RetrogeneDB ID: retro_btau_468

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 12:38817376..38818725(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNRNPK
• Ensembl ID: ENSBTAG00000021131
• Aliases: HNRNPK, HNRPK
• Description: Heterogeneous nuclear ribonucleoprotein K [Source:UniProtKB/Swiss-Prot;Acc:Q3T0D0]

Sequence

>retro_btau_468
GAGGAAACCTTTACCAAAACCAGTGTCAAATTTGGTAAATGCCCTGCTGAAGATATGGAAGAGGAACAAGCTTTTAAAAG
ATTTAGAAATACTGATGAGATGGTTGAATTATGTATTCTGCTTCAAAGCAAGAATGCTGGGGCAGTGATAGGAAAAGGAG
GCAAGAATATTAAGGCTCTCCATACAGACTACAATTGCCAGTGTTTCAGTCCCAGACAGCAGTGACTCCCAGCGCATATT
GAGCATCAGTGCTGATATTGAAATGATTGGAGAATTTCTGAAGAAAATCATCCCGACCTTGGAAGACGGCCTGCAGTTGC
CATCACCCACCACAACCAGCCAGCTCCCACTTGAATCTGATGTTGTGGAATGCTTACATTGCCAACACTATAAAGGAAGC
GACTTTGACTGTGATATGAGACTATTGATTCATCAGAGCACAGCAGGAGGAATTATTGGAGTCAAAGGTGCTAAAATCAA
AGAACTTTGAGAGAACACTCAGACAACAGTCAAGCTTTTCCAGGAATGTTGTCCTCAATCTACTGACACAGTCGTTCTTA
TTGGGGGAAAACCTGATAGGTTTGGAGAGTTCATAAAGATCATCCTTGATCTTATATCTGAGTCTCCCACTAAAGGACAT
GCTCAACCTCATGATCCCAATTTTTATGATGAAATCTATAATTATGGTGGTTTTACAATGATGTTTGATGACCACCGTGG
ACGTCCTGTGGGAATCCCCATTCAGGGAAGAGGTGGCTTTGACGGAATGCTACCTGGTCTGGGTAGGGGGTCCCATGCCT
CCTTCCAGAAGAGATTATGATGATATGAGACCTTGTCAAGGACCTCTTTCACCCCCTCCTGGACGAGTTGGCCAGGGTGG
AAGTAGAGTTCGGAATTTTCCTCTTCCACCACCACCACCACCTAGAGGAGGAGATTTAATATCCTATTATAGAAGAGGAA
GACCTGGACACCGTTACCATGGCATGATTGGTTTCAGTGCTGATGAAACCTGGGACTCTGCAATAGACACATGGAGCCTC
TCAGAGTGGCAGATGGCTTCTGAACCACAGGGTGGCTCTGGATATGATTATTCCTATGCAGGGGGTCATGCCTCATACGG
TGATCTTGGTGGACCTATTATTACAACACAACTATTCCCCAAAATTTGGCTGGATCTTATGGGCAAAGGTGGTAAGTGGA
TTAAACAAATCAGTCATGAGTCAAAAGCTTCCATCATAATTGAGGAGCCTTTAGAAGGATCCAAAGATCAGATCATTACC
ATTACAGGAACATAGGACCAGATATAAAATGTACAGTATTTGCTGCAAATCAGTGTGAAGCAGTATTCT

Alignment

ORF - retro_btau_468 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.1 %
• Parental protein coverage: 97.63 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EETFPNTETNGEFGKRPAEDMEEEQAFKRSRNTDEMVELRILLQSKNAGAVIGKGGKNIKALRTDYN-AS
          EETF..T.T...FGK.PAEDMEEEQAFKR.RNTDEMVEL.ILLQSKNAGAVIGKGGKNIKAL.TDYN.AS
Retrocopy EETF--TKTSVKFGKCPAEDMEEEQAFKRFRNTDEMVELCILLQSKNAGAVIGKGGKNIKALHTDYN>AS

Parental  VSVPDSSGPERILSISADIETIGEILKKIIPTLEEGLQLPSPTATSQLPLESDAVECLNYQHYKGSDFDC
          VSVPDSS...RILSISADIE.IGE.LKKIIPTLE.GLQLPSPT.TSQLPLESD.VECL..QHYKGSDFDC
Retrocopy VSVPDSSDSQRILSISADIEMIGEFLKKIIPTLEDGLQLPSPTTTSQLPLESDVVECLHCQHYKGSDFDC

