RetrogeneDB ID: retro_mmus_3271

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 9:43683050..43683512(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Srm
• Ensembl ID: ENSMUSG00000006442
• Aliases: Srm, AA407669, SpdST, SpdSy
• Description: spermidine synthase [Source:MGI Symbol;Acc:MGI:102690]

Sequence

>retro_mmus_3271
ATGGAGCCTGTCCCCAATGGCCCAGCCGCGCTCGGCCCTGCTGCCATCCATAAGGGCTGGTTCCGAGAGACCTGCAGCCT
GTGGCCCGGCCAAGCCCTGTCGCTGCAAGTGGAGCAGCTGCTGCACCACCGGCGCTCGCGGTAACAAGACATCCTTGTCT
TCCTGAGTAAAACCTACAGCAACGTGCTGGTTCTGGATGGTGTCATCCAGTGTACTGAGAGGGACGAGTTCTTCTACCAG
GAGATGATCGCCAACCTGCCGCTCTACAACCACCCCAACCCGTGGAAGGTGCTGATCATCGGGGGTGAAGATGGGAGCGC
CCTACGGGAAGTGGTGAAGCACCCCTCTGTGGAGTCTGTGGTCCAGTGCGAGATCGATGAGGATGCCATTAAAGTCTCTT
AGAAGTTCCTGCCTGGCATAGCTGTTGGCTTCTCCAGCTCAAAGCTGACTATCCATGTGGGT

Alignment

ORF - retro_mmus_3271 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.01 %
• Parental protein coverage: 50.99 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEPGPDGPAAPGPAAIREGWFRETCSLWPGQALSLQVEQLLHHRRSRYQDILVFRSKTYGNVLVLDGVIQ
          MEP.P.GPAA.GPAAI..GWFRETCSLWPGQALSLQVEQLLHHRRSR.QDILVF.SKTY.NVLVLDGVIQ
Retrocopy MEPVPNGPAALGPAAIHKGWFRETCSLWPGQALSLQVEQLLHHRRSR*QDILVFLSKTYSNVLVLDGVIQ

Parental  CTERDEFSYQEMIANLPLCSHPNPRKVLIIGGGDGGVLREVVKHPSVESVVQCEIDEDVIEVSKKFLPGM
          CTERDEF.YQEMIANLPL..HPNP.KVLIIGG.DG..LREVVKHPSVESVVQCEIDED.I.VS.KFLPG.
Retrocopy CTERDEFFYQEMIANLPLYNHPNPWKVLIIGGEDGSALREVVKHPSVESVVQCEIDEDAIKVS*KFLPGI

Parental  AVGFSSSKLTLHVG
          AVGFSSSKLT.HVG
Retrocopy AVGFSSSKLTIHVG

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	28.90 RPM
SRP007412_cerebellum	0.00 RPM	20.58 RPM
SRP007412_heart	0.00 RPM	10.12 RPM
SRP007412_kidney	0.00 RPM	10.49 RPM
SRP007412_liver	0.00 RPM	22.91 RPM
SRP007412_testis	0.00 RPM	5.53 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3271 was not detected

EST

No EST(s) were mapped for retro_mmus_3271 retrocopy.

TSS

No TSS is located nearby retro_mmus_3271 retrocopy 5' end.

Lab

retro_mmus_3271 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3271 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002354	4 retrocopies	retro_cjac_2131, retro_cjac_2524, retro_cjac_3331, retro_cjac_4025,
Dasypus novemcinctus	ENSDNOG00000013348	1 retrocopy	retro_dnov_338,
Gorilla gorilla	ENSGGOG00000014385	1 retrocopy	retro_ggor_1756,
Macropus eugenii	ENSMEUG00000007002	2 retrocopies	retro_meug_1330, retro_meug_887,
Macaca mulatta	ENSMMUG00000019321	2 retrocopies	retro_mmul_1500, retro_mmul_2259,
Mus musculus	ENSMUSG00000006442	1 retrocopy	retro_mmus_3271 ,