RetrogeneDB ID: retro_mmus_762

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 11:16635111..16636066(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000048149
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Ublcp1
• Ensembl ID: ENSMUSG00000041231
• Aliases: Ublcp1, 4930527B16Rik, 8430435I17Rik, BC002236
• Description: ubiquitin-like domain containing CTD phosphatase 1 [Source:MGI Symbol;Acc:MGI:1933105]

Sequence

>retro_mmus_762
ATGGCACTCCCCATCATAGTGAAATGGGGTGGGCAGGAGTACTCAGTGACCACGCTCTCAGAAGATGATACTGTGCTGGA
TCTTAAACAGTTCCTCAAGACCCTTACGGGAGTGCTCCCAGAGCGCCAGAAGTTACTAGGGCTCAAAGTTAAAGGCAAAC
CTGCAGAAAATGATGTTAAGCTTGGAGCTCTCAAACTGAAACCAAATACTAAAATCATGATGATGGGAACTCGAGAGGAG
AGCTTGGAAGATGTCTTATGTCCTCCTCCTGACAATGATGATGTCATCAATGATTTTGACATTGAAGATGAAGTAGTTGA
AGTAGAAAATAGGGAGGAAAACCTCCTGAAGGTCTCTCGCAGAGTCAAGGAGTACAAGGTGGAGGTGCTGAACCCTCCCC
GGGAGGGCAAGAAGCTCCTGGTGCTGGATGGTGACTATACACTGTTTGATCATAGGTCTTGTGCAGAGACTGGGGTAGAG
TTAATGAGACCATTATCTTCATGAATTTCTAACATCTGCATATGAAGATTATGACATTGTTATTTGGTCTGCAACAAATA
TGAAGTGGATTGAAGCTAAAATGCAAGAGCTGGGCGTGAGCACAAATGCCAACTATAAGATTACCTTCATGCTGGACAGT
GCGGCCATGATCACTGTGCACACGCCCCGGAGAGGGCTCATTGACGTGAAGCCTCTTGGTGTCATTTGGGGAAAGTTTTC
TGAATTCTACAGCAAAAAGAACACCATTATGTTTGATGATATAGGAAGAAATTTTCTAATGAATCCACAAAATGGACTGA
AGATAAGGCCTTTCATGAAAGCTCATCTAAACCGTGATAAAGACAAGGAACTGGTGAAGCTCACTCAGTACCTCAAGGAG
ATCGCTAAGCTTGATGACTTCTTGGAGCTGAATCACAAGTACTGGGAGAGGTGTCTATCAAAGAAGCAAGGACAG

Alignment

ORF - retro_mmus_762 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.75 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MALPIIVKWGGQEYSVTTLSEDDTVLDLKQFLKTLTGVLPERQKLLGLKVKGKPAENDVKLGALKLKPNT
          MALPIIVKWGGQEYSVTTLSEDDTVLDLKQFLKTLTGVLPERQKLLGLKVKGKPAENDVKLGALKLKPNT
Retrocopy MALPIIVKWGGQEYSVTTLSEDDTVLDLKQFLKTLTGVLPERQKLLGLKVKGKPAENDVKLGALKLKPNT

Parental  KIMMMGTREESLEDVLCPPPDNDDVINDFDIEDEVVEVENREENLLKVSRRVKEYKVEVLNPPREGKKLL
          KIMMMGTREESLEDVLCPPPDNDDVINDFDIEDEVVEVENREENLLKVSRRVKEYKVEVLNPPREGKKLL
Retrocopy KIMMMGTREESLEDVLCPPPDNDDVINDFDIEDEVVEVENREENLLKVSRRVKEYKVEVLNPPREGKKLL

Parental  VLDVDYTLFDHRSCAETGVELMRP-YLHEFLTSAYEDYDIVIWSATNMKWIEAKMKELGVSTNANYKITF
          VLD.DYTLFDHRSCAETGVELMRP.YLHEFLTSAYEDYDIVIWSATNMKWIEAKM.ELGVSTNANYKITF
Retrocopy VLDGDYTLFDHRSCAETGVELMRP>YLHEFLTSAYEDYDIVIWSATNMKWIEAKMQELGVSTNANYKITF

Parental  MLDSAAMITVHTPRRGLIDVKPLGVIWGKFSEFYSKKNTIMFDDIGRNFLMNPQNGLKIRPFMKAHLNRD
          MLDSAAMITVHTPRRGLIDVKPLGVIWGKFSEFYSKKNTIMFDDIGRNFLMNPQNGLKIRPFMKAHLNRD
Retrocopy MLDSAAMITVHTPRRGLIDVKPLGVIWGKFSEFYSKKNTIMFDDIGRNFLMNPQNGLKIRPFMKAHLNRD

Parental  KDKELVKLTQYLKEIAKLDDFLELNHKYWERYLSKKQGQ
          KDKELVKLTQYLKEIAKLDDFLELNHKYWER.LSKKQGQ
Retrocopy KDKELVKLTQYLKEIAKLDDFLELNHKYWERCLSKKQGQ

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	0.35 RPM	22.59 RPM
SRP007412_cerebellum	2.00 RPM	26.53 RPM
SRP007412_heart	0.16 RPM	14.04 RPM
SRP007412_kidney	1.10 RPM	20.37 RPM
SRP007412_liver	0.63 RPM	13.44 RPM
SRP007412_testis	1.14 RPM	8.51 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_762 was not detected

EST

No EST(s) were mapped for retro_mmus_762 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_11207	150 libraries	159 libraries	640 libraries	101 libraries	22 libraries

The graphical summary, for retro_mmus_762 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_762 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_762 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007691	1 retrocopy	retro_chof_51,
Echinops telfairi	ENSETEG00000000170	1 retrocopy	retro_etel_1142,
Microcebus murinus	ENSMICG00000010060	2 retrocopies	retro_mmur_1083, retro_mmur_1319,
Myotis lucifugus	ENSMLUG00000006359	1 retrocopy	retro_mluc_1367,
Monodelphis domestica	ENSMODG00000008063	2 retrocopies	retro_mdom_1251, retro_mdom_1351,
Mustela putorius furo	ENSMPUG00000013396	1 retrocopy	retro_mputfur_1098,
Mus musculus	ENSMUSG00000041231	1 retrocopy	retro_mmus_762 ,
Oryctolagus cuniculus	ENSOCUG00000002224	1 retrocopy	retro_ocun_1036,
Tupaia belangeri	ENSTBEG00000008983	1 retrocopy	retro_tbel_41,
Tursiops truncatus	ENSTTRG00000005876	1 retrocopy	retro_ttru_761,