RetrogeneDB ID: retro_mdom_1949

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 8:280764726..280765077(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL23
• Ensembl ID: ENSMODG00000012634
• Aliases: None
• Description: ribosomal protein L23 [Source:HGNC Symbol;Acc:10316]

Sequence

>retro_mdom_1949
CTGGGTTTCCTAATGTGTGTAGTCATCAGTTGGCCTGATAATGCAAGTGCCAAGAACCTGTGCATCATCTCTGTGAATGG
GGATTAAAGGAAAACTGAGCAGGCTTCCTGAAGCTGGTGTGGGTGACCTCCTAAGGACCACAGTCAAAAAGGGAAACCAG
AGTTCCAAAAAAGGTTCATCCAGCAATGATAATTTGGTCACAGAAATCATAGCAGAGAAAGAAGGAGTGTTTCTATATTT
TGAAGACAATGCAGAGGTCATAGTAAATAACAAAGGCAAGATGAAAAGTTTAGCCATTATGGAGCTGGTTGCCAACAAGT
GGCCAGGACTTCATCTAATGCCAGCAACATT

Alignment

ORF - retro_mdom_1949 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.84 %
• Parental protein coverage: 87.14 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  LGLPVGAVINCADNTGAKNLYIISVKG-IKGRLNRLPAAGVGDMVMATVKKG-KPELRK-KVHPAVVIRQ
          LG.....VI...DN..AKNL.IISV.G.IKG.L.RLP.AGVGD....TVKKG.KPE..K.KVHPA..I..
Retrocopy LGFLMCVVISWPDNASAKNLCIISVNG>IKGKLSRLPEAGVGDLLRTTVKKG<KPEFQK<KVHPAMIIWS

Parental  RKSYRRK-DGVFLYFEDNAGVIVNNKGEMKGSAITGPVAKECADLWP-RIASNAGSI
          .KS..RK..GVFLYFEDNA.VIVNNKG.MK..AI...VA......WP.R..SNA..I
Retrocopy QKS*QRK<EGVFLYFEDNAEVIVNNKGKMKSLAIMELVANK----WP<RTSSNASNI

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_1949 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1949 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 12 parental genes, and 79 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004268	6 retrocopies	retro_amel_1791, retro_amel_226, retro_amel_308, retro_amel_880, retro_amel_918, retro_amel_990,
Callithrix jacchus	ENSCJAG00000008311	9 retrocopies	retro_cjac_1129, retro_cjac_1483, retro_cjac_2283, retro_cjac_2598, retro_cjac_2639, retro_cjac_2772, retro_cjac_2885, retro_cjac_3128, retro_cjac_3831,
Gorilla gorilla	ENSGGOG00000025082	9 retrocopies	retro_ggor_1574, retro_ggor_1744, retro_ggor_1746, retro_ggor_2416, retro_ggor_2508, retro_ggor_256, retro_ggor_2710, retro_ggor_2757, retro_ggor_504,
Latimeria chalumnae	ENSLACG00000004430	1 retrocopy	retro_lcha_16,
Macaca mulatta	ENSMMUG00000004502	9 retrocopies	retro_mmul_1598, retro_mmul_1705, retro_mmul_1955, retro_mmul_2366, retro_mmul_2391, retro_mmul_384, retro_mmul_928, retro_mmul_930, retro_mmul_935,
Monodelphis domestica	ENSMODG00000012634	3 retrocopies	retro_mdom_1949 , retro_mdom_527, retro_mdom_916,
Mustela putorius furo	ENSMPUG00000015075	2 retrocopies	retro_mputfur_1138, retro_mputfur_1324,
Nomascus leucogenys	ENSNLEG00000000642	7 retrocopies	retro_nleu_1506, retro_nleu_181, retro_nleu_2056, retro_nleu_2337, retro_nleu_2988, retro_nleu_574, retro_nleu_8,
Oryctolagus cuniculus	ENSOCUG00000013915	6 retrocopies	retro_ocun_1027, retro_ocun_1196, retro_ocun_1270, retro_ocun_1919, retro_ocun_251, retro_ocun_482,
Otolemur garnettii	ENSOGAG00000012445	7 retrocopies	retro_ogar_1050, retro_ogar_1645, retro_ogar_1695, retro_ogar_2250, retro_ogar_277, retro_ogar_3145, retro_ogar_539,
Ochotona princeps	ENSOPRG00000001957	10 retrocopies	retro_opri_1079, retro_opri_1216, retro_opri_137, retro_opri_14, retro_opri_178, retro_opri_202, retro_opri_224, retro_opri_481, retro_opri_639, retro_opri_684,
Rattus norvegicus	ENSRNOG00000004107	10 retrocopies	retro_rnor_1195, retro_rnor_1539, retro_rnor_1622, retro_rnor_2445, retro_rnor_2483, retro_rnor_2688, retro_rnor_2981, retro_rnor_347, retro_rnor_498, retro_rnor_941,