RetrogeneDB ID: retro_mmus_2038

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:60274946..60275375(-)
• Located in intron of: ENSMUSG00000060703

Retrocopy information

• Ensembl ID: ENSMUSG00000080198
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Rpl10a
• Ensembl ID: ENSMUSG00000037805
• Aliases: Rpl10a, CsA-19, Nedd6
• Description: ribosomal protein L10A [Source:MGI Symbol;Acc:MGI:1343877]

Sequence

>retro_mmus_2038
GATGAAGCCAAGGCTGTGGATATCCCCCACATGGACATCGAGGCGCTCAAGAAGCTTAACAAGAACAAGAAGTTGGTCAA
GAAGCTGGCCAAGAAGTACGATGCCTTTTTGGCCTCCGAGTCTCTGATTAAGCAGATCCCACGTATCCTGGGCCCAGGCC
TAAACAAGGCTGGCAAGTTCCCCTCCCTGCTGACACACAATGAAAACATGGTAGCCAAAGTGGATGAGGTGAAATCTACA
ATCAAGTTCCAGATGAAGAAGGTGCTCTGTCTGGCCGTCGCTGTCGGCCACGTGAAGATGATCGATGATGAGCTAGTCTA
CAACATTCATCTGGCTGTCAATTTCTTGGTGTCCTTGCTCAAGAAAAACTGGCAAAACGTGCGGGCTCTGTACATCAAGA
GCACCATGGGCAAGCCCCAGCGTCTGTAT

Alignment

ORF - retro_mmus_2038 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.91 %
• Parental protein coverage: 65.9 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DEAKAVDIPHMDIEALKKLNKNKKLVKKLAKKYDAFLASESLIKQIPRILGPGLNKAGKFPSLLTHNENM
          DEAKAVDIPHMDIEALKKLNK............DAFLASESLIKQIPRILGPGLNKAGKFPSLLTHNENM
Retrocopy DEAKAVDIPHMDIEALKKLNKXXXXXXXXXXXXDAFLASESLIKQIPRILGPGLNKAGKFPSLLTHNENM

Parental  VAKVDEVKSTIKFQMKKVLCLAVAVGHVKMTDDELVYNIHLAVNFLVSLLKKNWQNVRALYIKSTMGKPQ
          VAKVDEVKSTIKFQMKKVLCLAVAVGHVKM.DDELVYNIHLAVNFLVSLLKKNWQNVRALYIKSTMGKPQ
Retrocopy VAKVDEVKSTIKFQMKKVLCLAVAVGHVKMIDDELVYNIHLAVNFLVSLLKKNWQNVRALYIKSTMGKPQ

Parental  RLY
          RLY
Retrocopy RLY

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	0.02 RPM	27.90 RPM
SRP007412_cerebellum	0.00 RPM	18.45 RPM
SRP007412_heart	0.00 RPM	34.83 RPM
SRP007412_kidney	0.04 RPM	40.04 RPM
SRP007412_liver	0.14 RPM	39.90 RPM
SRP007412_testis	0.09 RPM	16.47 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2038 was not detected

EST

No EST(s) were mapped for retro_mmus_2038 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_87851	46 libraries	36 libraries	404 libraries	334 libraries	252 libraries

The graphical summary, for retro_mmus_2038 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_mmus_2038 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2038 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 47 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019494	4 retrocopies	retro_btau_138, retro_btau_1501, retro_btau_1634, retro_btau_87,
Dasypus novemcinctus	ENSDNOG00000012921	3 retrocopies	retro_dnov_157, retro_dnov_1917, retro_dnov_469,
Equus caballus	ENSECAG00000014090	2 retrocopies	retro_ecab_512, retro_ecab_517,
Macropus eugenii	ENSMEUG00000005760	6 retrocopies	retro_meug_1337, retro_meug_1578, retro_meug_2066, retro_meug_407, retro_meug_541, retro_meug_705,
Microcebus murinus	ENSMICG00000012458	3 retrocopies	retro_mmur_1381, retro_mmur_384, retro_mmur_93,
Monodelphis domestica	ENSMODG00000013766	2 retrocopies	retro_mdom_276, retro_mdom_499,
Mus musculus	ENSMUSG00000037805	8 retrocopies	retro_mmus_1110, retro_mmus_1304, retro_mmus_1422, retro_mmus_149, retro_mmus_1737, retro_mmus_2038 , retro_mmus_2652, retro_mmus_452,
Ornithorhynchus anatinus	ENSOANG00000014574	1 retrocopy	retro_oana_86,
Pongo abelii	ENSPPYG00000016529	10 retrocopies	retro_pabe_1208, retro_pabe_1597, retro_pabe_2614, retro_pabe_2759, retro_pabe_3302, retro_pabe_3315, retro_pabe_3377, retro_pabe_357, retro_pabe_451, retro_pabe_475,
Sarcophilus harrisii	ENSSHAG00000002047	1 retrocopy	retro_shar_438,
Sus scrofa	ENSSSCG00000001543	7 retrocopies	retro_sscr_1169, retro_sscr_1174, retro_sscr_120, retro_sscr_246, retro_sscr_379, retro_sscr_461, retro_sscr_465,