RetrogeneDB ID: retro_mmus_312

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:43409598..43409922(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Golga7
• Ensembl ID: ENSMUSG00000015341
• Aliases: Golga7, AB041568, C130038N16Rik, GCP16, GOLGA3AP1, HSPC041, R75586
• Description: golgi autoantigen, golgin subfamily a, 7 [Source:MGI Symbol;Acc:MGI:1931029]

Sequence

>retro_mmus_312
GCCAGTGTCCCGGGGAAGGTGCTCATTCAGCAAGACTATGGCAGTGGCACGTGCTGCCAGTTCCAGACCAAGTTCCCCGT
GGAGCTGGAGAACAAGATTGATAGACAGCAGTTTGAAGAATCAGTTTGAACTCTAAATAACCTTTATGCAGAAGCAGAGA
AACTTGGGGGCCAGTTATATCTTGAAGGCCTTTTGGCTTGTTTAACAGCATACACCATCTTCTTATGCATGGAAACTCAT
TATGAGAAGGTCTTGAAGAAAGTCTCCAAAAACATTCAAGAACAGAATGCTCCCCAAGGCCTCCTCCTAACAGACCCCAC
TGAG

Alignment

ORF - retro_mmus_312 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.93 %
• Parental protein coverage: 81.75 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  APVSGKVFIQRDYSSGTRCQFQTKFPAELENRIDRQQFEETVRTLNNLYAEAEKLGGQSYLEGCLACLTA
          A.V.GKV.IQ.DY.SGT.CQFQTKFP.ELEN.IDRQQFEE.V.TLNNLYAEAEKLGGQ.YLEG.LACLTA
Retrocopy ASVPGKVLIQQDYGSGTCCQFQTKFPVELENKIDRQQFEESV*TLNNLYAEAEKLGGQLYLEGLLACLTA

Parental  YTIFLCMETHYEKVLKKVSKYIQEQNEKIYAPQGLLLTDPIE
          YTIFLCMETHYEKVLKKVSK.IQEQN....APQGLLLTDP.E
Retrocopy YTIFLCMETHYEKVLKKVSKNIQEQN----APQGLLLTDPTE

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	27.33 RPM
SRP007412_cerebellum	0.00 RPM	25.05 RPM
SRP007412_heart	0.00 RPM	13.42 RPM
SRP007412_kidney	0.00 RPM	21.16 RPM
SRP007412_liver	0.00 RPM	24.17 RPM
SRP007412_testis	0.00 RPM	19.35 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_312 was not detected

EST

No EST(s) were mapped for retro_mmus_312 retrocopy.

TSS

No TSS is located nearby retro_mmus_312 retrocopy 5' end.

Lab

retro_mmus_312 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_312 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 35 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002741	1 retrocopy	retro_amel_1785,
Dasypus novemcinctus	ENSDNOG00000009976	2 retrocopies	retro_dnov_194, retro_dnov_45,
Erinaceus europaeus	ENSEEUG00000013699	1 retrocopy	retro_eeur_588,
Felis catus	ENSFCAG00000018740	3 retrocopies	retro_fcat_1209, retro_fcat_1958, retro_fcat_975,
Homo sapiens	ENSG00000147533	1 retrocopy	retro_hsap_3862,
Loxodonta africana	ENSLAFG00000009146	1 retrocopy	retro_lafr_273,
Microcebus murinus	ENSMICG00000000940	1 retrocopy	retro_mmur_721,
Myotis lucifugus	ENSMLUG00000014516	2 retrocopies	retro_mluc_1348, retro_mluc_787,
Monodelphis domestica	ENSMODG00000010474	2 retrocopies	retro_mdom_1034, retro_mdom_1528,
Mus musculus	ENSMUSG00000015341	3 retrocopies	retro_mmus_2687, retro_mmus_312 , retro_mmus_3572,
Nomascus leucogenys	ENSNLEG00000012577	1 retrocopy	retro_nleu_3014,
Oryctolagus cuniculus	ENSOCUG00000007546	1 retrocopy	retro_ocun_1503,
Otolemur garnettii	ENSOGAG00000003707	2 retrocopies	retro_ogar_2968, retro_ogar_3484,
Pongo abelii	ENSPPYG00000018542	1 retrocopy	retro_pabe_276,
Pan troglodytes	ENSPTRG00000020193	1 retrocopy	retro_ptro_2632,
Rattus norvegicus	ENSRNOG00000017956	1 retrocopy	retro_rnor_2793,
Sarcophilus harrisii	ENSSHAG00000016094	2 retrocopies	retro_shar_123, retro_shar_626,
Ictidomys tridecemlineatus	ENSSTOG00000004024	3 retrocopies	retro_itri_1181, retro_itri_1774, retro_itri_359,
Tarsius syrichta	ENSTSYG00000005197	3 retrocopies	retro_tsyr_1835, retro_tsyr_359, retro_tsyr_714,
Tursiops truncatus	ENSTTRG00000003557	3 retrocopies	retro_ttru_1289, retro_ttru_1410, retro_ttru_516,