RetrogeneDB ID: retro_mmus_1403

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 15:73407627..73408238(-)
• Located in intron of: ENSMUSG00000022607

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: Ptplb
• Ensembl ID: ENSMUSG00000035376
• Aliases: Ptplb, 6330408J20Rik, AI255777, AI481689, HACD2
• Description: protein tyrosine phosphatase-like (proline instead of catalytic arginine), member b [Source:MGI Symbol;Acc:MGI:1918007]

Sequence

>retro_mmus_1403
GCGGCGACTGCAGCGACCAAGGGGAATGGGGGCGGTAGTGGCCAAGCCGGGGCTGGCGACAGCAGCGGCGCCCAGAAGAA
GAAGGGCCCTGGGCCTGTGGCCACGGTGTACCTGGTCATCTACAATGTGGTGATGACTCGGGGTGGTTGGTGATAGCAGT
TGGGCTGGTGATAGCATACCTGGCTAAGGGGAGCTACCATAGCCTTTATTATTCAATAGAAAGGCCTTTGAAGTTCTTCC
AAACAGGAGCCTTACTGGAGATTTTACATTGTGCTATAGGGATTGTGTCATCTTCTGTTGTCCTGACTTCTTTCCAGGTG
ATGTCAAGAGTTTTCCTAATATGGGCAGTGACACATAGTGTCAAAGAGGTGCAGAGTGAAGACAGTGTACTTCTGTTTGT
CATTGCCTGGACAATCACGGAAATTATCCGTTACTCCTTTTACACATTCAGTCTATTAAACCATCTGCCTTACATCATCA
AATGGGCCAGGTACACACTTTTCATCGTGCTGTACCCAATGGGAGTGACAAGAGAGCTCCTCACAATATACGCAGCTCTG
CCCTTTGTCTGGCAGGCCGGCCTGTACTCCATCAGCTTACCTAACAAATAC

Alignment

ORF - retro_mmus_1403 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.12 %
• Parental protein coverage: 80.31 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AATAATKGNGGGSGRVGAGDSSGARKKKGPGPVATAYLVIYNVVMT-AGWLVIAVGLVRAYLAKGSYHSL
          AATAATKGNGGGSG..GAGDSSGA.KKKGPGPVAT.YLVIYNVVMT..GWLVIAVGLV.AYLAKGSYHSL
Retrocopy AATAATKGNGGGSGQAGAGDSSGAQKKKGPGPVATVYLVIYNVVMT<SGWLVIAVGLVIAYLAKGSYHSL

Parental  YYSIERPLKFFQTGALLEILHCAIGIVPSSVVLTSFQVMSRVFLIWAVTHSVKEVQSEDSVLLFVIAWTI
          YYSIERPLKFFQTGALLEILHCAIGIV.SSVVLTSFQVMSRVFLIWAVTHSVKEVQSEDSVLLFVIAWTI
Retrocopy YYSIERPLKFFQTGALLEILHCAIGIVSSSVVLTSFQVMSRVFLIWAVTHSVKEVQSEDSVLLFVIAWTI

Parental  TEIIRYSFYTFSLLNHLPYIIKWARYTLFIVLYPMGVTGELLTIYAALPFVRQAGLYSISLPNKY
          TEIIRYSFYTFSLLNHLPYIIKWARYTLFIVLYPMGVT.ELLTIYAALPFV.QAGLYSISLPNKY
Retrocopy TEIIRYSFYTFSLLNHLPYIIKWARYTLFIVLYPMGVTRELLTIYAALPFVWQAGLYSISLPNKY

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	0.19 RPM	24.55 RPM
SRP007412_cerebellum	0.13 RPM	15.85 RPM
SRP007412_heart	0.09 RPM	4.30 RPM
SRP007412_kidney	0.64 RPM	28.43 RPM
SRP007412_liver	0.68 RPM	26.52 RPM
SRP007412_testis	0.46 RPM	29.04 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1403 was not detected

EST

No EST(s) were mapped for retro_mmus_1403 retrocopy.

TSS

No TSS is located nearby retro_mmus_1403 retrocopy 5' end.

Lab

retro_mmus_1403 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1403 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000035376	1 retrocopy	retro_mmus_1403 ,
Mus musculus	ENSMUSG00000063275	1 retrocopy	retro_mmus_2120,
Otolemur garnettii	ENSOGAG00000014549	1 retrocopy	retro_ogar_2949,