RetrogeneDB ID: retro_mmus_177

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 9:64235238..64235940(+)
• Located in intron of: ENSMUSG00000004936

Retrocopy information

• Ensembl ID: ENSMUSG00000035337
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Uchl3
• Ensembl ID: ENSMUSG00000022111
• Aliases: None
• Description: ubiquitin carboxyl-terminal esterase L3 (ubiquitin thiolesterase) [Source:MGI Symbol;Acc:MGI:1355274]

Sequence

>retro_mmus_177
ATGGAGGGTCAACGCTGGCTGCCACTGGAGGCCAACCCTGAGGTCACCAACCAGTTTCTCAAGCAATTAGGCCTGCATCC
TAACTGGCAGTTTGTTGATGTGTACGGGATGGAGTCTGAACTTCTTAGCATCATACCAAGACCAGTGTGCGCAGTGTTAC
TCCTCTTCCCTATCACAGAAAAGTATGAAGTCTTCAGAACAGAAGAGGAAGAAAAGATAAAATCTCAAGGACAAGATGTG
ACATCATCAGTATATTTTATGAAACAAACCATCAGCAATGCCTGTGGAACGATTGGAACGATTGGACTAATCCATGCCAT
TGCAAACAACAAAGACAAGGTGCACTTTGAATCAGGGTCAACATTGAAAAAGTTCCTGGAGGAGTCTGTATCAATGAGCC
CTGAAGAGAGAGCCAAATACCTGGAGAACTATGACGCTATTCGAGTTACTCATGAAACCAGTGCACATGAAGGTCAGACT
GAGGCACCAAGTATAGATGAAAAAGTAGATCTTCATTTTATTGCGTTAGTACATGTAGATGGGCATCTCTATGAATTAGA
TGGATGGAAACCATTTCCAATTAACCATGGGAAAACTAGCGATGAGACGTTGTTAGAGGATGTCATAAAAGTTTGCAAGA
AGTTCATGGAACGTGACCCTGATGAGTTAAGATTTAATGCAATTGCTCTCTCGGCAGCATAG

Alignment

ORF - retro_mmus_177 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.28 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEGQRWLPLEANPEVTNQFLKQLGLHPNWQFVDVYGMEPELLSMVPRPVCAVLLLFPITEKYEVFRTEEE
          MEGQRWLPLEANPEVTNQFLKQLGLHPNWQFVDVYGME.ELLS..PRPVCAVLLLFPITEKYEVFRTEEE
Retrocopy MEGQRWLPLEANPEVTNQFLKQLGLHPNWQFVDVYGMESELLSIIPRPVCAVLLLFPITEKYEVFRTEEE

Parental  EKIKSQGQDVTSSVYFMKQTISNAC---GTIGLIHAIANNKDKMHFESGSTLKKFLEESVSMSPEERAKF
          EKIKSQGQDVTSSVYFMKQTISNAC...GTIGLIHAIANNKDK.HFESGSTLKKFLEESVSMSPEERAK.
Retrocopy EKIKSQGQDVTSSVYFMKQTISNACGTIGTIGLIHAIANNKDKVHFESGSTLKKFLEESVSMSPEERAKY

Parental  LENYDAIRVTHETSAHEGQTEAPSIDEKVDLHFIALVHVDGHLYELDGRKPFPINHGKTSDETLLEDAIE
          LENYDAIRVTHETSAHEGQTEAPSIDEKVDLHFIALVHVDGHLYELDG.KPFPINHGKTSDETLLED.I.
Retrocopy LENYDAIRVTHETSAHEGQTEAPSIDEKVDLHFIALVHVDGHLYELDGWKPFPINHGKTSDETLLEDVIK

Parental  VCKKFMERDPDELRFNAIALSAA
          VCKKFMERDPDELRFNAIALSAA
Retrocopy VCKKFMERDPDELRFNAIALSAA

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	0.28 RPM	14.23 RPM
SRP007412_cerebellum	0.26 RPM	10.68 RPM
SRP007412_heart	0.31 RPM	12.64 RPM
SRP007412_kidney	0.50 RPM	12.42 RPM
SRP007412_liver	0.46 RPM	7.86 RPM
SRP007412_testis	2.42 RPM	52.60 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_177 was not detected

EST

No EST(s) were mapped for retro_mmus_177 retrocopy.

TSS

No TSS is located nearby retro_mmus_177 retrocopy 5' end.

Lab

retro_mmus_177 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_177 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000012261	1 retrocopy	retro_cpor_1217,
Equus caballus	ENSECAG00000024190	1 retrocopy	retro_ecab_400,
Myotis lucifugus	ENSMLUG00000003442	1 retrocopy	retro_mluc_362,
Mus musculus	ENSMUSG00000022111	1 retrocopy	retro_mmus_177 ,
Oryctolagus cuniculus	ENSOCUG00000006789	1 retrocopy	retro_ocun_382,
Otolemur garnettii	ENSOGAG00000017114	1 retrocopy	retro_ogar_2285,
Rattus norvegicus	ENSRNOG00000009530	1 retrocopy	retro_rnor_2227,