RetrogeneDB ID: retro_mmus_294

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:9450655..9451743(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Hibch
• Ensembl ID: ENSMUSG00000041426
• Aliases: Hibch, 2610509I15Rik, AI648812
• Description: 3-hydroxyisobutyryl-Coenzyme A hydrolase [Source:MGI Symbol;Acc:MGI:1923792]

Sequence

>retro_mmus_294
AGTGTTATTCTGCAACAACTGAGAATGTCCATGCACACAGAAGCTGCAGAAGTGCTACTGGAGAGGAGAGGCTGTGCAGG
GGTCATAACACTCAACAGACTCAATGCACTGAGTCTGAATATGATCCAGCAGATCTATCCACAGCTAAAGAAGTGGAAAC
AAGACCTTGACACATTCCTGATCATCATAAAGGGAGCCTGAGGAAAGGCCTTTTGTGCTGGAGTGGACATCAAAGCACTC
TCAGAAGCTAAAAAAGCGAGACAGAATTGGACTCATGATGTATTCAGAGAAGAATACATCCTGAACAATGCAATTGCATC
TTGTCAGAAACCATATGTTGCCCTTATTGATGGAATCACCATGTTTGGGGAAGTTGGTCTTTCAGTTCATGGTCATTTCC
GAGTGGCTACAGAAAGGTCTCTCTTTGCTATGCCAGAAACAGGAATAGGACTATTTCCTGATGTGGGTAGAGGTTATTTC
CTGCCAACATTTCAAGGAAAACTGGGTTACTTCCTTGCACTGACAGGACACAGATTAAAAGGAAGAGATGTGCACAGAGC
GGGAATTGACACACACTTTGTAGATTCAGAAAAGTTGCATGTGTTGGAGGAGGAGCTGTTAGCCTTAAACTCACCTCCAG
CTGAGGATGTTGCAGGTGTCTTAGAAAACTATCATGCCAAGTCCAAGATGGATCAAGACAAATCTTTATATTTGAGGAAC
ACATGGGCAAAATAAACAGTTGTTTTTCAGCCAATACCATGGAACAGATAATTGAAAACTTATGGCAAAATGGATCACCT
TTTGCCATAGAATAGATGAAGGTAATTAATAAAATGTCTCTGACATCACTAAAGATCACACGAAGGCAGCTCATGGAGGG
TTCTTCAAAGACCTTGCAAGAGGTACTGACCATGGAATATCGGTTAACTCAAGCATGTATGGAAGGTTATAACTTTCATG
AAGGTGTTAGAGTTGTTATCATTGACAAAGACCAGACTTCAACATGGAAACCAGCCAGTCTAAAAGATTTTACTGATAAA
GATTTGAATAGTTATTTTAAATCTCTGGGAAGCACTGATTTGAAATTC

Alignment

ORF - retro_mmus_294 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.19 %
• Parental protein coverage: 95.06 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SVILQHLRMSMHTEAAEVLLERRGCGGVITLNRPKFLNALSLNMIRQIYPQLKTWEQDPDTFLIIIKGAG
          SVILQ.LRMSMHTEAAEVLLERRGC.GVITLNR...LNALSLNMI.QIYPQLK.W.QD.DTFLIIIKGA.
Retrocopy SVILQQLRMSMHTEAAEVLLERRGCAGVITLNR---LNALSLNMIQQIYPQLKKWKQDLDTFLIIIKGA*

Parental  GKAFCAGGDIKALSEAKKARQNLTQDLFREEYILNNAIASCQKPYVALIDGITMGGGVGLSVHGQFRVAT
          GKAFCAG.DIKALSEAKKARQN.T.D.FREEYILNNAIASCQKPYVALIDGITM.G.VGLSVHG.FRVAT
Retrocopy GKAFCAGVDIKALSEAKKARQNWTHDVFREEYILNNAIASCQKPYVALIDGITMFGEVGLSVHGHFRVAT

Parental  ERSLFAMPETGIGLFPDVGGGYFLPRLQGKLGYFLALTGYRLKGRDVHRAGIATHFVDSEKLRVLEEELL
          ERSLFAMPETGIGLFPDVG.GYFLP..QGKLGYFLALTG.RLKGRDVHRAGI.THFVDSEKL.VLEEELL
Retrocopy ERSLFAMPETGIGLFPDVGRGYFLPTFQGKLGYFLALTGHRLKGRDVHRAGIDTHFVDSEKLHVLEEELL

Parental  ALKSPSAEDVAGVLESYHAKSKMDQDKSI-IFEEHMDKINSCFSANTVEQIIENLRQDGSPFAIEQMKVI
          AL.SP.AEDVAGVLE.YHAKSKMDQDKS..IFEEHM.KINSCFSANT.EQIIENL.Q.GSPFAIE.MKVI
Retrocopy ALNSPPAEDVAGVLENYHAKSKMDQDKSL<IFEEHMGKINSCFSANTMEQIIENLWQNGSPFAIE*MKVI

Parental  NKMSPTSLKITLRQLMEGSSKTLQEVLIMEYRITQACMEGHDFHEGVRAVLIDKDQTPKWKPANLKDVTD
          NKMS.TSLKIT.RQLMEGSSKTLQEVL.MEYR.TQACMEG..FHEGVR.V.IDKDQT..WKPA.LKD.TD
Retrocopy NKMSLTSLKITRRQLMEGSSKTLQEVLTMEYRLTQACMEGYNFHEGVRVVIIDKDQTSTWKPASLKDFTD

Parental  EDLNSYFKSLGSSDLKF
          .DLNSYFKSLGS.DLKF
Retrocopy KDLNSYFKSLGSTDLKF

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	0.00 RPM	10.54 RPM
SRP007412_cerebellum	0.00 RPM	12.90 RPM
SRP007412_heart	0.00 RPM	49.19 RPM
SRP007412_kidney	0.02 RPM	44.95 RPM
SRP007412_liver	0.00 RPM	53.63 RPM
SRP007412_testis	0.05 RPM	4.85 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_294 was not detected

EST

No EST(s) were mapped for retro_mmus_294 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_77718	862 libraries	192 libraries	16 libraries	1 library	1 library

The graphical summary, for retro_mmus_294 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_294 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_294 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000003341	1 retrocopy	retro_fcat_890,
Homo sapiens	ENSG00000198130	1 retrocopy	retro_hsap_3285,
Gorilla gorilla	ENSGGOG00000004988	1 retrocopy	retro_ggor_1317,
Macaca mulatta	ENSMMUG00000007283	1 retrocopy	retro_mmul_2062,
Mus musculus	ENSMUSG00000041426	1 retrocopy	retro_mmus_294 ,
Nomascus leucogenys	ENSNLEG00000006646	1 retrocopy	retro_nleu_1351,
Pongo abelii	ENSPPYG00000013021	2 retrocopies	retro_pabe_2714, retro_pabe_2827,
Pan troglodytes	ENSPTRG00000012741	1 retrocopy	retro_ptro_2222,
Tupaia belangeri	ENSTBEG00000004132	1 retrocopy	retro_tbel_3398,