RetrogeneDB ID: retro_mmus_1668

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 17:79933511..79934572(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Eif3h
• Ensembl ID: ENSMUSG00000022312
• Aliases: Eif3h, 1110008A16Rik, 40kD, 9430017H16Rik, EIF3-P40, EIF3-gamma, Eif3s3
• Description: eukaryotic translation initiation factor 3, subunit H [Source:MGI Symbol;Acc:MGI:1915385]

Sequence

>retro_mmus_1668
ATGGCGTCGCGCAAGGAAGGCACCGGCTCCACTGCCACCTCCTCCAGTTCTGCTGGCGGCACGGTGGGGAAGGGCAAAGG
CAAGGGCGGCTCTGGAGATTCGGTGGTGAAGCAGGTGCAGATCGACGGCCTGGTAGTATTAAAGATAATCAAACATTATC
AAGAAGAAGGACAAGGAACTGAGGTTGTTCAGGGAGTGCTCCTGGGTCTGGTTGTAGAAGATCGACTAGAGATGACCAAC
TGCTTCCCGTTCCCCCCAGCACACGGAGGATGATGCTGACTTTGATGAGGTACAGTATCAGATGGAGATGATGCGCAGCC
TTCGCCATGTCAACATTGATCACCTCCACGTGGGCTGGTATCAGTCCACATATTACGGCTCCTTCGTTACCCGGGCGCTT
CTGGATTCTCAGTTCAGCTACCAGCACGCCATTGAAGAGTCTGTCGTCCTCATTTATGATCCCATAAAAACTGCCCAAGG
ATCTCTCTCTCGCTGAAGGCATACATGACTGACTCCTAAACGGATGGAAGTTTGTAAAGAGAAGGACTTTTCCCCTGAAG
CACTGAAAAAGGCAAGCATCACCTTTGAGCACATGTTTGAAGAAGTGCCGATTGTGATTAAAAACTCACATCTGATCAGT
GTCCTTATGTGGGAGCTTGAGAAGAAGTCAGCTGTGGCGGATAAGCACGAATTGCTCAGTCTTGCTAGCAGCAATCATCT
GGGGGAAGAATCTCCAGCTGCTGATGGACCCGGTGGATGAAATGAGCCAGGACATAATCAAATACAACACAGACGTGCGG
AACACCAGTAAACAGCAGCAGCAGAAACATCAGAATCAGCAGCGCCGCCAACAGGAGAATATGCAGCGTCGGAGTCGAGG
CGAGCCCCCACTCCCTGAGGAGGACCTCTCTAAACTCTTCAAGCCCCACCAGGCCCCTGCCAGGATGGATTCACTGCTCA
TTGCAGGCCAGATGAACACTTACTGCCAGAACATCAAGGAGTTCACTGCCCAAAACTTAGGCAAACTCTTCATGGCCCAG
GCTCTTCAAGAATACAATAAT

Alignment

ORF - retro_mmus_1668 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.08 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MASRKEGTGSTATSSGSAGGAVGKGKGKGGSGDSAVKQVQIDGLVVLKIIKHYQEEGQGTEVVQGVLLGL
          MASRKEGTGSTATSS.SAGG.VGKGKGKGGSGDS.VKQVQIDGLVVLKIIKHYQEEGQGTEVVQGVLLGL
Retrocopy MASRKEGTGSTATSSSSAGGTVGKGKGKGGSGDSVVKQVQIDGLVVLKIIKHYQEEGQGTEVVQGVLLGL

Parental  VVEDRLEITNCFPF-PQHTEDDADFDEVQYQMEMMRSLRHVNIDHLHVGWYQSTYYGSFVTRALLDSQFS
          VVEDRLE.TNCFPF.PQHTEDDADFDEVQYQMEMMRSLRHVNIDHLHVGWYQSTYYGSFVTRALLDSQFS
Retrocopy VVEDRLEMTNCFPF>PQHTEDDADFDEVQYQMEMMRSLRHVNIDHLHVGWYQSTYYGSFVTRALLDSQFS

Parental  YQHAIEESVVLIYDPIKTAQGSLSLKAYR-LTPKLMEVCKEKDFSPEALKKASITFEHMFEEVPIVIKNS
          YQHAIEESVVLIYDPIKTAQGSLS......LTPK.MEVCKEKDFSPEALKKASITFEHMFEEVPIVIKNS
Retrocopy YQHAIEESVVLIYDPIKTAQGSLSR*RHT*LTPKRMEVCKEKDFSPEALKKASITFEHMFEEVPIVIKNS

Parental  HLINVLMWELEKKSAVADKHELLSLASSNHL-GKSLQLLMDRVDEMSQDIIKYNTYMRNTSKQQQQKHQY
          HLI.VLMWELEKKSAVADKHELLSLASSNHL.GK.LQLLMD.VDEMSQDIIKYNT..RNTSKQQQQKHQ.
Retrocopy HLISVLMWELEKKSAVADKHELLSLASSNHL>GKNLQLLMDPVDEMSQDIIKYNTDVRNTSKQQQQKHQN

Parental  QQRRQQENMQRQSRGEPPLPEEDLSKLFKPHQAPARMDSLLIAGQINTYCQNIKEFTAQNLGKLFMAQAL
          QQRRQQENMQR.SRGEPPLPEEDLSKLFKPHQAPARMDSLLIAGQ.NTYCQNIKEFTAQNLGKLFMAQAL
Retrocopy QQRRQQENMQRRSRGEPPLPEEDLSKLFKPHQAPARMDSLLIAGQMNTYCQNIKEFTAQNLGKLFMAQAL

Parental  QEYNN
          QEYNN
Retrocopy QEYNN

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	0.12 RPM	70.11 RPM
SRP007412_cerebellum	0.09 RPM	95.44 RPM
SRP007412_heart	0.19 RPM	117.92 RPM
SRP007412_kidney	0.17 RPM	105.30 RPM
SRP007412_liver	0.11 RPM	95.31 RPM
SRP007412_testis	0.73 RPM	123.68 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1668 was not detected

EST

No EST(s) were mapped for retro_mmus_1668 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_56876	412 libraries	50 libraries	304 libraries	250 libraries	56 libraries

The graphical summary, for retro_mmus_1668 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_1668 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1668 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000000816	1 retrocopy	retro_cfam_2073,
Callithrix jacchus	ENSCJAG00000005910	1 retrocopy	retro_cjac_3023,
Echinops telfairi	ENSETEG00000000324	1 retrocopy	retro_etel_24,
Macropus eugenii	ENSMEUG00000015663	4 retrocopies	retro_meug_1223, retro_meug_1244, retro_meug_1790, retro_meug_376,
Monodelphis domestica	ENSMODG00000004154	1 retrocopy	retro_mdom_1243,
Mus musculus	ENSMUSG00000022312	1 retrocopy	retro_mmus_1668 ,
Oryctolagus cuniculus	ENSOCUG00000007534	1 retrocopy	retro_ocun_608,
Otolemur garnettii	ENSOGAG00000008905	1 retrocopy	retro_ogar_2043,
Sorex araneus	ENSSARG00000009067	1 retrocopy	retro_sara_69,
Sarcophilus harrisii	ENSSHAG00000014977	1 retrocopy	retro_shar_561,
Ictidomys tridecemlineatus	ENSSTOG00000001403	1 retrocopy	retro_itri_420,