RetrogeneDB ID: retro_mmus_1585

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 17:61397321..61398245(+)
• Located in intron of: None

Retrocopy information

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

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_1585
TTCAGAACCCCTGGGGGAAGCTTTGGTGGCAGAGGCAAGAGAGGAGGACAAGGAAGACAAGGAGGCTTTGGTGGTGGAAG
AGGAGACTTTGGCAGTGGAGATCGAGGCGGAGGGTGGCTTCAGGGCACAGGAAGGTGGAGGTGGCAGAGGTGGAGGCTTC
TAATCTGGGGGCAACTGGGGTCGAGGTGGTGGCCGGGGAGGCAAGAGAGGAAACCAATCAGGGAAGAATGTGATGTTGTT
GCCGCATTGGTATGAAGATGTGTTTATCTGTTGCGGAAAGGAGGATGCCCTTGTCGCAAAGAATCTGATCCCTGTAGAAT
CTGTGTAAGGAGAGAAGAGAGACTCTATTTCAGAAGGAGATGACAATTTTGAGTAGGGAGCCTGGAACCCCTTCGGCTGG
CAGCAGCAAATCTGGGCAACGTAGACCAGAGCCACATCAAACCTGGGCCCAAGGTGCTCTACCTTGGAGCAGCCTCAGGC
ACCACTGTCTCCCACATCTCTGATATTGTCGGCCCGGATGGTCTGGTATATACAGTTGAGCTCTCCCACCACTCTGGCCA
TGATCCCATCAACTTGGCCAAGAAGAGGACCAGAATAATTCCTGTAATTGAAGATGTTCCGCACCCTCACAAATACGCAA
GCATATCACAATGGTGGATGTCACCTTGGCTTATGTGGACCAGCCAGATCAAACCCATATTGTGGCCCTGAATGCCCACA
CATTCCTGCGGAATGGAGGTCACTTTGTGATTTCCATTAAGGCCAACTGCATTGACTCTGCAGCCTCAGCAGAAGCTTCA
TCTGAAGTGAAGAAGATGTAGCAAGAGAACATGAAGCCCCAGGAGCAGCTGACGCTAGAGCCTTGTGAATGAGACTGCAC
TGTGTGTTGTAGGTGTATACAGGCCACCTCCCTACATGAAGAAC

Alignment

ORF - retro_mmus_1585 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.13 %
• Parental protein coverage: 94.8 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  FGDRGGRGGGRGGRGGFGGGRGGFGG--GGRGRGG-GGG-GFRGRGGGGGRGGGFQSGGNRGRGGGRGGK
          F...GG..GGR.G..........FGG..G..G.G..GGG.GFR...GGGGRGGGF.SGGN.GRGGGRGGK
Retrocopy FRTPGGSFGGR-GKXXXXXXXXXFGGGRGDFGSGDRGGG>GFRAQEGGGGRGGGF*SGGNWGRGGGRGGK

Parental  RGNQSGKNVMVEPHRHEGVFICRGKEDALVTKNLVPGESVYGEKRVSISEGDDKIEYRAWN-PFRSKLAA
          RGNQSGKNVM..PH..E.VFIC.GKEDALV.KNL.P.ESV.GEKR.SISEGDD..E..AWN.P.R..LAA
Retrocopy RGNQSGKNVMLLPHWYEDVFICCGKEDALVAKNLIPVESV*GEKRDSISEGDDNFE*GAWN<PLR--LAA

Parental  AILGGVDQIHIKPGAKVLYLGAASGTTVSHVSDIVGPDGLVYAVEFSHRSGRDLINLAKKRTNIIPVIED
          A.LG.VDQ.HIKPG.KVLYLGAASGTTVSH.SDIVGPDGLVY.VE.SH.SG.D.INLAKKRT.IIPVIED
Retrocopy ANLGNVDQSHIKPGPKVLYLGAASGTTVSHISDIVGPDGLVYTVELSHHSGHDPINLAKKRTRIIPVIED

Parental  ARHPHKY-RMLIAMVDVIFADVAQPDQTRIVALNAHTFLRNGGHFVISIKANCIDSTASAEAVFASEVKK
          ..HPHKY.R..I.MVDV..A.V.QPDQT.IVALNAHTFLRNGGHFVISIKANCIDS.ASAEA...SEVKK
Retrocopy VPHPHKY<RKHITMVDVTLAYVDQPDQTHIVALNAHTFLRNGGHFVISIKANCIDSAASAEA--SSEVKK

Parental  MQQENMKPQEQLTLEPYERDHAV-VVGVYRPPPKVKN
          M.QENMKPQEQLTLEP.E.D..V.VVGVYRPPP..KN
Retrocopy M*QENMKPQEQLTLEPCE*DCTV>VVGVYRPPPYMKN

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	0.00 RPM	9.37 RPM
SRP007412_cerebellum	0.00 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	0.00 RPM	21.31 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_1585 was not detected

EST

No EST(s) were mapped for retro_mmus_1585 retrocopy.

TSS

No TSS is located nearby retro_mmus_1585 retrocopy 5' end.

Lab

retro_mmus_1585 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1585 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,