RetrogeneDB ID: retro_mmus_1899

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:30159395..30160363(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000085401
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Slc39a1
• Ensembl ID: ENSMUSG00000052310
• Aliases: Slc39a1, Zip1, Zirtl
• Description: solute carrier family 39 (zinc transporter), member 1 [Source:MGI Symbol;Acc:MGI:1353474]

Sequence

>retro_mmus_1899
ATGGGGTCCTGGGGGAACCAGAGCTCCTGGTGTGGCGCCCAGAAGCAGTCGCATTGGAGCCCTCGGTGCCAGTAGGGCTG
GAGGGGAAACTGGGGGCCCTGGTGCTGCTGCTGCTGACACTCATCGGCAGCCTGGTACCTGTCTGTGTGCTTCGAAGGTC
AGGTGCTAACCATGAAGCTTCAGCCTCGGGCCAGAAAGCCCTGAGCCTCGTCAGCTGCTTCGCAGGAGGAGTCTTTTTGG
CTACATGTCTTCTGGACCTGCTGCCTGACTACCTGGCTGCCATAGATGAGGCCTTGGAGGCCCTGCATGTGACGCTTCAG
TTCCCCTTGCAAGAATTCATCTTGGCCATGGGTTTCTTCCTGGTCCTGGTGATGGAGCAAATCACGCTGGCTTACAAGGA
ACAGTCCAGTCCACCCCATTCGAAAGAGACAAGGGCTCTACTGGGCACAGTGAATGGTGGGCCTCAGCATTGGCATGATG
GACCAGGGATCCCCCAGGCCGGCGGAACTCCAGCAGCTCCCTCAGCCCTGCGTGCTTGTGTCCCGGTCTTCTCCTTAGCC
TTGCACTCAGTATTTGAGGGCCTGGCTGTAGGGTTGCAGCGAGACAGGGCTCGGGCAATGGAGCTGTGCCTAGCTCTGCT
GCTTCACAGGGGCATTCTGGCAGTCAGCCTGTCCCTGCGGCTGCTACAGAGCCACCTACGTGTGCAGGTGGTGGCTGGCT
GCGGGATCCTCTTCTCATGTATGACACCTCTGGGCATCGGGTTGGGTGCAGCTCTGGCAGAGTCAGCTGGGCCTCTGCAC
CAGCTGGCCCAATCTGTTCTAGAGGGCATGGCAGCTGGCACCTTCCTCTATATCACCTTCCTGGAAATTCTACCCCAGGA
ACTGGCCACTTCTGAGCAGAGGATCCTCAAGGTCATTCTGCTCCTAGCAGGCTTTGCCCTGCTCACTGGCCTTCTCTTTG
TCCAAATC

Alignment

ORF - retro_mmus_1899 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.62 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGPWG-EPELLVWRPEAVASEPSVPVGLEVKLGALVLLLLLTLICSLVPVCVLRRSGANHEASASGQKAL
          MG.WG.EPELLVWRPEAVA.EPSVPVGLE.KLGALVLLLL.TLI.SLVPVCVLRRSGANHEASASGQKAL
Retrocopy MGSWG<EPELLVWRPEAVALEPSVPVGLEGKLGALVLLLL-TLIGSLVPVCVLRRSGANHEASASGQKAL

Parental  SLVSCFAGGVFLATCLLDLLPDYLAAIDEALEALHVTLQFPLQEFILAMGFFLVLVMEQITLAYKEQTSP
          SLVSCFAGGVFLATCLLDLLPDYLAAIDEALEALHVTLQFPLQEFILAMGFFLVLVMEQITLAYKEQ.SP
Retrocopy SLVSCFAGGVFLATCLLDLLPDYLAAIDEALEALHVTLQFPLQEFILAMGFFLVLVMEQITLAYKEQSSP

Parental  PHPEETRALLGTVNGGPQHWHDGPGIPQAGGTPAAPSALRACVLVFSLALHSVFEGLAVGLQRDRARAME
          PH..ETRALLGTVNGGPQHWHDGPGIPQAGGTPAAPSALRACV.VFSLALHSVFEGLAVGLQRDRARAME
Retrocopy PHSKETRALLGTVNGGPQHWHDGPGIPQAGGTPAAPSALRACVPVFSLALHSVFEGLAVGLQRDRARAME

Parental  LCLALLLHKGILAVSLSLRLLQSHLRVQVVAGCGILFSCMTPLGIGLGAALAESAGPLHQLAQSVLEGMA
          LCLALLLH.GILAVSLSLRLLQSHLRVQVVAGCGILFSCMTPLGIGLGAALAESAGPLHQLAQSVLEGMA
Retrocopy LCLALLLHRGILAVSLSLRLLQSHLRVQVVAGCGILFSCMTPLGIGLGAALAESAGPLHQLAQSVLEGMA

Parental  AGTFLYITFLEILPQELATSEQRILKVILLLAGFALLTGLLFVQI
          AGTFLYITFLEILPQELATSEQRILKVILLLAGFALLTGLLFVQI
Retrocopy AGTFLYITFLEILPQELATSEQRILKVILLLAGFALLTGLLFVQI

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	19.04 RPM
SRP007412_cerebellum	0.00 RPM	18.15 RPM
SRP007412_heart	0.03 RPM	37.95 RPM
SRP007412_kidney	0.00 RPM	38.96 RPM
SRP007412_liver	0.03 RPM	42.36 RPM
SRP007412_testis	0.00 RPM	14.59 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1899 was not detected

EST

No EST(s) were mapped for retro_mmus_1899 retrocopy.

TSS

No TSS is located nearby retro_mmus_1899 retrocopy 5' end.

Lab

retro_mmus_1899 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1899 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
Callithrix jacchus	ENSCJAG00000010006	1 retrocopy	retro_cjac_1476,
Macropus eugenii	ENSMEUG00000006754	1 retrocopy	retro_meug_1551,
Microcebus murinus	ENSMICG00000010310	1 retrocopy	retro_mmur_162,
Myotis lucifugus	ENSMLUG00000013282	1 retrocopy	retro_mluc_2366,
Macaca mulatta	ENSMMUG00000005007	1 retrocopy	retro_mmul_28,
Mus musculus	ENSMUSG00000052310	1 retrocopy	retro_mmus_1899 ,
Oryctolagus cuniculus	ENSOCUG00000003045	1 retrocopy	retro_ocun_1792,