RetrogeneDB ID: retro_mmus_3517

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:121913226..121913991(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000084110
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Trim5
• Ensembl ID: ENSMUSG00000060441
• Aliases: Trim5, EG667823, Gm8833
• Description: tripartite motif-containing 5 [Source:MGI Symbol;Acc:MGI:3646853]

Sequence

>retro_mmus_3517
TCAGACATAGAAATACTGCAGGGTGTGGAGAACATCATAAAACGGAGTCATACTTTTTCGATGAAGAAGCCCAAAACCAT
CGCCAGGGAACAAAGAAAGTTCAGAGCTCCTGACCTGCAAGGCATGCTGCAAGTGCTGCAAGAGGTCGCAGAGGCTCAAC
GCTACTGGGTTCAGGTGACCCTGGTTCAAAACAACCATCCAAACATTGCCATTACTGACGACAAAAGACAAGTACGATAT
GAAGACCACCAAGCAAGTAATCTTATACCCGGGTGTGAAAACTCTCATGAAGGCGTCCTGGGACATCCAGCTATCCAATC
TGGAAAACATTACTGGGAAGTAGATGTGTCTAGAAAAGGTGCTTGGGTTCTGGGGTTAAGTGATGGAAGCTACCTCTTCT
GTCCAATATTTCATTCAAATGCTGAAAGAAATCGTTTATTTTGTAGGGGGATTAAGAATGATTCACATTATCAACCAAAA
TATGGCTTCTGGGTTATAGGGCTGTGGAAAAAGTCTGAGTATAATGCTTTTGAGGAGTGTCCTTTCACAGGCAAGCCCAG
TGTCTTGTCCCTGTCTCTGATGGTCCCGCCCTGTCGTGTTGGTGTTTTCCTTGACTATGCAGCTGGCACTCTCTCATTTT
ACAATATTTCCAACAATGGGACTCTTATCTACAGATTCTGTACAGCTTCCTTTCCTGATAGGGTTTTTCCATATTTTAAT
CCCACGGGAAGTTCAGAGCCGATGACAATTTGCTGGCCAGACTCT

Alignment

ORF - retro_mmus_3517 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.25 %
• Parental protein coverage: 51.31 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SDIEILQGVENIIKRSLTFSMKKPKTIAREQRKFRAPDLQGMLQVLQEVTEAQRYWVQVTLVQNNHPNIA
          SDIEILQGVENIIKRS.TFSMKKPKTIAREQRKFRAPDLQGMLQVLQEV.EAQRYWVQVTLVQNNHPNIA
Retrocopy SDIEILQGVENIIKRSHTFSMKKPKTIAREQRKFRAPDLQGMLQVLQEVAEAQRYWVQVTLVQNNHPNIA

Parental  ITDDKRQVRYEDHQASNLIHECENSHEGVLGHPAIQSGKHYWEVDVSGKGAWVLGLSDGSYLFCPIFHSN
          ITDDKRQVRYEDHQASNLI..CENSHEGVLGHPAIQSGKHYWEVDVS.KGAWVLGLSDGSYLFCPIFHSN
Retrocopy ITDDKRQVRYEDHQASNLIPGCENSHEGVLGHPAIQSGKHYWEVDVSRKGAWVLGLSDGSYLFCPIFHSN

Parental  AERNRLFCRGIKNDSHYQPKYGFWVIGLWKKSVYNAFEECPFTGKPSVLTLSLMVPPCRVGVFLDYAAGT
          AERNRLFCRGIKNDSHYQPKYGFWVIGLWKKS.YNAFEECPFTGKPSVL.LSLMVPPCRVGVFLDYAAGT
Retrocopy AERNRLFCRGIKNDSHYQPKYGFWVIGLWKKSEYNAFEECPFTGKPSVLSLSLMVPPCRVGVFLDYAAGT

Parental  LSFYNISNNGTLIYRFCTASFPDRVFPYFNPTGSSEPMTICWPDS
          LSFYNISNNGTLIYRFCTASFPDRVFPYFNPTGSSEPMTICWPDS
Retrocopy LSFYNISNNGTLIYRFCTASFPDRVFPYFNPTGSSEPMTICWPDS

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	0.56 RPM
SRP007412_cerebellum	0.26 RPM	1.56 RPM
SRP007412_heart	0.03 RPM	1.56 RPM
SRP007412_kidney	0.31 RPM	5.79 RPM
SRP007412_liver	0.14 RPM	3.44 RPM
SRP007412_testis	0.00 RPM	0.69 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3517 was not detected

EST

No EST(s) were mapped for retro_mmus_3517 retrocopy.

TSS

No TSS is located nearby retro_mmus_3517 retrocopy 5' end.

Lab

retro_mmus_3517 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3517 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000060441	1 retrocopy	retro_mmus_3517 ,