RetrogeneDB ID: retro_mmus_1834

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 19:43280797..43281694(+)
• Located in intron of: ENSMUSG00000074852

Retrocopy information

• Ensembl ID: ENSMUSG00000047509
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Lztfl1
• Ensembl ID: ENSMUSG00000025245
• Aliases: Lztfl1, 5530402H04Rik, 6130400H19Rik, AI414725, AW048545
• Description: leucine zipper transcription factor-like 1 [Source:MGI Symbol;Acc:MGI:1934860]

Sequence

>retro_mmus_1834
ATGGCAGAGTTGGGCCTAAATGAGCACCATCAAAATGAGGTCATTAATTACATGCATTTTGCTCGTTCAAAAAGAGGCTT
GAGACTTAAAACGGTAGATTCTTGCTTTCAGGACCTCAAAGACAGCAGGCTGGTGGAGGAGACTTTCACCATTGATGAGG
TTTCAGAAGTCCTAAATGGGCTGCAGGCTGTGGTACACAGTGAGGTGGAGTCTGAGCTCATCAATACAGCTTACACCAAT
GTCCTGCTCCTACGGCAGCTGTTCTCCCAAGCTGAGAAGTGGTATCTAAAGCTACAGACAGACATCTCTGAACTTGAAAA
CAGAGAATTATTAGAACAAGTTGCTGAATTTGAAAAGGCAGAATTTGTATCTTCAAGTAAAAAGCCCATCATAGATATCA
CAAAGCCTAAGCTTGTTCCGATTAATGAAGGTGGAACTACAGAGCTCCTAAACAAGGAAATTTTAAGACTTCAACAAGAG
AATGAAAAACTAAAGTCAAGGCTGAAGACCATTGAAATACAGGCTGTAAATGCTCTGGATGAGAAGTCAAAATTGGAAGG
AGTACTTCAAGATTTACAGCTCAATCAAGAAAACCAACAGGATTTTCTAAAGGCCCAAGACTTGGATGACTTGGAAAATA
CAGTTGCAACTCTTAGGAGTGAATTTCAGAAGACACTTAATGACAAGACAGAAAGCCAAAAATCTTTGGAGGAGAACCTA
GCAGCAGCCAAACATGACCTCCTCAGAGTACAGGAGCAGCTGAGCATGGCTGAAAAGGAGTTAGAGAAGAAATTTCAACA
AACAGCAGCTTATCGAAACATGAAAGAGATTCTCACCAAAAAGAATGATCAAATCAAAGACCTATGGAAAAGACTGGCAA
AATATGAATCTGAAGAT

Alignment

ORF - retro_mmus_1834 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.99 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAELGLNEHHQNEVINYMRFARSKRGLRLKTVDSCFQDLKDSRLVEETFTIDEVSEVLNGLQAVVHSEVE
          MAELGLNEHHQNEVINYM.FARSKRGLRLKTVDSCFQDLKDSRLVEETFTIDEVSEVLNGLQAVVHSEVE
Retrocopy MAELGLNEHHQNEVINYMHFARSKRGLRLKTVDSCFQDLKDSRLVEETFTIDEVSEVLNGLQAVVHSEVE

Parental  SELINTAYTNVLLLRQLFSQAEKWYLKLQTDISELENRELLEQVAEFEKAEFVSSSKKPIIDITKPKLVP
          SELINTAYTNVLLLRQLFSQAEKWYLKLQTDISELENRELLEQVAEFEKAEFVSSSKKPIIDITKPKLVP
Retrocopy SELINTAYTNVLLLRQLFSQAEKWYLKLQTDISELENRELLEQVAEFEKAEFVSSSKKPIIDITKPKLVP

Parental  INEGGTTELLNKEILRLQQENEKLKSRLKTIEIQAVNALDEKSKLERVLQDLQLDQENQQDLLKAQDLDD
          INEGGTTELLNKEILRLQQENEKLKSRLKTIEIQAVNALDEKSKLE.VLQDLQL.QENQQD.LKAQDLDD
Retrocopy INEGGTTELLNKEILRLQQENEKLKSRLKTIEIQAVNALDEKSKLEGVLQDLQLNQENQQDFLKAQDLDD

Parental  LENTVATLRSEFQKTLNDKTENQKSLEENLAAAKHDLLRVQEQLSMAEKELEKKFQQTAAYRNMKEILTK
          LENTVATLRSEFQKTLNDKTE.QKSLEENLAAAKHDLLRVQEQLSMAEKELEKKFQQTAAYRNMKEILTK
Retrocopy LENTVATLRSEFQKTLNDKTESQKSLEENLAAAKHDLLRVQEQLSMAEKELEKKFQQTAAYRNMKEILTK

Parental  KNDQIKDLRKRLAKYESED
          KNDQIKDL.KRLAKYESED
Retrocopy KNDQIKDLWKRLAKYESED

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	0.05 RPM	36.42 RPM
SRP007412_cerebellum	0.00 RPM	20.49 RPM
SRP007412_heart	0.03 RPM	9.65 RPM
SRP007412_kidney	0.06 RPM	14.23 RPM
SRP007412_liver	0.00 RPM	5.05 RPM
SRP007412_testis	0.32 RPM	38.10 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1834 was not detected

EST

No EST(s) were mapped for retro_mmus_1834 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_65044	225 libraries	253 libraries	526 libraries	51 libraries	17 libraries

The graphical summary, for retro_mmus_1834 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_1834 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1834 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003899	1 retrocopy	retro_chof_1935,
Echinops telfairi	ENSETEG00000013761	1 retrocopy	retro_etel_1726,
Loxodonta africana	ENSLAFG00000010237	1 retrocopy	retro_lafr_155,
Mus musculus	ENSMUSG00000025245	3 retrocopies	retro_mmus_1834 , retro_mmus_3266, retro_mmus_3276,
Procavia capensis	ENSPCAG00000009783	1 retrocopy	retro_pcap_313,