RetrogeneDB ID: retro_mmus_1375

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 15:96202307..96203088(+)
• Located in intron of: ENSMUSG00000097536

Retrocopy information

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

Parental gene information

• Parental gene symbol: Eif3i
• Ensembl ID: ENSMUSG00000028798
• Aliases: Eif3i, 36kDa, D4Ertd632e, Eif3s2, Trip1
• Description: eukaryotic translation initiation factor 3, subunit I [Source:MGI Symbol;Acc:MGI:1860763]

Sequence

>retro_mmus_1375
GGAGCTGTGTGGAGTGCGGATGTTGACTGGAACACTACTCATGTCCCTCCTGGCTCAGTTGACAACAGCTGTTGTCTCTG
GGATTGTGAAACAGGGAAGCAGTTGGTTCCACTCAGGACCAACTCAGCTGTCCGAGCCTGTGGCATTGACTTTCAGGGGA
ATATTATCATGTTCTTCACAGACACAAAGATGGCCTACCAATGTTTTGTGAGCTTCTTTGATCTATGGGATCTGAGCCAA
ATCAACAGCAATGAGCCCTACATGAAGATGCCCAGCAAGATTCCAAGATCACCGTGCTGTTTGGGGACCCCTGGGGACAC
ACATCATTGAAAGCCATGAGAGTAGAAAGAGCTCAGCCAACACAGTGCCAAGTCTAGAGAGGTCTTGGTTAATGTTAAAG
AGCACCATGGCAGGTCACTGTCATCCAGTTGTCTAGAGGCATGACCATGTGTGTCACCACATCCAAGGACAGCACAGCCA
AGCAACTTGACTCCATAAGTCTTGACTATCAGGAGACTTTCCAAACACAATGTTCCATCAACTCCACTACTCTCTCTCTC
ATCTGTGACCATGTGGTACTGGAAAGGTGTCAGGAAGCCAGAGATAAAACCACAGCCTCCACCAGGATTGACAAGTTTGA
GGCCAGGTTCTCCCAGTTGGCATTTGAAGGAGAGTTTGAAAGCCTCAAGGGCCACTTTGGACCTATCAACAGTATTGCCT
TGCATCCTGATGGCAAGAGCTACAGCCTCATGGCTAAGCTGGTGATGTATGCATCCACTAT

Alignment

ORF - retro_mmus_1375 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.53 %
• Parental protein coverage: 80.31 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  GAVWCVDADWDTKHVLTGSADNSCRLWDCETGKQLALLKTNSAVRTCGFDFGGNIIMFSTDKQMGYQCFV
          GAVW..D.DW.T.HV..GS.DNSC.LWDCETGKQL..L.TNSAVR.CG.DF.GNIIMF.TD..M.YQCFV
Retrocopy GAVWSADVDWNTTHVPPGSVDNSCCLWDCETGKQLVPLRTNSAVRACGIDFQGNIIMFFTDTKMAYQCFV

Parental  SFFDLRDPSQIDSNEPYMKIPCN-DSKITSAVWGPLGECVIAGH-ESGELNQYSAKSGEVLVNVKEHSR-
          SFFDL.D.SQI.SNEPYMK.P...DSKIT.....P.G........E..EL.Q.SAKS.EVLVNVKEH...
Retrocopy SFFDLWDLSQINSNEPYMKMPSK<DSKITVLFGDPWGHTSLKAM>E*KELSQHSAKSREVLVNVKEHHG<

Parental  QINDIQLSRDMTMFVTASKDNTAKLFDSTTLEHQKTFRTERPVNSAALSPNYDHVVLGGGQEAMDVTTTS
          Q...IQLSR.MTM.VT.SKD.TAK..DS..L..Q.TF.T....NS..LS...DHVVL...QEA.D.TT.S
Retrocopy QVTVIQLSRGMTMCVTTSKDSTAKQLDSISLDYQETFQTQCSINSTTLSLICDHVVLERCQEARDKTTAS

Parental  TRIGKFEARFFHLAFEEEFGRVKGHFGPINSVAFHPDGKSYS-SGGEDGYVRIHY
          TRI.KFEARF..LAFE.EF...KGHFGPINS.A.HPDGKSYS...G..G.V.IHY
Retrocopy TRIDKFEARFSQLAFEGEFESLKGHFGPINSIALHPDGKSYS<PHG*AGDVCIHY

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	65.53 RPM
SRP007412_cerebellum	0.04 RPM	62.83 RPM
SRP007412_heart	0.00 RPM	60.95 RPM
SRP007412_kidney	0.00 RPM	76.29 RPM
SRP007412_liver	0.00 RPM	63.57 RPM
SRP007412_testis	0.32 RPM	60.19 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1375 was not detected

EST

No EST(s) were mapped for retro_mmus_1375 retrocopy.

TSS

No TSS is located nearby retro_mmus_1375 retrocopy 5' end.

Lab

retro_mmus_1375 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1375 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006810	1 retrocopy	retro_cjac_3104,
Echinops telfairi	ENSETEG00000008047	1 retrocopy	retro_etel_1497,
Loxodonta africana	ENSLAFG00000017026	1 retrocopy	retro_lafr_1073,
Monodelphis domestica	ENSMODG00000017481	2 retrocopies	retro_mdom_1054, retro_mdom_822,
Mus musculus	ENSMUSG00000028798	2 retrocopies	retro_mmus_1375 , retro_mmus_607,
Mus musculus	ENSMUSG00000030224	1 retrocopy	retro_mmus_794,
Rattus norvegicus	ENSRNOG00000047185	1 retrocopy	retro_rnor_1548,