RetrogeneDB ID: retro_mmus_79

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 16:13677038..13677977(+)
• Located in intron of: ENSMUSG00000022684

Retrocopy information

• Ensembl ID: ENSMUSG00000079737
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

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_79
ATGCTTCATATCCCGGTCATCCTTGGTCACCGTCCAGGATCAGTGTACAGAAGAGACAAGATGTGGCCTAACAGATCATA
TGATGAAGTACCTCAGAATGTCTCCAGTGATGAATCTACCCTGAGGAAAACAAGAGGTGATCTTTCTGCAAGCCAACAGC
ATGAGTGCGGGGATGAGAAAGATGACTTTAGAAGAAACTGTTCCTCTTCTTCCCATTACTCAGAACAGCAGTCTCCCCAT
AAAGGGGCTTCTTGTTTTTCCAGAAAATCAGGTATAGATCAGAAGAACTCCCCACACAGCAGATCTGGATCCAGTGGAAG
CCATTCTCCAAAACAAAGCAAACTGCATTCTTCCCATGGGTCAGAGCTTAGGAAGTCCGAGCATGCTCATTCCTCCTACA
AACGGCACAGTGAAGAAAAGCCAGAAGGAGGTAAAAAGAGGGCTGGCCAGTCTTTGAAAACATCAAGAGACACACACCCA
AAAAGTTCTTCAGCAGTTCCTTCGTCAGAAAGTTTAAACAAACTCAAAAGGCTTGATGAAAAGGGACGTCCTAAAGCTGC
AAGCAGGCAAGCTGTAGAAAAGCCAATGATGGCAGATGAAAGTGACTTACCTAAAATTTCTGAGTTTGAAGTTGGATTCT
CAGAACTTATGGATCAGCCACAAGAACCTGGGTCAAACAAAAAAGATCATACAGAATTCATTGATGACCAAGTAACCAAT
CGCCGTAAAGCAATAGTGTCAAAGACCAAGGAAATTGAACAAGCCTACTACCAAGACTGTGAGACCTTCGGAATGGTGGT
GAAAATGCTGGTTGAAAAAGACGCTTCATTAGAAAGGCCCATTCAGTTTGCGCTCCGGCAGAATTTACATGAACTAAGTG
AGCGCTGTGTGGAGGAGCTCAGGCAGTTCATTGCAGATTATGATGCTGCTGCTTCCTAA

Alignment

ORF - retro_mmus_79 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.36 %
• Parental protein coverage: 91.99 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PRSHPSDESGYRWLRDDHSTSRQPDYRDMRDGFRRKSFYSSHYSRDRSPHKRDAPFFRESPVGRKDSPHS
          P....SDES..R..R.D.S.S.Q....D..D.FRR....SSHYS...SPHK....F.R.S....K.SPHS
Retrocopy PQNVSSDESTLRKTRGDLSASQQHECGDEKDDFRRNCSSSSHYSEQQSPHKGASCFSRKSGIDQKNSPHS

Parental  RSGSSVSSRSYSPERSRTHSFHQSQHRKSSRVGASYKRQNEAIRGRGKERSIQSVKTSRDASPSSSSAVA
          RSG...SS.S.SP..S..HS.H.S..RKS.....SYKR..E.....GK.R..QS.KTSRD..P.SSSAV.
Retrocopy RSG---SSGSHSPKQSKLHSSHGSELRKSEHAHSSYKRHSEEKPEGGKKRAGQSLKTSRDTHPKSSSAVP

Parental  SSKALDKPSRLTEKELAEAESKWANETLEKSDESNLAEMNEFEAGSTAPLFIDQTEEPESNTVDGTELYE
          SS..L.K..RL.EK....A.S..A.E.....DES.L....EFE.G.......DQ..EP.SN..D.TE...
Retrocopy SSESLNKLKRLDEKGRPKAASRQAVEKPMMADESDLPKISEFEVGFSE--LMDQPQEPGSNKKDHTEFID

Parental  DSQLSNRSKAIASKTKEIEQVYRQDCETFGMVVKMLIEKDPSLEKSVQFALRQNLHEIGERCVEELKRFI
          D.Q..NR.KAI.SKTKEIEQ.Y.QDCETFGMVVKML.EKD.SLE...QFALRQNLHE..ERCVEEL..FI
Retrocopy D-QVTNRRKAIVSKTKEIEQAYYQDCETFGMVVKMLVEKDASLERPIQFALRQNLHELSERCVEELRQFI

Parental  TEYDNSA
          ..YD..A
Retrocopy ADYDAAA

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	1.14 RPM	30.37 RPM
SRP007412_cerebellum	1.17 RPM	25.23 RPM
SRP007412_heart	0.81 RPM	15.60 RPM
SRP007412_kidney	0.92 RPM	21.46 RPM
SRP007412_liver	1.67 RPM	12.23 RPM
SRP007412_testis	0.55 RPM	52.74 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_79 was not detected

EST

2 EST(s) were mapped to retro_mmus_79 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AA408436	13677477	13677716	98.8	236	2	232
AI155450	13676955	13677428	100	473	0	473

TSS

No TSS is located nearby retro_mmus_79 retrocopy 5' end.

Lab

retro_mmus_79 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_79 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,