RetrogeneDB ID: retro_mmus_621

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 10:16424169..16424668(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Sgta
• Ensembl ID: ENSMUSG00000004937
• Aliases: Sgta, 5330427H01Rik, AI194281, D10Ertd190e, Sgt, Stg
• Description: small glutamine-rich tetratricopeptide repeat (TPR)-containing, alpha [Source:MGI Symbol;Acc:MGI:1098703]

Sequence

>retro_mmus_621
CAGGACTGTGAGCACACCATTGGCATTGATCTCCAATACAGCCAGGCCTATGGCCTCATGGGCCTTGCGCTGTCCAGTCT
GAACAAACGTGGAGGCTGTGGTGTACTACAAGAAAACCCTGGAGATGGATTCTGACAACTACTCGTACAAGTTTAACCTC
AAGATTGCAGAGTTACAGGAGGCACCGAGCCCCACGGGTGGCATGGGCACCTTAGACATAGGTGGCTTGCTGAACAACCC
ACACTTCATCACCATGGGTTGGATCTTAATGTACAGCCCCCAACTGCAGCAGTTCATGTTGAACATGATCTCTGGAGGCC
ATAACCCTCTGGGCACTCCAGGCAGCAGTCCACAGCAGAGTGACCTGGCCAGCCTCATCCAGGTGGACCAGCAGTTTGCA
CACTAGATGGAGCAGCAGAACTCAGAATTCGTGGAGCAAATCCAGAGCCAGGTAGTACGCAGCCAGACACCCAGGGCCAG
CCATGAGGTGCAGCAAGAT

Alignment

ORF - retro_mmus_621 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.71 %
• Parental protein coverage: 53.65 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QDCERAIGIDPGYSKAYGRMGLALSSLNKHA-EAVAYYKKALELDPDNDTYKSNLKIAELKLREAPSPTG
          QDCE..IGID..YS.AYG.MGLALSSLNK.....V.Y.KK.LE.D.DN..YK.NLKIAE..L.EAPSPTG
Retrocopy QDCEHTIGIDLQYSQAYGLMGLALSSLNKRG>AVVYY-KKTLEMDSDNYSYKFNLKIAE--LQEAPSPTG

Parental  GVGSLDIAGLLNNPHFITMASSLMNSPQLQQLMSGMISGGHNPLGTPGSSPQQSDLASLIQAGQQFAQQM
          G.G.LDI.GLLNNPHFITM...LM.SPQLQQ.M..MISGGHNPLGTPGSSPQQSDLASLIQ..QQFA..M
Retrocopy GMGTLDIGGLLNNPHFITMGWILMYSPQLQQFMLNMISGGHNPLGTPGSSPQQSDLASLIQVDQQFAH*M

Parental  QQQNPEFVEQIRSQVVRSRTPSASHEEQQE
          .QQN.EFVEQI.SQVVRS.TP.ASHE.QQ.
Retrocopy EQQNSEFVEQIQSQVVRSQTPRASHEVQQD

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	79.13 RPM
SRP007412_cerebellum	0.00 RPM	97.87 RPM
SRP007412_heart	0.00 RPM	77.55 RPM
SRP007412_kidney	0.00 RPM	76.42 RPM
SRP007412_liver	0.00 RPM	50.49 RPM
SRP007412_testis	0.00 RPM	131.04 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_621 was not detected

EST

No EST(s) were mapped for retro_mmus_621 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_2009	145 libraries	195 libraries	618 libraries	109 libraries	5 libraries

The graphical summary, for retro_mmus_621 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_621 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_621 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005257	1 retrocopy	retro_amel_1169,
Equus caballus	ENSECAG00000010381	2 retrocopies	retro_ecab_723, retro_ecab_780,
Monodelphis domestica	ENSMODG00000004900	1 retrocopy	retro_mdom_277,
Mus musculus	ENSMUSG00000004937	1 retrocopy	retro_mmus_621 ,
Sarcophilus harrisii	ENSSHAG00000011900	1 retrocopy	retro_shar_39,