RetrogeneDB ID: retro_mmus_2072

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:104714308..104714671(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000074997
• Aliases: Pin1rt1, OTTMUSG00000014964, Pin1-ps1, Pin1l
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Pin1
• Ensembl ID: ENSMUSG00000032171
• Aliases: Pin1, 0610025L01Rik, D9Bwg1161e
• Description: protein (peptidyl-prolyl cis/trans isomerase) NIMA-interacting 1 [Source:MGI Symbol;Acc:MGI:1346036]

Sequence

>retro_mmus_2072
GGCAGCAGCAAGAACGGCCAGGGTGAGCCTGCCAGGGTGCGCTGCTCACACCTGCTGGTGAAGCACAGCCAATCTCGGAG
GCCCTCATCCTGGCGCCAGGAAAAGATCACCAGGAGCAAGGAGGAGGCCCTGGAGCTCATCAATGGCTACATCCGGAAGA
TTAAGTCAGGAGAGGAGGACTTTGAATCTCTGGCCTCACAGTTCAGTGACTGCAGCTCTGCCAAAGCCAGGGGAGACCTG
GGTGCCTTCAGCAGAGGACAGATGGAGAAACCGTTTGAGGATGCATCGTTTGCTCTACGGACTGGGGAGATGAGTGGGCC
CGTGTTCACGGAGTCAGGCATCCATATCATCCTGCGCACAGAA

Alignment

ORF - retro_mmus_2072 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.87 %
• Parental protein coverage: 73.33 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GSSKNGQGEPAKVRCSHLLVKHSQSRRPSSWRQEKITRSKEEALELINGYIQKIKSGEEDFESLASQFSD
          GSSKNGQGEPA.VRCSHLLVKHSQSRRPSSWRQEKITRSKEEALELINGYI.KIKSGEEDFESLASQFSD
Retrocopy GSSKNGQGEPARVRCSHLLVKHSQSRRPSSWRQEKITRSKEEALELINGYIRKIKSGEEDFESLASQFSD

Parental  CSSAKARGDLGPFSRGQMQKPFEDASFALRTGEMSGPVFTDSGIHIILRTE
          CSSAKARGDLG.FSRGQM.KPFEDASFALRTGEMSGPVFT.SGIHIILRTE
Retrocopy CSSAKARGDLGAFSRGQMEKPFEDASFALRTGEMSGPVFTESGIHIILRTE

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	40.44 RPM
SRP007412_cerebellum	0.04 RPM	33.30 RPM
SRP007412_heart	0.00 RPM	28.64 RPM
SRP007412_kidney	0.04 RPM	21.23 RPM
SRP007412_liver	0.00 RPM	10.13 RPM
SRP007412_testis	1.51 RPM	22.23 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2072 was not detected

EST

No EST(s) were mapped for retro_mmus_2072 retrocopy.

TSS

No TSS is located nearby retro_mmus_2072 retrocopy 5' end.

Lab

retro_mmus_2072 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2072 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006079	1 retrocopy	retro_cjac_2925,
Homo sapiens	ENSG00000127445	1 retrocopy	retro_hsap_168,
Gorilla gorilla	ENSGGOG00000006008	1 retrocopy	retro_ggor_252,
Microcebus murinus	ENSMICG00000001996	1 retrocopy	retro_mmur_1157,
Mus musculus	ENSMUSG00000032171	1 retrocopy	retro_mmus_2072 ,
Nomascus leucogenys	ENSNLEG00000011999	1 retrocopy	retro_nleu_980,
Pongo abelii	ENSPPYG00000009537	1 retrocopy	retro_pabe_462,
Pan troglodytes	ENSPTRG00000010452	1 retrocopy	retro_ptro_159,
Rattus norvegicus	ENSRNOG00000020474	1 retrocopy	retro_rnor_1220,
Tupaia belangeri	ENSTBEG00000003793	1 retrocopy	retro_tbel_1546,