RetrogeneDB ID: retro_mmus_278

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 13:21495305..21495695(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000078139
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Isca1
• Ensembl ID: ENSMUSG00000044792
• Aliases: Isca1, 1810010A06Rik, Hbld2
• Description: iron-sulfur cluster assembly 1 homolog (S. cerevisiae) [Source:MGI Symbol;Acc:MGI:1916296]

Sequence

>retro_mmus_278
ATGTCGGCGTCGTTGGTCCGCGCCACCGTGTGGGCCGTGAGCAAGAGAAAACTGCAGCCCACGCGGGCGGCCCTCACACT
GACCCCCTCTGCTGTAAACAAGATAAAACAACTTCTTAAAGACAAACCTGAGCATGTGGGTCTGAAAGTTGGCGTGCGAA
CCAGGGGCTGTAATGGCCTCTCTTACAGCCTGGAGTACACAAAGACAAAAGGAGATTCTGATGAAGAAGTTATTCAAGAT
GGAGTCCGAGTGTTCATCGAGAAGAAAGCACAGCTAACCCTGTTAGGAACAGAGATGGACTATGTGGAAGACAAACTGTC
CAGTGAGTTTGTGTTCAATAACCCCAACATCAAGGGAACCTGTGGCTGCGGTGAGAGCTTTCACGTGTGA

Alignment

ORF - retro_mmus_278 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.22 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSASLVRATVRAVSKRKLQPTRAALTLTPSAVNKIKQLLKDKPEHVGLKVGVRTRGCNGLSYSLEYTKTK
          MSASLVRATV.AVSKRKLQPTRAALTLTPSAVNKIKQLLKDKPEHVGLKVGVRTRGCNGLSYSLEYTKTK
Retrocopy MSASLVRATVWAVSKRKLQPTRAALTLTPSAVNKIKQLLKDKPEHVGLKVGVRTRGCNGLSYSLEYTKTK

Parental  GDSDEEVIQDGVRVFIEKKAQLTLLGTEMDYVEDKLSSEFVFNNPNIKGTCGCGESFHV
          GDSDEEVIQDGVRVFIEKKAQLTLLGTEMDYVEDKLSSEFVFNNPNIKGTCGCGESFHV
Retrocopy GDSDEEVIQDGVRVFIEKKAQLTLLGTEMDYVEDKLSSEFVFNNPNIKGTCGCGESFHV

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	0.23 RPM	46.45 RPM
SRP007412_cerebellum	0.96 RPM	26.49 RPM
SRP007412_heart	0.31 RPM	64.50 RPM
SRP007412_kidney	0.98 RPM	29.74 RPM
SRP007412_liver	0.41 RPM	13.98 RPM
SRP007412_testis	2.70 RPM	31.38 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_278 was not detected

EST

No EST(s) were mapped for retro_mmus_278 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_27726	333 libraries	145 libraries	426 libraries	137 libraries	31 libraries
TSS #2	TSS_27727	528 libraries	480 libraries	59 libraries	3 libraries	2 libraries

The graphical summary, for retro_mmus_278 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_278 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_278 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 24 parental genes, and 65 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000046526	2 retrocopies	retro_btau_1787, retro_btau_506,
Canis familiaris	ENSCAFG00000001336	1 retrocopy	retro_cfam_1087,
Callithrix jacchus	ENSCJAG00000001940	6 retrocopies	retro_cjac_1623, retro_cjac_1734, retro_cjac_1870, retro_cjac_2608, retro_cjac_350, retro_cjac_672,
Cavia porcellus	ENSCPOG00000011872	2 retrocopies	retro_cpor_1383, retro_cpor_768,
Dasypus novemcinctus	ENSDNOG00000010652	5 retrocopies	retro_dnov_1162, retro_dnov_142, retro_dnov_1956, retro_dnov_431, retro_dnov_95,
Equus caballus	ENSECAG00000011465	1 retrocopy	retro_ecab_936,
Echinops telfairi	ENSETEG00000016537	1 retrocopy	retro_etel_1857,
Homo sapiens	ENSG00000135070	6 retrocopies	retro_hsap_1556, retro_hsap_1768, retro_hsap_1975, retro_hsap_2314, retro_hsap_317, retro_hsap_3329,
Gorilla gorilla	ENSGGOG00000007518	2 retrocopies	retro_ggor_1182, retro_ggor_92,
Microcebus murinus	ENSMICG00000003889	1 retrocopy	retro_mmur_1399,
Myotis lucifugus	ENSMLUG00000001288	1 retrocopy	retro_mluc_1620,
Macaca mulatta	ENSMMUG00000003399	3 retrocopies	retro_mmul_1230, retro_mmul_1365, retro_mmul_2211,
Monodelphis domestica	ENSMODG00000003559	1 retrocopy	retro_mdom_583,
Mus musculus	ENSMUSG00000044792	1 retrocopy	retro_mmus_278 ,
Nomascus leucogenys	ENSNLEG00000005129	5 retrocopies	retro_nleu_1674, retro_nleu_1725, retro_nleu_2330, retro_nleu_2618, retro_nleu_2782,
Oryctolagus cuniculus	ENSOCUG00000010945	1 retrocopy	retro_ocun_1685,
Otolemur garnettii	ENSOGAG00000015628	5 retrocopies	retro_ogar_1267, retro_ogar_1545, retro_ogar_2186, retro_ogar_2813, retro_ogar_935,
Pongo abelii	ENSPPYG00000019339	5 retrocopies	retro_pabe_1287, retro_pabe_2043, retro_pabe_2744, retro_pabe_2745, retro_pabe_367,
Pan troglodytes	ENSPTRG00000021075	7 retrocopies	retro_ptro_1047, retro_ptro_1185, retro_ptro_1316, retro_ptro_1689, retro_ptro_2149, retro_ptro_256, retro_ptro_2842,
Pteropus vampyrus	ENSPVAG00000004588	1 retrocopy	retro_pvam_956,
Rattus norvegicus	ENSRNOG00000018343	4 retrocopies	retro_rnor_1177, retro_rnor_1805, retro_rnor_2254, retro_rnor_2956,
Sus scrofa	ENSSSCG00000010953	1 retrocopy	retro_sscr_558,
Tarsius syrichta	ENSTSYG00000012826	2 retrocopies	retro_tsyr_1060, retro_tsyr_1698,
Tursiops truncatus	ENSTTRG00000004231	1 retrocopy	retro_ttru_1317,