RetrogeneDB ID: retro_mmus_1154

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 13:118598056..118598525(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Plscr3
• Ensembl ID: ENSMUSG00000019461
• Aliases: Plscr3, 2210403O21Rik, 2610037N06Rik, ESTM3, X83310
• Description: phospholipid scramblase 3 [Source:MGI Symbol;Acc:MGI:1917560]

Sequence

>retro_mmus_1154
CTGCTCTGCGGTACCCACTGTCTGCTTTGTGTCCACCTAGCAGTCCCAGAGGATCCGGAATTCCCTGCCTCCACCACCCA
CTCCACTGTGGCTGCAGCTGCAGTTCATGTGGTCTTCAGGACACGGAAGTACATGCTCCACTCGGGACCACTGCCGACCA
TGTGCAACCTACCTGGCCACCCATCCTTCCTAAACTTTCTATCCTAGACTTTGATTACCAAACTGTCCTTTGAGGGGTGG
GGCTTTCCGGAAGTGCGGTTGTGATACAGAGGCCAGTTTTGAAATAAAGACTAAGGATGGTTCTTGAAGAGTGGGCCTCA
TCTGTGAGGGGTTGCTTGGAGGGTAGCTTGGAGAAGCACTCACAGACGCTGATGGCTTTGTCCTACATTTCCCTGTAGAT
CCAGATGTCAGAGTGAAGGCCATGCACCTGGGAGCCACATTCCCTGTTGATTATGTGTTCTTCCAGAAG

Alignment

ORF - retro_mmus_1154 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.23 %
• Parental protein coverage: 52.7 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LCCGARRPFRIRLADPGDRE-VLRLLRPLHCGCSCCPCGLQEMEVQAPPGTTIGHVLQTWHPFLPKFSIL
          L.CG........LA.P.D.E....L..PLHCGCSC..CGLQ..EV.AP.GTT..HV..TW.P.LPK.SIL
Retrocopy LLCGTHCLLCVHLAVPEDPE<IPCLHHPLHCGCSCSSCGLQDTEVHAPLGTTADHVQPTWPPILPKLSIL

Parental  DADRQPVLRVVGPCWT-CGCGTDTNFEVKTKDESRSVGRISK-QWGGLLREALTDADDFGLQFPVDLDVK
          D.D.Q.VL..VG.....CGC.T...FE.KTKD.S..VG.I.....GG.L.EALTDAD.F.L.FPVD.DV.
Retrocopy DFDYQTVL*GVGLSGS<CGCDTEASFEIKTKDGS*RVGLICEGLLGG*LGEALTDADGFVLHFPVDPDVR

Parental  VKAVLLGATFLIDYMFFEK
          VKA..LGATF..DY.FF.K
Retrocopy VKAMHLGATFPVDYVFFQK

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	10.49 RPM
SRP007412_cerebellum	0.00 RPM	13.46 RPM
SRP007412_heart	0.00 RPM	18.71 RPM
SRP007412_kidney	0.06 RPM	15.67 RPM
SRP007412_liver	0.00 RPM	6.31 RPM
SRP007412_testis	0.00 RPM	2.42 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1154 was not detected

EST

No EST(s) were mapped for retro_mmus_1154 retrocopy.

TSS

No TSS is located nearby retro_mmus_1154 retrocopy 5' end.

Lab

retro_mmus_1154 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1154 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Latimeria chalumnae	ENSLACG00000011730	1 retrocopy	retro_lcha_14,
Mus musculus	ENSMUSG00000019461	1 retrocopy	retro_mmus_1154 ,
Mus musculus	ENSMUSG00000032369	1 retrocopy	retro_mmus_462,