RetrogeneDB ID: retro_mmus_1736

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 18:73730981..73731433(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Egfl7
• Ensembl ID: ENSMUSG00000026921
• Aliases: Egfl7, VE-statin, Zneu1
• Description: EGF-like domain 7 [Source:MGI Symbol;Acc:MGI:2449923]

Sequence

>retro_mmus_1736
TCCTATCTCCGCAGCCTTGGGCCTATTCCCACCAGGCCTCACTATGTCTGCTGCCTTGGTTGGAAGAGGGGCTGTGAGCT
CACTAGGGATTGTAGAACAGCAACCTGCCAGCCTCCATGTGGGGATGAGGGAGTCACATCCATTCAGACCATCATCACTG
CCCCGTGTGATGGCAGGGAGATGCTTGCCGGACAGATATGAATGAATGCACTTCTGGAAAGGCCAGTTGTCCCCAACACT
ATGTCAATAAGGTGGGCAAGTACTGGTGCCAGTGTTGGGAGGGGCAAAGCCCATCTATAGACGGGATGTTCTGCCTGCCC
AGGGGAGCCCCCTCCCTGGTGACCCCAAACCCCTCAACAGGAGTGGCAGCGTGGTGAGGGAGGAGGTGCTCGGGCTGCAA
GTCCTGGGTTGACATGCTAGAGCAAAAACTGCAGTTGGTGCTGGCCCCAATG

Alignment

ORF - retro_mmus_1736 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.74 %
• Parental protein coverage: 54.32 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  AYRRSPGVTPARPRYACCPGWKRTSGLPGACGAAICQPPCGNGG-SCIRPGHCRCPVGWQGDTCQTDVDE
          .Y.RS.G..P.RP.Y.CC.GWKR...L...C..A.CQPPCG..G.S.I...H..CPV.WQGD.C.TD..E
Retrocopy SYLRSLGPIPTRPHYVCCLGWKRGCELTRDCRTATCQPPCGDEG<SHIHSDHHHCPV*WQGDACRTDMNE

Parental  CSTGEASCPQRCVNTVGSYWCQGWEGQSPSADGTRCLSKEGPSPVAPNPTAGV-DSMAREEVYRLQAR-V
          C..G.ASCPQ..VN.VG.YWCQ.WEGQSPS.DG..CL....PS.V.PNP..GV..S..REEV..LQ...V
Retrocopy CTSGKASCPQHYVNKVGKYWCQCWEGQSPSIDGMFCLPRGAPSLVTPNPSTGV<GSVVREEVLGLQVL>V

Parental  DVLEQKLQLVLAPL
          D.LEQKLQLVLAP.
Retrocopy DMLEQKLQLVLAPM

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	15.16 RPM
SRP007412_cerebellum	0.00 RPM	10.90 RPM
SRP007412_heart	0.00 RPM	64.25 RPM
SRP007412_kidney	0.02 RPM	31.61 RPM
SRP007412_liver	0.00 RPM	15.10 RPM
SRP007412_testis	0.00 RPM	4.44 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1736 was not detected

EST

No EST(s) were mapped for retro_mmus_1736 retrocopy.

TSS

No TSS is located nearby retro_mmus_1736 retrocopy 5' end.

Lab

retro_mmus_1736 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1736 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Rattus norvegicus	retro_rnor_1362

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003952	1 retrocopy	retro_amel_1056,
Canis familiaris	ENSCAFG00000019575	1 retrocopy	retro_cfam_945,
Mustela putorius furo	ENSMPUG00000011294	1 retrocopy	retro_mputfur_329,
Mus musculus	ENSMUSG00000026921	1 retrocopy	retro_mmus_1736 ,
Rattus norvegicus	ENSRNOG00000019388	1 retrocopy	retro_rnor_1362,