RetrogeneDB ID: retro_mmus_1569

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 17:37130908..37131502(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000092223
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Pbdc1
• Ensembl ID: ENSMUSG00000031226
• Aliases: Pbdc1, 2610029G23Rik
• Description: polysaccharide biosynthesis domain containing 1 [Source:MGI Symbol;Acc:MGI:1914933]

Sequence

>retro_mmus_1569
ATGGATGCTGCTGGCGAAAGTGAAGAGCTGGTCTCTGGGGAAGCGTTGTCCATAGCCCATGCTCTCTCTCACTCTCCGGA
GTCATATGGCAACGGCCCTGATATTGAAATGGCTTGAGCCATTCGAGCAATGCAGCATGCTGAAATCTATTATAAACTGA
TTCATCAGCTGACCCACAGTTTCTGAAACTCACCAAAGTAGATGACCAAATCTGAGTTCCATTCCGTGAGATTTTTGAGA
CACTCAGGGTAGATGTATTGGACCCAGAAGAACTCAAATCAGAATCAGCTAAAGAAAAGTGGAGACCATTCTGCTTAAAA
TTTGAAGGGATCGTAGAAGATTATAACTACGGGACTTTACTGCGACTGGATTGTTTCCAGGGCTACTCTGAAGAGAACAC
CATCTTTGCACCCAGGATTCAATTTTTTTGCCATTGAAATTGCTCGGAACCGGGAAGGCTATAACAAAGCAGTTTCCATC
AGTATTCAGGACAAAGAAGGAGAGGAAGGAGCTGGCAATAAAGAAGAAGAAGCTGAGAAAGGAGCTGGTAGTGGAGGAGA
AAAAGAGGAAGGAGCCAACAGAGAAGGAGAAAAG

Alignment

ORF - retro_mmus_1569 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92. %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MDAAGESEEPVSGEALSIAHALSHPPESYGNDPDIEMAWAIRAMQHAEVYYKLI-SSVDPQFLKLTKVDD
          MDAAGESEE.VSGEALSIAHALSH.PESYGN.PDIEMA.AIRAMQHAE.YYKLI.SS.DPQFLKLTKVDD
Retrocopy MDAAGESEELVSGEALSIAHALSHSPESYGNGPDIEMA*AIRAMQHAEIYYKLI<SSADPQFLKLTKVDD

Parental  QIYSEFREIFETLRVDVLDPEELKSESAKEKWRPFCLKFEGIVEDYNYGTLLRLDCSQGYTEENTIFAPR
          QI...FREIFETLRVDVLDPEELKSESAKEKWRPFCLKFEGIVEDYNYGTLLRLDC.QGY.EENTIFAPR
Retrocopy QI*VPFREIFETLRVDVLDPEELKSESAKEKWRPFCLKFEGIVEDYNYGTLLRLDCFQGYSEENTIFAPR

Parental  IQ-FFAIEIARNREGYNKAVSVSIQDKEGEEGAGNKEEAAEKGADSGGEKEEGANREGEK
          IQ.FFAIEIARNREGYNKAVS.SIQDKEGEEGAGNKEE.AEKGA.SGGEKEEGANREGEK
Retrocopy IQ>FFAIEIARNREGYNKAVSISIQDKEGEEGAGNKEEEAEKGAGSGGEKEEGANREGEK

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	12.20 RPM
SRP007412_cerebellum	0.00 RPM	9.77 RPM
SRP007412_heart	0.00 RPM	8.72 RPM
SRP007412_kidney	0.02 RPM	13.59 RPM
SRP007412_liver	0.00 RPM	8.27 RPM
SRP007412_testis	0.09 RPM	8.42 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1569 was not detected

EST

No EST(s) were mapped for retro_mmus_1569 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_53874	573 libraries	457 libraries	42 libraries	0 libraries	0 libraries

The graphical summary, for retro_mmus_1569 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_mmus_1569 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1569 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000017228	2 retrocopies	retro_cfam_1588, retro_cfam_944,
Callithrix jacchus	ENSCJAG00000018571	1 retrocopy	retro_cjac_1880,
Equus caballus	ENSECAG00000009882	1 retrocopy	retro_ecab_532,
Erinaceus europaeus	ENSEEUG00000001116	1 retrocopy	retro_eeur_377,
Monodelphis domestica	ENSMODG00000009685	2 retrocopies	retro_mdom_1002, retro_mdom_572,
Mus musculus	ENSMUSG00000031226	1 retrocopy	retro_mmus_1569 ,
Oryctolagus cuniculus	ENSOCUG00000001088	3 retrocopies	retro_ocun_1017, retro_ocun_1402, retro_ocun_595,
Otolemur garnettii	ENSOGAG00000015205	1 retrocopy	retro_ogar_3063,
Rattus norvegicus	ENSRNOG00000002662	3 retrocopies	retro_rnor_1703, retro_rnor_1705, retro_rnor_826,
Sarcophilus harrisii	ENSSHAG00000017872	1 retrocopy	retro_shar_132,
Tupaia belangeri	ENSTBEG00000003411	3 retrocopies	retro_tbel_3448, retro_tbel_494, retro_tbel_979,