RetrogeneDB ID: retro_mmus_607

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 10:124523446..124524381(+)
• Located in intron of: None

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_607
ATCATGCAGATCAAGTATAACCATGAAGTATAACCTCCTCTTCACTGTGGCTAAAGACCCTCTCTTCAATGTGTGTTGCT
CAGACAACGGCGAGAGGCTAGGCACCTACATGGGCCACACTGGACCTGTGTGGTGTGTGGATGCTGACTGGGACACCAAG
CATGTCCTTACTGGTTCAGCTGACAACAACTGTTGTCTCTGGGACTGTGAAACAGGGAAGCAGCTGTCTCTACTCAAGAC
CAACTCAGCTGTCCGGACCTGTGGCTTTGACTTTGGGGGGCAACATCATTATGTTCTCCACAGACAAGCAGATGGGGTAT
CCATGTTTTGTAAGCTTCTTTGATCTGCAGGATCCAAGCCAAACCGACAGAAATGAGCCTTACATGAAGATTCCCTGTAA
TGATTCCAAGATCACCAGTGCTATCTGGGGACCCCTGGGGGAGTGCATCATTGCAGAAGAGCGGAGAGCTCAACAAGTAT
AGCGCCAAGTCTGGAGAGGTGTTGGTGAACGTTAAGGAGCACTCTCGGCAGATCAATGACATCCAGTTGTCTAGAAACAT
GACCATGTTTGTCACTGCATCCAAGGACAACACAGCTAAGCTCTTCGGCTCTACTTGTCTTGAACATGAGAAGACTTTCC
TAACAGAACGTCCAGTCAACTCGGCTGCTCTCTCTCCCAACTATGACCATGTGGTTCTGGGAGGTGGTCAGGAAGCCACA
GATGTCACCACAACCTACACCAGGTTTGGCAAGTTTGAGGCCAGGTTCTTCCATTTGGCTTTTGAGGAAGAGTTTGGAAG
AGTAAAGGGCCACTTTGGACCAATCAACAGTGTTGCCTTCCATCTTGATGGCAAGAGCTACAGCAGCGTGGCAAAGATGC
TTTTGTCCATATCCACTACTTTGACCCACAGGACTTTGAGTTTAAGTTTGAGGCC

Alignment

ORF - retro_mmus_607 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.86 %
• Parental protein coverage: 96.31 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  ITQIKYNREG-DLLFTVAKDPIVNVWYSVNGERLGTYMGHTGAVWCVDADWDTKHVLTGSADNSCRLWDC
          I.QIKYN.E...LLFTVAKDP..NV..S.NGERLGTYMGHTG.VWCVDADWDTKHVLTGSADN.C.LWDC
Retrocopy IMQIKYNHEV>NLLFTVAKDPLFNVCCSDNGERLGTYMGHTGPVWCVDADWDTKHVLTGSADNNCCLWDC

Parental  ETGKQLALLKTNSAVRTCGFDFGG-NIIMFSTDKQMGYQCFVSFFDLRDPSQIDSNEPYMKIPCNDSKIT
          ETGKQL.LLKTNSAVRTCGFDFGG.NIIMFSTDKQMGY.CFVSFFDL.DPSQ.D.NEPYMKIPCNDSKIT
Retrocopy ETGKQLSLLKTNSAVRTCGFDFGG>NIIMFSTDKQMGYPCFVSFFDLQDPSQTDRNEPYMKIPCNDSKIT

Parental  SAVWG-PLGECVIAGHESGELNQYSAKSGEVLVNVKEHSRQINDIQLSRDMTMFVTASKDNTAKLFDSTT
          SA.WG.P.G........SGELN.YSAKSGEVLVNVKEHSRQINDIQLSR.MTMFVTASKDNTAKLF.ST.
Retrocopy SAIWG>PWGSASL--QKSGELNKYSAKSGEVLVNVKEHSRQINDIQLSRNMTMFVTASKDNTAKLFGSTC

Parental  LEHQKTFRTERPVNSAALSPNYDHVVLGGGQEAMDVTTTSTRIGKFEARFFHLAFEEEFGRVKGHFGPIN
          LEH.KTF.TERPVNSAALSPNYDHVVLGGGQEA.DVTTT.TR.GKFEARFFHLAFEEEFGRVKGHFGPIN
Retrocopy LEHEKTFLTERPVNSAALSPNYDHVVLGGGQEATDVTTTYTRFGKFEARFFHLAFEEEFGRVKGHFGPIN

Parental  SVAFHPDGKSYSS-GGEDGYVRIHYFDPQYFEFEFEA
          SVAFH.DGKSYSS..G.D..V.IHYFDPQ.FEF.FEA
Retrocopy SVAFHLDGKSYSS<RGKDAFVHIHYFDPQDFEFKFEA

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	65.53 RPM
SRP007412_cerebellum	0.87 RPM	62.83 RPM
SRP007412_heart	0.00 RPM	60.95 RPM
SRP007412_kidney	0.75 RPM	76.29 RPM
SRP007412_liver	0.38 RPM	63.57 RPM
SRP007412_testis	0.69 RPM	60.19 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_607 was not detected

EST

No EST(s) were mapped for retro_mmus_607 retrocopy.

TSS

No TSS is located nearby retro_mmus_607 retrocopy 5' end.

Lab

retro_mmus_607 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_607 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,