RetrogeneDB ID: retro_mmus_547

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 10:34898249..34898829(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Gstm5
• Ensembl ID: ENSMUSG00000004032
• Aliases: None
• Description: glutathione S-transferase, mu 5 [Source:MGI Symbol;Acc:MGI:1309466]

Sequence

>retro_mmus_547
AGCGCCATGTCTATGACACTGGGCTATTGGAACACCCGCGGACTGACTCACTCCATCTGCTTGCTCCTGGAATACACAGA
TTCAAGCTATGAGGAGAAGAGATATGTCATGGGGGATGCCCCCAACTTTGACCGAAGCCAGTGGCTGAGTGAGAAATTCA
ATCTTGGCCTGGATTTTCCCAATCTGCCCTACTTAATTGATGGGTCACACAAGGTCACCCAGAGCAATGCCATCCTGCGC
TACCTTGTCCGGAAGAACAACCTGTGGAGAGACAGAGGAGGAGAGGATCCGTGTGGATACTTTGGAGAACCAGGTTATGG
ACACCCGCATACAGCTCATGATAGTTTGCTGCAGTCCCGATTTTGAGAAGCAGAAGCCAGAGTTCTTGAAGGCCATCCCT
GAGAAAATGAAGCTCTATTCTGAGTTCCTGGGCAAGAGGCCATGGTTTGCAGGGGACAAGGTCACCTATGTGGATTTCCT
TGCTTATGACATTCTTGACCAGTACCGTATGTTTGAGCCCAAGTGCCTGGACGCCTTCCCAAACCTGAGGGACTTCTTGG
CCTGCTTCGAGGCAAAAGAA

Alignment

ORF - retro_mmus_547 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.03 %
• Parental protein coverage: 86.61 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SSKSMVLGYWDIRGLAHAIRMLLEFTDTSYEEKRYICGEAPDYDRSQWLDVKFKLDLDFPNLPYLMDGKN
          S..SM.LGYW..RGL.H.I..LLE.TD.SYEEKRY..G.AP..DRSQWL..KF.L.LDFPNLPYL.DG..
Retrocopy SAMSMTLGYWNTRGLTHSICLLLEYTDSSYEEKRYVMGDAPNFDRSQWLSEKFNLGLDFPNLPYLIDGSH

Parental  KITQSNAILRYIARKHNMCGD-TEEEKIRVDIMENQIMDFRMQLVRLCYNSNHENLKPQYLEQLPAQLKQ
          K.TQSNAILRY..RK.N...D..EE..IRVD..ENQ.MD.R.QL...C.....E..KP..L...P...K.
Retrocopy KVTQSNAILRYLVRKNNLWRD>EEE-RIRVDTLENQVMDTRIQLMIVCCSPDFEKQKPEFLKAIPEKMKL

Parental  FSLFLGKFTWFAGEKLTFVDFLTYDVLDQNRIFEPKCLDEFPNLKAFMCRFEALE
          .S.FLGK..WFAG.K.T.VDFL.YD.LDQ.R.FEPKCLD.FPNL..F...FEA.E
Retrocopy YSEFLGKRPWFAGDKVTYVDFLAYDILDQYRMFEPKCLDAFPNLRDFLACFEAKE

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	0.05 RPM	85.39 RPM
SRP007412_cerebellum	0.00 RPM	46.03 RPM
SRP007412_heart	0.12 RPM	24.84 RPM
SRP007412_kidney	0.42 RPM	66.55 RPM
SRP007412_liver	1.28 RPM	9.67 RPM
SRP007412_testis	0.14 RPM	970.81 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_547 was not detected

EST

No EST(s) were mapped for retro_mmus_547 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_3004	884 libraries	130 libraries	26 libraries	7 libraries	25 libraries

The graphical summary, for retro_mmus_547 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_547 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_547 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005380	2 retrocopies	retro_chof_1850, retro_chof_1989,
Callithrix jacchus	ENSCJAG00000003168	1 retrocopy	retro_cjac_4,
Erinaceus europaeus	ENSEEUG00000014211	1 retrocopy	retro_eeur_112,
Echinops telfairi	ENSETEG00000005817	2 retrocopies	retro_etel_1074, retro_etel_1910,
Homo sapiens	ENSG00000134202	1 retrocopy	retro_hsap_2419,
Microcebus murinus	ENSMICG00000005185	1 retrocopy	retro_mmur_1571,
Macaca mulatta	ENSMMUG00000008029	2 retrocopies	retro_mmul_610, retro_mmul_941,
Monodelphis domestica	ENSMODG00000001899	1 retrocopy	retro_mdom_331,
Mus musculus	ENSMUSG00000004032	2 retrocopies	retro_mmus_491, retro_mmus_547 ,
Mus musculus	ENSMUSG00000027890	1 retrocopy	retro_mmus_204,
Mus musculus	ENSMUSG00000038155	1 retrocopy	retro_mmus_521,
Mus musculus	ENSMUSG00000058135	1 retrocopy	retro_mmus_2692,
Nomascus leucogenys	ENSNLEG00000003302	1 retrocopy	retro_nleu_1895,
Pan troglodytes	ENSPTRG00000001063	2 retrocopies	retro_ptro_1393, retro_ptro_1709,
Rattus norvegicus	ENSRNOG00000047034	1 retrocopy	retro_rnor_963,
Sus scrofa	ENSSSCG00000006821	2 retrocopies	retro_sscr_10, retro_sscr_855,
Tarsius syrichta	ENSTSYG00000006736	1 retrocopy	retro_tsyr_145,
Tursiops truncatus	ENSTTRG00000009682	1 retrocopy	retro_ttru_1828,