Parental  ELRLLIHQSLAGGIIGVKGAKIKELRENTQTTIKLFQECCPQSTDRVVLIGGKPDRVVECIKIILDLISE
          ..RLLIHQS.AGGIIGVKGAKIKEL.ENTQTT.KLFQECCPQSTD.VVLIGGKPDR..E.IKIILDLISE
Retrocopy DMRLLIHQSTAGGIIGVKGAKIKEL*ENTQTTVKLFQECCPQSTDTVVLIGGKPDRFGEFIKIILDLISE

Parental  SPIKGRAQPYDPNFYDETYDYGGFTMMFDDRRGRPVGFPMRGRGGFDRMPPGRG-GRPMPPSRRDYDDMS
          SP.KG.AQP.DPNFYDE.Y.YGGFTMMFDD.RGRPVG.P..GRGGFD.M.PG.G.G.PMPPSRRDYDDM.
Retrocopy SPTKGHAQPHDPNFYDEIYNYGGFTMMFDDHRGRPVGIPIQGRGGFDGMLPGLG>GGPMPPSRRDYDDMR

Parental  PRRGPPPPPPGRGGRGGSRARNLPLPPPPPPRGGDLMAYDRRGRPGDRYDGMVGFSADETWDSAIDTWSP
          P..GP..PPPGR.G.GGSR.RN.PLPPPPPPRGGDL..Y.RRGRPG.RY.GM.GFSADETWDSAIDTWS.
Retrocopy PCQGPLSPPPGRVGQGGSRVRNFPLPPPPPPRGGDLISYYRRGRPGHRYHGMIGFSADETWDSAIDTWSL

Parental  SEWQMAYEPQGGSGYDYSYAGGRGSYGDLGGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKID
          SEWQMA.EPQGGSGYDYSYAGG..SYGDLGGPIITTQ...PK.......GKGG..IKQI.HES.ASI.I.
Retrocopy SEWQMASEPQGGSGYDYSYAGGHASYGDLGGPIITTQL-FPK-IWLDLMGKGGKWIKQISHESKASIIIE

Parental  EPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQYA
          EPLEGS.D.IITITGT.DQI.N.QYLLQ.SVKQY.
Retrocopy EPLEGSKDQIITITGT*DQI*NVQYLLQISVKQYS

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	152.70 RPM
ERP005899_muscle	0.00 RPM	323.33 RPM
SRP017611_brain	0.00 RPM	248.13 RPM
SRP017611_kidney	0.00 RPM	348.52 RPM
SRP017611_liver	0.00 RPM	189.30 RPM
SRP030211_testis	0.02 RPM	307.99 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_468 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_468 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_468 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 31 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020757	1 retrocopy	retro_btau_175,
Bos taurus	ENSBTAG00000021131	2 retrocopies	retro_btau_468 , retro_btau_605,
Homo sapiens	ENSG00000165119	3 retrocopies	retro_hsap_2323, retro_hsap_2674, retro_hsap_3385,
Microcebus murinus	ENSMICG00000015780	3 retrocopies	retro_mmur_1562, retro_mmur_235, retro_mmur_448,
Myotis lucifugus	ENSMLUG00000005871	2 retrocopies	retro_mluc_128, retro_mluc_561,
Macaca mulatta	ENSMMUG00000018871	1 retrocopy	retro_mmul_2111,
Monodelphis domestica	ENSMODG00000008402	1 retrocopy	retro_mdom_1666,
Mus musculus	ENSMUSG00000021546	2 retrocopies	retro_mmus_1131, retro_mmus_2137,
Otolemur garnettii	ENSOGAG00000007478	3 retrocopies	retro_ogar_2635, retro_ogar_2966, retro_ogar_3086,
Pongo abelii	ENSPPYG00000019327	3 retrocopies	retro_pabe_2105, retro_pabe_2106, retro_pabe_42,
Sarcophilus harrisii	ENSSHAG00000017109	1 retrocopy	retro_shar_820,
Tupaia belangeri	ENSTBEG00000001289	1 retrocopy	retro_tbel_2491,
Tursiops truncatus	ENSTTRG00000004906	1 retrocopy	retro_ttru_1622,
Tursiops truncatus	ENSTTRG00000016693	7 retrocopies	retro_ttru_1144, retro_ttru_180, retro_ttru_1922, retro_ttru_444, retro_ttru_813, retro_ttru_930, retro_ttru_937,