RetrogeneDB ID: retro_mmus_10

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 8:67514231..67515590(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000030735
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Tufm
• Ensembl ID: ENSMUSG00000073838
• Aliases: Tufm, 2300002G02Rik, C76308, C76389, EF-TuMT, EFTU
• Description: Tu translation elongation factor, mitochondrial [Source:MGI Symbol;Acc:MGI:1923686]

Sequence

>retro_mmus_10
ATGGCGGCAGCCACTCTATTGCGAGCGACGCCCCGCTTCAGCGGTCTCTGCGCCAGCCCGACCCCATTTCTGCAAGGTCG
GCTGCGGCCGCTGAAGGCTCCCGCATCACCCTTCTTGTGTCGCGGCCTAGCTGTGGAGGCCAAGAAGACTTATGTACGCG
ACAAGCCCCATGTGAATGTGGGTACCATCGGACATGTGGACCATGGCAAGACCACCCTGACTGCAGCCATCACGAAAATT
CTAGCCGAGGGAGGTGGAGCTAAGTTCAAGAAGTACGAGGAGATAGACAATGCCCCAGAGGAGCGAGCTCGGGGCATCAC
CATCAATGCAGCCCATGTGGAGTATAGCACTGCTGCCCGACACTATGCCCACACAGACTGTCCTGGTCATGCAGATTATG
TTAAGAATATGATCACAGGCACTGCCCCCCTGGATGGCTGTATCCTGGTGGTGGCAGCTAATGATAGCCCCATGCCCCAG
ACCCGAGAGCACTTACTGCTAGCTAAACAGATTGGGGTAGAACATGTTGTGGTGTACGTGAACAAGGCAGACGCTGTCCA
GGACTCAGAGATGGTGGAGTTAGTCGAGCTGGAGATCCGGGAGCTGCTCACCGAGTTTGGCTATAAAGGAGAGGAAACTC
CAGTCATTGTAGGCTCGGCTCTCTGTGCCCTTGAGCAACGTGACCCTGAGCTAGGCGTGAAGTCAGTGCAGAAGCTCCTG
GATGCTGTGGACACCTACATCCCAGTGCCCACCCGGGACCTGGACAAGCCCTTCCTGCTCCCTGTAGAGTCAGTCTACTC
TATTCCTGGCCGGGGCACAGTGGTGACAGGTACATTAGAGCGTGGCATTTTGAAGAAAGGAGATGAGTGTGAGTTGCTGG
GACATAACAAGAACATCCGCACTGTGGTGACAGGCATTGAGATGTTCCACAAGAGCCTGGAGAGGGCTGAGGCAGGGGAT
AACCTGGGTGCTCTGGTCCGAGGCTTAAAGCGCGAAGATTTGAGGCGTGGCTTGGTCATGGTCAAGCCAGGCTCCATCCA
ACCCCACCAGAAGGTGGAGGCCCAGGTTTATATCCTCAGCAAGGAGGAAGGTGGCCGCCACAAACCCTTTGTATCTCATT
TCATGCCCGTCATGTTCTCCCTGACCTGGGACATGGCCTGTCGAGTCATCTTGCCTCCAGGGAAGGAACTTGCCATGCCT
GGAGAGGACTTGAAGCTTAGTCTAATCTTGCGGCAGCCCATGATCTTAGAGAAAGGCCAACGTTTCACCTTGAGGGATGG
CAACAAGACCATTGGCACTGGCCTTGTTACTGATGTACCAGCCATGACTGAGGAGGACAAGAACATCAAGTGGAGCTGA

Alignment

ORF - retro_mmus_10 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.78 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAATLLRATPRFSGLCASPTPFLQGRLRPLKAPASPFLCRGLAVEAKKTYVRDKPHVNVGTIGHVDHGK
          MAAATLLRATPRFSGLCASPTPFLQGRLRPLKAPASPFLCRGLAVEAKKTYVRDKPHVNVGTIGHVDHGK
Retrocopy MAAATLLRATPRFSGLCASPTPFLQGRLRPLKAPASPFLCRGLAVEAKKTYVRDKPHVNVGTIGHVDHGK

