RetrogeneDB ID: retro_mmus_3502

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:105141134..105141940(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000082245
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Sms
• Ensembl ID: ENSMUSG00000071708
• Aliases: Sms, AI427066, Gy, SPMSY, SpmST, gyro
• Description: spermine synthase [Source:MGI Symbol;Acc:MGI:109490]

Sequence

>retro_mmus_3502
AAAGAATTGAGTCAAGACAGTACTGGGCGGGTGAAGCAATTACCACCCATAGTTCGAGGAGGGGCCATTGACAGATACTG
GCCTACTGCTGATGGGCGCCTGGCTGAGTATGACATAGATGAAGTGGTGTATGATGAAGATTCACCCTATCAGAACATTA
AAATCCTACACTCAGAGCAGTTTGGGAATACTCTCATCCTCAGCGGGGATGTTAATTTGGCAGAGAGTGACTTGGCATAT
ACCCGTGCCATCATGGGCAGTGGTAAAAAAGACTACACTGGCAAAGATGTACTGATTCTGGGAGGCGGCGATGGAGGCAT
ATTGTGTGAAATTGTCAAACTGAAGCCAAAGATGGTCACTATGGTAGAGATTGACCAAATGGTCACTGATGGATGTAAGA
AATGCATGCGGAGAACATGTGGAGATGTCTTAGACAATCTTAAAGGAGACTGCTATCAGGGTCTTATAGAAGACTGAATC
CCAGTACTGAAGAGGTTTGCCAAAGAAGGGAGAGAGTTTGATTATGTGATTAGTGATTTGACAGTTGTCCCTAACTCTAC
TCTCCAGAAGAAGATTGCACATGGGAGTTCCTCAGACTGATTCTCGACCTGTTGATGAAGGTTCTGAAACAGGCTGGAAA
ATACTTCACACAGGGGAACTGTGTCAACTTTACTGAAGCCCTGTCGCTCTATGACGAACAGCTGGGGTGTCTGTATTGTC
TTGTGGAATTCTCAAAAGAGATTGTCTGTGTCCCTTCATACTTGGAATTGTGGGTATTTTACACTGTTTGGAAGAAAGCT
GAGCCT

Alignment

ORF - retro_mmus_3502 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.74 %
• Parental protein coverage: 73.5 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KELSQDSTGRVKRLPPIVRGGAIDRYWPTADGRLVEYDIDEVVYDEDSPYQNIKILHSKQFGNILILSGD
          KELSQDSTGRVK.LPPIVRGGAIDRYWPTADGRL.EYDIDEVVYDEDSPYQNIKILHS.QFGN.LILSGD
Retrocopy KELSQDSTGRVKQLPPIVRGGAIDRYWPTADGRLAEYDIDEVVYDEDSPYQNIKILHSEQFGNTLILSGD

Parental  VNLAESDLAYTRAIMGSGKEDYTGKDVLILGGGDGGILCEIVKLKPKMVTMVEIDQMVIDGCKKYMRRTC
          VNLAESDLAYTRAIMGSGK.DYTGKDVLILGGGDGGILCEIVKLKPKMVTMVEIDQMV.DGCKK.MRRTC
Retrocopy VNLAESDLAYTRAIMGSGKKDYTGKDVLILGGGDGGILCEIVKLKPKMVTMVEIDQMVTDGCKKCMRRTC

Parental  GDVLDNLRGDCYQVLIEDCIPVLKMYAKEGREFDYVINDLTAVPIST-SPEEDSTWDFLRLILDLSMKVL
          GDVLDNL.GDCYQ.LIED.IPVLK..AKEGREFDYVI.DLT.VP.ST.SPEED.TW.FLRLILDL.MKVL
Retrocopy GDVLDNLKGDCYQGLIED*IPVLKRFAKEGREFDYVISDLTVVPNST<SPEEDCTWEFLRLILDLLMKVL

Parental  KQDGKYFTQGNCVNLTEALSLYEEQLGRLYCPVEFSKEIVCVPSYLELWVFYTVWKKAKP
          KQ.GKYFTQGNCVN.TEALSLY.EQLG.LYC.VEFSKEIVCVPSYLELWVFYTVWKKA.P
Retrocopy KQAGKYFTQGNCVNFTEALSLYDEQLGCLYCLVEFSKEIVCVPSYLELWVFYTVWKKAEP

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	0.02 RPM	66.02 RPM
SRP007412_cerebellum	0.00 RPM	67.91 RPM
SRP007412_heart	0.03 RPM	24.97 RPM
SRP007412_kidney	0.02 RPM	31.51 RPM
SRP007412_liver	0.00 RPM	2.79 RPM
SRP007412_testis	0.00 RPM	2.24 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3502 was not detected

EST

No EST(s) were mapped for retro_mmus_3502 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_154752	369 libraries	467 libraries	229 libraries	7 libraries	0 libraries

The graphical summary, for retro_mmus_3502 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_3502 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3502 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013284	3 retrocopies	retro_cfam_1076, retro_cfam_1995, retro_cfam_613,
Callithrix jacchus	ENSCJAG00000033933	1 retrocopy	retro_cjac_518,
Cavia porcellus	ENSCPOG00000006176	2 retrocopies	retro_cpor_729, retro_cpor_889,
Echinops telfairi	ENSETEG00000010098	2 retrocopies	retro_etel_1066, retro_etel_1540,
Homo sapiens	ENSG00000102172	5 retrocopies	retro_hsap_243, retro_hsap_3168, retro_hsap_3193, retro_hsap_3611, retro_hsap_4826,
Gorilla gorilla	ENSGGOG00000003123	3 retrocopies	retro_ggor_1335, retro_ggor_2437, retro_ggor_3009,
Myotis lucifugus	ENSMLUG00000013185	3 retrocopies	retro_mluc_471, retro_mluc_530, retro_mluc_92,
Macaca mulatta	ENSMMUG00000020392	2 retrocopies	retro_mmul_2003, retro_mmul_2574,
Monodelphis domestica	ENSMODG00000007897	1 retrocopy	retro_mdom_412,
Mus musculus	ENSMUSG00000071708	6 retrocopies	retro_mmus_2162, retro_mmus_2170, retro_mmus_2837, retro_mmus_3502 , retro_mmus_3628, retro_mmus_994,
Nomascus leucogenys	ENSNLEG00000009955	4 retrocopies	retro_nleu_1664, retro_nleu_2200, retro_nleu_2208, retro_nleu_2755,
Pongo abelii	ENSPPYG00000020182	4 retrocopies	retro_pabe_2649, retro_pabe_2810, retro_pabe_3752, retro_pabe_38,
Rattus norvegicus	ENSRNOG00000007688	2 retrocopies	retro_rnor_1934, retro_rnor_938,
Tupaia belangeri	ENSTBEG00000012109	3 retrocopies	retro_tbel_1630, retro_tbel_1893, retro_tbel_3570,