RetrogeneDB ID: retro_mmus_973

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 12:101221995..101222418(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Myl1
• Ensembl ID: ENSMUSG00000061816
• Aliases: Myl1, AI325107, MLC1f, MLC3f, Mylf
• Description: myosin, light polypeptide 1 [Source:MGI Symbol;Acc:MGI:97269]

Sequence

>retro_mmus_973
GACTTCAAGGAGGCATTTCTCCTGTTTGACAGAACAGGTGAATGCAAGATCACCTTAAGTCAGGTGGGAGACGTCCTCCG
GGCTCTGGGCACCAATCCCATCAATGCAGAGGTCAAGAAGGTTCTTGGGAACCCCAGCAATGAAGAGATGAATGCTAAGA
AAATCGAGTTTGAACAGTTTCTGCCCATGATGCAAGCTATCTCCAACAACAAGGACCAGGGAGGTTATGAAGATTTCGTT
GAGGGTCTGCGTGTCTTCGACAAGGAGGACAATGGCACCGTCATGGGTGCTGAACTCCGCCATGTCCTCGCCACTCTGGG
AGAGAAGATGAAGGAGGAAGAGGTAGAAGCGTTGCTGGCAGGCCAGGAGGACTCCAATGGCTGCATCAACTAGGAAGCTT
TTGTCAAACACATCATGTCTGTC

Alignment

ORF - retro_mmus_973 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.87 %
• Parental protein coverage: 94. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DFKEAFLLFDRTGECKITLSQVGDVLRALGTNPTNAEVKKVLGNPSNEEMNAKKIEFEQFLPMMQAISNN
          DFKEAFLLFDRTGECKITLSQVGDVLRALGTNP.NAEVKKVLGNPSNEEMNAKKIEFEQFLPMMQAISNN
Retrocopy DFKEAFLLFDRTGECKITLSQVGDVLRALGTNPINAEVKKVLGNPSNEEMNAKKIEFEQFLPMMQAISNN

Parental  KDQGGYEDFVEGLRVFDKEGNGTVMGAELRHVLATLGEKMKEEEVEALLAGQEDSNGCINYEAFVKHIMS
          KDQGGYEDFVEGLRVFDKE.NGTVMGAELRHVLATLGEKMKEEEVEALLAGQEDSNGCIN.EAFVKHIMS
Retrocopy KDQGGYEDFVEGLRVFDKEDNGTVMGAELRHVLATLGEKMKEEEVEALLAGQEDSNGCIN*EAFVKHIMS

Parental  V
          V
Retrocopy V

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	0.26 RPM
SRP007412_cerebellum	0.00 RPM	0.39 RPM
SRP007412_heart	0.28 RPM	25.59 RPM
SRP007412_kidney	0.02 RPM	4.97 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.05 RPM	0.23 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_973 was not detected

EST

No EST(s) were mapped for retro_mmus_973 retrocopy.

TSS

No TSS is located nearby retro_mmus_973 retrocopy 5' end.

Lab

retro_mmus_973 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_973 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008609	2 retrocopies	retro_chof_1485, retro_chof_2467,
Macropus eugenii	ENSMEUG00000006905	5 retrocopies	retro_meug_1796, retro_meug_21, retro_meug_537, retro_meug_87, retro_meug_914,
Mus musculus	ENSMUSG00000061816	1 retrocopy	retro_mmus_973 ,
Mus musculus	ENSMUSG00000090841	7 retrocopies	retro_mmus_1281, retro_mmus_1504, retro_mmus_2328, retro_mmus_3231, retro_mmus_3333, retro_mmus_3358, retro_mmus_434,
Sorex araneus	ENSSARG00000002568	1 retrocopy	retro_sara_196,
Tarsius syrichta	ENSTSYG00000007599	3 retrocopies	retro_tsyr_1284, retro_tsyr_1539, retro_tsyr_2003,