RetrogeneDB ID: retro_mmus_1766

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 18:37652435..37652907(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Uxt
• Ensembl ID: ENSMUSG00000001134
• Aliases: Uxt, 0910002B17Rik
• Description: ubiquitously expressed transcript [Source:MGI Symbol;Acc:MGI:1277988]

Sequence

>retro_mmus_1766
ATGGCGACGCCCCCGATACGGCGGGCCTTGGATACGGTGGGGGAGAAAGTGCTGCGGTACGAGACCTTTATCAGTGACGT
ACTGCAGCGAGACTTGCAAAAGGTGCTGGATCATTGAGACAAGGTATATGAGCAGCTGTCCGTATATCTTCAACTAAGAA
ATGTCATTGAGCGACTCCAGGAAACTAATCACTCGGAGTTATATATGCAGGTGGATTTGGGCTGTAACTTCTTCGTTGAC
ACAGTGGTCCCAGATACTTCACGCATCTATGTGGCCCTGGGATATGGTTTTTTTCCTGGAACTGACACTGGCTGAAGCAC
TCAAGTTCATTGACCGAAAGAGTTCTCTCCTCACAGAGCTCAGCGACAGCCTCACCAAGGACTCCATGAATATCAAGGCC
CATATCCACATGATGCTAGAGGGACTTAGAGAACTATAAGGCCTGCAGAATTTCCCAGAGCCATCTCCCCAT

Alignment

ORF - retro_mmus_1766 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.47 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MATPPKRRALDTVGEKVLRYETFISDVLQRDLQKVLDHRDKVYEQLSVYLQLRNVIERLQETNHSELYMQ
          MATPP.RRALDTVGEKVLRYETFISDVLQRDLQKVLDH.DKVYEQLSVYLQLRNVIERLQETNHSELYMQ
Retrocopy MATPPIRRALDTVGEKVLRYETFISDVLQRDLQKVLDH*DKVYEQLSVYLQLRNVIERLQETNHSELYMQ

Parental  VDLGCNFFVDTVVPDTSRIYVALGYGFF-LELTLAEALKFIDRKSSLLTELSDSLTKDSMNIKAHIHMML
          VDLGCNFFVDTVVPDTSRIYVALGYGFF.LELTLAEALKFIDRKSSLLTELSDSLTKDSMNIKAHIHMML
Retrocopy VDLGCNFFVDTVVPDTSRIYVALGYGFF>LELTLAEALKFIDRKSSLLTELSDSLTKDSMNIKAHIHMML

Parental  EGLRELQGLQNFPEPSPH
          EGLREL.GLQNFPEPSPH
Retrocopy EGLREL*GLQNFPEPSPH

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	2.27 RPM
SRP007412_cerebellum	0.04 RPM	1.82 RPM
SRP007412_heart	0.12 RPM	6.23 RPM
SRP007412_kidney	0.10 RPM	6.80 RPM
SRP007412_liver	0.05 RPM	4.86 RPM
SRP007412_testis	0.09 RPM	1.42 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_1766 was not detected

EST

No EST(s) were mapped for retro_mmus_1766 retrocopy.

TSS

No TSS is located nearby retro_mmus_1766 retrocopy 5' end.

Lab

retro_mmus_1766 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1766 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000009154	1 retrocopy	retro_cpor_1302,
Dipodomys ordii	ENSDORG00000001025	1 retrocopy	retro_dord_627,
Erinaceus europaeus	ENSEEUG00000006151	1 retrocopy	retro_eeur_543,
Macropus eugenii	ENSMEUG00000003352	1 retrocopy	retro_meug_59,
Microcebus murinus	ENSMICG00000016263	1 retrocopy	retro_mmur_1156,
Mustela putorius furo	ENSMPUG00000013405	1 retrocopy	retro_mputfur_999,
Mus musculus	ENSMUSG00000001134	3 retrocopies	retro_mmus_1424, retro_mmus_1766 , retro_mmus_715,
Rattus norvegicus	ENSRNOG00000009893	5 retrocopies	retro_rnor_521, retro_rnor_522, retro_rnor_683, retro_rnor_692, retro_rnor_882,
Tarsius syrichta	ENSTSYG00000012719	2 retrocopies	retro_tsyr_237, retro_tsyr_778,