Parental  TTLTAAITKILAEGGGAKFKKYEEIDNAPEERARGITINAAHVEYSTAARHYAHTDCPGHADYVKNMITG
          TTLTAAITKILAEGGGAKFKKYEEIDNAPEERARGITINAAHVEYSTAARHYAHTDCPGHADYVKNMITG
Retrocopy TTLTAAITKILAEGGGAKFKKYEEIDNAPEERARGITINAAHVEYSTAARHYAHTDCPGHADYVKNMITG

Parental  TAPLDGCILVVAANDGPMPQTREHLLLAKQIGVEHVVVYVNKADAVQDSEMVELVELEIRELLTEFGYKG
          TAPLDGCILVVAAND.PMPQTREHLLLAKQIGVEHVVVYVNKADAVQDSEMVELVELEIRELLTEFGYKG
Retrocopy TAPLDGCILVVAANDSPMPQTREHLLLAKQIGVEHVVVYVNKADAVQDSEMVELVELEIRELLTEFGYKG

Parental  EETPVIVGSALCALEQRDPELGVKSVQKLLDAVDTYIPVPTRDLDKPFLLPVESVYSIPGRGTVVTGTLE
          EETPVIVGSALCALEQRDPELGVKSVQKLLDAVDTYIPVPTRDLDKPFLLPVESVYSIPGRGTVVTGTLE
Retrocopy EETPVIVGSALCALEQRDPELGVKSVQKLLDAVDTYIPVPTRDLDKPFLLPVESVYSIPGRGTVVTGTLE

Parental  RGILKKGDECELLGHNKNIRTVVTGIEMFHKSLERAEAGDNLGALVRGLKREDLRRGLVMVKPGSIQPHQ
          RGILKKGDECELLGHNKNIRTVVTGIEMFHKSLERAEAGDNLGALVRGLKREDLRRGLVMVKPGSIQPHQ
Retrocopy RGILKKGDECELLGHNKNIRTVVTGIEMFHKSLERAEAGDNLGALVRGLKREDLRRGLVMVKPGSIQPHQ

Parental  KVEAQVYILSKEEGGRHKPFVSHFMPVMFSLTWDMACRVILPPGKELAMPGEDLKLSLILRQPMILEKGQ
          KVEAQVYILSKEEGGRHKPFVSHFMPVMFSLTWDMACRVILPPGKELAMPGEDLKLSLILRQPMILEKGQ
Retrocopy KVEAQVYILSKEEGGRHKPFVSHFMPVMFSLTWDMACRVILPPGKELAMPGEDLKLSLILRQPMILEKGQ

Parental  RFTLRDGNKTIGTGLVTDVPAMTEEDKNIKWS
          RFTLRDGNKTIGTGLVTDVPAMTEEDKNIKWS
Retrocopy RFTLRDGNKTIGTGLVTDVPAMTEEDKNIKWS

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	0.21 RPM	16.84 RPM
SRP007412_cerebellum	0.22 RPM	20.76 RPM
SRP007412_heart	0.87 RPM	81.00 RPM
SRP007412_kidney	0.65 RPM	58.15 RPM
SRP007412_liver	0.25 RPM	38.53 RPM
SRP007412_testis	0.09 RPM	16.74 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_10 was not detected

EST

No EST(s) were mapped for retro_mmus_10 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_143140	685 libraries	352 libraries	33 libraries	2 libraries	0 libraries

The graphical summary, for retro_mmus_10 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_10 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_10 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000016474	1 retrocopy	retro_dord_278,
Homo sapiens	ENSG00000178952	1 retrocopy	retro_hsap_1816,
Macropus eugenii	ENSMEUG00000011131	1 retrocopy	retro_meug_1783,
Monodelphis domestica	ENSMODG00000015564	1 retrocopy	retro_mdom_384,
Mus musculus	ENSMUSG00000073838	1 retrocopy	retro_mmus_10 ,
Ornithorhynchus anatinus	ENSOANG00000013114	1 retrocopy	retro_oana_36,
Oryctolagus cuniculus	ENSOCUG00000002683	1 retrocopy	retro_ocun_333,
Pan troglodytes	ENSPTRG00000007939	1 retrocopy	retro_ptro_1174,
Rattus norvegicus	ENSRNOG00000018604	1 retrocopy	retro_rnor_1134,
Vicugna pacos	ENSVPAG00000009541	1 retrocopy	retro_vpac_346,
Drosophila melanogaster	FBgn0033184	1 retrocopy	retro_dmel_52,