RetrogeneDB ID: retro_mmus_3561

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:169369331..169370003(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000081137
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Pphln1
• Ensembl ID: ENSMUSG00000036167
• Aliases: Pphln1, CR, HSPC206, HSPC232
• Description: periphilin 1 [Source:MGI Symbol;Acc:MGI:1917029]

Sequence

>retro_mmus_3561
AAAAGGGATGCTCCTTTCGTCAGAGAATCAACTGCAGGGTGGAAGAACTCCCAACACAACAGATCTGGCTCCATTATCAG
TGGTAGAAGCTATGCTCTGGAGCAAAGTAAGACACATTTATCTCCTAAGTCTCAGAATACACTTAAAGATGGATCCAAGC
AATCTTTGAAAATTTCAAGAGATAATTCATCCCCAAGATCATCAGCAGTTTCTTCATCCAAGATGTTAGACAAAACCATC
AAGCTAACTGAGAAGGAACTTGCTGAGGCTGAAAGCAAGTGGGCTAACGAAACACTAGAGCAGTCCAACAAAAATCACTT
GACTGAAATTTCTAAGTTTCAGGTGAGATCCATGGCACCCCTAGTTATTGATCAGACAGAAGGACCCAAGTCAAATACAG
AAAATGCCATAGCAATGAATGAAGACAGCCAACTTAGCAGCCGCACTAAAGCCATCATATCGAAGACCAAACAGATCGAG
GAGGTTTACCTACAATATTGTGAGACTTTTGCAATAGTGGTGAAAATGCTGCTTGACAAAGACCCCTCATTACAAAAGTC
TATCCAGTTTGCACTGAGACAAAATTTACAGGAAATGAGTGAGCGCTGTGTTGAAGAACTCAACTGTTTCATTACTGAGT
ATGATAATTCTCAAGATTTCGGAGACCCTTTT

Alignment

ORF - retro_mmus_3561 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.78 %
• Parental protein coverage: 76.79 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KRDAPFFRESPVGRKDSPHSRSGSSVSSRSYSPERSRTHSFHQSQHRSKERSIQSVKTSRDASPSSSSAV
          KRDAPF.RES..G.K.S.H.RSGS..S.RSY..E.S.TH....SQ...K..S.QS.K.SRD.S...SSAV
Retrocopy KRDAPFVRESTAGWKNSQHNRSGSIISGRSYALEQSKTHLSPKSQNTLKDGSKQSLKISRDNSSPRSSAV

Parental  ASSKALDKPSRLTEKELAEAESKWANETLEKSDESNLAEMNEFEAGSTAPLFIDQTEEPESNTVDGTELY
          .SSK.LDK...LTEKELAEAESKWANETLE.S....L.E...F...S.APL.IDQTE.P.SNT.......
Retrocopy SSSKMLDKTIKLTEKELAEAESKWANETLEQSNKNHLTEISKFQVRSMAPLVIDQTEGPKSNTENAIAMN

Parental  EDSQLSNRSKAIASKTKEIEQVYRQDCETFGMVVKMLIEKDPSLEKSVQFALRQNLHEIGERCVEELKRF
          EDSQLS.R.KAI.SKTK.IE.VY.Q.CETF..VVKML..KDPSL.KS.QFALRQNL.E..ERCVEEL..F
Retrocopy EDSQLSSRTKAIISKTKQIEEVYLQYCETFAIVVKMLLDKDPSLQKSIQFALRQNLQEMSERCVEELNCF

Parental  ITEYDNSAQDFGDPF
          ITEYDNS.QDFGDPF
Retrocopy ITEYDNS-QDFGDPF

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	3.18 RPM	30.37 RPM
SRP007412_cerebellum	3.56 RPM	25.23 RPM
SRP007412_heart	0.12 RPM	15.60 RPM
SRP007412_kidney	0.15 RPM	21.46 RPM
SRP007412_liver	0.03 RPM	12.23 RPM
SRP007412_testis	4.25 RPM	52.74 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_3561 was not detected

EST

No EST(s) were mapped for retro_mmus_3561 retrocopy.

TSS

No TSS is located nearby retro_mmus_3561 retrocopy 5' end.

Lab

retro_mmus_3561 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3561 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010693	1 retrocopy	retro_chof_1231,
Callithrix jacchus	ENSCJAG00000017726	1 retrocopy	retro_cjac_1547,
Cavia porcellus	ENSCPOG00000012266	2 retrocopies	retro_cpor_744, retro_cpor_745,
Dasypus novemcinctus	ENSDNOG00000002007	1 retrocopy	retro_dnov_1790,
Equus caballus	ENSECAG00000016067	1 retrocopy	retro_ecab_209,
Mus musculus	ENSMUSG00000036167	3 retrocopies	retro_mmus_1657, retro_mmus_3561 , retro_mmus_79,
Otolemur garnettii	ENSOGAG00000004012	2 retrocopies	retro_ogar_1387, retro_ogar_2103,
Tarsius syrichta	ENSTSYG00000010740	1 retrocopy	retro_tsyr_2044,