RetrogeneDB ID: retro_mmus_535

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 10:22343438..22345478(+)
• Located in intron of: ENSMUSG00000053219

Retrocopy information

• Ensembl ID: ENSMUSG00000097245
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Aco2
• Ensembl ID: ENSMUSG00000022477
• Aliases: Aco2, Aco-2, Aco3, D10Wsu183e
• Description: aconitase 2, mitochondrial [Source:MGI Symbol;Acc:MGI:87880]

Sequence

>retro_mmus_535
ATGGCTCCTTACAGCCTCCTGGTCACCCGGCTGCAGAAGGCCCTGGGTGTGGGGCAGTACCATGTGGCCTCTGTCCTGTG
CCAAAGGGCCAAGGTGGCCATGAGCCATTTTGAGCCCAGTGAGTACATCCGATATGACCTGCTAGAGAAGAACATTAACA
TTGTCTGTAAACGGTTGAACCGGCCTCTTACTCTCTCAGAGAAGATTGTGTATGGACACCTGGATGACCCAGCCAATTGG
GAGATCGAGCAGGGAAAGACATATCTGCGTTTATGGCCTGACCGGGTGGCCATGCAGGATGCCACAGGACAGATGGCTAT
GCTACAGTTCATTAGCAGTGGGCTGCCCAAGGTGGCTGTACCATCAACCATCCACTGTGATCATCTGATTGAGGCCCAGG
TTGGGGGTGAGAAAGACCTGCGCAGGGCCAAGGACATAAACCAGGAAGTGTATAATTTCCTGGCAACTGCAGGTGCCAAG
TATGGCGTGGGCTTCTGGACGCCTGGAACTGGGATCATTTACCAGATCATTCTAGAAAACTATGCATACCCTGGAGTTCT
TCTGATTGGCACTGACTCGCACACCCCCAATGGTGGTGGCCTGGGAGGCATCTGCATTAGAGTAAGGGGTGCTGATGCTG
TGGATGTTATGGCTGGGATCCCCTGGGAGCTGAAGTGTCCCAAGGTGATTGGTGTGAAGCTGACAGGCTCCCTCTCTAGT
TGGACCTCACCCAAAGATGTGATCCTGAAACTGGCAGGTATCCTCACAGTGAAAGGTGGCACAGGTGCTATTGTGGAATA
CCATGGACCCGGTGTCGATTCCATCTCCTGCACTGGCATGGCAACTATCTGCAACATGGGTGCAGAAATTGGGGCCACTA
TATCAGTGTTCCCATACAACCACAGGATGAAAGGTACCTGAGCAAGACAGGCCGAACAGACATTGCCAACCTAGCAGAAG
AATTCAAGGATCACTTAGTGCCTGATCCTGGCTGCCAGTATGACCAAGTGATTGAAATTAACTTCAATGAGCTAAAGCCA
CATATCAATGGGCCCTTTACCCCTGACTTGGCTCATCCAGTGGCAGATGTGGGGACTGTGGCAGAGAAGGAAGGCTGGCC
TCTGGACATCTGAGTAGGTTTGATTGGCAGCTGCACCAATTCAATCTACGAGGACATGGGACGATCAGCAGCTGTGGCTA
AGCAGGCATTGGTCCATGGACTCAAGTGCAAGCCCCAGTTCACCATCACCCCAGGCTCTGAGCAGATCCGTGCTGCTATT
GAGCGGGATGGCTATGCACAGATCCTAAGGGATGTGGGTGGAATCGTTTTGGCCAATGCCTGTGGCTCTTGCATTGGCCA
GTGGGACAGAAAAGACATCAAGAGGGGGGAGAAGAATACAATCGTCACCTTCTACAACAAGAACTTCATAGGCCGTAATG
ATGCAAACCCTGAGACCCATGCCTTTGTCACATCCCCAGAGATTGTCACAGCTCTGGCCATTGCGGGGAAGCCTGAAGTT
CAATCCAGAAACTGACTTCTTGACAGGCAAGGATGGCAAGAAGTTCAAGTTGGAGGCTCCAGATGCAGACGAGCTTCCCC
GATCGGACTTTGATCCAGGGCAGGACACATACCAGCACCCCCCTAAGGACAGCAGTGGGCAGCGGGTGGATGTGAGCCCT
ACCAGCCAGCACCTACAGCTCCTGGAGCCTTTTGACAAGTGGGACGGCAAAGACCTTGAGGACCTGCAAATCCTCATCAA
GGTCAAAGGGAAGTGCACCACAGACCACATTTCTGCTGCCAGCCCCTGGCTCAAGTTCCGTGGTCATCTGGATAACATCT
CTAACAACCTGCTCATCGGTGCCATCAACATCGAAAATGGTAAAGCCAACTCTGTACGAAATGCTGTCACCCAGGAGTTT
GGCCCTGTACCTGACACTGCTCGCTACTACAAGAAACATGGCATCAGGTGGGTGGTGATTGGAGATGAGAACGATGGTGA
GGGCTCAAGCTGGGAGCATGCAGCACTGGAGCCTCGCCAT

