RetrogeneDB ID: retro_mdom_464

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:682720573..682720786(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS21
• Ensembl ID: ENSMODG00000016769
• Aliases: None
• Description: ribosomal protein S21 [Source:HGNC Symbol;Acc:10409]

Sequence

>retro_mdom_464
GTGCCATGGAAGTGCTCTGCGAGCCACAGGATCAGCGGAGCCAAGGACCATGCATCCATCCAGATGAACATGGCCGAGGT
TGATAAGGTCACAGGCAGGTTCAATGGCCAATTTAAAACATATGTAATTTGTGGAGCAATTCGCAGAATGGGAGAATCTG
ATGACTCTATTCTCCAGCTGGCAAAAAATAATGGTATTGTCTCAAAGAACTTC

Alignment

ORF - retro_mdom_464 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.14 %
• Parental protein coverage: 65.74 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VPRKCSASNRIIGAKDHASIQMNVAEVDKVTGRFNGQFKTYAICGAIRRMGESDDSILRLAKNDGIVSKN
          VP.KCSAS.RI.GAKDHASIQMN.AEVDKVTGRFNGQFKTY.ICGAIRRMGESDDSIL.LAKN.GIVSKN
Retrocopy VPWKCSASHRISGAKDHASIQMNMAEVDKVTGRFNGQFKTYVICGAIRRMGESDDSILQLAKNNGIVSKN

Parental  F
          F
Retrocopy F

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	350.08 RPM
SRP007412_cerebellum	0.00 RPM	372.48 RPM
SRP007412_heart	0.00 RPM	714.28 RPM
SRP007412_kidney	0.00 RPM	1154.86 RPM
SRP007412_liver	0.00 RPM	1063.87 RPM
SRP007412_testis	0.00 RPM	159.31 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_464 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_464 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 77 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017399	2 retrocopies	retro_amel_1783, retro_amel_87,
Bos taurus	ENSBTAG00000020795	2 retrocopies	retro_btau_174, retro_btau_1780,
Canis familiaris	ENSCAFG00000012676	4 retrocopies	retro_cfam_1055, retro_cfam_1687, retro_cfam_1896, retro_cfam_28,
Callithrix jacchus	ENSCJAG00000014195	5 retrocopies	retro_cjac_2266, retro_cjac_2572, retro_cjac_629, retro_cjac_82, retro_cjac_884,
Cavia porcellus	ENSCPOG00000001965	4 retrocopies	retro_cpor_1156, retro_cpor_1268, retro_cpor_262, retro_cpor_584,
Homo sapiens	ENSG00000171858	6 retrocopies	retro_hsap_1179, retro_hsap_1883, retro_hsap_2300, retro_hsap_2949, retro_hsap_3026, retro_hsap_4303,
Gorilla gorilla	ENSGGOG00000023745	7 retrocopies	retro_ggor_131, retro_ggor_1380, retro_ggor_1647, retro_ggor_2043, retro_ggor_2089, retro_ggor_2875, retro_ggor_917,
Latimeria chalumnae	ENSLACG00000012753	1 retrocopy	retro_lcha_124,
Myotis lucifugus	ENSMLUG00000000346	3 retrocopies	retro_mluc_1009, retro_mluc_2136, retro_mluc_2282,
Monodelphis domestica	ENSMODG00000016769	1 retrocopy	retro_mdom_464 ,
Mus musculus	ENSMUSG00000039001	11 retrocopies	retro_mmus_1100, retro_mmus_1324, retro_mmus_1482, retro_mmus_1510, retro_mmus_1688, retro_mmus_1837, retro_mmus_2039, retro_mmus_2071, retro_mmus_2243, retro_mmus_576, retro_mmus_992,
Ornithorhynchus anatinus	ENSOANG00000003361	2 retrocopies	retro_oana_102, retro_oana_107,
Otolemur garnettii	ENSOGAG00000016673	12 retrocopies	retro_ogar_1013, retro_ogar_1339, retro_ogar_1742, retro_ogar_2111, retro_ogar_2176, retro_ogar_2532, retro_ogar_2703, retro_ogar_2921, retro_ogar_3119, retro_ogar_3214, retro_ogar_3256, retro_ogar_719,
Pongo abelii	ENSPPYG00000011205	8 retrocopies	retro_pabe_1562, retro_pabe_157, retro_pabe_2446, retro_pabe_2505, retro_pabe_3503, retro_pabe_365, retro_pabe_710, retro_pabe_986,
Pan troglodytes	ENSPTRG00000013708	1 retrocopy	retro_ptro_42,
Rattus norvegicus	ENSRNOG00000006325	2 retrocopies	retro_rnor_128, retro_rnor_172,
Sus scrofa	ENSSSCG00000021825	1 retrocopy	retro_sscr_7,
Ictidomys tridecemlineatus	ENSSTOG00000001029	5 retrocopies	retro_itri_1027, retro_itri_1487, retro_itri_637, retro_itri_82, retro_itri_849,