RetrogeneDB ID: retro_mmus_1139

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 13:100946407..100946815(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000096789
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: H3f3a
• Ensembl ID: ENSMUSG00000060743
• Aliases: H3f3a, H3.3A
• Description: H3 histone, family 3A [Source:MGI Symbol;Acc:MGI:1097686]

Sequence

>retro_mmus_1139
ATGGCTCGTACAAAGCAGACTGCCCGCAAATCCACCGGTGGTAAAGCACCCAGGAAACAACTGGCTACAAAAGCCGCTCG
CAAGAGTGTGCCCTCTACTGGAGGGGTGAAGAAACCTCATCGTTACAGGCCTGGTACTGTGGCACTCCGTGAAATCAGAC
GCTATCAGAAGTCCACTGAACTTCTGATCCGCAAGCTCCCCTTTCAGGGTCTGGTGCGAGAAATTGCTCAGGACTTCAAA
ACAGATCTGCGCTTCCAGAGTGCAGCTATTGGTGCTTTGCAGGAGGCAAGTGAGGCCTATCTGGTTGGCCTTTTTGAAGA
TACCAATCTGTGTGCTATCCATGCCAAACGTGTAACAATTATGCCAAAAGATATCCAGCTAGCACGCCGCATATGCGGAG
AACGTGCT

Alignment

ORF - retro_mmus_1139 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.79 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MARTKQTARKSTGGKAPRKQLATKAARKSAPSTGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQR
          MARTKQTARKSTGGKAPRKQLATKAARKS.PSTGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQ.
Retrocopy MARTKQTARKSTGGKAPRKQLATKAARKSVPSTGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQG

Parental  LVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA
          LVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRI.GERA
Retrocopy LVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRICGERA

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	0.05 RPM	12.50 RPM
SRP007412_cerebellum	0.04 RPM	12.64 RPM
SRP007412_heart	0.03 RPM	12.70 RPM
SRP007412_kidney	0.00 RPM	15.34 RPM
SRP007412_liver	0.03 RPM	8.74 RPM
SRP007412_testis	0.00 RPM	30.87 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1139 was not detected

EST

No EST(s) were mapped for retro_mmus_1139 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_26182	181 libraries	342 libraries	494 libraries	55 libraries	0 libraries

The graphical summary, for retro_mmus_1139 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_1139 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1139 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 95 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009765	3 retrocopies	retro_amel_1636, retro_amel_1794, retro_amel_192,
Choloepus hoffmanni	ENSCHOG00000009661	10 retrocopies	retro_chof_1580, retro_chof_1635, retro_chof_1911, retro_chof_2281, retro_chof_2294, retro_chof_2343, retro_chof_2546, retro_chof_454, retro_chof_517, retro_chof_530,
Cavia porcellus	ENSCPOG00000004707	7 retrocopies	retro_cpor_1059, retro_cpor_1390, retro_cpor_1524, retro_cpor_432, retro_cpor_695, retro_cpor_842, retro_cpor_853,
Loxodonta africana	ENSLAFG00000021624	4 retrocopies	retro_lafr_172, retro_lafr_410, retro_lafr_546, retro_lafr_832,
Myotis lucifugus	ENSMLUG00000015447	10 retrocopies	retro_mluc_146, retro_mluc_1571, retro_mluc_2286, retro_mluc_2344, retro_mluc_2364, retro_mluc_246, retro_mluc_2468, retro_mluc_2500, retro_mluc_392, retro_mluc_613,
Mus musculus	ENSMUSG00000016559	18 retrocopies	retro_mmus_1058, retro_mmus_1188, retro_mmus_1269, retro_mmus_1535, retro_mmus_1635, retro_mmus_2021, retro_mmus_2083, retro_mmus_2377, retro_mmus_2771, retro_mmus_2867, retro_mmus_2972, retro_mmus_3002, retro_mmus_3144, retro_mmus_3477, retro_mmus_3667, retro_mmus_896, retro_mmus_961, retro_mmus_962,
Mus musculus	ENSMUSG00000060743	19 retrocopies	retro_mmus_1053, retro_mmus_1116, retro_mmus_1139 , retro_mmus_1151, retro_mmus_1254, retro_mmus_2285, retro_mmus_2614, retro_mmus_2934, retro_mmus_3009, retro_mmus_3213, retro_mmus_3425, retro_mmus_395, retro_mmus_498, retro_mmus_808, retro_mmus_884, retro_mmus_885, retro_mmus_886, retro_mmus_959, retro_mmus_960,
Oryctolagus cuniculus	ENSOCUG00000024644	2 retrocopies	retro_ocun_185, retro_ocun_217,
Pongo abelii	ENSPPYG00000008636	1 retrocopy	retro_pabe_2662,
Ictidomys tridecemlineatus	ENSSTOG00000024226	8 retrocopies	retro_itri_315, retro_itri_449, retro_itri_465, retro_itri_505, retro_itri_649, retro_itri_695, retro_itri_764, retro_itri_771,
Tupaia belangeri	ENSTBEG00000006177	13 retrocopies	retro_tbel_110, retro_tbel_1274, retro_tbel_15, retro_tbel_170, retro_tbel_2335, retro_tbel_3341, retro_tbel_3342, retro_tbel_3820, retro_tbel_391, retro_tbel_487, retro_tbel_592, retro_tbel_783, retro_tbel_978,