RetrogeneDB ID: retro_mmus_1141

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 13:103159911..103160831(-)
• Located in intron of: ENSMUSG00000034751

Retrocopy information

• Ensembl ID: ENSMUSG00000091577
• 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_1141
GGTTTCAGCACCCGTGGGGGCGGCTTTGGTGGAGGAGGCAGAGGAGGCCAAAGTGGCCGAGGAGGCTTTGGCGGTTGAGG
TTGAGGCAGAGGGGGTGGTGGCTTCAGGGGACAAGGAGGTGGAAGTGGCAGAGGTGGAGGCTTCCGGTCTGGGGGCAGCC
AGGGTCGAGGTGGTGGCCAGGGAAGCAAGAGAGGAAATCAGTCAGGGAAGAATGTGATGGTGGAGCCGCATCAGCATGAA
GGTATCTTTATCTGTCGCGGAAAGGAGGATGCCCTTGTCACAAAGAATCTGGTCCCTGGAGAGTCTGTGTATGGAGAGAA
GAGAGTCTCTATTTCAGAAGGAGATGACAGAATTGAGTACCAAACCTGGAACCCCTTCCACTCCAAACTGGCAGCAGCAG
TCCTTGGCGGCGTAGACCAGATCCACATCAAGTGGGGGGCCAAGGTGCTCTACCTTGGGACAGCCTCAGGCACCACCATC
TCCCATGTCTCTGATATTGTTGGCTGGGATGGTCTGGTCTACGCAGTTGAGTTCTCCCACCACTCTGGCTTGACCTCATC
AACTTGGCCAAGAAGAGGACCAACATTATTCCTCGAATTGAAGATGCTCGACACCCACACAAATACCACATGCTTATCAC
AATGGTGGATGTCATCTTTGCCGACGTGGCCCAGCCAGACCAAACCCGGATTGTGACCCTGAATGCCCACACCTTCCTGC
GGAATGGAGGACACTTTGTGATTTCCATTAAGGCCAACGGCATTGACCCCACAGCCTCAGCAGAAGCTGTGTTTGCATCT
GAAGTGAAGAAGATGCAGCAAGAGACCATGAAGCCCCAGGAGCTGCTGACGCTAGAGCCTTATGAATGAAACCAAGCTGT
GGTTGTGGGTGTGTACAGGCCATCTCCCAAGGCAAAGAAC

Alignment

ORF - retro_mmus_1141 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.26 %
• Parental protein coverage: 95.11 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GFGDRGGRGGGRGGRGGFGGGRGGFGGGGRGRGGGGGGFRGRGGGGGRGGGFQSGGNRGRGGGRGGKRGN
          GF..RGG..GG.GGRGG...GRGGFGG.G.GRGGGG..FRG.GGG.GRGGGF.SGG..GRGGG.G.KRGN
Retrocopy GFSTRGGGFGG-GGRGG-QSGRGGFGG*G*GRGGGG--FRGQGGGSGRGGGFRSGGSQGRGGGQGSKRGN

Parental  QSGKNVMVEPHRHEGVFICRGKEDALVTKNLVPGESVYGEKRVSISEGDDKIEYRAWNPFRSKLAAAILG
          QSGKNVMVEPH.HEG.FICRGKEDALVTKNLVPGESVYGEKRVSISEGDD.IEY..WNPF.SKLAAA.LG
Retrocopy QSGKNVMVEPHQHEGIFICRGKEDALVTKNLVPGESVYGEKRVSISEGDDRIEYQTWNPFHSKLAAAVLG

Parental  GVDQIHIKPGAKVLYLGAASGTTVSHVSDIVGPDGLVYAVEFSHRSG-RDLINLAKKRTNIIPVIEDARH
          GVDQIHIK.GAKVLYLG.ASGTT.SHVSDIVG.DGLVYAVEFSH.SG..DLINLAKKRTNIIP.IEDARH
Retrocopy GVDQIHIKWGAKVLYLGTASGTTISHVSDIVGWDGLVYAVEFSHHSG<LDLINLAKKRTNIIPRIEDARH

Parental  PHKYRMLIAMVDVIFADVAQPDQTRIVALNAHTFLRNGGHFVISIKANCIDSTASAEAVFASEVKKMQQE
          PHKY.MLI.MVDVIFADVAQPDQTRIV.LNAHTFLRNGGHFVISIKAN.ID.TASAEAVFASEVKKMQQE
Retrocopy PHKYHMLITMVDVIFADVAQPDQTRIVTLNAHTFLRNGGHFVISIKANGIDPTASAEAVFASEVKKMQQE

Parental  NMKPQEQLTLEPYERDHAVVVGVYRPPPKVKN
          .MKPQE.LTLEPYE...AVVVGVYRP.PK.KN
Retrocopy TMKPQELLTLEPYE*NQAVVVGVYRPSPKAKN

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	9.37 RPM
SRP007412_cerebellum	0.00 RPM	12.46 RPM
SRP007412_heart	0.09 RPM	19.27 RPM
SRP007412_kidney	0.06 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 actvity near the 5' end of retro_mmus_1141 was not detected

EST

No EST(s) were mapped for retro_mmus_1141 retrocopy.

TSS

No TSS is located nearby retro_mmus_1141 retrocopy 5' end.

Lab

retro_mmus_1141 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1141 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,