RetrogeneDB ID: retro_mmus_1609

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 17:6121210..6122062(-)
• Located in intron of: ENSMUSG00000034377

Retrocopy information

• Ensembl ID: ENSMUSG00000051639
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Fbl
• Ensembl ID: ENSMUSG00000046865
• Aliases: Fbl, AL022665, FIB, FLRN, RNU3IP1
• Description: fibrillarin [Source:MGI Symbol;Acc:MGI:95486]

Sequence

>retro_mmus_1609
GGCGGTGGAGGTCGAGGCGGAGGGGGTGGTGGCTTCAGGGGACGAGGAGGTGGCGGTGGCCGAGGTGGGGGCTTCCAGTC
TGGGGGCAACCGGGGTCGAGGTGGTGGCCGGGGAGGCAAGAGAGGAAACCAGTCAGGGAAGAATGTGATGGTGGAGCCGC
ATCGGCATGAAGGTGTCTTTATCTGTCTCGGAAAGGAGGATGATCTTGTCACAAAGAATCTGGTCCCTGGAGAGTCTGTG
TATGGAGAGAAGAGAGTCTCTATTTCAGAAGGAGATGACAAAATTGAGTACAGAGCCTGGAACCCCTTCCGCTCCAAGCT
GGCAGCAGCTATCCTGGGCGGCGTAGACCAGATCCACATCAAGCCAGGAGCCAAGGTGCTCTACCTTGGGGCAGCCTCAG
GCACCACCGTCTCCCACGTCTCTGATATTGTCGGCCCGGATGGTCTGGTCTACGCAGTTGAGTTCTCCCACCGCTCTGGC
CGTGACCTCATCAACTTGGCCAAGAAGAGGACTAACATTATTCCTGTAATTGAAGATGCTCGACACCCACACAAATACCG
CATGCTTATCGCAATGGTGGATGTCATCTTTGCCGATGTGGCCCAGCCAGACCAAACCCGAATTGTGGCCCTGAACGCCC
ACACCTTCCTGCGGAATGGAGGACACTTTGTGATTTCCATTAAGGCCAACTGCATTGACTCCACTGCGTCAGCAGAGGCT
GTGTTTGCATCTGAAGTGAAGAAGATGCAGCAGGAGAACATGAAGCCGCAGGAGCAGCTGACGCTAGAGCCTTATGAGCG
AGACCACGCCGTGGTTGTCGGTGTGTACAGGCCACCTCCCAAGGTGAAGAAC

Alignment

ORF - retro_mmus_1609 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.94 %
• Parental protein coverage: 86.85 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GGRGRGGGGGGFRGRGGGGGRGGGFQSGGNRGRGGGRGGKRGNQSGKNVMVEPHRHEGVFICRGKEDALV
          GG.GRGGGGGGFRGRGGGGGRGGGFQSGGNRGRGGGRGGKRGNQSGKNVMVEPHRHEGVFIC.GKED.LV
Retrocopy GGGGRGGGGGGFRGRGGGGGRGGGFQSGGNRGRGGGRGGKRGNQSGKNVMVEPHRHEGVFICLGKEDDLV

Parental  TKNLVPGESVYGEKRVSISEGDDKIEYRAWNPFRSKLAAAILGGVDQIHIKPGAKVLYLGAASGTTVSHV
          TKNLVPGESVYGEKRVSISEGDDKIEYRAWNPFRSKLAAAILGGVDQIHIKPGAKVLYLGAASGTTVSHV
Retrocopy TKNLVPGESVYGEKRVSISEGDDKIEYRAWNPFRSKLAAAILGGVDQIHIKPGAKVLYLGAASGTTVSHV

Parental  SDIVGPDGLVYAVEFSHRSGRDLINLAKKRTNIIPVIEDARHPHKYRMLIAMVDVIFADVAQPDQTRIVA
          SDIVGPDGLVYAVEFSHRSGRDLINLAKKRTNIIPVIEDARHPHKYRMLIAMVDVIFADVAQPDQTRIVA
Retrocopy SDIVGPDGLVYAVEFSHRSGRDLINLAKKRTNIIPVIEDARHPHKYRMLIAMVDVIFADVAQPDQTRIVA

Parental  LNAHTFLRNGGHFVISIKANCIDSTASAEAVFASEVKKMQQENMKPQEQLTLEPYERDHAVVVGVYRPPP
          LNAHTFLRNGGHFVISIKANCIDSTASAEAVFASEVKKMQQENMKPQEQLTLEPYERDHAVVVGVYRPPP
Retrocopy LNAHTFLRNGGHFVISIKANCIDSTASAEAVFASEVKKMQQENMKPQEQLTLEPYERDHAVVVGVYRPPP

Parental  KVKN
          KVKN
Retrocopy KVKN

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	0.91 RPM	9.37 RPM
SRP007412_cerebellum	1.13 RPM	12.46 RPM
SRP007412_heart	0.81 RPM	19.27 RPM
SRP007412_kidney	1.29 RPM	22.25 RPM
SRP007412_liver	1.26 RPM	22.80 RPM
SRP007412_testis	10.47 RPM	21.31 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1609 was not detected

EST

No EST(s) were mapped for retro_mmus_1609 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_55934	675 libraries	331 libraries	59 libraries	4 libraries	3 libraries

The graphical summary, for retro_mmus_1609 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_1609 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1609 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002579	1 retrocopy	retro_btau_108,
Canis familiaris	ENSCAFG00000005412	1 retrocopy	retro_cfam_1697,
Homo sapiens	ENSG00000105202	1 retrocopy	retro_hsap_99,
Macropus eugenii	ENSMEUG00000014684	1 retrocopy	retro_meug_1077,
Microcebus murinus	ENSMICG00000007686	1 retrocopy	retro_mmur_1127,
Mus musculus	ENSMUSG00000046865	4 retrocopies	retro_mmus_1141, retro_mmus_1585, retro_mmus_1609 , retro_mmus_89,
Nomascus leucogenys	ENSNLEG00000014234	1 retrocopy	retro_nleu_1947,
Otolemur garnettii	ENSOGAG00000006463	2 retrocopies	retro_ogar_3102, retro_ogar_504,
Pan troglodytes	ENSPTRG00000010982	2 retrocopies	retro_ptro_2208, retro_ptro_3074,
Pteropus vampyrus	ENSPVAG00000010849	1 retrocopy	retro_pvam_231,
Rattus norvegicus	ENSRNOG00000019229	4 retrocopies	retro_rnor_1082, retro_rnor_1780, retro_rnor_643, retro_rnor_75,
Sus scrofa	ENSSSCG00000030510	1 retrocopy	retro_sscr_39,
Tupaia belangeri	ENSTBEG00000007755	2 retrocopies	retro_tbel_3774, retro_tbel_3974,