Alignment

ORF - retro_mmus_535 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.16 %
• Parental protein coverage: 87.18 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAPYSLLVTRLQKALGVRQYHVASVLCQRAKVAMSHFEPSEYIRYDLLEKNINIVRKRLNRPLTLSEKIV
          MAPYSLLVTRLQKALGV.QYHVASVLCQRAKVAMSHFEPSEYIRYDLLEKNINIV.KRLNRPLTLSEKIV
Retrocopy MAPYSLLVTRLQKALGVGQYHVASVLCQRAKVAMSHFEPSEYIRYDLLEKNINIVCKRLNRPLTLSEKIV

Parental  YGHLDDPANQEIERGKTYLRLRPDRVAMQDATAQMAMLQFISSGLPKVAVPSTIHCDHLIEAQVGGEKDL
          YGHLDDPAN.EIE.GKTYLRL.PDRVAMQDAT.QMAMLQFISSGLPKVAVPSTIHCDHLIEAQVGGEKDL
Retrocopy YGHLDDPANWEIEQGKTYLRLWPDRVAMQDATGQMAMLQFISSGLPKVAVPSTIHCDHLIEAQVGGEKDL

Parental  RRAKDINQEVYNFLATAGAKYGVGFWRPGSGIIHQIILENYAYPGVLLIGTDSHTPNGGGLGGICIGVGG
          RRAKDINQEVYNFLATAGAKYGVGFW.PG.GII.QIILENYAYPGVLLIGTDSHTPNGGGLGGICI.V.G
Retrocopy RRAKDINQEVYNFLATAGAKYGVGFWTPGTGIIYQIILENYAYPGVLLIGTDSHTPNGGGLGGICIRVRG

Parental  ADAVDVMAGIPWELKCPKVIGVKLTGSLSGWTSPKDVILKVAGILTVKGGTGAIVEYHGPGVDSISCTGM
          ADAVDVMAGIPWELKCPKVIGVKLTGSLS.WTSPKDVILK.AGILTVKGGTGAIVEYHGPGVDSISCTGM
Retrocopy ADAVDVMAGIPWELKCPKVIGVKLTGSLSSWTSPKDVILKLAGILTVKGGTGAIVEYHGPGVDSISCTGM

Parental  ATICNMGAEIGATTSVFPYNHRMK-KYLSKTGRTDIANLAEEFKDHLVPDPGCQYDQVIEINLNELKPHI
          ATICNMGAEIGAT.SVFPYNHRMK..YLSKTGRTDIANLAEEFKDHLVPDPGCQYDQVIEIN.NELKPHI
Retrocopy ATICNMGAEIGATISVFPYNHRMK<RYLSKTGRTDIANLAEEFKDHLVPDPGCQYDQVIEINFNELKPHI

