RetrogeneDB ID: retro_mmus_1072

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 13:3138787..3140112(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ptbp1
• Ensembl ID: ENSMUSG00000006498
• Aliases: Ptbp1, AA407203, AL033359, HNRPI, PTB-1, PTB2, PTB3, PTB4, Ptb, pPTB
• Description: polypyrimidine tract binding protein 1 [Source:MGI Symbol;Acc:MGI:97791]

Sequence

>retro_mmus_1072
ATGGACGGCATCGTCCCAGACATAGCAGTCGGTACAAAGCAGGGATCCGACGAGCTCTTCTCCACGTGTGTCAGCAACGG
CCCCTTCATCATGAGCAGCTCTGCCTCAGCAGCCAATGGAAACGATAGCAAGAAGTTCAAAGGTGACAACAGGAGCGCAG
GAGTCCCTTCCAGAGTCATCCACGTCAGAAAGCTGCCCAGCGATGTCACTGAGGGCGAGGTCATCTCCCTAGGGCTGCCC
TTTGGAAAGGTTACCAACCTTCTTATGCTGAAGGGGAAGAACCAGGCCTTCACTGAAATGAACACAGAGGAGACTGCCAA
CACTATGGTTAACTACTATACATCGGTAGCGCCAGTGCTTCGTGGACAGCCCATCTACATCCAGTTCTCCAACCACAAAG
AGCTCGAGACCGACAGCTCGCCCAACCAGGCACGTGCCCAGGCAGCCCTGCAGGCTGTAAACTCTGTCCATTCTGGAAAC
CTGGCCTTGGCAGCGTCTGCTGCTGCCGTAGACGCAGGAATGGCAATGGCAGGGCAGAGTCCAGCGCTCAGGATCATTGT
CGAAAACCTTTTCTACCCAGTGACCCTGGACATGGTGCACCAGATCTTCTCTAAGTTTGGCACCGTCCTGAAGATCATCA
CATTCACCAAGAACAACCAGTTCCAGGCGCTGCTGCAGTATGCTGACCCTGTGAGTGCCCAGCATGCCAAGCTGTCCCTG
GATGGCTAGAACATCTACAACGCCTGCTGCACGCTACGCATTGACTTCTCCAAGCTCACCAGTCTCAACATCAAATACAA
CAATGATAAGAGCAGAGACTACACTCGACCTGACCTGCCATCTGGAGACAGCCAGCCTTCACTAGACCAGACCATGGCAG
CAGCCTTTGGTGCGCCCGGCATAATGTCAGCCTCTCCATATGCAGGAGCCCGGTTCATCCCACCTCAGGCCGCAGGCCTC
TCTGTCCCTAATGTCCATGGAGCCTTGGCTCCCCTGGCCATCTCGTCTGCTGCTGCTGCTGCTGCGGCCAGCTGCATTGC
CATCCCAGGGTTGGCAGGTGCTGGGAATTCCGTCCTTTTGGTCAGCAACCTGAACCCTGAGATAGTCACACCCCAAAGCC
TCTTTATTCTCTTCGGCGTCTACGGTGATGTGCAGCGGGTGAAGATCCTGTTCAATAAGGAGAAGCGCTTGTGCAGATGG
CAGACGGCAGCCAGGCCCAGCTGGCCATGAGCCACATGAACGGGCACAAGCACGGGAAGTCAGTGCGCATCACACTGTCC
AAGCATCAGAGTGTGCAGCTGCCTCGGGAGGGTCAGGAGGACCAG

Alignment

ORF - retro_mmus_1072 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.1 %
• Parental protein coverage: 80.72 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MDGIVPDIAVGTKRGSDELFSTCVSNGPFIMSSSASAANGNDSKKFKGDNRSAGVPSRVIHVRKLPSDVT
          MDGIVPDIAVGTK.GSDELFSTCVSNGPFIMSSSASAANGNDSKKFKGDNRSAGVPSRVIHVRKLPSDVT
Retrocopy MDGIVPDIAVGTKQGSDELFSTCVSNGPFIMSSSASAANGNDSKKFKGDNRSAGVPSRVIHVRKLPSDVT

