RetrogeneDB ID: retro_mdom_1302

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:349592142..349592910(+)
• Located in intron of: ENSMODG00000023996

Retrocopy information

• Ensembl ID: ENSMODG00000023995
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_mdom_1302
ATGATGCTGAGCACCAAAGGAGAAGAAGGCTTTGTGGTGAAGGTCCGGGGCTTGCCATGGTCATGCTCAGCCAGTGACAT
CCAACAATTCTTCTCAGAATGCAAAATTCAAAATGGGGCAGCAGGCATTCATTTCATTTATACCAGAGAGGGCAGACCAA
GTGGAGAGGCATTTGTTGAACTTGAATCTGAAGATGAAGTCACACTGGCTTTGAAAAAAGATAGAGAAACTATGGGACAC
AGATATGTGGAAGTATTCAAGTCAAACAACATTGAAATGGATTGGGTGTTGAAGCATACTGCTCCAAATAGTCTTGATAC
TGCCAGTGATGGCTTTGTGCGCCTTAGGGGACTCCCATTTAGGTGTAACAAGGAAGAAATCGTTCAGTTCTTTTCAGGGC
TGGAAATCATGCCAAATGGGATAACATTGCCAGTGGACTTCCAAGGGAGGAACAGTGGCGAAGCCTTCGTGCAGTTTGCT
TCACAGGAAATAGCTGAAAAGGCTCTAAAGAAACACAAGGAAAGAATAGGGCACAGGTACATTGAAATCTTCAAGAGCAG
CCAGGCAGAAGCTCAGACCCATTATGATCCTCCTCGAAAGCTAATGGCTAAGCAGCGTCCAGGTCCTTATGACAGACCTC
AGGCAGGCAGAGGCTATAGCACTCTAGGTAGAGGAGTTGGGTTTGCAGGAATGAGATGTGGTGCCTATGAAGCTGGATAC
AGAGGCTATGATGACTACAACTGGTATAATGATGATTACTGCTTTGGA

Alignment

ORF - retro_mdom_1302 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.94 %
• Parental protein coverage: 58.31 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MMLSTEGGEGFVVKVRGLPWSCSADEVQRFFSECKIQNGASGIRFIYTREGRPSGEAFVELESEDEVKLA
          MMLST.G.EGFVVKVRGLPWSCSA...Q.FFSECKIQNGA.GI.FIYTREGRPSGEAFVELESEDEV.LA
Retrocopy MMLSTKGEEGFVVKVRGLPWSCSASDIQQFFSECKIQNGAAGIHFIYTREGRPSGEAFVELESEDEVTLA

Parental  LKKDRETMGHRYVEVFKSNNVEMDWVLKHTGPNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNG
          LKKDRETMGHRYVEVFKSNN.EMDWVLKHT.PNS.DTA.DGFVRLRGLPF.C.KEEIVQFFSGLEI.PNG
Retrocopy LKKDRETMGHRYVEVFKSNNIEMDWVLKHTAPNSLDTASDGFVRLRGLPFRCNKEEIVQFFSGLEIMPNG

Parental  ITLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKSSRAEVRTHYDPPRKLMAMQRPGPY
          ITLPVDFQGR..GEAFVQFASQEIAEKALKKHKERIGHRYIEIFKSS.AE..THYDPPRKLMA.QRPGPY
Retrocopy ITLPVDFQGRNSGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKSSQAEAQTHYDPPRKLMAKQRPGPY

Parental  DRPGAGRGYNSIGRGAGFERMRRGAYGGGYGGYDDYNGYNDGYGFG
          DRP.AGRGY...GRG.GF..MR.GAY..GY.GYDDYN.YND.Y.FG
Retrocopy DRPQAGRGYSTLGRGVGFAGMRCGAYEAGYRGYDDYNWYNDDYCFG

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	0.00 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_1302 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1302 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,