RetrogeneDB ID: retro_mmus_2192

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 3:99500549..99501379(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000080832
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: M6pr
• Ensembl ID: ENSMUSG00000007458
• Aliases: M6pr, CD-MPR, Mpr46
• Description: mannose-6-phosphate receptor, cation dependent [Source:MGI Symbol;Acc:MGI:96904]

Sequence

>retro_mmus_2192
ATGTTCCCCTTCTCTGGCTGCTGGAGGACTGAACTGTTATTGTTGCTACTCCTGGCTGTGGCTGTGAGAGAATCCTGGCA
GACAGAAGAAAAATCGTGTGACCTGGTAGGAGAGAAGGATAAGGAGTCAAAGAACAAGGTGGCTCTCCTGGAGAGGTTCC
GGCCACTGTTTAACAAAAGTTTTGAGAGTACTGTGGGCCAGGGCTCAGACACATACAGCTACATATTCAGAGTATGCCGG
GAAGCTAGCAACCACTCCTCTGGAGCAGGCCTGGTCCAGATCAACAAAAGCAATGACAAGGAGACAGTGGTTGGGAGAAC
CAACGAGACTCACATCTTGAATGGAAGTAATTGGATCATGCTGATAGATAAAGGGGGTGATGAATATGACAACCACTGTG
GCAAAGAGCAGCGCGTGCAGTGGTGATGATCTGCAATCGGCACACACTAGCGGCTAATTTTAACCCAGTGTCTGAGGAAC
GAGGCAAAGTCCAGGATTGCTTCTACCTCTTTGAGATGGATAGCAGTCTGGCCTGTTCACCAGAGGTCTCACACCTCAGT
GTGGGCTCGATCTTACTTGTCATATTTGCATCGTTGGTTGCTGTCTATATCATTGGGGGTTTCTTATACTAGCGATTGGT
AGTGGGGGCCAAGGGAATGGAGCAGTTTCCTCATCTGGCCTTCTGGCAGGATCTTGGCAACCTAGTAGCTGATGGTTGTG
ACTTTGTGTGCCGTTCCAAACCCCGCAATGTGCCTGCAGCATATCGTGGAGTGGGGGATGACCAGCTGGGGGAAGAGTAG
GAAGAAAGGGATGATCATCTGCTACCAATG

Alignment

ORF - retro_mmus_2192 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.42 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MFPFSGCWRTELLLLLLLAVAVRESWQIEEKSCDLVGEKDKESKNEVALLERLRPLFNKSFESTVGQGSD
          MFPFSGCWRTELLLLLLLAVAVRESWQ.EEKSCDLVGEKDKESKN.VALLER.RPLFNKSFESTVGQGSD
Retrocopy MFPFSGCWRTELLLLLLLAVAVRESWQTEEKSCDLVGEKDKESKNKVALLERFRPLFNKSFESTVGQGSD

Parental  TYSYIFRVCREASNHSSGAGLVQINKSNDKETVVGRINETHIFNGSNWIMLIYKGGDEYDNHCGKEQR-R
          TYSYIFRVCREASNHSSGAGLVQINKSNDKETVVGR.NETHI.NGSNWIMLI.KGGDEYDNHCGKEQR.R
Retrocopy TYSYIFRVCREASNHSSGAGLVQINKSNDKETVVGRTNETHILNGSNWIMLIDKGGDEYDNHCGKEQR<R

Parental  AVVMISCNRHTLAANFNPVSEERGKVQDCFYLFEMDSSLACSPEVSHLSVGSILLVIFASLVAVYIIGGF
          AVVMI.CNRHTLAANFNPVSEERGKVQDCFYLFEMDSSLACSPEVSHLSVGSILLVIFASLVAVYIIGGF
Retrocopy AVVMI-CNRHTLAANFNPVSEERGKVQDCFYLFEMDSSLACSPEVSHLSVGSILLVIFASLVAVYIIGGF

Parental  LYQRLVVGAKGMEQFPHLAFWQDLGNLVADGCDFVCRSKPRNVPAAYRGVGDDQLGEESEERDDHLLPM
          LY.RLVVGAKGMEQFPHLAFWQDLGNLVADGCDFVCRSKPRNVPAAYRGVGDDQLGEE.EERDDHLLPM
Retrocopy LY*RLVVGAKGMEQFPHLAFWQDLGNLVADGCDFVCRSKPRNVPAAYRGVGDDQLGEE*EERDDHLLPM

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	0.14 RPM	67.10 RPM
SRP007412_cerebellum	0.35 RPM	77.98 RPM
SRP007412_heart	0.09 RPM	42.87 RPM
SRP007412_kidney	0.50 RPM	148.95 RPM
SRP007412_liver	0.30 RPM	90.17 RPM
SRP007412_testis	0.14 RPM	30.92 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2192 was not detected

EST

No EST(s) were mapped for retro_mmus_2192 retrocopy.

TSS

No TSS is located nearby retro_mmus_2192 retrocopy 5' end.

Lab

retro_mmus_2192 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2192 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000003538	1 retrocopy	retro_dnov_2250,
Mus musculus	ENSMUSG00000007458	1 retrocopy	retro_mmus_2192 ,
Oryctolagus cuniculus	ENSOCUG00000017823	1 retrocopy	retro_ocun_1931,
Otolemur garnettii	ENSOGAG00000005610	1 retrocopy	retro_ogar_629,
Tarsius syrichta	ENSTSYG00000005689	2 retrocopies	retro_tsyr_1665, retro_tsyr_882,