RetrogeneDB ID: retro_mmus_1997

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:157901535..157902009(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000062846
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Ube2i
• Ensembl ID: ENSMUSG00000015120
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2I [Source:MGI Symbol;Acc:MGI:107365]

Sequence

>retro_mmus_1997
ATGTCGGGGATCGCCCTCAGCCGCCTTGCGCAGGAAAGGAAAGCCTGGAGGAAGGACCACCCTTTTGGCTTTGTAGCTGT
CCCAACAAAGAACCCTGATGGCACAATGAACCTGATGAACGGGGAGTGCGCTATCCCTGGAAAGAAGGGGACTCCATGGG
AAGGAGGCTTGTTCAAGCTACGGATGCTTTTCAAAGATGACTATCCGTCCTCACCACCAAAATGTAAATTTGAGCCCCCA
CTGTTTCATCCAAACGTGTATCCTTCTGGCACAGTGTGCCTGTCCATCCTGGAGGAAGACAAGGACTGGAGGCCAGCTAT
CACCATCAAACAGATCTTATTAGGAATACAAGAACTTCTAAATGAACCAAATATTCAAGACCCAGCTCAAGCAGAGGCCT
ACACAATTTACTGCCAAAACAGAGTGGAATATGAGAAAAGGGTCCGAGCACAAGCGAAGAAGTTTGCCCCCTCA

Alignment

ORF - retro_mmus_1997 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.37 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSGIALSRLAQERKAWRKDHPFGFVAVPTKNPDGTMNLMNWECAIPGKKGTPWEGGLFKLRMLFKDDYPS
          MSGIALSRLAQERKAWRKDHPFGFVAVPTKNPDGTMNLMN.ECAIPGKKGTPWEGGLFKLRMLFKDDYPS
Retrocopy MSGIALSRLAQERKAWRKDHPFGFVAVPTKNPDGTMNLMNGECAIPGKKGTPWEGGLFKLRMLFKDDYPS

Parental  SPPKCKFEPPLFHPNVYPSGTVCLSILEEDKDWRPAITIKQILLGIQELLNEPNIQDPAQAEAYTIYCQN
          SPPKCKFEPPLFHPNVYPSGTVCLSILEEDKDWRPAITIKQILLGIQELLNEPNIQDPAQAEAYTIYCQN
Retrocopy SPPKCKFEPPLFHPNVYPSGTVCLSILEEDKDWRPAITIKQILLGIQELLNEPNIQDPAQAEAYTIYCQN

Parental  RVEYEKRVRAQAKKFAPS
          RVEYEKRVRAQAKKFAPS
Retrocopy RVEYEKRVRAQAKKFAPS

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	33.22 RPM
SRP007412_cerebellum	0.00 RPM	37.17 RPM
SRP007412_heart	0.03 RPM	21.79 RPM
SRP007412_kidney	0.02 RPM	34.86 RPM
SRP007412_liver	0.03 RPM	30.97 RPM
SRP007412_testis	0.05 RPM	63.17 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1997 was not detected

EST

No EST(s) were mapped for retro_mmus_1997 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_82479	274 libraries	174 libraries	146 libraries	335 libraries	143 libraries

The graphical summary, for retro_mmus_1997 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_1997 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1997 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007721	1 retrocopy	retro_amel_1843,
Bos taurus	ENSBTAG00000038866	1 retrocopy	retro_btau_1470,
Canis familiaris	ENSCAFG00000031449	4 retrocopies	retro_cfam_1363, retro_cfam_1991, retro_cfam_2090, retro_cfam_541,
Callithrix jacchus	ENSCJAG00000013249	1 retrocopy	retro_cjac_2914,
Cavia porcellus	ENSCPOG00000010431	1 retrocopy	retro_cpor_156,
Equus caballus	ENSECAG00000015831	1 retrocopy	retro_ecab_350,
Felis catus	ENSFCAG00000027291	2 retrocopies	retro_fcat_1994, retro_fcat_873,
Loxodonta africana	ENSLAFG00000018318	1 retrocopy	retro_lafr_541,
Myotis lucifugus	ENSMLUG00000008229	2 retrocopies	retro_mluc_1112, retro_mluc_1327,
Macaca mulatta	ENSMMUG00000003654	1 retrocopy	retro_mmul_981,
Mustela putorius furo	ENSMPUG00000015763	1 retrocopy	retro_mputfur_1234,
Mus musculus	ENSMUSG00000015120	4 retrocopies	retro_mmus_1341, retro_mmus_1997 , retro_mmus_3182, retro_mmus_3419,
Nomascus leucogenys	ENSNLEG00000008525	1 retrocopy	retro_nleu_1298,
Otolemur garnettii	ENSOGAG00000001428	4 retrocopies	retro_ogar_2367, retro_ogar_2731, retro_ogar_548, retro_ogar_641,
Rattus norvegicus	ENSRNOG00000017907	11 retrocopies	retro_rnor_1051, retro_rnor_1448, retro_rnor_1764, retro_rnor_1913, retro_rnor_2036, retro_rnor_2147, retro_rnor_2301, retro_rnor_2423, retro_rnor_2927, retro_rnor_708, retro_rnor_832,
Sarcophilus harrisii	ENSSHAG00000007034	1 retrocopy	retro_shar_218,
Sus scrofa	ENSSSCG00000021560	1 retrocopy	retro_sscr_319,
Ictidomys tridecemlineatus	ENSSTOG00000010233	3 retrocopies	retro_itri_1341, retro_itri_1459, retro_itri_1601,