RetrogeneDB ID: retro_mmus_1233

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 14:118952324..118952748(+)
• Located in intron of: ENSMUSG00000022136

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ccdc58
• Ensembl ID: ENSMUSG00000075229
• Aliases: Ccdc58, A930007B11Rik, AI413631
• Description: coiled-coil domain containing 58 [Source:MGI Symbol;Acc:MGI:2146423]

Sequence

>retro_mmus_1233
ATGGCGGCACCCAGTGGCAGTGTGAACTGTGAAGAGTTCGCCTAGTTCCAGGAATTACTCAAGGTGATGAGGACAATTGA
TTGCAGAATAGTACATGAATTAAACACTACGGTTCCAACAGCTTCCTTTGCAGGGAAAATCGATGCCAGCCAAACCTGTA
AACAGCTGTATGAGTCTTTGTTGGCAGCTCATGTCAGTAGGGACAGAGTTATAAAGAACTGTATTGCCCAGACCTCAGCA
GTAGTAAAAAGTCTCCGAGAAGAGAGAAAAGAACCTGGATGACTTAATGTTATTAAAGCGACTTAGAAAAGAACAGACAA
AGTTGAAATGAATGCAGTCAGAACTAAATGTCGAAGTGGTCAATGACAGAAGCTGGAAGGTGTTTAATGAACGCTGAGTT
CACTTCAAGCCTCCAAAGAATGAG

Alignment

ORF - retro_mmus_1233 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.83 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAAPSGSVNCEEFAEFQELLKVMRTIDDRIVHELNTTVPTASFAGKIDASQTCKQLYESLMAAHVSRDRV
          MAAPSGSVNCEEFA.FQELLKVMRTID.RIVHELNTTVPTASFAGKIDASQTCKQLYESL.AAHVSRDRV
Retrocopy MAAPSGSVNCEEFA*FQELLKVMRTIDCRIVHELNTTVPTASFAGKIDASQTCKQLYESLLAAHVSRDRV

Parental  IKNCIAQTSAVVKSLREEREKNLDDLTLLKRLRKEQTK-LKWMQSELNVEEVVNDRSWKVFNERCRVHFK
          IKNCIAQTSAVVKSLREER.K....L...K...K...K.LK.MQSELNV.EVVNDRSWKVFNER..VHFK
Retrocopy IKNCIAQTSAVVKSLREER-KEPG*LNVIKAT*KRTDK>LK*MQSELNV-EVVNDRSWKVFNER-*VHFK

Parental  PPKNE
          PPKNE
Retrocopy PPKNE

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	3.39 RPM
SRP007412_cerebellum	0.00 RPM	3.69 RPM
SRP007412_heart	0.03 RPM	7.81 RPM
SRP007412_kidney	0.06 RPM	9.22 RPM
SRP007412_liver	0.05 RPM	17.07 RPM
SRP007412_testis	0.41 RPM	10.47 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1233 was not detected

EST

No EST(s) were mapped for retro_mmus_1233 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_32546	391 libraries	504 libraries	174 libraries	1 library	2 libraries

The graphical summary, for retro_mmus_1233 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_mmus_1233 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1233 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 26 parental genes, and 66 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011138	4 retrocopies	retro_btau_1723, retro_btau_1791, retro_btau_1815, retro_btau_328,
Choloepus hoffmanni	ENSCHOG00000004505	1 retrocopy	retro_chof_1072,
Callithrix jacchus	ENSCJAG00000008132	2 retrocopies	retro_cjac_294, retro_cjac_4115,
Dasypus novemcinctus	ENSDNOG00000005535	1 retrocopy	retro_dnov_743,
Equus caballus	ENSECAG00000023743	2 retrocopies	retro_ecab_1088, retro_ecab_458,
Echinops telfairi	ENSETEG00000003564	3 retrocopies	retro_etel_1361, retro_etel_228, retro_etel_980,
Homo sapiens	ENSG00000160124	3 retrocopies	retro_hsap_1871, retro_hsap_1910, retro_hsap_676,
Gorilla gorilla	ENSGGOG00000001964	9 retrocopies	retro_ggor_132, retro_ggor_1369, retro_ggor_1370, retro_ggor_1939, retro_ggor_2951, retro_ggor_2952, retro_ggor_2953, retro_ggor_582, retro_ggor_722,
Loxodonta africana	ENSLAFG00000016049	1 retrocopy	retro_lafr_227,
Myotis lucifugus	ENSMLUG00000000937	2 retrocopies	retro_mluc_2530, retro_mluc_634,
Macaca mulatta	ENSMMUG00000011919	4 retrocopies	retro_mmul_1104, retro_mmul_2414, retro_mmul_2531, retro_mmul_723,
Monodelphis domestica	ENSMODG00000018298	1 retrocopy	retro_mdom_1936,
Mustela putorius furo	ENSMPUG00000004777	1 retrocopy	retro_mputfur_194,
Mus musculus	ENSMUSG00000075229	1 retrocopy	retro_mmus_1233 ,
Nomascus leucogenys	ENSNLEG00000000291	6 retrocopies	retro_nleu_1236, retro_nleu_1248, retro_nleu_2697, retro_nleu_390, retro_nleu_435, retro_nleu_683,
Oryctolagus cuniculus	ENSOCUG00000002682	2 retrocopies	retro_ocun_724, retro_ocun_839,
Otolemur garnettii	ENSOGAG00000003190	2 retrocopies	retro_ogar_2498, retro_ogar_817,
Pongo abelii	ENSPPYG00000013486	5 retrocopies	retro_pabe_1551, retro_pabe_3694, retro_pabe_3695, retro_pabe_544, retro_pabe_768,
Pteropus vampyrus	ENSPVAG00000012707	2 retrocopies	retro_pvam_1127, retro_pvam_1318,
Rattus norvegicus	ENSRNOG00000031653	2 retrocopies	retro_rnor_1013, retro_rnor_1576,
Sorex araneus	ENSSARG00000004054	1 retrocopy	retro_sara_596,
Sus scrofa	ENSSSCG00000025107	2 retrocopies	retro_sscr_1053, retro_sscr_835,
Ictidomys tridecemlineatus	ENSSTOG00000004419	1 retrocopy	retro_itri_247,
Tupaia belangeri	ENSTBEG00000003196	6 retrocopies	retro_tbel_208, retro_tbel_2214, retro_tbel_2781, retro_tbel_2882, retro_tbel_4574, retro_tbel_846,
Tursiops truncatus	ENSTTRG00000013399	1 retrocopy	retro_ttru_72,
Vicugna pacos	ENSVPAG00000002150	1 retrocopy	retro_vpac_445,