RetrogeneDB ID: retro_mmus_2464

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 4:57413716..57414082(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000081540
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Ormdl3
• Ensembl ID: ENSMUSG00000038150
• Aliases: Ormdl3, 2810011N17Rik, AI315223
• Description: ORM1-like 3 (S. cerevisiae) [Source:MGI Symbol;Acc:MGI:1913862]

Sequence

>retro_mmus_2464
GGACTCCTGCATGTCGTGCTGCTGAGCATTCCCTTTGTGAGCGTCCCTGTCGTCTGGACCCTCACCAACCTTATCCACAA
CCTGGGCATGTACGTCTTTCTGCACACCGTGAAAGGGACACCCTTCGAGACTCCAGACCAAGGCAAAGCAAGGTTGCTGA
CCCACTGGGAGCAGATGGACCACGAGGTTCAGTTCACAGCCTCTAGGAAGTTCTTAACCATCACGCCTATTGTGCTGTAC
TTCCTCACCAGCTTCTACACCAAGTATGACCAAGTCCATTTCATACTCAACACAGTGTCCTTGATGACTGTGCTCATGCC
CAAGTTTCCCCAGCTCCACGGAGTCCGGATCTTTGGAATCAATAAG

Alignment

ORF - retro_mmus_2464 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.9 %
• Parental protein coverage: 79.74 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GLLHVVLLSIPFVSVPVVWTLTNLIHNLGMYIFLHTVKGTPFETPDQGKARLLTHWEQMDYGVQFTASRK
          GLLHVVLLSIPFVSVPVVWTLTNLIHNLGMY.FLHTVKGTPFETPDQGKARLLTHWEQMD..VQFTASRK
Retrocopy GLLHVVLLSIPFVSVPVVWTLTNLIHNLGMYVFLHTVKGTPFETPDQGKARLLTHWEQMDHEVQFTASRK

Parental  FLTITPIVLYFLTSFYTKYDQVHFILNTVSLMTVLIPKLPQLHGVRIFGINK
          FLTITPIVLYFLTSFYTKYDQVHFILNTVSLMTVL.PK.PQLHGVRIFGINK
Retrocopy FLTITPIVLYFLTSFYTKYDQVHFILNTVSLMTVLMPKFPQLHGVRIFGINK

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	35.65 RPM
SRP007412_cerebellum	0.00 RPM	45.03 RPM
SRP007412_heart	0.00 RPM	36.17 RPM
SRP007412_kidney	0.02 RPM	31.22 RPM
SRP007412_liver	0.03 RPM	55.00 RPM
SRP007412_testis	0.05 RPM	68.75 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2464 was not detected

EST

No EST(s) were mapped for retro_mmus_2464 retrocopy.

TSS

No TSS is located nearby retro_mmus_2464 retrocopy 5' end.

Lab

retro_mmus_2464 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2464 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000031660	1 retrocopy	retro_fcat_730,
Macropus eugenii	ENSMEUG00000000957	3 retrocopies	retro_meug_1234, retro_meug_130, retro_meug_2052,
Mus musculus	ENSMUSG00000025353	1 retrocopy	retro_mmus_2646,
Mus musculus	ENSMUSG00000038150	1 retrocopy	retro_mmus_2464 ,
Sarcophilus harrisii	ENSSHAG00000014339	1 retrocopy	retro_shar_372,