Parental  NGPFTPDLAHPVADVGTVAEKEGWPLDIRVGLIGSCTNSSYEDMGRSAAVAKQALAHGLKCKSQFTITPG
          NGPFTPDLAHPVADVGTVAEKEGWPLDI.VGLIGSCTNS.YEDMGRSAAVAKQAL.HGLKCK.QFTITPG
Retrocopy NGPFTPDLAHPVADVGTVAEKEGWPLDI*VGLIGSCTNSIYEDMGRSAAVAKQALVHGLKCKPQFTITPG

Parental  SEQIRATIERDGYAQILRDVGGIVLANACGPCIGQWDRKDIKKGEKNTIVTSYNRNFTGRNDANPETHAF
          SEQIRA.IERDGYAQILRDVGGIVLANACG.CIGQWDRKDIK.GEKNTIVT.YN.NF.GRNDANPETHAF
Retrocopy SEQIRAAIERDGYAQILRDVGGIVLANACGSCIGQWDRKDIKRGEKNTIVTFYNKNFIGRNDANPETHAF

Parental  VTSPEIVTALAIA-GTLKFNPETDFLTGKDGKKFKLEAPDADELPRSDFDPGQDTYQHPPKDSSGQRVDV
          VTSPEIVTALAIA.G.LKFNPETDFLTGKDGKKFKLEAPDADELPRSDFDPGQDTYQHPPKDSSGQRVDV
Retrocopy VTSPEIVTALAIA>GSLKFNPETDFLTGKDGKKFKLEAPDADELPRSDFDPGQDTYQHPPKDSSGQRVDV

Parental  SPTSQRLQLLEPFDKWDGKDLEDLQILIKVKGKCTTDHISAAGPWLKFRGHLDNISNNLLIGAINIENGK
          SPTSQ.LQLLEPFDKWDGKDLEDLQILIKVKGKCTTDHISAA.PWLKFRGHLDNISNNLLIGAINIENGK
Retrocopy SPTSQHLQLLEPFDKWDGKDLEDLQILIKVKGKCTTDHISAASPWLKFRGHLDNISNNLLIGAINIENGK

Parental  ANSVRNAVTQEFGPVPDTARYYKKHGIRWVVIGDENYGEGSSREHAALEPRH
          ANSVRNAVTQEFGPVPDTARYYKKHGIRWVVIGDEN.GEGSS.EHAALEPRH
Retrocopy ANSVRNAVTQEFGPVPDTARYYKKHGIRWVVIGDENDGEGSSWEHAALEPRH

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	0.68 RPM	403.43 RPM
SRP007412_cerebellum	0.87 RPM	495.96 RPM
SRP007412_heart	4.58 RPM	2501.31 RPM
SRP007412_kidney	2.71 RPM	1359.28 RPM
SRP007412_liver	0.41 RPM	243.59 RPM
SRP007412_testis	0.18 RPM	147.33 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_535 was not detected

EST

No EST(s) were mapped for retro_mmus_535 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_2495	468 libraries	467 libraries	133 libraries	4 libraries	0 libraries
TSS #2	TSS_2496	423 libraries	509 libraries	136 libraries	4 libraries	0 libraries
TSS #3	TSS_2497	516 libraries	400 libraries	149 libraries	6 libraries	1 library

The graphical summary, for retro_mmus_535 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_535 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_535 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000100412	2 retrocopies	retro_hsap_2583, retro_hsap_324,
Myotis lucifugus	ENSMLUG00000002472	1 retrocopy	retro_mluc_2566,
Macaca mulatta	ENSMMUG00000001454	2 retrocopies	retro_mmul_647, retro_mmul_694,
Mus musculus	ENSMUSG00000022477	1 retrocopy	retro_mmus_535 ,
Nomascus leucogenys	ENSNLEG00000015482	2 retrocopies	retro_nleu_1519, retro_nleu_1767,
Pongo abelii	ENSPPYG00000011871	1 retrocopy	retro_pabe_1903,
Pan troglodytes	ENSPTRG00000014428	1 retrocopy	retro_ptro_260,
Drosophila melanogaster	FBgn0010100	1 retrocopy	retro_dmel_56,