RetrogeneDB ID: retro_mmus_290

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:4771130..4772196(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Pdhb
• Ensembl ID: ENSMUSG00000021748
• Aliases: Pdhb, 2610103L06Rik, AL024199, C81408
• Description: pyruvate dehydrogenase (lipoamide) beta [Source:MGI Symbol;Acc:MGI:1915513]

Sequence

>retro_mmus_290
ATGGCGGTGGTGGCTGGTCTGGTGCGGGGACCCTTGCGGCAGGTTTCCAGGCGTTTTCACCGCTCGGCGCCCGCAGCGGT
GCAGTTGACAGTTCGTGAAGCTAATAATCAAGGTACGGATGAAGAACTAGAAAGAGATGAAAAAGTTTTTCTGCTTGGGG
AAGAAGTTGCCCAGTATGACGGTGCATACAAGGTTAGCAGAGGCCTGTGGAAGAAATACGGTGACAAGAGGATCATCGAC
ACCCCCATCTCAGAGATGGGCTTTGCTGGAATTGCTGTTGGTGCAGCCTGTGGCTGGGTTGCGGCCCATCTGTGAATTTA
TGACCTTCAATTTCTCTATGCAAGCTATTGACCAGGTTATAAACTCAGCTGCCAAGACTTACTATATGTCCGCTGGCCTT
CACCCTGTGCCCATAGTATTCAGGGGGCCCAATGGCGCCTCAGCAGGTGTAGCTGCTCAGCACTCGCAATGCTTTGCTGC
ATGGTATGGGCACTGCCCAGGTTTAAAAGTGGTCAGCCCCTGGAATTCCGAGGATGCAAAAGGACTTATTAAATCGGCTA
TTCGTGATAATAGCCCAGTGGTAATGCTAGAAAATGAACTGATGTATGGAGTTGCATTTGAAGTTCCTGCAGAAGCTCAG
TCAAAAGATTTCCTGATTCCTATTGGAAAAGCCAAAATTGAAAGGCAAGGGACCCACATCACTGTAGTTGCCCATTCAAG
CCCAGTGGGCCACTGCCTAGAAGCTGCAGCTGTATTGTCTAAAGAGGGAATTGAATGTGAGGTAATAAATCTGCGTACCA
TCAGACCAATGCACATTGAAGCCATAGAAGCCAGTGTGATGAAGACATACCATCTCGTGACTGTGGAAGGAGGCTGGCCA
CAATTTGGAGTAGGAGCTGAGATTTGTGCCAGAATTATGGAAGGCCCTGCATTCAACTTCCTTGATGCCCCTGCCGTTCC
TGTCACTGGTGCTGATGTCCCTATGCCTTACGCAAAGGTCCTAGAAGACAACTCCGTACCTCAGGTCAAAGACATCATAT
TTGCAGTAAGGAAGACTTTGAACATC

Alignment

ORF - retro_mmus_290 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.28 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAVVAGLVRGPLRQASGLLKRRFHRSAPAAVQLTVREAINQGMDEELERDEKVFLLGEEVAQYDGAYKVS
          MAVVAGLVRGPLRQ.S....RRFHRSAPAAVQLTVREA.NQG.DEELERDEKVFLLGEEVAQYDGAYKVS
Retrocopy MAVVAGLVRGPLRQVS----RRFHRSAPAAVQLTVREANNQGTDEELERDEKVFLLGEEVAQYDGAYKVS

Parental  RGLWKKYGDKRIIDTPISEMGFAGIAVGAA-MAGLRPICEFMTFNFSMQAIDQVINSAAKTYYMSAGLQP
          RGLWKKYGDKRIIDTPISEMGFAGIAVGAA..AGLRPICEFMTFNFSMQAIDQVINSAAKTYYMSAGL.P
Retrocopy RGLWKKYGDKRIIDTPISEMGFAGIAVGAA>VAGLRPICEFMTFNFSMQAIDQVINSAAKTYYMSAGLHP

Parental  VPIVFRGPNGASAGVAAQHSQCFAAWYGHCPGLKVVSPWNSEDAKGLIKSAIRDNNPVVMLENELMYGVA
          VPIVFRGPNGASAGVAAQHSQCFAAWYGHCPGLKVVSPWNSEDAKGLIKSAIRDN.PVVMLENELMYGVA
Retrocopy VPIVFRGPNGASAGVAAQHSQCFAAWYGHCPGLKVVSPWNSEDAKGLIKSAIRDNSPVVMLENELMYGVA

Parental  FELPAEAQSKDFLIPIGKAKIERQGTHITVVAHSRPVGHCLEAAAVLSKEGIECEVINLRTIRPMDIEAI
          FE.PAEAQSKDFLIPIGKAKIERQGTHITVVAHS.PVGHCLEAAAVLSKEGIECEVINLRTIRPM.IEAI
Retrocopy FEVPAEAQSKDFLIPIGKAKIERQGTHITVVAHSSPVGHCLEAAAVLSKEGIECEVINLRTIRPMHIEAI

Parental  EASVMKTNHLVTVEGGWPQFGVGAEICARIMEGPAFNFLDAPAVRVTGADVPMPYAKVLEDNSVPQVKDI
          EASVMKT.HLVTVEGGWPQFGVGAEICARIMEGPAFNFLDAPAV.VTGADVPMPYAKVLEDNSVPQVKDI
Retrocopy EASVMKTYHLVTVEGGWPQFGVGAEICARIMEGPAFNFLDAPAVPVTGADVPMPYAKVLEDNSVPQVKDI

Parental  IFAVKKTLNI
          IFAV.KTLNI
Retrocopy IFAVRKTLNI

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	0.33 RPM	71.35 RPM
SRP007412_cerebellum	0.22 RPM	79.68 RPM
SRP007412_heart	1.40 RPM	392.12 RPM
SRP007412_kidney	0.69 RPM	188.28 RPM
SRP007412_liver	0.11 RPM	87.66 RPM
SRP007412_testis	0.14 RPM	99.71 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_290 was not detected

EST

No EST(s) were mapped for retro_mmus_290 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_74668	346 libraries	99 libraries	311 libraries	259 libraries	57 libraries

The graphical summary, for retro_mmus_290 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_290 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_290 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021724	1 retrocopy	retro_btau_596,
Canis familiaris	ENSCAFG00000007340	2 retrocopies	retro_cfam_1215, retro_cfam_2031,
Callithrix jacchus	ENSCJAG00000019739	1 retrocopy	retro_cjac_3875,
Dasypus novemcinctus	ENSDNOG00000006937	1 retrocopy	retro_dnov_1090,
Monodelphis domestica	ENSMODG00000002398	1 retrocopy	retro_mdom_614,
Mus musculus	ENSMUSG00000021748	1 retrocopy	retro_mmus_290 ,
Oryctolagus cuniculus	ENSOCUG00000015632	1 retrocopy	retro_ocun_342,
Procavia capensis	ENSPCAG00000016595	1 retrocopy	retro_pcap_261,
Sarcophilus harrisii	ENSSHAG00000008480	1 retrocopy	retro_shar_5,
Ictidomys tridecemlineatus	ENSSTOG00000019553	2 retrocopies	retro_itri_1349, retro_itri_249,
Tupaia belangeri	ENSTBEG00000016148	2 retrocopies	retro_tbel_1651, retro_tbel_3170,