Parental  EGEVISLGLPFGKVTNLLMLKGKNQAFIEMNTEEAANTMVNYYTSVAPVLRGQPIYIQFSNHKELKTDSS
          EGEVISLGLPFGKVTNLLMLKGKNQAF.EMNTEE.ANTMVNYYTSVAPVLRGQPIYIQFSNHKEL.TDSS
Retrocopy EGEVISLGLPFGKVTNLLMLKGKNQAFTEMNTEETANTMVNYYTSVAPVLRGQPIYIQFSNHKELETDSS

Parental  PNQARAQAALQAVNSVQSGNLALAASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVL
          PNQARAQAALQAVNSV.SGNLALAASAAAVDAGMAMAGQSP.LRIIVENLFYPVTLD..HQIFSKFGTVL
Retrocopy PNQARAQAALQAVNSVHSGNLALAASAAAVDAGMAMAGQSPALRIIVENLFYPVTLDMVHQIFSKFGTVL

Parental  KIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTSLNVKYNNDKSRDYTRPDLP
          KIITFTKNNQFQALLQYADPVSAQHAKLSLDG.NIYNACCTLRIDFSKLTSLN.KYNNDKSRDYTRPDLP
Retrocopy KIITFTKNNQFQALLQYADPVSAQHAKLSLDG*NIYNACCTLRIDFSKLTSLNIKYNNDKSRDYTRPDLP

Parental  SGDSQPSLDQTMAAAFGAPGIMSASPYAGAGFPPTFAIPQAAGLSVPNVHGALAPLAIPSAAAAAAASRI
          SGDSQPSLDQTMAAAFGAPGIMSASPYAGA.F.P....PQAAGLSVPNVHGALAPLAI........AS.I
Retrocopy SGDSQPSLDQTMAAAFGAPGIMSASPYAGARFIP----PQAAGLSVPNVHGALAPLAISXXXXXXXASCI

Parental  AIPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKEN-ALVQMADGSQAQLAMSHLN
          AIPGLAGAGNSVLLVSNLNPE.VTPQSLFILFGVYGDVQRVKILFN.KE..ALVQMADGSQAQLAMSH.N
Retrocopy AIPGLAGAGNSVLLVSNLNPEIVTPQSLFILFGVYGDVQRVKILFN-KEK<ALVQMADGSQAQLAMSHMN

Parental  GHKLHGKSVRITLSKHQSVQLPREGQEDQ
          GHK.HGKSVRITLSKHQSVQLPREGQEDQ
Retrocopy GHK-HGKSVRITLSKHQSVQLPREGQEDQ

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	22.78 RPM
SRP007412_cerebellum	0.00 RPM	31.78 RPM
SRP007412_heart	0.06 RPM	33.18 RPM
SRP007412_kidney	0.04 RPM	81.75 RPM
SRP007412_liver	0.11 RPM	63.82 RPM
SRP007412_testis	5.72 RPM	68.52 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1072 was not detected

EST

No EST(s) were mapped for retro_mmus_1072 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_28389	285 libraries	538 libraries	240 libraries	8 libraries	1 library
TSS #2	TSS_28390	330 libraries	551 libraries	188 libraries	2 libraries	1 library

The graphical summary, for retro_mmus_1072 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_1072 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1072 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Ciona savignyi	ENSCSAVG00000007421	1 retrocopy	retro_csav_17,
Equus caballus	ENSECAG00000018845	1 retrocopy	retro_ecab_330,
Echinops telfairi	ENSETEG00000006890	1 retrocopy	retro_etel_1573,
Macropus eugenii	ENSMEUG00000006710	2 retrocopies	retro_meug_1447, retro_meug_67,
Myotis lucifugus	ENSMLUG00000003320	1 retrocopy	retro_mluc_755,
Mus musculus	ENSMUSG00000006498	1 retrocopy	retro_mmus_1072 ,
Rattus norvegicus	ENSRNOG00000010448	2 retrocopies	retro_rnor_1994, retro_rnor_2478,