RetrogeneDB ID: retro_mmus_2304

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 3:132655397..132655782(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Sub1
• Ensembl ID: ENSMUSG00000022205
• Aliases: Sub1, AI842364, P15, P9, Pc4, Rpo2tc1
• Description: SUB1 homolog (S. cerevisiae) [Source:MGI Symbol;Acc:MGI:104811]

Sequence

>retro_mmus_2304
ATGCCTAAATCAAAGGAACTGTTTCTTCAAGCTCCTCAGGCAGTGATCCAGAAAGCGAAGTTGAAAAAAGGTTAAAGAGG
AAAAAGCAAGTTGTTCCAGAGAAACCCATGAAGAAGCAGCAGCCTGGTGAGACTTCTAGAGCGCTGGCATCCATCCTCCA
AGCAGAGCAGCAGCAGCAGAGATGACAACGTGTTCCACATTGGAAAGATGAGATATGTCAGTGTTCAGGACTTTAAAGGA
AAACTTCTAATTGATACTAGAGAATACTGGATGGACTCAGAAGGTGAAATGAAGCCAGGGAGAAAAGGTATTTCTTTAAA
CATGGAACAATGGAGCCCACTGAAGAACCAGATGATCTGACACAGATGATGCAGTGAGAAAGCTG

Alignment

ORF - retro_mmus_2304 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.21 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MPKSKEL-VSSSSSGSDSDSEVEKKLKRKKQAVPEKPVKKQKPGETSRALAS-SKQSSS-SRDDNMFQIG
          MPKSKEL.VSSSSSGSD..SEVEK.LKRKKQ.VPEKP.KKQ.PGETSRALAS.S...SS.SRDDN.F.IG
Retrocopy MPKSKEL<VSSSSSGSDPESEVEKRLKRKKQVVPEKPMKKQQPGETSRALAS>SSKQSSSSRDDNVFHIG

Parental  KMRYVSVRDFKGKILIDIREYWMDSEGEMKPGRKGISLNMEQWSQLKEQI-SDIDDAVRKL
          KMRYVSV.DFKGK.LID.REYWMDSEGEMKPGRKGISLNMEQWS.LK.Q..SD.DDAVRKL
Retrocopy KMRYVSVQDFKGKLLIDTREYWMDSEGEMKPGRKGISLNMEQWSPLKNQM>SDTDDAVRKL

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	0.02 RPM	139.31 RPM
SRP007412_cerebellum	0.04 RPM	55.84 RPM
SRP007412_heart	0.00 RPM	30.23 RPM
SRP007412_kidney	0.02 RPM	39.71 RPM
SRP007412_liver	0.00 RPM	43.50 RPM
SRP007412_testis	0.00 RPM	61.52 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2304 was not detected

EST

No EST(s) were mapped for retro_mmus_2304 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_92326	635 libraries	358 libraries	64 libraries	10 libraries	5 libraries

The graphical summary, for retro_mmus_2304 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_2304 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2304 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 25 parental genes, and 83 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006238	2 retrocopies	retro_amel_1331, retro_amel_794,
Canis familiaris	ENSCAFG00000018879	5 retrocopies	retro_cfam_1266, retro_cfam_1536, retro_cfam_1916, retro_cfam_2010, retro_cfam_215,
Callithrix jacchus	ENSCJAG00000018718	2 retrocopies	retro_cjac_1908, retro_cjac_484,
Cavia porcellus	ENSCPOG00000005584	4 retrocopies	retro_cpor_1114, retro_cpor_1481, retro_cpor_834, retro_cpor_854,
Dasypus novemcinctus	ENSDNOG00000007611	5 retrocopies	retro_dnov_1230, retro_dnov_161, retro_dnov_1822, retro_dnov_2156, retro_dnov_400,
Dipodomys ordii	ENSDORG00000013916	2 retrocopies	retro_dord_85, retro_dord_98,
Felis catus	ENSFCAG00000006012	2 retrocopies	retro_fcat_1052, retro_fcat_1313,
Homo sapiens	ENSG00000113387	2 retrocopies	retro_hsap_1662, retro_hsap_3934,
Gorilla gorilla	ENSGGOG00000027033	3 retrocopies	retro_ggor_1063, retro_ggor_1254, retro_ggor_2645,
Loxodonta africana	ENSLAFG00000011006	1 retrocopy	retro_lafr_19,
Macropus eugenii	ENSMEUG00000007770	4 retrocopies	retro_meug_1155, retro_meug_1820, retro_meug_2038, retro_meug_500,
Microcebus murinus	ENSMICG00000014535	2 retrocopies	retro_mmur_1115, retro_mmur_17,
Myotis lucifugus	ENSMLUG00000013685	6 retrocopies	retro_mluc_1649, retro_mluc_1696, retro_mluc_1785, retro_mluc_226, retro_mluc_2346, retro_mluc_621,
Macaca mulatta	ENSMMUG00000011470	2 retrocopies	retro_mmul_2318, retro_mmul_993,
Monodelphis domestica	ENSMODG00000020410	3 retrocopies	retro_mdom_840, retro_mdom_841, retro_mdom_895,
Mustela putorius furo	ENSMPUG00000015185	2 retrocopies	retro_mputfur_186, retro_mputfur_295,
Mus musculus	ENSMUSG00000022205	4 retrocopies	retro_mmus_1118, retro_mmus_2304 , retro_mmus_2586, retro_mmus_3606,
Oryctolagus cuniculus	ENSOCUG00000006262	5 retrocopies	retro_ocun_1227, retro_ocun_1313, retro_ocun_1661, retro_ocun_1714, retro_ocun_902,
Otolemur garnettii	ENSOGAG00000009012	6 retrocopies	retro_ogar_1130, retro_ogar_1272, retro_ogar_218, retro_ogar_2481, retro_ogar_340, retro_ogar_525,
Ochotona princeps	ENSOPRG00000012887	2 retrocopies	retro_opri_495, retro_opri_941,
Pongo abelii	ENSPPYG00000015379	2 retrocopies	retro_pabe_124, retro_pabe_1371,
Rattus norvegicus	ENSRNOG00000050563	12 retrocopies	retro_rnor_1040, retro_rnor_1137, retro_rnor_1203, retro_rnor_1496, retro_rnor_1692, retro_rnor_1693, retro_rnor_1863, retro_rnor_2721, retro_rnor_2986, retro_rnor_420, retro_rnor_572, retro_rnor_735,
Sarcophilus harrisii	ENSSHAG00000014986	1 retrocopy	retro_shar_628,
Ictidomys tridecemlineatus	ENSSTOG00000019364	2 retrocopies	retro_itri_570, retro_itri_571,
Tarsius syrichta	ENSTSYG00000014069	2 retrocopies	retro_tsyr_528, retro_tsyr_895,