RetrogeneDB ID: retro_mmus_2896

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 7:12603822..12604645(+)
• Located in intron of: ENSMUSG00000096002

Retrocopy information

• Ensembl ID: ENSMUSG00000082872
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Psip1
• Ensembl ID: ENSMUSG00000028484
• Aliases: Psip1, AA408851, AU015605, Dfs70, Ledgfa, Ledgfb, Psip2
• Description: PC4 and SFRS1 interacting protein 1 [Source:MGI Symbol;Acc:MGI:2142116]

Sequence

>retro_mmus_2896
GAAGTTGAATCTAAACTGATAATTTTAGCTAAACCAGGGGTTACATCAACCTCTGATTCAGTAGACGAAAATGATCAAGA
GGGTGAAAAGAAGAGAAAGGGTGGAAGGAACTTCCAGGCTGCTCACGGGAGGAACATGCTAAAAGGCCAACATGAGAAAG
AAGCTGGAGATCGGAAACGCAAAGCAGGAGGAACAAATGGAAACTGAGCAGCAGAATAAAGATGAAGGAAAGAAACCAGA
AGTTAAGAAAGTGGAGAAGAAGCGAGAAACATCAATGGATTCTCGACTTCAAAGGATACATGCTGAAATTAAAAATTCAC
TCAAAATTGATAATCTAGATGTGAACAGATGCATAGAGGCACTAGGTGAACTTGCTTTACTTCAGGTAACAATGCAACAA
GGTCAGAAACACACAGAGATGATCACAACCCTGAAGAAAATACAGCAGTTCAAAGTCAGTCAAGTTATCATGGAAAAGTC
TACAATGTTATATAACAAGTTTAAGAATATGTTTTCGGTTGGTGAAGGAGATTCAGACATCACCCAAGTGCTGAACAAAT
CTCTTGCTGAACAGAGACAGCATGAGGAAGCAAATAAAACCAAAGACCAGGGGAAGAAAGGGCCAAACAAAAAGCTAGAG
AAGGAACACACAGGTACGAAGAGCCTAAATGGCAGATCTGATGCTCAAGAGAGTAACCATCCACAGCATAATGGTGACAG
TAACGAAGACAGCAAAGACAGCCACGAGGCCAGCAGTAAGACAAAGCCACCTGGAGAAGAGAGAGAGGCTGAAATATCTC
TGAAAGAGTCTACACTAGATCAC

Alignment

ORF - retro_mmus_2896 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.09 %
• Parental protein coverage: 51.89 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EVESKRKNLAKPGVTSTSDSEDEDDQEGEKKRKGGRNFQAAHRRNMLKGQHEKEAGDRKR-KQEEQMETE
          EVESK...LAKPGVTSTSDS.DE.DQEGEKKRKGGRNFQAAH.RNMLKGQHEKEAGDRKR.KQEEQMETE
Retrocopy EVESKLIILAKPGVTSTSDSVDENDQEGEKKRKGGRNFQAAHGRNMLKGQHEKEAGDRKR>KQEEQMETE

Parental  QQNKDEGKKPEVKKVEKKRETSMDSRLQRIHAEIKNSLKIDNLDVNRCIEALDELASLQVTMQQAQKHTE
          QQNKDEGKKPEVKKVEKKRETSMDSRLQRIHAEIKNSLKIDNLDVNRCIEAL.ELA.LQVTMQQ.QKHTE
Retrocopy QQNKDEGKKPEVKKVEKKRETSMDSRLQRIHAEIKNSLKIDNLDVNRCIEALGELALLQVTMQQGQKHTE

Parental  MITTLKKIRRFKVSQVIMEKSTMLYNKFKNMFLVGEGDSVITQVLNKSLAEQRQHEEANKTKDQGKKGPN
          MITTLKKI..FKVSQVIMEKSTMLYNKFKNMF.VGEGDS.ITQVLNKSLAEQRQHEEANKTKDQGKKGPN
Retrocopy MITTLKKIQQFKVSQVIMEKSTMLYNKFKNMFSVGEGDSDITQVLNKSLAEQRQHEEANKTKDQGKKGPN

Parental  KKLEKEPTGTKSLNGGSDAQESNHPQHNGDSNEDGKDSREASSKTKPPGEEREAEISLKESTLDN
          KKLEKE.TGTKSLNG.SDAQESNHPQHNGDSNED.KDS.EASSKTKPPGEEREAEISLKESTLD.
Retrocopy KKLEKEHTGTKSLNGRSDAQESNHPQHNGDSNEDSKDSHEASSKTKPPGEEREAEISLKESTLDH

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	0.05 RPM	125.58 RPM
SRP007412_cerebellum	0.00 RPM	114.89 RPM
SRP007412_heart	0.00 RPM	13.82 RPM
SRP007412_kidney	0.02 RPM	19.00 RPM
SRP007412_liver	0.00 RPM	13.95 RPM
SRP007412_testis	0.14 RPM	216.12 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2896 was not detected

EST

No EST(s) were mapped for retro_mmus_2896 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_128497	615 libraries	379 libraries	75 libraries	1 library	2 libraries
TSS #2	TSS_128498	885 libraries	156 libraries	29 libraries	1 library	1 library

The graphical summary, for retro_mmus_2896 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_2896 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2896 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012471	1 retrocopy	retro_cjac_4069,
Homo sapiens	ENSG00000164985	1 retrocopy	retro_hsap_4136,
Mus musculus	ENSMUSG00000004897	1 retrocopy	retro_mmus_3647,
Mus musculus	ENSMUSG00000028484	1 retrocopy	retro_mmus_2896 ,
Pan troglodytes	ENSPTRG00000020786	1 retrocopy	retro_ptro_2811,
Tupaia belangeri	ENSTBEG00000000715	1 retrocopy	retro_tbel_364,