RetrogeneDB ID: retro_btau_1013

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 23:44090793..44091596(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FBLIM1
• Ensembl ID: ENSBTAG00000018725
• Aliases: None
• Description: Filamin-binding LIM protein 1 [Source:UniProtKB/Swiss-Prot;Acc:Q1JQB5]

Sequence

>retro_btau_1013
ATGGCCTCCAAGCCTGAGAAGAGGGTCGCCTCATCTGTCTTTATCACCCTGGTGCCCCCACGTCGAGATGAGGCTGTGGT
TGAGGAGGTGAGGCGAGCAGCTTGTGAGGCCCAGCCTGGCCACCCCTGGGAATCTCCTGCCCCCACAAAGGCACCCGGGG
CTGGCTCGGTGGGAAAGCTCCGTTCCTGGATGCCTCCTGGCAGGACTGCAGCCCCAGGGCCAGCTGTTCCACCTCCGCTC
TCCAATGGAGGGTGTCACTTCCTTCTCGCCCTTGGACGTTGATGATGCTCTTCCAGACCCGGACCTCCTCCCACCTCTGC
CTCCACCCCCTCCAGTGGACCTGCCCCTCCTGACAAAGAGCCCCCTCCGCGATGGGGGCACCACTCATTTCAGACTTGGG
GCAGTTGCACCTGCCCCTCCCCCTCCCCCATCCCAGCACAGGCCCTGGTGGAGGGGCCTCCACTGCAGCCTCGGCCCAGT
CATCTCAAGCCCGCAGAGGAGGAGCTGCTGCCCACCACTCCAAAGAGCCTGTCGGCTTCCCTGAGAGAGACATCTGTGCC
TTCTGCCGCAAGACTGTGTCCCCCCGAGAGCTGGGCGTAGAGGCCATGGAGAGGCAGTACCCGCCCAGTGCTTCACGTGC
CGTGTCTGCCGCCAACGGCTGGCCGGGCAGAGCTTCTACCAGAAGGATGGGCGGCCCCTCTGTGAAGCCTGCTACCAGGA
CACCTGGAGAAGTGTGCCAAGTGTGCAAGGTTGTCCGGGAGCGCATCATCCGGGCCCTAGGCCAGGCCTTCCACCCCTCC
TGT

Alignment

ORF - retro_btau_1013 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79. %
• Parental protein coverage: 71.69 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  MASKPEKRVASSVFITLVPPRRDEAVVEEVRRAACEAWPGRPWES-APTKAPGAGSVGKLRSWMPPGRAA
          MASKPEKRVASSVFITLVPPRRDEAVVEEVRRAACEA.PG.PWES.APTKAPGAGSVGKLRSWMPPGR.A
Retrocopy MASKPEKRVASSVFITLVPPRRDEAVVEEVRRAACEAQPGHPWESPAPTKAPGAGSVGKLRSWMPPGRTA

Parental  APGPAVPPQLSNGGC-SLPP-PPLDVDDALPDLDLLPPPPPPPAADLP-PPDEEPHSAMGASLISDLEQL
          APGPAVPP.LSNGGC.SLP...PLDVDDALPD.DLLPP.PPPP..DLP.PPD.EP....G..........
Retrocopy APGPAVPPPLSNGGC<SLPS<SPLDVDDALPDPDLLPPLPPPPPVDLP<PPDKEPPPRWGHHSFQTWGSC

Parental  HLPPPPP-PPQALVEGPPLQPRPSHLKPAEEEL-PPPPE-EPVSFPEREASTDICAFCHKTVSPRELAVE
          ..P.P.P.P.QALVEGPPLQPRPSHLKPAEEEL.P..P..EPV.FPER....DICAFC.KTVSPREL.VE
Retrocopy TCPSPSPIPAQALVEGPPLQPRPSHLKPAEEELLPTTPK<EPVGFPER----DICAFCRKTVSPRELGVE

Parental  AMKRQYH-AQCFTCRVCRRQLAGQSFYQKDGRPLCEPCYQDT-LEKCGKCG-EVVREHIIRALGQAFHPS
          AM.RQY..AQCFTCRVCR..LAGQSFYQKDGRPLCE.CYQDT.LEKC.KC...VVRE.IIRALGQAFHPS
Retrocopy AMERQYP<AQCFTCRVCRQRLAGQSFYQKDGRPLCEACYQDT<LEKCAKCA<KVVRERIIRALGQAFHPS

Parental  C
          C
Retrocopy C

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	1.01 RPM
ERP005899_muscle	0.11 RPM	80.82 RPM
SRP017611_brain	0.00 RPM	8.54 RPM
SRP017611_kidney	0.24 RPM	43.33 RPM
SRP017611_liver	0.00 RPM	1.21 RPM
SRP030211_testis	0.02 RPM	8.71 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1013 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1013 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1013 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000018725	1 retrocopy	retro_btau_1013 ,
Bos taurus	ENSBTAG00000024772	1 retrocopy	retro_btau_1521,
Homo sapiens	ENSG00000162458	2 retrocopies	retro_hsap_4898, retro_hsap_778,
Gorilla gorilla	ENSGGOG00000015190	2 retrocopies	retro_ggor_3058, retro_ggor_645,
Macaca mulatta	ENSMMUG00000032243	2 retrocopies	retro_mmul_1095, retro_mmul_2635,
Nomascus leucogenys	ENSNLEG00000007650	2 retrocopies	retro_nleu_1265, retro_nleu_2840,
Pongo abelii	ENSPPYG00000001837	2 retrocopies	retro_pabe_3809, retro_pabe_751,
Pan troglodytes	ENSPTRG00000000208	2 retrocopies	retro_ptro_3266, retro_ptro_544,
Pteropus vampyrus	ENSPVAG00000009000	1 retrocopy	retro_pvam_415,