RetrogeneDB ID: retro_btau_1735

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: X:35340346..35340658(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NUDCD2
• Ensembl ID: ENSBTAG00000014772
• Aliases: None
• Description: nudC domain-containing protein 2 [Source:RefSeq peptide;Acc:NP_001035643]

Sequence

>retro_btau_1735
GTGGCCACAGGATCCTCAAGGTAGTGGCAGGGCAAACTCTTTGACTCTACAATAGCTGATGAGGGAACATGGACTCTGGA
GGATAGAAAAATGATCCATATTGTTTTTACAAAGATGAGGAGAGATGCAAAAAATTGTTGGACTTATCTTCCAGAATATG
AATATACAGCTCACCCTTGGGTTCAAGACCAAATGCAGAGAAAACTTACATTAGGGAGATTCCAGAAAGAAAATCCTGGT
TTTGACTTCAGCGGAGCAGAAATCTCAGGAAACTACACTAAAGGTGGACCAGATTTCTCGAATCATGAGAAA

Alignment

ORF - retro_btau_1735 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.85 %
• Parental protein coverage: 66.24 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LAVGGREILKGKLFDSTIADEGTWTLEDRKMVRIVLTKTKRDAANCWTSLLESDYAADPWVQDQMQRKLT
          .A.G......GKLFDSTIADEGTWTLEDRKM..IV.TK..RDA.NCWT.L.E..Y.A.PWVQDQMQRKLT
Retrocopy VATGSSR*WQGKLFDSTIADEGTWTLEDRKMIHIVFTKMRRDAKNCWTYLPEYEYTAHPWVQDQMQRKLT

Parental  LERFQKENPGFDFSGAEISGNYTKGGPDFSNLEK
          L.RFQKENPGFDFSGAEISGNYTKGGPDFSN.EK
Retrocopy LGRFQKENPGFDFSGAEISGNYTKGGPDFSNHEK

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	32.66 RPM
ERP005899_muscle	0.00 RPM	17.05 RPM
SRP017611_brain	0.00 RPM	8.86 RPM
SRP017611_kidney	0.00 RPM	17.78 RPM
SRP017611_liver	0.00 RPM	14.88 RPM
SRP030211_testis	0.00 RPM	18.92 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1735 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1735 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1735 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005270	1 retrocopy	retro_amel_535,
Bos taurus	ENSBTAG00000014772	1 retrocopy	retro_btau_1735 ,
Callithrix jacchus	ENSCJAG00000015367	1 retrocopy	retro_cjac_2093,
Cavia porcellus	ENSCPOG00000000877	1 retrocopy	retro_cpor_936,
Dipodomys ordii	ENSDORG00000014291	1 retrocopy	retro_dord_188,
Macropus eugenii	ENSMEUG00000004802	1 retrocopy	retro_meug_1673,
Myotis lucifugus	ENSMLUG00000001670	1 retrocopy	retro_mluc_1154,
Monodelphis domestica	ENSMODG00000007641	2 retrocopies	retro_mdom_1058, retro_mdom_2016,
Ornithorhynchus anatinus	ENSOANG00000021414	1 retrocopy	retro_oana_122,
Oryctolagus cuniculus	ENSOCUG00000005783	1 retrocopy	retro_ocun_819,
Otolemur garnettii	ENSOGAG00000024929	3 retrocopies	retro_ogar_1486, retro_ogar_1696, retro_ogar_482,
Sarcophilus harrisii	ENSSHAG00000007551	1 retrocopy	retro_shar_559,
Ictidomys tridecemlineatus	ENSSTOG00000028665	1 retrocopy	retro_itri_1770,
Tupaia belangeri	ENSTBEG00000000307	1 retrocopy	retro_tbel_507,
Tarsius syrichta	ENSTSYG00000008090	1 retrocopy	retro_tsyr_1638,