RetrogeneDB ID: retro_mdom_1037

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:307974783..307975078(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: H3F3A
• Ensembl ID: ENSMODG00000005983
• Aliases: None
• Description: H3 histone, family 3A [Source:HGNC Symbol;Acc:4764]

Sequence

>retro_mdom_1037
AGGAAAAGCACCCTCTCTACTAGCCAGGGCAAAAAACTTCACTGTTTCAGAAGTATTGTGAATCTTCATGAAATTCAGTG
TTACTAGAAATCAACAGAGTGTTTAGTCAGGAAACTCTTTTTTTCAGTGATTGAGGCAGGAGATTACTCAGAAATTCAAA
ACAATCTTGAGGTTCCAGATTGCAGCTATTGGTACCCTCCAGGAGGCTATTAAAGCATATTTGATGGGTCTTTTTAAAGG
TACCAATCTATGTGTCAGCAATGCCAAGAGAGTCACTATCATGCCCAAAGACATC

Alignment

ORF - retro_mdom_1037 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64. %
• Parental protein coverage: 72.79 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RKSAPSTGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPF-QRLVREIAQDFKTDLRFQSAAIGALQE
          RKS..ST...KK.H..R...V.L.EI..Y.KSTE.L.RKL.F.Q.L..EI.Q.FKT.LRFQ.AAIG.LQE
Retrocopy RKSTLSTSQGKKLHCFR-SIVNLHEIQCY*KSTECLVRKLFF>Q*LRQEITQKFKTILRFQIAAIGTLQE

Parental  ASEAYLVGLFEDTNLCAIHAKRVTIMPKDI
          A..AYL.GLF..TNLC...AKRVTIMPKDI
Retrocopy AIKAYLMGLFKGTNLCVSNAKRVTIMPKDI

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_1037 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1037 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 18 parental genes, and 99 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014588	7 retrocopies	retro_amel_1023, retro_amel_1026, retro_amel_144, retro_amel_570, retro_amel_687, retro_amel_711, retro_amel_903,
Bos taurus	ENSBTAG00000024561	3 retrocopies	retro_btau_156, retro_btau_204, retro_btau_47,
Canis familiaris	ENSCAFG00000004916	2 retrocopies	retro_cfam_1117, retro_cfam_622,
Canis familiaris	ENSCAFG00000016119	4 retrocopies	retro_cfam_168, retro_cfam_1845, retro_cfam_650, retro_cfam_673,
Erinaceus europaeus	ENSEEUG00000013796	1 retrocopy	retro_eeur_2,
Felis catus	ENSFCAG00000003617	4 retrocopies	retro_fcat_1085, retro_fcat_1953, retro_fcat_592, retro_fcat_830,
Felis catus	ENSFCAG00000030424	5 retrocopies	retro_fcat_1251, retro_fcat_1532, retro_fcat_1533, retro_fcat_2011, retro_fcat_674,
Gadus morhua	ENSGMOG00000014306	1 retrocopy	retro_gmor_9,
Macaca mulatta	ENSMMUG00000031483	9 retrocopies	retro_mmul_108, retro_mmul_147, retro_mmul_201, retro_mmul_213, retro_mmul_215, retro_mmul_286, retro_mmul_337, retro_mmul_346, retro_mmul_7,
Monodelphis domestica	ENSMODG00000005983	3 retrocopies	retro_mdom_1037 , retro_mdom_1132, retro_mdom_175,
Mustela putorius furo	ENSMPUG00000013811	3 retrocopies	retro_mputfur_1159, retro_mputfur_787, retro_mputfur_881,
Nomascus leucogenys	ENSNLEG00000001577	2 retrocopies	retro_nleu_25, retro_nleu_35,
Otolemur garnettii	ENSOGAG00000024312	11 retrocopies	retro_ogar_1086, retro_ogar_1790, retro_ogar_1863, retro_ogar_2364, retro_ogar_2463, retro_ogar_2581, retro_ogar_2746, retro_ogar_3415, retro_ogar_478, retro_ogar_842, retro_ogar_955,
Otolemur garnettii	ENSOGAG00000025933	14 retrocopies	retro_ogar_1285, retro_ogar_1364, retro_ogar_1449, retro_ogar_1575, retro_ogar_1576, retro_ogar_2200, retro_ogar_2316, retro_ogar_2449, retro_ogar_2634, retro_ogar_3235, retro_ogar_42, retro_ogar_733, retro_ogar_937, retro_ogar_952,
Pongo abelii	ENSPPYG00000008636	1 retrocopy	retro_pabe_2662,
Pan troglodytes	ENSPTRG00000002045	20 retrocopies	retro_ptro_1045, retro_ptro_1704, retro_ptro_1770, retro_ptro_1867, retro_ptro_1954, retro_ptro_2098, retro_ptro_2183, retro_ptro_2228, retro_ptro_2229, retro_ptro_2230, retro_ptro_2232, retro_ptro_2233, retro_ptro_2363, retro_ptro_279, retro_ptro_2834, retro_ptro_2936, retro_ptro_2978, retro_ptro_300, retro_ptro_3111, retro_ptro_3164,
Pteropus vampyrus	ENSPVAG00000008459	2 retrocopies	retro_pvam_218, retro_pvam_52,
Tursiops truncatus	ENSTTRG00000015889	7 retrocopies	retro_ttru_1094, retro_ttru_1306, retro_ttru_18, retro_ttru_451, retro_ttru_738, retro_ttru_814, retro_ttru_92,