RetrogeneDB ID: retro_mmus_89

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 11:35797489..35798434(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000051062
• Aliases: Fbll1, AI595406
• Status: KNOWN_PROTEIN_CODING

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_89
ATGAAACCCGCGGGCGGCCGCGGCGGCTGGGGCTGGGGTGGCGGCAAGGGAGGCAGCAAGGGAGGTGACACGGGCTCAGG
GACCAAAGGCGGCTTCGGGGCACGCACACGCGGCTCCAGCGGCGGCGGCCGGGGCCGGGGACGAGGCGGCGGCGGGGGCG
GCGGGGGCGGCGGCGGCGACAGGCAGCGACGCGGCGGTCCAGGCAAGAACAAGAACCGCCGCAAGAAGGGCATCACGGTG
TCGGTGGAGCCGCATCGGCACGAGGGCGTGTTCATCTACCGCGGCGCGGAGGATGCTCTGGTCACACTGAACATGGTGCC
TGGAGTCTCGGTGTACGGCGAGAAGCGCGTCACCGTGATGGAGAACGGGGAGAAACAGGAGTACCGCACGTGGAATCCCT
TCCGCTCCAAATTGGCAGCGGCCATCCTGGGCGGCGTGGACCAGATCCACATCAAGCCCAAGTCCAAAGTGTTGTACCTG
GGCGCCGCCTCCGGAACCACTGTCTCACACGTCTCCGACATCATCGGCCCCGACGGCCTGGTCTATGCGGTTGAATTCTC
CCATCGCGCCGGCCGCGATCTGGTCAACGTGGCCAAGAAGCGCACCAACATCATCCCGGTGCTGGAAGATGCCCGGCACC
CGCTCAAGTATCGCATGCTCATTGGCATGGTGGACGTGATCTTCGCCGATGTGGCCCAGCCAGATCAGTCGCGCATCGTG
GCGCTTAACGCCCACACCTTTCTGCGCAACGGAGGCCACTTTCTCATTTCCATCAAGGCCAACTGCATCGACTCCACAGC
GTCTGCCGAGGCCGTGTTTGCTTCTGAGGTGAGGAAGCTGCAACAGGAGAACTTGAAGCCACAGGAGCAGCTGACTCTGG
AGCCCTACGAAAGGGACCACGCCGTCGTCGTCGGGGTCTATCGGCCCCCACCCAAGAGCAAGTAG

Alignment

ORF - retro_mmus_89 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.37 %
• Parental protein coverage: 96.02 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GGRGGFGDRGGRGGGRGGRGGFGGGRGGFGGGGRGRGGGGGGFRGRGGGGGRGGGFQSGGNRGRGGGRG-
          GGRGG.G..GG.GG..GG..G..G..GGFG...RG..GGG.G.RGRGGGGG.GGG...GG.R.R.GG.G.
Retrocopy GGRGGWGWGGGKGGSKGGDTG-SGTKGGFGARTRGSSGGGRG-RGRGGGGGGGGG---GGDRQRRGGPGK

Parental  GKRGNQSGKNVMVEPHRHEGVFICRGKEDALVTKNLVPGESVYGEKRVSISEGDDKIEYRAWNPFRSKLA
          .K.....G..V.VEPHRHEGVFI.RG.EDALVT.N.VPG.SVYGEKRV...E...K.EYR.WNPFRSKLA
Retrocopy NKNRRKKGITVSVEPHRHEGVFIYRGAEDALVTLNMVPGVSVYGEKRVTVMENGEKQEYRTWNPFRSKLA

Parental  AAILGGVDQIHIKPGAKVLYLGAASGTTVSHVSDIVGPDGLVYAVEFSHRSGRDLINLAKKRTNIIPVIE
          AAILGGVDQIHIKP..KVLYLGAASGTTVSHVSDI.GPDGLVYAVEFSHR.GRDL.N.AKKRTNIIPV.E
Retrocopy AAILGGVDQIHIKPKSKVLYLGAASGTTVSHVSDIIGPDGLVYAVEFSHRAGRDLVNVAKKRTNIIPVLE

Parental  DARHPHKYRMLIAMVDVIFADVAQPDQTRIVALNAHTFLRNGGHFVISIKANCIDSTASAEAVFASEVKK
          DARHP.KYRMLI.MVDVIFADVAQPDQ.RIVALNAHTFLRNGGHF.ISIKANCIDSTASAEAVFASEV.K
Retrocopy DARHPLKYRMLIGMVDVIFADVAQPDQSRIVALNAHTFLRNGGHFLISIKANCIDSTASAEAVFASEVRK

Parental  MQQENMKPQEQLTLEPYERDHAVVVGVYRPPPKVK
          .QQEN.KPQEQLTLEPYERDHAVVVGVYRPPPK.K
Retrocopy LQQENLKPQEQLTLEPYERDHAVVVGVYRPPPKSK

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	13.78 RPM	9.37 RPM
SRP007412_cerebellum	8.51 RPM	12.46 RPM
SRP007412_heart	0.00 RPM	19.27 RPM
SRP007412_kidney	0.00 RPM	22.25 RPM
SRP007412_liver	0.00 RPM	22.80 RPM
SRP007412_testis	4.12 RPM	21.31 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_89 was not detected

EST

No EST(s) were mapped for retro_mmus_89 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_12351	813 libraries	74 libraries	71 libraries	22 libraries	92 libraries

The graphical summary, for retro_mmus_89 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_89 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_89 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Rattus norvegicus	retro_rnor_75

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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,