RetrogeneDB ID: retro_mmus_291

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:6380393..6381029(+)
• Located in intron of: ENSMUSG00000087247

Retrocopy information

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

Parental gene information

• Parental gene symbol: Mospd1
• Ensembl ID: ENSMUSG00000023074
• Aliases: Mospd1, 1810018L05Rik
• Description: motile sperm domain containing 1 [Source:MGI Symbol;Acc:MGI:1917630]

Sequence

>retro_mmus_291
ATGCATCAACAAAAAAGACAACCAGAGTTAGTGGAAGGGAATCTTCCTGTCTTTGTGTTTCCCACGGAGCTAATATTTTA
TGCAGATGATCAGTCAACACATAAACAAGTGTTGACTCTGTACAATCCCTATGAGTTTGCTTTAAAGTTCAAAGTTTTGT
GTACGACTCCAAATAAGTATGTTGTCGTTGATGCTGCTGGTGCAGTGAAGCCACAGAGCTGTGTGGATATTGTGATTCGT
CATAGAGATGTTTGATTCTGTCACTATGGTGTGATAGACAAATTCCGCCTCCAGGTTTCTGAACAAAGCCAGAGGAAGGC
CTTGGGAAGGAAAGAGGTTATTGCCACCCTTCTCCCGTCTGCTAAAGAACAACAGAAGGAAGAGGAGAAGAGAATAAAGG
AACACTTAACCGAGAGTGTGTTTTTTGAGTAGTCATGTCAACCAGAAAACAGAGCCGTCTCTTCAGGACCTAGTTTGCTA
ACTGTCTTCCTGGGTGTGGGATGTATTGCGGCCCTGATGCTGCTTACTCTAGGGGATATGGAATCGCTGGTGCCTCTCTA
CCTCCACTTAAGTGTGAATCAAAAACTAGTGGCTGCTTATATCTTAGGTCTTATCACAATGGCTATACTTAGAACA

Alignment

ORF - retro_mmus_291 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.71 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MHQQKRQPELVEGNLPVFVFPTELIFYADDQSTHKQVLTLYNPYEFALKFKVLCTTPNKYVVVDAAGAVK
          MHQQKRQPELVEGNLPVFVFPTELIFYADDQSTHKQVLTLYNPYEFALKFKVLCTTPNKYVVVDAAGAVK
Retrocopy MHQQKRQPELVEGNLPVFVFPTELIFYADDQSTHKQVLTLYNPYEFALKFKVLCTTPNKYVVVDAAGAVK

Parental  PQCCVDIVIRHRDVRSCHYGVIDKFRLQVSEQSQRKALGRKEVIATLLPSAKEQQKEEEEKRIKEHLTES
          PQ.CVDIVIRHRDV..CHYGVIDKFRLQVSEQSQRKALGRKEVIATLLPSAKEQQK.EEEKRIKEHLTES
Retrocopy PQSCVDIVIRHRDV*FCHYGVIDKFRLQVSEQSQRKALGRKEVIATLLPSAKEQQK-EEEKRIKEHLTES

Parental  VFFEQSCQPENRAVSSGPSLLTVFLGVVCIAALMLPTLGDMESLVPLYLHLSVNQKLVAAYILGLITMAI
          VFFE.SCQPENRAVSSGPSLLTVFLGV.CIAALML.TLGDMESLVPLYLHLSVNQKLVAAYILGLITMAI
Retrocopy VFFE*SCQPENRAVSSGPSLLTVFLGVGCIAALMLLTLGDMESLVPLYLHLSVNQKLVAAYILGLITMAI

Parental  LRT
          LRT
Retrocopy LRT

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	7.24 RPM
SRP007412_cerebellum	0.00 RPM	5.86 RPM
SRP007412_heart	0.03 RPM	15.63 RPM
SRP007412_kidney	0.00 RPM	13.01 RPM
SRP007412_liver	0.03 RPM	6.47 RPM
SRP007412_testis	0.00 RPM	1.28 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_291 was not detected

EST

No EST(s) were mapped for retro_mmus_291 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_75510	782 libraries	281 libraries	7 libraries	2 libraries	0 libraries

The graphical summary, for retro_mmus_291 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_291 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_291 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001304	1 retrocopy	retro_amel_683,
Choloepus hoffmanni	ENSCHOG00000007386	5 retrocopies	retro_chof_1202, retro_chof_1623, retro_chof_201, retro_chof_2295, retro_chof_675,
Dasypus novemcinctus	ENSDNOG00000013117	4 retrocopies	retro_dnov_1825, retro_dnov_2650, retro_dnov_2660, retro_dnov_926,
Macaca mulatta	ENSMMUG00000022505	1 retrocopy	retro_mmul_133,
Monodelphis domestica	ENSMODG00000015178	1 retrocopy	retro_mdom_159,
Mus musculus	ENSMUSG00000023074	1 retrocopy	retro_mmus_291 ,
Otolemur garnettii	ENSOGAG00000005739	2 retrocopies	retro_ogar_2508, retro_ogar_528,
Sarcophilus harrisii	ENSSHAG00000011544	1 retrocopy	retro_shar_21,
Sus scrofa	ENSSSCG00000012686	1 retrocopy	retro_sscr_690,
Ictidomys tridecemlineatus	ENSSTOG00000008152	1 retrocopy	retro_itri_1303,
Tarsius syrichta	ENSTSYG00000006102	1 retrocopy	retro_tsyr_1785,