RetrogeneDB ID: retro_mmus_2120

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:162899082..162899511(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000083567
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Ptpla
• Ensembl ID: ENSMUSG00000063275
• Aliases: Ptpla, HACD1
• Description: protein tyrosine phosphatase-like (proline instead of catalytic arginine), member a [Source:MGI Symbol;Acc:MGI:1353592]

Sequence

>retro_mmus_2120
ATGGCGTCCAGTGAGGAGGACGGCACCAACGGCGCCTCCGAGGCCAGCGACGAGAAGGAAGCCGCCGGCAAGCGGAGACG
CCTAGGCTTACTGGCCACCGCCTGGCTCACCTTCTACAATATCGCCATGACGGCCGGGTGGTTGGTTCTTGCTATTGCTA
TGGCATGCTTTTATATGGAAAAAGGAACACACAGAGGTTTATATAAAAGCATTCAGAAGACACTTAAGTTTTTCCAAACA
TTTGCTTTGCTTGAGGTAGTCCATTGTCTGATCGGAATTGTACCCACTTCTGTGCTTGTGACTGGGGTCCAAGTGAGCTC
AAGAATCTTCATGGTGTGGCTCATTACTCACAGTATAAAACCCATACAATTTGTTTATCATCTTATATCCCGTTGGAGTT
GCTGGGGAACTTCTCACAATATACGCCGT

Alignment

ORF - retro_mmus_2120 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.6 %
• Parental protein coverage: 86.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MASSEEDGTNGASEASDEKEAAGKRRRLGLLATAWLTFYNIAMTAGWLVLAIAMVRFYMEKGTHRGLYKS
          MASSEEDGTNGASEASDEKEAAGKRRRLGLLATAWLTFYNIAMTAGWLVLAIAM..FYMEKGTHRGLYKS
Retrocopy MASSEEDGTNGASEASDEKEAAGKRRRLGLLATAWLTFYNIAMTAGWLVLAIAMACFYMEKGTHRGLYKS

Parental  IQKTLKFFQTFALLEVVHCLIGIVPTSVLVTGVQVSSRIFMVWLITHSIKPIQFVYHLISRWSCWGTSHN
          IQKTLKFFQTFALLEVVHCLIGIVPTSVLVTGVQVSSRIFMVWLITHSIKPIQFVYHLISRWSCWGTSHN
Retrocopy IQKTLKFFQTFALLEVVHCLIGIVPTSVLVTGVQVSSRIFMVWLITHSIKPIQFVYHLISRWSCWGTSHN

Parental  IRR
          IRR
Retrocopy IRR

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	3.18 RPM
SRP007412_cerebellum	0.26 RPM	2.82 RPM
SRP007412_heart	0.72 RPM	17.99 RPM
SRP007412_kidney	0.38 RPM	4.77 RPM
SRP007412_liver	0.16 RPM	3.00 RPM
SRP007412_testis	0.37 RPM	11.66 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2120 was not detected

EST

No EST(s) were mapped for retro_mmus_2120 retrocopy.

TSS

No TSS is located nearby retro_mmus_2120 retrocopy 5' end.

Lab

retro_mmus_2120 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2120 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000008663	1 retrocopy	retro_cjac_266,
Mus musculus	ENSMUSG00000035376	1 retrocopy	retro_mmus_1403,
Mus musculus	ENSMUSG00000063275	1 retrocopy	retro_mmus_2120 ,