RetrogeneDB ID: retro_mmus_495

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:143093844..143094606(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: Rpl4
• Ensembl ID: ENSMUSG00000032399
• Aliases: Rpl4, 2010004J23Rik
• Description: ribosomal protein L4 [Source:MGI Symbol;Acc:MGI:1915141]

Sequence

>retro_mmus_495
ATGGCTTGTGCCCGTCCCCTCATATCGGTGTACTCCGAAAAGGAAGAGTCATCTGGCAAGAATGTCACTTTGCCAGCTGT
GTTCAAAGCTCCCATTCGACCAGATATTGTGAACTTTGTTCACACCAACTTGAGAAAAAACAACAGACAACCCTATGCTG
TCAGTGAATTGGCAGGTCATCAGACCAGTGCTGAGTCTTGGGGTACTGGCAGAGCTGTGGCTCGAATTCCAAGAGTTCGA
GGTGGTGGGACCCACCGATCTGGCCAGGGTGCCTTTGGAAATATGTGTCGTGGGGGACGCATGTTTGCATCAACCAAAAC
TTGGCGTCGTTGGCACCGCAGAGTGAATACAACCCAAAAACGATATGCCATCTCTTCTGCCCTGGCTGCCTCGGCCTTAC
CAGCTTTGGTGATGTCTAAAGGTCATCGTATTGAGGAGATTCCTGAGCTGCCGCTGGTGGTTGAAGATAAGGTTGAAGGT
TACAAGAAGACCAAGGAGGCTGTTCAGCTGCTTAAGAAGCTTAAAGCTTGGAATGACACCAAAAAGGTCTATGCCTCTCA
GAGAATGAGAGCTGGCAAGGGCAAAATGAGAAACGGATGGCGGATCCAGCGCAGGGTGCCCTGCATCATCTATAACGAAG
ATAATGGTATCATCAAGGCCTTCCGGAACATCCCTGCTATTACTCTGCTTAATGTAAGCAAGCTGAACATTTTGAAACTT
GCTCCTGGTGGGCATGTGGGCCGTTTCTGCATCTGGACAGAG

Alignment

ORF - retro_mmus_495 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.46 %
• Parental protein coverage: 60.62 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MACARPLISVYSEKGESSGKNVTLPAVFKAPIRPDIVNFVHTNLRKNNRQPYAVSELAGHQTSAESWGTG
          MACARPLISVYSEK.ESSGKNVTLPAVFKAPIRPDIVNFVHTNLRKNNRQPYAVSELAGHQTSAESWGTG
Retrocopy MACARPLISVYSEKEESSGKNVTLPAVFKAPIRPDIVNFVHTNLRKNNRQPYAVSELAGHQTSAESWGTG

Parental  RAVARIPRVRGGGTHRSGQGAFGNMCRGGRMFAPTKTWRRWHRRVNTTQKRYAICSALAASALPALVMSK
          RAVARIPRVRGGGTHRSGQGAFGNMCRGGRMFA.TKTWRRWHRRVNTTQKRYAI.SALAASALPALVMSK
Retrocopy RAVARIPRVRGGGTHRSGQGAFGNMCRGGRMFASTKTWRRWHRRVNTTQKRYAISSALAASALPALVMSK

Parental  GHRIEEVPELPLVVEDKVEGYKKTKEAVQLLKKLKAWNDIKKVYASQRMRAGKGKMRNRRRIQRRGPCII
          GHRIEE.PELPLVVEDKVEGYKKTKEAVQLLKKLKAWND.KKVYASQRMRAGKGKMRN..RIQRR.PCII
Retrocopy GHRIEEIPELPLVVEDKVEGYKKTKEAVQLLKKLKAWNDTKKVYASQRMRAGKGKMRNGWRIQRRVPCII

Parental  YNEDNGIIKAFRNIPGITLLNVSKLNILKLAPGGHVGRFCIWTE
          YNEDNGIIKAFRNIP.ITLLNVSKLNILKLAPGGHVGRFCIWTE
Retrocopy YNEDNGIIKAFRNIPAITLLNVSKLNILKLAPGGHVGRFCIWTE

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	0.30 RPM	285.80 RPM
SRP007412_cerebellum	0.30 RPM	190.23 RPM
SRP007412_heart	0.31 RPM	262.33 RPM
SRP007412_kidney	0.44 RPM	289.94 RPM
SRP007412_liver	0.33 RPM	315.41 RPM
SRP007412_testis	0.23 RPM	138.45 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_495 was not detected

EST

No EST(s) were mapped for retro_mmus_495 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_69999	23 libraries	6 libraries	149 libraries	205 libraries	689 libraries

The graphical summary, for retro_mmus_495 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_495 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_495 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 42 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005211	2 retrocopies	retro_btau_101, retro_btau_610,
Canis familiaris	ENSCAFG00000017309	1 retrocopy	retro_cfam_72,
Callithrix jacchus	ENSCJAG00000007491	2 retrocopies	retro_cjac_251, retro_cjac_945,
Cavia porcellus	ENSCPOG00000003055	1 retrocopy	retro_cpor_370,
Echinops telfairi	ENSETEG00000000337	3 retrocopies	retro_etel_1876, retro_etel_2195, retro_etel_226,
Felis catus	ENSFCAG00000012293	4 retrocopies	retro_fcat_1136, retro_fcat_189, retro_fcat_505, retro_fcat_567,
Gorilla gorilla	ENSGGOG00000003695	4 retrocopies	retro_ggor_1023, retro_ggor_2008, retro_ggor_2831, retro_ggor_304,
Myotis lucifugus	ENSMLUG00000011809	2 retrocopies	retro_mluc_121, retro_mluc_198,
Macaca mulatta	ENSMMUG00000016844	2 retrocopies	retro_mmul_2160, retro_mmul_649,
Monodelphis domestica	ENSMODG00000009657	2 retrocopies	retro_mdom_656, retro_mdom_944,
Mustela putorius furo	ENSMPUG00000000337	3 retrocopies	retro_mputfur_1205, retro_mputfur_411, retro_mputfur_570,
Mus musculus	ENSMUSG00000032399	2 retrocopies	retro_mmus_2863, retro_mmus_495 ,
Nomascus leucogenys	ENSNLEG00000012938	4 retrocopies	retro_nleu_1041, retro_nleu_1062, retro_nleu_2385, retro_nleu_887,
Oryctolagus cuniculus	ENSOCUG00000008794	3 retrocopies	retro_ocun_1134, retro_ocun_630, retro_ocun_631,
Ochotona princeps	ENSOPRG00000007792	1 retrocopy	retro_opri_735,
Pongo abelii	ENSPPYG00000006578	1 retrocopy	retro_pabe_152,
Rattus norvegicus	ENSRNOG00000009378	5 retrocopies	retro_rnor_1192, retro_rnor_1621, retro_rnor_2061, retro_rnor_2484, retro_rnor_949,