestica	ENSMODG00000009436	3 retrocopies	retro_mdom_1301, retro_mdom_1302, retro_mdom_333 ,
Mustela putorius furo	ENSMPUG00000000693	1 retrocopy	retro_mputfur_156,
Mus musculus	ENSMUSG00000007850	1 retrocopy	retro_mmus_142,
Nomascus leucogenys	ENSNLEG00000026658	3 retrocopies	retro_nleu_1668, retro_nleu_28, retro_nleu_48,
Otolemur garnettii	ENSOGAG00000012631	2 retrocopies	retro_ogar_208, retro_ogar_498,
Ochotona princeps	ENSOPRG00000003513	1 retrocopy	retro_opri_11,
Procavia capensis	ENSPCAG00000006715	1 retrocopy	retro_pcap_4,
Pongo abelii	ENSPPYG00000016121	1 retrocopy	retro_pabe_110,
Pteropus vampyrus	ENSPVAG00000007670	1 retrocopy	retro_pvam_23,
Rattus norvegicus	ENSRNOG00000003399	1 retrocopy	retro_rnor_340,
Sorex araneus	ENSSARG00000003024	1 retrocopy	retro_sara_29,
Sarcophilus harrisii	ENSSHAG00000018204	1 retrocopy	retro_shar_674,
Sus scrofa	ENSSSCG00000014022	1 retrocopy	retro_sscr_70,
Ictidomys tridecemlineatus	ENSSTOG00000016376	2 retrocopies	retro_itri_66, retro_itri_78,
Vicugna pacos	ENSVPAG00000007485	2 retrocopies	retro_vpac_594, retro_vpac_614,