RetrogeneDB ID: retro_mmus_249

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 3:85915782..85916070(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000044330
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Higd1a
• Ensembl ID: ENSMUSG00000038412
• Aliases: Higd1a, 2210020B17Rik, 7420700H20Rik, AI303276, AW049839, HIMP1, Hig1
• Description: HIG1 domain family, member 1A [Source:MGI Symbol;Acc:MGI:1930666]

Sequence

>retro_mmus_249
ATGTCAACCAACACAGACCTTTCTCTCTCTTCATACGATGAAGGTCAGGGTTCTAAGTTTATTCGGAAAGCTAAGGAGAC
ACTGTTTGTCCCCATTGGAATGGCGGGCTTTGCAGCGATTGTTGCCTATGGGTTGTACAAGCTGAAGAGCAGAGGAAATA
CAAAGATGTCCATTCACTTGATCCACATGCGTGTAGCAGCCCAGGGCTTTGTTGTGGGGGCCATGACTCTTGGTATGGGC
TACTCCATGTATCAGGAATTCTGGGCCAACCCTAAGCCTAAGCCTTAG

Alignment

ORF - retro_mmus_249 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.95 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSTNTDLSLSSYDEGQGSKFIRKAKETPFVPIGMAGFAAIVAYGLYKLKSRGNTKMSIHLIHMRVAAQGF
          MSTNTDLSLSSYDEGQGSKFIRKAKET.FVPIGMAGFAAIVAYGLYKLKSRGNTKMSIHLIHMRVAAQGF
Retrocopy MSTNTDLSLSSYDEGQGSKFIRKAKETLFVPIGMAGFAAIVAYGLYKLKSRGNTKMSIHLIHMRVAAQGF

Parental  VVGAMTLGMGYSMYQEFWANPKPKP
          VVGAMTLGMGYSMYQEFWANPKPKP
Retrocopy VVGAMTLGMGYSMYQEFWANPKPKP

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	45.74 RPM
SRP007412_cerebellum	0.00 RPM	45.16 RPM
SRP007412_heart	0.31 RPM	45.33 RPM
SRP007412_kidney	0.10 RPM	27.20 RPM
SRP007412_liver	0.08 RPM	20.02 RPM
SRP007412_testis	0.09 RPM	25.80 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_249 was not detected

EST

No EST(s) were mapped for retro_mmus_249 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_96446	223 libraries	343 libraries	422 libraries	70 libraries	14 libraries

The graphical summary, for retro_mmus_249 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_249 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_249 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 114 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012431	1 retrocopy	retro_amel_679,
Choloepus hoffmanni	ENSCHOG00000009079	10 retrocopies	retro_chof_1067, retro_chof_1609, retro_chof_171, retro_chof_180, retro_chof_1978, retro_chof_2028, retro_chof_2253, retro_chof_495, retro_chof_546, retro_chof_81,
Callithrix jacchus	ENSCJAG00000032668	9 retrocopies	retro_cjac_1056, retro_cjac_1703, retro_cjac_3001, retro_cjac_3044, retro_cjac_3211, retro_cjac_4111, retro_cjac_514, retro_cjac_79, retro_cjac_920,
Cavia porcellus	ENSCPOG00000000703	11 retrocopies	retro_cpor_1263, retro_cpor_1517, retro_cpor_314, retro_cpor_347, retro_cpor_420, retro_cpor_800, retro_cpor_973, retro_cpor_974, retro_cpor_975, retro_cpor_976, retro_cpor_977,
Equus caballus	ENSECAG00000010978	1 retrocopy	retro_ecab_755,
Echinops telfairi	ENSETEG00000007493	4 retrocopies	retro_etel_1278, retro_etel_1741, retro_etel_1957, retro_etel_767,
Felis catus	ENSFCAG00000000537	2 retrocopies	retro_fcat_1479, retro_fcat_414,
Homo sapiens	ENSG00000181061	13 retrocopies	retro_hsap_1003, retro_hsap_1221, retro_hsap_1313, retro_hsap_205, retro_hsap_2391, retro_hsap_2411, retro_hsap_2969, retro_hsap_3269, retro_hsap_391, retro_hsap_3975, retro_hsap_4079, retro_hsap_884, retro_hsap_996,
Gorilla gorilla	ENSGGOG00000016759	3 retrocopies	retro_ggor_1025, retro_ggor_148, retro_ggor_951,
Macaca mulatta	ENSMMUG00000018783	11 retrocopies	retro_mmul_1093, retro_mmul_1296, retro_mmul_2057, retro_mmul_2164, retro_mmul_2298, retro_mmul_495, retro_mmul_568, retro_mmul_603, retro_mmul_792, retro_mmul_804, retro_mmul_966,
Monodelphis domestica	ENSMODG00000013605	6 retrocopies	retro_mdom_1618, retro_mdom_176, retro_mdom_1937, retro_mdom_1988, retro_mdom_948, retro_mdom_970,
Mustela putorius furo	ENSMPUG00000011870	3 retrocopies	retro_mputfur_1112, retro_mputfur_1287, retro_mputfur_892,
Mus musculus	ENSMUSG00000038412	1 retrocopy	retro_mmus_249 ,
Otolemur garnettii	ENSOGAG00000011358	3 retrocopies	retro_ogar_1546, retro_ogar_2641, retro_ogar_2844,
Ochotona princeps	ENSOPRG00000016072	1 retrocopy	retro_opri_564,
Pongo abelii	ENSPPYG00000013974	16 retrocopies	retro_pabe_1014, retro_pabe_1096, retro_pabe_1776, retro_pabe_2159, retro_pabe_2196, retro_pabe_2462, retro_pabe_2707, retro_pabe_3136, retro_pabe_3199, retro_pabe_322, retro_pabe_3269, retro_pabe_3348, retro_pabe_398, retro_pabe_434, retro_pabe_672, retro_pabe_841,
Pan troglodytes	ENSPTRG00000014802	1 retrocopy	retro_ptro_89,
Rattus norvegicus	ENSRNOG00000019428	1 retrocopy	retro_rnor_36,
Sus scrofa	ENSSSCG00000011290	1 retrocopy	retro_sscr_1026,
Ictidomys tridecemlineatus	ENSSTOG00000009681	3 retrocopies	retro_itri_1636, retro_itri_775, retro_itri_879,
Tupaia belangeri	ENSTBEG00000002324	5 retrocopies	retro_tbel_1136, retro_tbel_1451, retro_tbel_1608, retro_tbel_1991, retro_tbel_4525,
Tursiops truncatus	ENSTTRG00000009760	8 retrocopies	retro_ttru_1001, retro_ttru_1090, retro_ttru_120, retro_ttru_1292, retro_ttru_330, retro_ttru_362, retro_ttru_632, retro_ttru_79,