RetrogeneDB ID: retro_mmus_18

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 18:43476954..43477746(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000043424
• Aliases: Eif3j2, ENSMUSG00000043424, Eif3j-2, Gm9781, eIF3 p35, eIF3j-B
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Eif3j1
• Ensembl ID: ENSMUSG00000027236
• Aliases: None
• Description: eukaryotic translation initiation factor 3, subunit J1 [Source:MGI Symbol;Acc:MGI:1925905]

Sequence

>retro_mmus_18
ATGGCGGCGGCGGCGGCGGCGGCGGCGGCAGCGGCGGCGGGGGACTCAGACTCTTGGGACGCGGACACGTTCTCTATGGA
GGACCCGGTGCGGAAGGTCGCGGGCGGCGGCACGGCCGGCGGGGACCGCTGGGAAGGCGAGGACGAGGACGAGGACGTGA
AGGATAACTGGGATGATGATGATGATGAAAATAAAGAGGAAGCAGAAGTCAAACCAGAAGTAAAAATTTCAGAGAAGAAA
AAAATAGCAGAAAAGATAAAAGAGAAAGAACGGCAGCAGAAGAAAAGGCAAGAAGAAATTAAAAAGAGGTTAGAAGAACC
TGAAGAATCTAAAGTACTAACACCTGAAGAGCAATTAGCAGATAAACTCCGGCTAAAGAAATTACAGGAAGAGTCAGACC
TTGAATTAGCAAAAGAAACTTTTGGTGTTAATAATACCGTTTATGGAATAGATGCTATGAACCCATCTTCAAGAGATGAC
TTCACAGAGTTTGGAAAGTTACTAAAAGATAAAATTACACAATATGAAAAATCACTATATTATGCCAGTTTTTTGGAAGC
CTTAGTTCGGGATGTCTGTATTTCATTGGAAATTGATGACTTGAAAAAGATTACCAACTCATTGACTGTGCTCTGCAGTG
AAAAACAGAAGCAAGAAAAGCAAAGCAAAGCCAAAAAGAAGAAGAAAGGCGTGGTTCCTGGAGGGGGATTAAAGGCCACC
ATGAAAGACGACCTGGCAGATTATGGTGGATATGAAGGAGGCTATGTACAAGACTATGAAGACTTCATGTGA

Alignment

ORF - retro_mmus_18 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100. %
• Parental protein coverage: 99.62 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AAAAAAAAAAGDSDSWDADTFSMEDPVRKVAGGGTAGGDRWEGEDEDEDVKDNWDDDDDENKEEAEVKPE
          AAAAAAAAAAGDSDSWDADTFSMEDPVRKVAGGGTAGGDRWEGEDEDEDVKDNWDDDDDENKEEAEVKPE
Retrocopy AAAAAAAAAAGDSDSWDADTFSMEDPVRKVAGGGTAGGDRWEGEDEDEDVKDNWDDDDDENKEEAEVKPE

Parental  VKISEKKKIAEKIKEKERQQKKRQEEIKKRLEEPEESKVLTPEEQLADKLRLKKLQEESDLELAKETFGV
          VKISEKKKIAEKIKEKERQQKKRQEEIKKRLEEPEESKVLTPEEQLADKLRLKKLQEESDLELAKETFGV
Retrocopy VKISEKKKIAEKIKEKERQQKKRQEEIKKRLEEPEESKVLTPEEQLADKLRLKKLQEESDLELAKETFGV

Parental  NNTVYGIDAMNPSSRDDFTEFGKLLKDKITQYEKSLYYASFLEALVRDVCISLEIDDLKKITNSLTVLCS
          NNTVYGIDAMNPSSRDDFTEFGKLLKDKITQYEKSLYYASFLEALVRDVCISLEIDDLKKITNSLTVLCS
Retrocopy NNTVYGIDAMNPSSRDDFTEFGKLLKDKITQYEKSLYYASFLEALVRDVCISLEIDDLKKITNSLTVLCS

Parental  EKQKQEKQSKAKKKKKGVVPGGGLKATMKDDLADYGGYEGGYVQDYEDFM
          EKQKQEKQSKAKKKKKGVVPGGGLKATMKDDLADYGGYEGGYVQDYEDFM
Retrocopy EKQKQEKQSKAKKKKKGVVPGGGLKATMKDDLADYGGYEGGYVQDYEDFM

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	0.09 RPM	10.54 RPM
SRP007412_cerebellum	0.17 RPM	7.43 RPM
SRP007412_heart	0.22 RPM	15.94 RPM
SRP007412_kidney	0.19 RPM	10.01 RPM
SRP007412_liver	0.33 RPM	14.12 RPM
SRP007412_testis	0.27 RPM	16.10 RPM

ChIP-Seq

RNA Polymerase II actvity may be related with retro_mmus_18 in 2 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF001XVA	POLR2A	18:43477717..43477798
ENCFF001YKA	POLR2A	18:43477584..43477967

EST

No EST(s) were mapped for retro_mmus_18 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_59418	324 libraries	259 libraries	203 libraries	169 libraries	117 libraries

The graphical summary, for retro_mmus_18 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_18 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_18 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002412	1 retrocopy	retro_cjac_589,
Cavia porcellus	ENSCPOG00000012396	3 retrocopies	retro_cpor_1357, retro_cpor_1358, retro_cpor_500,
Dipodomys ordii	ENSDORG00000008339	7 retrocopies	retro_dord_208, retro_dord_364, retro_dord_451, retro_dord_470, retro_dord_633, retro_dord_738, retro_dord_746,
Equus caballus	ENSECAG00000008716	1 retrocopy	retro_ecab_635,
Echinops telfairi	ENSETEG00000005052	1 retrocopy	retro_etel_1376,
Homo sapiens	ENSG00000104131	1 retrocopy	retro_hsap_4189,
Gorilla gorilla	ENSGGOG00000000548	2 retrocopies	retro_ggor_1687, retro_ggor_41,
Macropus eugenii	ENSMEUG00000010372	1 retrocopy	retro_meug_256,
Microcebus murinus	ENSMICG00000005006	1 retrocopy	retro_mmur_100,
Monodelphis domestica	ENSMODG00000017696	1 retrocopy	retro_mdom_141,
Mus musculus	ENSMUSG00000027236	1 retrocopy	retro_mmus_18 ,
Nomascus leucogenys	ENSNLEG00000005568	1 retrocopy	retro_nleu_2848,
Oryctolagus cuniculus	ENSOCUG00000005376	1 retrocopy	retro_ocun_1350,
Otolemur garnettii	ENSOGAG00000004694	1 retrocopy	retro_ogar_1227,
Pongo abelii	ENSPPYG00000006431	1 retrocopy	retro_pabe_3429,