RetrogeneDB ID: retro_mdom_1003

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:186285134..186285500(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL22
• Ensembl ID: ENSMODG00000006225
• Aliases: None
• Description: ribosomal protein L22 [Source:HGNC Symbol;Acc:10315]

Sequence

>retro_mdom_1003
AGAAGAAAAGTGATGAAGAGCAGCAAAACAAATAAGCAAGTCCTCCAATTTACTCTGGATTGCACATATCCGGTAGAAGA
TGGGATTATGGGTGCAGTTGATTTTAAGCAATTCTTGCAAGAACAAATAAAGTAAATGGAAAGACCAATAACCTCAGTGA
AGGTGGAGGGGTTATGGTTATTGAGAGATTCAAAAGTAAAATAACCAGGTATGAGACCCACTTATTTTCTAAAGTGTATT
TCAAGTACCTTAGAAGGAATTATTTTAAAAGAACAATTTATAAGATTGACTATGTAAATTGCCAATAACAAGGAAAGCTA
TGATTTACATTATTTCCAGATTATACAGGATGAAAAGGGAAAGGAT

Alignment

ORF - retro_mdom_1003 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.11 %
• Parental protein coverage: 94.53 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KKSVMKGGKKKKQVLKFTLDCTHPVEDGIMDAANFEQFLQERI-KVNGKAGNL--GGGVVTIERSKSKIT
          ...VMK..K..KQVL.FTLDCT.PVEDGIM.A..F.QFLQE.I.KVNGK..NL..GGGV..IER.KSKIT
Retrocopy RRKVMKSSKTNKQVLQFTLDCTYPVEDGIMGAVDFKQFLQEQI<KVNGKTNNLSEGGGVMVIERFKSKIT

Parental  VTSEVPFSKRYLKYLTKKYLK-KNNLRDWL-RVVANSKESYELRYFQINQDEEEEE
          ......FSK.Y.KYL...Y.K.KNNL.D.L....AN.KESY.L.YFQI.QDE....
Retrocopy RYETHLFSKVYFKYLRRNYFK<KNNL*D*L<M*IANNKESYDLHYFQIIQDEKGKD

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_1003 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1003 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 10 parental genes, and 57 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009864	7 retrocopies	retro_amel_1219, retro_amel_1247, retro_amel_1775, retro_amel_1793, retro_amel_369, retro_amel_830, retro_amel_870,
Bos taurus	ENSBTAG00000014423	4 retrocopies	retro_btau_1491, retro_btau_566, retro_btau_694, retro_btau_892,
Gorilla gorilla	ENSGGOG00000027739	10 retrocopies	retro_ggor_1111, retro_ggor_1652, retro_ggor_1655, retro_ggor_1708, retro_ggor_1757, retro_ggor_2268, retro_ggor_2567, retro_ggor_37, retro_ggor_531, retro_ggor_613,
Macropus eugenii	ENSMEUG00000008801	1 retrocopy	retro_meug_65,
Macaca mulatta	ENSMMUG00000018347	12 retrocopies	retro_mmul_1004, retro_mmul_1044, retro_mmul_1047, retro_mmul_1512, retro_mmul_2209, retro_mmul_2264, retro_mmul_2467, retro_mmul_2601, retro_mmul_271, retro_mmul_445, retro_mmul_469, retro_mmul_80,
Monodelphis domestica	ENSMODG00000006225	1 retrocopy	retro_mdom_1003 ,
Mustela putorius furo	ENSMPUG00000007087	6 retrocopies	retro_mputfur_1074, retro_mputfur_1277, retro_mputfur_134, retro_mputfur_1433, retro_mputfur_578, retro_mputfur_873,
Pongo abelii	ENSPPYG00000001951	11 retrocopies	retro_pabe_1196, retro_pabe_1213, retro_pabe_1435, retro_pabe_166, retro_pabe_248, retro_pabe_3114, retro_pabe_349, retro_pabe_3782, retro_pabe_3817, retro_pabe_590, retro_pabe_966,
Sarcophilus harrisii	ENSSHAG00000018731	1 retrocopy	retro_shar_597,
Sus scrofa	ENSSSCG00000003367	4 retrocopies	retro_sscr_257, retro_sscr_276, retro_sscr_497, retro_sscr_509,