RetrogeneDB ID: retro_btau_1133

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 27:30509115..30509874(-)
• Located in intron of: ENSBTAG00000010241

Retrocopy information

• Ensembl ID: ENSBTAG00000005639
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NIP30
• Ensembl ID: ENSBTAG00000002242
• Aliases: FAM192A, NIP30
• Description: protein FAM192A [Source:RefSeq peptide;Acc:NP_001014944]

Sequence

>retro_btau_1133
ATGGATGGAGGGGATGATGGTAACCTTGTTATCAAAAAGAGGTTTGTATCTGAGGCAGAGCTAGATGAACGGCGCAAAAG
GAGACAAGAAGAATGGGAAAAAGTTCGAAAACCTGAAGATCCAGAAGAATGCCCAGAGGAGGTTTATGACCCTCGGTCCC
TGTATGAAAGGCTACAGGAACAGAAAGACAGGAAGCAGCAGGAGTATGAAGAACAGTTCAAATTCAAAAACATGGTAAGA
GGCTTAGATGAAGATGAGACCAACTTCCTTGATGAGGTTTCTCGGCAGCAAGAGCTAATAGAAAAACAGCGAAGAGAAGA
AGAACTGAAAAAACTGAAGGAATACAGAAGTAATCTCAACAAGGTTGGAATTTCTTCAGAAAACAAGAAGGAAGTGGAGA
AGAAAGCTGTGAAACCCATAGAAACCAAGAACAAGTTCTCCCAGGCAAAGCTGTTGGCAGGAGCTGTGAAGCATAAGAGT
TCAGAGAGTGGAAACAGTGTGAAAAGACTGAAATCTGACCCTGACCCAGATGACAAGAATCAAGAAGCCTCGTCCTGCGT
GTCTCTGGGAAGCACCTCCCTGAGCAGTCCCTCCATCCGCTGTCCATCCGCGGCTGTCTGTATTGGCATCCTCCCGGGCC
TGGGCGCCTACTCCGGGAGCAGCGACTCTGAGTCCAGCTCAGACAGCGAAGGCACCATCAACGCCACGGGCAAGATCGTC
TCCTCCATCTTCCGAACCAACACCTTCCTCGAGGTCCCC

Alignment

ORF - retro_btau_1133 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.81 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDGGDDGNLVIKKRFVSEAELDERRKRRQEEWEKVRKPEDPEECPEEVYDPRSLYERLQEQKDRKQQEYE
          MDGGDDGNLVIKKRFVSEAELDERRKRRQEEWEKVRKPEDPEECPEEVYDPRSLYERLQEQKDRKQQEYE
Retrocopy MDGGDDGNLVIKKRFVSEAELDERRKRRQEEWEKVRKPEDPEECPEEVYDPRSLYERLQEQKDRKQQEYE

Parental  EQFKFKNMVRGLDEDETNFLDEVSRQQELIEKQRREEELKELKEYRSNLNKVGISSENKKEVEKKAVKPI
          EQFKFKNMVRGLDEDETNFLDEVSRQQELIEKQRREEELK.LKEYRSNLNKVGISSENKKEVEKKAVKPI
Retrocopy EQFKFKNMVRGLDEDETNFLDEVSRQQELIEKQRREEELKKLKEYRSNLNKVGISSENKKEVEKKAVKPI

Parental  ETKNKFSQAKLLAGAVKHKSSESGNSVKRLKSDPDPDDKNQEASSCVSLGSTSLSSPSIHCPSAAVCIGI
          ETKNKFSQAKLLAGAVKHKSSESGNSVKRLKSDPDPDDKNQEASSCVSLGSTSLSSPSI.CPSAAVCIGI
Retrocopy ETKNKFSQAKLLAGAVKHKSSESGNSVKRLKSDPDPDDKNQEASSCVSLGSTSLSSPSIRCPSAAVCIGI

Parental  LPGLGAYSGSSDSESSSDSEGTINATGKIVSSIFRTNTFLEAP
          LPGLGAYSGSSDSESSSDSEGTINATGKIVSSIFRTNTFLE.P
Retrocopy LPGLGAYSGSSDSESSSDSEGTINATGKIVSSIFRTNTFLEVP

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	0.07 RPM	4.61 RPM
ERP005899_muscle	0.05 RPM	18.63 RPM
SRP017611_brain	0.18 RPM	12.06 RPM
SRP017611_kidney	0.24 RPM	10.85 RPM
SRP017611_liver	0.08 RPM	5.13 RPM
SRP030211_testis	1.65 RPM	72.29 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1133 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1133 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1133 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002242	1 retrocopy	retro_btau_1133 ,
Cavia porcellus	ENSCPOG00000001392	1 retrocopy	retro_cpor_122,
Equus caballus	ENSECAG00000009324	1 retrocopy	retro_ecab_710,
Echinops telfairi	ENSETEG00000014379	1 retrocopy	retro_etel_930,
Homo sapiens	ENSG00000172775	1 retrocopy	retro_hsap_2994,
Gorilla gorilla	ENSGGOG00000003938	1 retrocopy	retro_ggor_2074,
Macaca mulatta	ENSMMUG00000013492	1 retrocopy	retro_mmul_189,
Mus musculus	ENSMUSG00000031774	1 retrocopy	retro_mmus_428,
Nomascus leucogenys	ENSNLEG00000002716	1 retrocopy	retro_nleu_745,
Ochotona princeps	ENSOPRG00000006909	2 retrocopies	retro_opri_175, retro_opri_579,
Pongo abelii	ENSPPYG00000007382	1 retrocopy	retro_pabe_2480,
Pan troglodytes	ENSPTRG00000008148	1 retrocopy	retro_ptro_2025,
Tarsius syrichta	ENSTSYG00000013300	1 retrocopy	retro_tsyr_884,
Tursiops truncatus	ENSTTRG00000012791	1 retrocopy	retro_ttru_1884,
Vicugna pacos	ENSVPAG00000005973	1 retrocopy	retro_vpac_321,