RetrogeneDB ID: retro_mmus_2159

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 3:55847419..55848065(+)
• Located in intron of: ENSMUSG00000027799

Retrocopy information

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

Parental gene information

• Parental gene symbol: Sec13
• Ensembl ID: ENSMUSG00000030298
• Aliases: Sec13, 1110003H02Rik, Sec13l1, Sec13r
• Description: SEC13 homolog (S. cerevisiae) [Source:MGI Symbol;Acc:MGI:99832]

Sequence

>retro_mmus_2159
AATGGACTCTGTCAGGCCCCTCATTACAATGGCCTGATCCTGGTCTATGGGAGTTCAGATGGGGCCACCTCACTGCCAAC
CTACACAGGAGAAGGCCAGTGGGAAGTGAAGAAGATTAACAATGCTCACACGATTGGCTGTAATGCTGCCAGTTGGGCCC
CAGCTGCTGTGCCTGGAAGCCTTATAGACTAACATCAGGACAGAAACCTAATTACATCAAGAAATTTGCATCAAGTGGCT
GTGACAACCTCATCAAGCTGTGGAGGGAAGAGGAGAACGGCCAGTGGGAGGAGGAACAAAAGCTAGAGGCACACGGAGTC
TGGGTTCAAGATGTTGCCTGGGCCCCTCCATTGGCTTGCCCACCAGCACCACTACCAGCTGCTCTCAGGACAATCGAGTG
ATTATTTGGACCTGCCATGGTGCCTCAGGCAATATGTGGTCATCTAAACTCCTACACAAGTTCAATGATGTGGTGTGGCA
TGTGAGCTGGCCCATCACAGTGAACATCCTGGCTATGTTAGGTGGAGGCAATAAAGTGACCCTGTGGAAAGAATCTGTGG
ATGGACAGTGGGTGTGCATCAGTGATGTCAACAAAGGCCAGGGTTCTGGGTCAGCCTCCATCACAGAGGCCCAACAGAAT
GAGCAG

Alignment

ORF - retro_mmus_2159 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.94 %
• Parental protein coverage: 67.08 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NSVCWAPHDYGLILACGSSDGAISLLTYTGEGQWEVKKINNAHTIGCNAVSWAPAVVPGSLID-QPSGQK
          N..C.APH..GLIL..GSSDGA.SL.TYTGEGQWEVKKINNAHTIGCNA.SWAPA.VPGSLID...SGQK
Retrocopy NGLCQAPHYNGLILVYGSSDGATSLPTYTGEGQWEVKKINNAHTIGCNAASWAPAAVPGSLID<LTSGQK

Parental  PNYIKKFASGGCDNLIKLWREEEDGQWKEEQKLEAHSDWVRDVAWAP-SIGLPTSTIASCSQDGRVFIWT
          PNYIKKFAS.GCDNLIKLWREEE.GQW.EEQKLEAH..WV.DVAWAP.SIGLPTST..SCSQD.RV.IWT
Retrocopy PNYIKKFASSGCDNLIKLWREEENGQWEEEQKLEAHGVWVQDVAWAP<SIGLPTSTTTSCSQDNRVIIWT

Parental  CDDASGNMWSPKLLHKFNDVVWHVSWSITANILAVSGGDNKVTLWKESVDGQWVCISDVNKGQGSVSASI
          C..ASGNMWS.KLLHKFNDVVWHVSW.IT.NILA..GG.NKVTLWKESVDGQWVCISDVNKGQGS.SASI
Retrocopy CHGASGNMWSSKLLHKFNDVVWHVSWPITVNILAMLGGGNKVTLWKESVDGQWVCISDVNKGQGSGSASI

Parental  TEGQQNEQ
          TE.QQNEQ
Retrocopy TEAQQNEQ

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	0.12 RPM	35.72 RPM
SRP007412_cerebellum	0.13 RPM	32.22 RPM
SRP007412_heart	0.00 RPM	40.28 RPM
SRP007412_kidney	0.06 RPM	53.05 RPM
SRP007412_liver	0.11 RPM	39.38 RPM
SRP007412_testis	7.78 RPM	46.06 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2159 was not detected

EST

No EST(s) were mapped for retro_mmus_2159 retrocopy.

TSS

No TSS is located nearby retro_mmus_2159 retrocopy 5' end.

Lab

retro_mmus_2159 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2159 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005118	1 retrocopy	retro_cfam_278,
Callithrix jacchus	ENSCJAG00000016439	2 retrocopies	retro_cjac_1574, retro_cjac_908,
Felis catus	ENSFCAG00000011245	1 retrocopy	retro_fcat_541,
Homo sapiens	ENSG00000157020	1 retrocopy	retro_hsap_2630,
Microcebus murinus	ENSMICG00000002401	1 retrocopy	retro_mmur_1509,
Mus musculus	ENSMUSG00000030298	2 retrocopies	retro_mmus_2159 , retro_mmus_3443,
Nomascus leucogenys	ENSNLEG00000004482	1 retrocopy	retro_nleu_642,
Otolemur garnettii	ENSOGAG00000017050	1 retrocopy	retro_ogar_1655,
Pongo abelii	ENSPPYG00000013658	1 retrocopy	retro_pabe_2333,
Pan troglodytes	ENSPTRG00000014619	1 retrocopy	retro_ptro_1774,
Rattus norvegicus	ENSRNOG00000010628	2 retrocopies	retro_rnor_1375, retro_rnor_1454,
Tursiops truncatus	ENSTTRG00000004395	1 retrocopy	retro_ttru_917,