RetrogeneDB ID: retro_mmus_2522

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 4:143611660..143612077(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000044377
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Trappc2
• Ensembl ID: ENSMUSG00000079317
• Aliases: None
• Description: trafficking protein particle complex 2 [Source:MGI Symbol;Acc:MGI:1913476]

Sequence

>retro_mmus_2522
ATGTCTGGGAGCTTCTACTTCGTAATTGTTGGCCACCATGATAATCCAGTTTTTGAAATGGAATTTTTGCCACCTGGGAA
AGCAGAATCCAAAGATGATCACCGTCATCTGAACCAGTTTATAGCTCATGCTGCTCTTGACCTTGTGGACGAAAATATGT
GGCTTTCGAACAACATGTACTTAAAAACGGTGGACAAATTTAATGAGTGAAAGACCACGCCTTAACTCTCTGCACATATG
AGATTTATTATGCTTCATGATGTGAGGCAAGAAGATGGGATAAAGAACTTCTTTACTGATGTCTATGATCTGTATATAAA
GTTTGCAATGAATCCATTTTATGAACCCAATTCTCCCATTCGATCGAGTGCATTCGACAGGAAAGTCCAATTTCTTGGGA
AGAAACACCTTTTAAGC

Alignment

ORF - retro_mmus_2522 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.57 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSGSFYFVIVGHHDNPVFEMEFLPPGKAESKDDHRHLNQFIAHAALDLVDENMWLSNNMYLKTVDKFNEW
          MSGSFYFVIVGHHDNPVFEMEFLPPGKAESKDDHRHLNQFIAHAALDLVDENMWLSNNMYLKTVDKFNE.
Retrocopy MSGSFYFVIVGHHDNPVFEMEFLPPGKAESKDDHRHLNQFIAHAALDLVDENMWLSNNMYLKTVDKFNE*

Parental  FVSAFVTAGHMRFIMLHDVRQEDGIKNFFTDVYDLYIKFAMNPFYEPNSPIRSSAFDRKVQFLGKKHLLS
          .......A.HMRFIMLHDVRQEDGIKNFFTDVYDLYIKFAMNPFYEPNSPIRSSAFDRKVQFLGKKHLLS
Retrocopy KTTP*LSA-HMRFIMLHDVRQEDGIKNFFTDVYDLYIKFAMNPFYEPNSPIRSSAFDRKVQFLGKKHLLS

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	0.09 RPM	11.12 RPM
SRP007412_cerebellum	0.04 RPM	7.16 RPM
SRP007412_heart	0.00 RPM	2.68 RPM
SRP007412_kidney	0.00 RPM	2.66 RPM
SRP007412_liver	0.03 RPM	1.20 RPM
SRP007412_testis	0.00 RPM	0.46 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2522 was not detected

EST

No EST(s) were mapped for retro_mmus_2522 retrocopy.

TSS

No TSS is located nearby retro_mmus_2522 retrocopy 5' end.

Lab

retro_mmus_2522 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2522 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000001719	1 retrocopy	retro_acar_53,
Canis familiaris	ENSCAFG00000011754	2 retrocopies	retro_cfam_1608, retro_cfam_368,
Homo sapiens	ENSG00000196459	1 retrocopy	retro_hsap_73,
Microcebus murinus	ENSMICG00000004690	1 retrocopy	retro_mmur_1022,
Macaca mulatta	ENSMMUG00000022619	1 retrocopy	retro_mmul_326,
Monodelphis domestica	ENSMODG00000017312	2 retrocopies	retro_mdom_1737, retro_mdom_1901,
Mus musculus	ENSMUSG00000079317	2 retrocopies	retro_mmus_198, retro_mmus_2522 ,
Otolemur garnettii	ENSOGAG00000002870	2 retrocopies	retro_ogar_369, retro_ogar_60,
Pan troglodytes	ENSPTRG00000021674	1 retrocopy	retro_ptro_72,
Sorex araneus	ENSSARG00000006353	1 retrocopy	retro_sara_244,
Ictidomys tridecemlineatus	ENSSTOG00000025097	1 retrocopy	retro_itri_1014,