RetrogeneDB ID: retro_btau_1850

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: X:112431671..112432313(-)
• Located in intron of: ENSBTAG00000047410

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB11A
• Ensembl ID: ENSBTAG00000018959
• Aliases: None
• Description: ras-related protein Rab-11A [Source:RefSeq peptide;Acc:NP_001033251]

Sequence

>retro_btau_1850
GGCACCCACGACGACGACTACAACTACCTCTTCAAAGCTGTCCTTATTGGAGATTCTGGTGTTGGAAAGAGTAATCTCCT
GTCTCGATTTGCTCAAAATGAGCTTAGTCTTGAAAGCAAGAGCACCATTGGAGTAGAGTTTGCAACAAGAAGCATCCAGG
TTGATGGGAAAACAATAAAGGTACAGATACAGGACTTGCCAGGGCAAGAACCATACCACAGTAGAACATCAGCATACTAT
TGTGGAGCTGTAGGTGCCTTATTGGTTTATGACATTGCTAAACATCTCACATATGAAAATGTAGAGCGATGGCTAAAAGA
ACTGAGAGATCATGCTGATAGTAATGTTGTTATCATGCCTGTGGGCAATAAGAGTGATTTGCACCATCTCAGAGCAGTTC
CTGCAGATGAATCAAGAGCTTTTGCAGAAGAAAACGATTTGTCATTCATCGAGACATCTGCTCTAGACCCTACAAATGTG
GAAGCTGGTTTTCAGACAATCTAGACAGAGATATACCGCATTGTTTCTCAGAAGCAAATGTCAGACAGACGTGAAAATAA
CATGTCTCCAGGCAACAATGTGGTTCCTATTCATGTTCCACCAACCACTGAAAACAAGCCAAAGGTGCAGTGCTGTCGGA
AC

Alignment

ORF - retro_btau_1850 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.98 %
• Parental protein coverage: 99.07 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GTRDDEYDYLFKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDGKTIKAQIWDTAGQE
          GT.DD.Y.YLFK.VLIGDSGVGKSNLLSRF..NE..LESKSTIGVEFATRSIQVDGKTIK.QI.D..GQE
Retrocopy GTHDDDYNYLFKAVLIGDSGVGKSNLLSRFAQNELSLESKSTIGVEFATRSIQVDGKTIKVQIQDLPGQE

Parental  RYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLKELRDHADSNIVIMLVGNKSDLRHLRAVPTDEARA
          .Y...TSAYY.GAVGALLVYDIAKHLTYENVERWLKELRDHADSN.VIM.VGNKSDL.HLRAVP.DE.RA
Retrocopy PYHSRTSAYYCGAVGALLVYDIAKHLTYENVERWLKELRDHADSNVVIMPVGNKSDLHHLRAVPADESRA

Parental  FAEKNGLSFIETSALDSTNVEAAFQTILTEIYRIVSQKQMSDRRENDMSPSNNVVPIHVPPTTENKPKVQ
          FAE.N.LSFIETSALD.TNVEA.FQTI.TEIYRIVSQKQMSDRREN.MSP.NNVVPIHVPPTTENKPKVQ
Retrocopy FAEENDLSFIETSALDPTNVEAGFQTI*TEIYRIVSQKQMSDRRENNMSPGNNVVPIHVPPTTENKPKVQ

Parental  CCQN
          CC.N
Retrocopy CCRN

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	22.78 RPM
ERP005899_muscle	0.05 RPM	80.19 RPM
SRP017611_brain	0.00 RPM	36.77 RPM
SRP017611_kidney	0.00 RPM	76.70 RPM
SRP017611_liver	0.00 RPM	16.84 RPM
SRP030211_testis	0.00 RPM	45.73 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1850 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1850 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1850 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000018959	1 retrocopy	retro_btau_1850 ,
Bos taurus	ENSBTAG00000044207	1 retrocopy	retro_btau_991,
Callithrix jacchus	ENSCJAG00000007333	1 retrocopy	retro_cjac_1050,
Echinops telfairi	ENSETEG00000004920	5 retrocopies	retro_etel_1150, retro_etel_2132, retro_etel_2214, retro_etel_694, retro_etel_837,
Homo sapiens	ENSG00000103769	1 retrocopy	retro_hsap_715,
Gorilla gorilla	ENSGGOG00000014252	2 retrocopies	retro_ggor_538, retro_ggor_605,
Myotis lucifugus	ENSMLUG00000008820	2 retrocopies	retro_mluc_1606, retro_mluc_2435,
Macaca mulatta	ENSMMUG00000008006	1 retrocopy	retro_mmul_2463,
Nomascus leucogenys	ENSNLEG00000012853	1 retrocopy	retro_nleu_467,
Petromyzon marinus	ENSPMAG00000009335	1 retrocopy	retro_pmar_25,
Pongo abelii	ENSPPYG00000006573	1 retrocopy	retro_pabe_618,
Pan troglodytes	ENSPTRG00000007188	1 retrocopy	retro_ptro_510,