RetrogeneDB ID: retro_mmus_1016

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 13:61917546..61918106(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Calcoco2
• Ensembl ID: ENSMUSG00000006056
• Aliases: Calcoco2, 2410154J16Rik, C77254, Ndp52, Ndp52l1
• Description: calcium binding and coiled-coil domain 2 [Source:MGI Symbol;Acc:MGI:1343177]

Sequence

>retro_mmus_1016
ATAGACCAGTGCCCCATACCTACCTTGCTAGGACATGGCAACTTCTCTCAGGTCCTGTTTAACAATGTTGAGAAGTTCTA
TGTTCCTGGAGGAGATGTCATGTGCTATTACACCCTCACTGAAAAGTTCATCCCTCATCCCAAGGCCTGGATCTGCATCT
TTAAAGTAGGATGGAAGACCACCCAGGAGTATTATACCTTCATGTGGGCTCCCTTGCAGAGAACGACCTAAACAAGGTGT
CAGCCACGCAGCAGGAAATCCAATTCAAAGCTTATTACCTTCTCAAGGATGAGGAGAGCTACCAGTTCTGCTATGTGGAT
GAAGATGGTTTGGTCCGGGGAACAAGTGTCCCTTTCCAGTTCTGTCCAGACCCTGACGAGGACATAAAGGTTGTTATCAA
TAAGGAAAGGGTAGAAGGGATGGAACAGCTCAGTGAGGAGCTTTACCAAGAAAACCTGGAACTAAAAGACAAGTATACTG
ACCTCCATGAGCAGCTTCAGAGGAAGCGGATGGTACTGGAAGCCACGCAGAGGATGAAAAAGACCTTAGAACAGGAAGTG

Alignment

ORF - retro_mmus_1016 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.19 %
• Parental protein coverage: 60. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MDQCPIPTLLEHGNFSQVLFNNVEKFYAPRGDIMCYYTLTEKFIPRRKDWIGIFKVGWK-TTQEY-YTFM
          .DQCPIPTLL.HGNFSQVLFNNVEKFY.P.GD.MCYYTLTEKFIP..K.WI.IFKVGWK.T...Y.Y...
Retrocopy IDQCPIPTLLGHGNFSQVLFNNVEKFYVPGGDVMCYYTLTEKFIPHPKAWICIFKVGWKTTQEYY<YLHV

Parental  WAPLPKDQNKDSATQQEIQFKAYYLPKDVERYQFCYVDEDGLVRGTSVPFQFCPDPDEDIMVVINKEKVE
          ......D.NK.SATQQEIQFKAYYL.KD.E.YQFCYVDEDGLVRGTSVPFQFCPDPDEDI.VVINKE.VE
Retrocopy GSLAENDLNKVSATQQEIQFKAYYLLKDEESYQFCYVDEDGLVRGTSVPFQFCPDPDEDIKVVINKERVE

Parental  EMEQLSEELYQQNQELKDKYADLHEQLQRKQVALEATQRVNKTLEHKV
          .MEQLSEELYQ.N.ELKDKY.DLHEQLQRK...LEATQR..KTLE..V
Retrocopy GMEQLSEELYQENLELKDKYTDLHEQLQRKRMVLEATQRMKKTLEQEV

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	0.02 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.14 RPM	0.14 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1016 was not detected

EST

No EST(s) were mapped for retro_mmus_1016 retrocopy.

TSS

No TSS is located nearby retro_mmus_1016 retrocopy 5' end.

Lab

retro_mmus_1016 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1016 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000006056	3 retrocopies	retro_mmus_1016 , retro_mmus_1108, retro_mmus_2097,
Otolemur garnettii	ENSOGAG00000011709	1 retrocopy	retro_ogar_3090,
Rattus norvegicus	ENSRNOG00000031074	1 retrocopy	retro_rnor_1194,
Ictidomys tridecemlineatus	ENSSTOG00000013395	1 retrocopy	retro_itri_1120,