RetrogeneDB ID: retro_mmus_1066

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 13:117229367..117229706(+)
• Located in intron of: ENSMUSG00000021728

Retrocopy information

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

Parental gene information

• Parental gene symbol: Rnf7
• Ensembl ID: ENSMUSG00000051234
• Aliases: Rnf7, Rbx2, SAG
• Description: ring finger protein 7 [Source:MGI Symbol;Acc:MGI:1337096]

Sequence

>retro_mmus_1066
ATGGCCGACGTGGAGGACGGCGAGGAACCCTGCGTCCTTTCTTCGCACTCCGGGAGCGCAGGCTCCAAGTCGGGAGGCGA
CAAGATGTTCTCTCTCAAGAAGTGTAACGCGGTAGCCATGTGGAGCTGGGACGTTGAGTGCGATACCTGTGCCATCTGCA
GGGTCCAGGTGATGGATGCCTGCCTTCGATGTCAAGCTGAAAACAAGCAAGAGGACTGTGTCCTGGTCTGGGGAGAGTGT
AACCATTCCTTCCACAACTGCTGCATGTCCCTGTGGGTGAAACAGAACAATCGCTGCCCTCTGTGCCAGCAGGACTGGGT
AGTCCAAAGAATCGGCAAA

Alignment

ORF - retro_mmus_1066 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.23 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MADVEDGEEPCVLSSHSGSAGSKSGGDKMFSLKKWNAVAMWSWDVECDTCAICRVQVMDACLRCQAENKQ
          MADVEDGEEPCVLSSHSGSAGSKSGGDKMFSLKK.NAVAMWSWDVECDTCAICRVQVMDACLRCQAENKQ
Retrocopy MADVEDGEEPCVLSSHSGSAGSKSGGDKMFSLKKCNAVAMWSWDVECDTCAICRVQVMDACLRCQAENKQ

Parental  EDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQQDWVVQRIGK
          EDCV.VWGECNHSFHNCCMSLWVKQNNRCPLCQQDWVVQRIGK
Retrocopy EDCVLVWGECNHSFHNCCMSLWVKQNNRCPLCQQDWVVQRIGK

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	0.14 RPM	31.38 RPM
SRP007412_cerebellum	0.91 RPM	30.31 RPM
SRP007412_heart	0.16 RPM	30.45 RPM
SRP007412_kidney	0.04 RPM	29.28 RPM
SRP007412_liver	0.00 RPM	11.63 RPM
SRP007412_testis	0.27 RPM	54.70 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1066 was not detected

EST

No EST(s) were mapped for retro_mmus_1066 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_26918	330 libraries	113 libraries	273 libraries	300 libraries	56 libraries

The graphical summary, for retro_mmus_1066 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_1066 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1066 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000007694	1 retrocopy	retro_cfam_1802,
Choloepus hoffmanni	ENSCHOG00000010742	3 retrocopies	retro_chof_2513, retro_chof_45, retro_chof_518,
Callithrix jacchus	ENSCJAG00000001991	2 retrocopies	retro_cjac_1391, retro_cjac_3943,
Dasypus novemcinctus	ENSDNOG00000005961	3 retrocopies	retro_dnov_1587, retro_dnov_2383, retro_dnov_294,
Homo sapiens	ENSG00000114125	1 retrocopy	retro_hsap_2790,
Gorilla gorilla	ENSGGOG00000001829	1 retrocopy	retro_ggor_1942,
Microcebus murinus	ENSMICG00000001353	1 retrocopy	retro_mmur_1140,
Macaca mulatta	ENSMMUG00000006648	2 retrocopies	retro_mmul_1223, retro_mmul_1440,
Monodelphis domestica	ENSMODG00000021232	1 retrocopy	retro_mdom_201,
Mus musculus	ENSMUSG00000022400	1 retrocopy	retro_mmus_1633,
Mus musculus	ENSMUSG00000051234	3 retrocopies	retro_mmus_1066 , retro_mmus_2450, retro_mmus_3,
Nomascus leucogenys	ENSNLEG00000004646	3 retrocopies	retro_nleu_2038, retro_nleu_2972, retro_nleu_687,
Otolemur garnettii	ENSOGAG00000008659	1 retrocopy	retro_ogar_2433,
Pongo abelii	ENSPPYG00000014167	2 retrocopies	retro_pabe_1446, retro_pabe_2228,
Pan troglodytes	ENSPTRG00000039248	1 retrocopy	retro_ptro_51,
Rattus norvegicus	ENSRNOG00000011663	5 retrocopies	retro_rnor_1858, retro_rnor_1859, retro_rnor_2262, retro_rnor_517, retro_rnor_624,
Ictidomys tridecemlineatus	ENSSTOG00000014964	3 retrocopies	retro_itri_1245, retro_itri_566, retro_itri_567,
Tupaia belangeri	ENSTBEG00000002917	2 retrocopies	retro_tbel_2202, retro_tbel_4027,
Tarsius syrichta	ENSTSYG00000007778	5 retrocopies	retro_tsyr_1222, retro_tsyr_1285, retro_tsyr_1410, retro_tsyr_2117, retro_tsyr_434,