RetrogeneDB ID: retro_btau_108

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 7:82834995..82835982(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000004657
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: FBL
• Ensembl ID: ENSBTAG00000002579
• Aliases: None
• Description: rRNA 2'-O-methyltransferase fibrillarin [Source:RefSeq peptide;Acc:NP_001192329]

Sequence

>retro_btau_108
ATGAAGTCTGCGGTGGGCTTGCGTCGTGGCGGGTCTGGCGGCCGTGGGGGTGGCGGCTGGGGCGGAGGGCGCGGAGGCGG
AGCGGGCAAGGGAGCAGGAGGCGACGGCGGCGGCCCGGGAGGCAAGGGCGGCTTCGGGGCGCGGACGCGCGGCTTCGGTG
GCGGCCGGGGCCGGGGGCGCGGTGGCGCCGGAGGAGACGGCCGGGGGGACCGCGGAGGCGGCGGGCAGCTGCGCGGCGTG
GCCAAGAACAAGAACCGCCGCAGGAAGAGCGTTTTGACGGTGTCAGTGGAACCGCACCGGCACGAGGGCGTCTTCATCTA
CCGCGGGGCGGAGGACGCGCTGGTCACGCTGAACATGGTGCCGGGCCAGTCGGTGTATGGCGAGCGGCGGGTCACGGTGA
CCGAGGGCGGCGAGAAGCTGGAATACCGCACGTGGAACCCCTTCCGCTCCAAGCTGGCCGCGGCCATCCTGGGCGGGGTC
GACCAGATTCACATCAAGCCCAAGTCCAAAGTGCTGTATCTGGGTGCCGCCTCGGGGACCACCGTGTCCCACGTCTCCGA
CATCATCGGCCCGGACGGCCTGGTCTACGCCGTTGAGTTCTCCCACCGCGCTGGCCGGGATCTCGTCAACGTGGCCAAGA
AGCGAACCAACATCATCCCGGTCCTCGAAGATGCACGGCACCCGCTCAAGTACCGCATGCTCATCGGCATGGTGGACGTG
ATCTTCGCCGACGTGGCACAGCCGGACCAGTCCCGCATAGTGGCTCTGAACGCCCACACCTTCCTGCGCAACGGGGGCCA
CTTCCTCATCTCCATCAAGGCCAACTGCATAGACTCCACTGCATCCGCGGAAGCGGTGTTCGCCTCTGAGGTGAGGAAGC
TGCAGCAGGAGAATTTAAAGCCTCAAGAGCAGCTGACTCTGGAGCCCTACGAAAGGGACCACGCTGTGGTGGTCGGGGTC
TATCGGCCTCTTCCTAAGAGCAGCAGC

Alignment

ORF - retro_btau_108 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.99 %
• Parental protein coverage: 99.07 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKPGFSPRGGGFGGRGGFGDRGGRGG----GRGGFGGGRGGFGGGRGRGGGGGGFRGRGRGG-GGRGGGF
          MK.....R.GG.GGRGG.G..GGRGG....G.GG.GGG.GG.GG...R..G.GG.RGRGRGG.GG.G.G.
Retrocopy MKSAVGLRRGGSGGRGGGGWGGGRGGGAGKGAGGDGGGPGGKGGFGARTRGFGGGRGRGRGGAGGDGRGD

Parental  QSGGNRGRGRGGKKGN--PSGKNVMVEPHRHEGVFICRGKEDALVTKNLVPGESVYGEKRVSISEGDDKI
          ..GG...RG....K.....S...V.VEPHRHEGVFI.RG.EDALVT.N.VPG.SVYGE.RV...EG..K.
Retrocopy RGGGGQLRGVAKNKNRRRKSVLTVSVEPHRHEGVFIYRGAEDALVTLNMVPGQSVYGERRVTVTEGGEKL

Parental  EYRAWNPFRSKLAAAILGGVDQIHIKPGAKVLYLGAASGTTVSHVSDIVGPDGLVYAVEFSHRSGRDLIN
          EYR.WNPFRSKLAAAILGGVDQIHIKP..KVLYLGAASGTTVSHVSDI.GPDGLVYAVEFSHR.GRDL.N
Retrocopy EYRTWNPFRSKLAAAILGGVDQIHIKPKSKVLYLGAASGTTVSHVSDIIGPDGLVYAVEFSHRAGRDLVN

Parental  LAKKRTNIIPVIEDARHPHKYRMLIAMVDVIFADVAQPDQTRIVALNAHTFLRNGGHFVISIKANCIDST
          .AKKRTNIIPV.EDARHP.KYRMLI.MVDVIFADVAQPDQ.RIVALNAHTFLRNGGHF.ISIKANCIDST
Retrocopy VAKKRTNIIPVLEDARHPLKYRMLIGMVDVIFADVAQPDQSRIVALNAHTFLRNGGHFLISIKANCIDST

Parental  ASAEAVFASEVKKMQQENMKPQEQLTLEPYERDHAVVVGVYRPPPK
          ASAEAVFASEV.K.QQEN.KPQEQLTLEPYERDHAVVVGVYRP.PK
Retrocopy ASAEAVFASEVRKLQQENLKPQEQLTLEPYERDHAVVVGVYRPLPK

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
ERP005899_liver	0.00 RPM	8.29 RPM
ERP005899_muscle	0.37 RPM	40.01 RPM
SRP017611_brain	6.85 RPM	6.99 RPM
SRP017611_kidney	0.18 RPM	15.59 RPM
SRP017611_liver	0.08 RPM	14.04 RPM
SRP030211_testis	27.37 RPM	33.54 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_108 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_108 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_108 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_99
Pan troglodytes	retro_ptro_2208
Sus scrofa	retro_sscr_39
Canis familiaris	retro_cfam_1697
Equus caballus	retro_ecab_308

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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,