RetrogeneDB ID: retro_mmus_3308

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 9:119162624..119163405(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ywhaq
• Ensembl ID: ENSMUSG00000076432
• Aliases: Ywhaq, 2700028P07Rik, AA409740, AU021156, R74690
• Description: tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, theta polypeptide [Source:MGI Symbol;Acc:MGI:891963]

Sequence

>retro_mmus_3308
ACTCGCGTCGCGGCCGCGGAGACTAGAAGGAGGACTCCGGATCCGGCTCGGCGCTTGCCCTCGCTCGCCATGGAGACCGA
GCTGATCTAGAAGGCCAAGCTGGCCGACATGGCCACCTGCATGAAAGCTGTGACAGAGCAGGGCGCCGAGCTGTCCAACG
AGGAGCACAACCTGCTGTCGGTGGCCTACAAAAACGTGGTAGGGGGCCGCAGGTCCGCCTGGAGGGTCATCTCGAGCATT
GAGCAGAAGACCGACACCTCTGACAAGACGTTGCAGCTGATCAAGGACTAATGGGGGAAAGTGGAATCGGAGCTGAGGTC
CATCTGCACCATGGTCCTGGAATTGTTGGATAAGTATTTGATAGCCAATGCAACTAATCCAGAGAGTAAGGTCTTCTATC
TGAACATGAAGGGAGATTATTTCCGGTATCTTGCTGAAGTAGCTTGTGGCGATGATCGAAAACAAACAATAGAAAATTCC
CAAGGAGCCTACCAAGAGGCATTTGATATAAGCAAGAAGGAGATGCAGCCTACGCATCTGATCCGCCTGGGGCTGGCTCT
TAACTTTTCTGTATTTTACTATGAGATCCTTAATAATCCAGAGCTTGCCTGCACACTGGCTAAAACGGCTTTTGATGAGG
CCATCACAGAGCTTGATACACTGAACGAAGACTCCTACAAAGACAGCACCCTCATCATGCAGTTGCTTAGAGACAACTTA
ACATTATGGACATCAGACAGTGCAGGGAGAAGAATGTGATGCAGCAGAGGGGGCCGAAAAC

Alignment

ORF - retro_mmus_3308 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.88 %
• Parental protein coverage: 86.14 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TRRRTPDPARRSPSLAMEKTELIQKAKLAEQAERYDDMATCMKAVTEQGAELSNEERNLLSVAYKNVVGG
          TR.......RR.P..A.....L.....L...A....DMATCMKAVTEQGAELSNEE.NLLSVAYKNVVGG
Retrocopy TRVAAAETRRRTPDPARRLPSLAMETELI*KA-KLADMATCMKAVTEQGAELSNEEHNLLSVAYKNVVGG

Parental  RRSAWRVISSIEQKTDTSDKKLQLIKDYREKVESELRSICTTVLELLDKYLIANATNPESKVFYLKMKGD
          RRSAWRVISSIEQKTDTSDK.LQLIKD...KVESELRSICT.VLELLDKYLIANATNPESKVFYL.MKGD
Retrocopy RRSAWRVISSIEQKTDTSDKTLQLIKD*WGKVESELRSICTMVLELLDKYLIANATNPESKVFYLNMKGD

Parental  YFRYLAEVACGDDRKQTIENSQGAYQEAFDISKKEMQPTHPIRLGLALNFSVFYYEILNNPELACTLAKT
          YFRYLAEVACGDDRKQTIENSQGAYQEAFDISKKEMQPTH.IRLGLALNFSVFYYEILNNPELACTLAKT
Retrocopy YFRYLAEVACGDDRKQTIENSQGAYQEAFDISKKEMQPTHLIRLGLALNFSVFYYEILNNPELACTLAKT

Parental  AFDEAIAELDTLNEDSYKDSTLIMQLLRDNLTLWTSDSA-GEECDAAEGAEN
          AFDEAI.ELDTLNEDSYKDSTLIMQLLRDNLTLWTSDSA.GEECDAAEGAEN
Retrocopy AFDEAITELDTLNEDSYKDSTLIMQLLRDNLTLWTSDSA>GEECDAAEGAEN

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	0.16 RPM	71.61 RPM
SRP007412_cerebellum	0.17 RPM	42.60 RPM
SRP007412_heart	0.00 RPM	9.62 RPM
SRP007412_kidney	0.04 RPM	23.25 RPM
SRP007412_liver	0.03 RPM	10.16 RPM
SRP007412_testis	0.32 RPM	33.98 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3308 was not detected

EST

No EST(s) were mapped for retro_mmus_3308 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_147604	388 libraries	391 libraries	274 libraries	17 libraries	2 libraries

The graphical summary, for retro_mmus_3308 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_3308 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3308 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 42 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000004925	1 retrocopy	retro_ecab_134,
Echinops telfairi	ENSETEG00000015359	4 retrocopies	retro_etel_1027, retro_etel_1048, retro_etel_235, retro_etel_65,
Felis catus	ENSFCAG00000007854	2 retrocopies	retro_fcat_1702, retro_fcat_771,
Myotis lucifugus	ENSMLUG00000005383	1 retrocopy	retro_mluc_1817,
Monodelphis domestica	ENSMODG00000014740	1 retrocopy	retro_mdom_1339,
Mus musculus	ENSMUSG00000022285	3 retrocopies	retro_mmus_163, retro_mmus_2187, retro_mmus_744,
Mus musculus	ENSMUSG00000076432	10 retrocopies	retro_mmus_1076, retro_mmus_1378, retro_mmus_1926, retro_mmus_2250, retro_mmus_2299, retro_mmus_2471, retro_mmus_2689, retro_mmus_3250, retro_mmus_3308 , retro_mmus_406,
Nomascus leucogenys	ENSNLEG00000013534	3 retrocopies	retro_nleu_2543, retro_nleu_750, retro_nleu_869,
Oryctolagus cuniculus	ENSOCUG00000010482	1 retrocopy	retro_ocun_1463,
Otolemur garnettii	ENSOGAG00000000547	3 retrocopies	retro_ogar_1047, retro_ogar_1732, retro_ogar_39,
Rattus norvegicus	ENSRNOG00000008104	5 retrocopies	retro_rnor_1569, retro_rnor_2065, retro_rnor_2123, retro_rnor_2180, retro_rnor_2746,
Sorex araneus	ENSSARG00000012476	4 retrocopies	retro_sara_1, retro_sara_162, retro_sara_179, retro_sara_23,
Tursiops truncatus	ENSTTRG00000000871	4 retrocopies	retro_ttru_1006, retro_ttru_1109, retro_ttru_1530, retro_ttru_1536,