RetrogeneDB ID: retro_mmus_510

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:162628359..162629007(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000091743
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Eif4e1b
• Ensembl ID: ENSMUSG00000074895
• Aliases: Eif4e1b, Eif4eloo, Gm273
• Description: eukaryotic translation initiation factor 4E family member 1B [Source:MGI Symbol;Acc:MGI:2685119]

Sequence

>retro_mmus_510
CCATCAGAAGCAACTGCGGAGGGAGTCCAAGCAGGAGAAGCCAGAGACCTTCCTGGCTCCCTTAAGACTCAGAGGAGGAA
GGCCCACAAAGAACATCCATCGGAGGTCCTGAGCAAGCTACACCCCTTGCAGTACAGGTGGGTTCTGTGGTTCTTCAAGA
ATGACCGAAGCCGGGCCTGGCAGGACAACCTGCAGCTAGTCTCCAAGTTTAACACTGTGGAGGACTTCTGGGTGATGTAC
AGCCATATCAAGCTAGCCAGCAAGCTCTCTTCCTGCTGTGACTATGCCCTATTCAAGGAAGGCATCCTGCCCATGTGGGA
AGACAACAGAAACAAGTGGGGTAGCCGCTGGCTGCTCAGCATTGACAAACAACTGCGCCACTTCGAACTGGACCGTCTGT
GGCTGGAGACGTTGGTGTGTCTGGTCGGGAACTGTTTTGAGGAATACAGCGGTGCTGTCGTGAACATCTGCACGAAGAGG
GACAAGATTGCCCTGTGGACGAATGAAGCAGAGGACAAAGCCGGAGTGATGCAGATCGGGCAAATATACAAAGAGCGCCT
GGGCATCCCTACGAAGACCATCCTTGGGTACCAGGCCCATGCAGACACTGCTGCCAAGAGCAACAACTTAGCAAACAAGT
TTGTGGTG

Alignment

ORF - retro_mmus_510 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.82 %
• Parental protein coverage: 90.16 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PSEATAEGVQAGEAKDLPGSLKTQRRKAHREHPPEVLSKLHPLQYRWVLWFFKNDRSRAWQDNLQLVTKF
          PSEATAEGVQAGEA.DLPGSLKTQRRKAH.EHP.EVLSKLHPLQYRWVLWFFKNDRSRAWQDNLQLV.KF
Retrocopy PSEATAEGVQAGEARDLPGSLKTQRRKAHKEHPSEVLSKLHPLQYRWVLWFFKNDRSRAWQDNLQLVSKF

Parental  NTVEDFWAVYSHIKLASKLSSGCDYALFKEGILPMWEDNRNKQGGRWLLSIDKQLRHFELDRLWLETLLC
          NTVEDFW..YSHIKLASKLSS.CDYALFKEGILPMWEDNRNK.G.RWLLSIDKQLRHFELDRLWLETL.C
Retrocopy NTVEDFWVMYSHIKLASKLSSCCDYALFKEGILPMWEDNRNKWGSRWLLSIDKQLRHFELDRLWLETLVC

Parental  LVGNCFEEYSREVCGAVVNIRTKRDKIALWTSEAEDKAGVMQIGQIYKERLGISTKTIIGYQAHADTAAK
          LVGNCFEEYS....GAVVNI.TKRDKIALWT.EAEDKAGVMQIGQIYKERLGI.TKTI.GYQAHADTAAK
Retrocopy LVGNCFEEYS----GAVVNICTKRDKIALWTNEAEDKAGVMQIGQIYKERLGIPTKTILGYQAHADTAAK

Parental  SNNLANKFVV
          SNNLANKFVV
Retrocopy SNNLANKFVV

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	0.00 RPM	0.02 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.00 RPM	0.55 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_510 was not detected

EST

No EST(s) were mapped for retro_mmus_510 retrocopy.

TSS

No TSS is located nearby retro_mmus_510 retrocopy 5' end.

Lab

retro_mmus_510 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_510 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003103	1 retrocopy	retro_btau_1679,
Erinaceus europaeus	ENSEEUG00000005920	1 retrocopy	retro_eeur_414,
Loxodonta africana	ENSLAFG00000027919	1 retrocopy	retro_lafr_866,
Monodelphis domestica	ENSMODG00000005097	3 retrocopies	retro_mdom_1779, retro_mdom_47, retro_mdom_710,
Mus musculus	ENSMUSG00000028156	6 retrocopies	retro_mmus_1059, retro_mmus_1478, retro_mmus_1872, retro_mmus_2362, retro_mmus_3462, retro_mmus_868,
Mus musculus	ENSMUSG00000074895	1 retrocopy	retro_mmus_510 ,
Nomascus leucogenys	ENSNLEG00000012532	1 retrocopy	retro_nleu_84,
Ochotona princeps	ENSOPRG00000008875	2 retrocopies	retro_opri_1088, retro_opri_21,
Tupaia belangeri	ENSTBEG00000001631	2 retrocopies	retro_tbel_3164, retro_tbel_3690,
Drosophila melanogaster	FBgn0035709	1 retrocopy	retro_dmel_68,